From benton at ohsu.edu Wed Oct 1 15:06:43 2014 From: benton at ohsu.edu (Erik Benton) Date: Wed, 1 Oct 2014 19:06:43 +0000 Subject: [Shrine-users] SSL configuration issues Message-ID: Hello all, We have 2 shrine nodes set up (let's call them alice and bob) and while we can query from alice to bob, we cannot query from bob to alice. We are using self-signed certificates at this time. We receive an exception when we try to connect: HTTP Status 500 - java.lang.Exception: Couldn't verify signature for message Alice shrine.log: 2014-Oct-01-11:35:23.950 INFO [SHRINE][AdapterResource][http-6060-1] Running request 326125229002396117 from user: i2b2demo:shrine of type UserRequestType 2014-Oct-01-11:35:23.951 INFO [SHRINE][AdapterService][http-6060-1] Incoming message had invalid signature: BroadcastMessage ? 2014-Oct-01-11:35:23.951 ERROR [SHRINE][AdapterResource][http-6060-1] Error processing request: java.lang.Exception: Couldn't verify signature for message BroadcastMessage Bob shrine.log: 2014-Oct-01-04:18:38.934 DEBUG [SHRINE][JerseyHttpClient][ForkJoinPool-1-worker-3] Got response from 'http://alice.ohsu.edu:6060/shrine/rest/adapter/requests': HttpResponse(500,'Apache Tomcat/6.0.41 - Error report ?

HTTP Status 500 - java.lang.Exception: Couldn't verify signature for message BroadcastMessage We performed the certificate exchange and we are currently using the http connector on port 6060 due to other issues with the SSLHandshakeExceptions that we saw back in June, due to the use of IP addresses. The shrine installers examples make heavy use of the IP address of the nodes so I'm not certain what the correct pattern is in this case. The question is of multiple parts: 1. What do I need to do to resolve the the invalid signature error, and why does work for one, but not the other? 2. When creating the certificates are there any other considerations that need to be made for identification of the certificate? 3. What are the considerations when configuring the downstreamNodes to use SSL? Thanks, Erik -- Erik Benton Research Associate / Informatics Software Developer Oregon Clinical + Translational Research Institute ? BioMedical Informatics Program Oregon Health & Science University From clint_gilbert at hms.harvard.edu Wed Oct 1 15:23:27 2014 From: clint_gilbert at hms.harvard.edu (Clint Gilbert) Date: Wed, 1 Oct 2014 15:23:27 -0400 Subject: [Shrine-users] SSL configuration issues In-Reply-To: References: Message-ID: <542C54AF.9090108@hms.harvard.edu> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Regarding 1), Shrine's signatures have a finite lifetime, and can expire and consequently be deemed invalid. Shrine's defaults makes this unlikely to happen - unless nodes' clocks are out of sync. Try checking your nodes' clocks and syncing them up if needed. On 10/01/2014 03:06 PM, Erik Benton wrote: > Hello all, > > We have 2 shrine nodes set up (let's call them alice and bob) and > while we can query from alice to bob, we cannot query from bob to > alice. We are using self-signed certificates at this time. > > We receive an exception when we try to connect: HTTP Status 500 - > java.lang.Exception: Couldn't verify signature for message > > Alice shrine.log: 2014-Oct-01-11:35:23.950 INFO > [SHRINE][AdapterResource][http-6060-1] Running request > 326125229002396117 from user: i2b2demo:shrine of type > UserRequestType 2014-Oct-01-11:35:23.951 INFO > [SHRINE][AdapterService][http-6060-1] Incoming message had invalid > signature: BroadcastMessage ? > > 2014-Oct-01-11:35:23.951 ERROR > [SHRINE][AdapterResource][http-6060-1] Error processing request: > java.lang.Exception: Couldn't verify signature for message > BroadcastMessage > > > Bob shrine.log: 2014-Oct-01-04:18:38.934 DEBUG > [SHRINE][JerseyHttpClient][ForkJoinPool-1-worker-3] Got response > from 'http://alice.ohsu.edu:6060/shrine/rest/adapter/requests': > HttpResponse(500,'Apache Tomcat/6.0.41 - Error > report ?
HTTP Status 500 - java.lang.Exception: > Couldn't verify signature for message BroadcastMessage > > We performed the certificate exchange and we are currently using > the http connector on port 6060 due to other issues with the > SSLHandshakeExceptions that we saw back in June, due to the use of > IP addresses. The shrine installers examples make heavy use of the > IP address of the nodes so I'm not certain what the correct pattern > is in this case. > > The question is of multiple parts: > > 1. What do I need to do to resolve the the invalid signature error, > and why does work for one, but not the other? > > 2. When creating the certificates are there any other > considerations that need to be made for identification of the > certificate? > > 3. What are the considerations when configuring the downstreamNodes > to use SSL? > > Thanks, Erik > > -- Erik Benton Research Associate / Informatics Software Developer > Oregon Clinical + Translational Research Institute ? BioMedical > Informatics Program Oregon Health & Science University > > > > _______________________________________________ Shrine-users > mailing list Shrine-users at open.med.harvard.edu > https://open.med.harvard.edu/mailman/listinfo/shrine-users > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iEYEARECAAYFAlQsVK8ACgkQ0GFaTS4nYxvgggCgj39uam7YCTyZDNVCl0yeyH4p 5soAnidLN5pE7pGD1Hs9dcsNPB2LtH+s =/299 -----END PGP SIGNATURE----- From beninato at ohsu.edu Wed Oct 1 17:08:45 2014 From: beninato at ohsu.edu (Peter Beninato) Date: Wed, 1 Oct 2014 21:08:45 +0000 Subject: [Shrine-users] i2b2 shrine - v1.17 - i2b2 virtual machine - shrine-webclient - ERROR Message-ID: <43ECC5435444BE479E03012738A1400F1514E376@EXMB03.ohsu.edu> Hi, I have attempted to shrinify the i2b2 VM, both vm v1.7.3, and v1.7.3a per the automated install instructions. The only difference from the v1.16.x install, is the subversion checkout, where I'm trying to use the shrine version 1.17 branch: svn co https://open.med.harvard.edu/svn/shrine/releases/1.17.0/code/install/i2b2-1.7/ quick_install I was able to use the VM webclient and run a query in both cases. However, when accessing the shrine-webclient: {URL}:6060\shrine-webclient When a query is run, there is an ERROR. In the tomcat opt/shrine/tomcat/logs/shrine.log, I see the following line: 2014-Oct-01-13:55:42.090 DEBUG [SHRINE][BufferingMultiplexer][ForkJoinPool-1-worker-1] Latest result count: 1; handled response Result(NodeId(Harvard),9 milliseconds,ErrorResponse(Exception while executing statement : Table 'shrine_query_history.SHRINE_QUERY' doesn't exist There is only an audit_entry table in mysql::shrine_query_history: AUDIT_ENTRY But in v1.16.2, there are other tables like shrine_query. Please advise. Sorry if I missed something. Mysqld is running. Thanks. _ Peter Beninato - OCTRI DW Developer Oregon Health & Science University 503-494-9985 beninato at ohsu.edu _ The information contained in this EMAIL message is confidential and protected by law. The information is intended only for the person or business identified in the document. If you are not the intended recipient, a sharing or copying the information will result in a violation of the law. If you have received this EMAIL by mistake, please notify the sender of this EMAIL and copy the Office of Information Privacy & Security at oips at ohsu.edu. Please remember to cite the NCRR/NCATS-funded CTSA grant (UL1RR024140) in any publications resulting from OCTRI funding, support services or consultations, and to submit your publication to PubMed Central. -------------- next part -------------- An HTML attachment was scrubbed... URL: From beninato at ohsu.edu Wed Oct 1 17:46:58 2014 From: beninato at ohsu.edu (Peter Beninato) Date: Wed, 1 Oct 2014 21:46:58 +0000 Subject: [Shrine-users] i2b2 shrine - v1.17 - i2b2 virtual machine - shrine-webclient - ERROR --> adapter.sql Message-ID: <43ECC5435444BE479E03012738A1400F1514E38D@EXMB03.ohsu.edu> Hi, I think the problem is here: https://open.med.harvard.edu/svn/shrine/releases/1.17.0/code/adapter/src/main/resources/adapter.sql It looks like in the CTAS statement, on the first table, create table SHRINE_QUERY, that the column in the script has a semicolon, and not a comma at the end. I think all the tables are then not created. has_been_run boolean not null default 0; FYI. -Peter From: Peter Beninato Sent: Wednesday, October 01, 2014 2:09 PM To: shrine-users at open.med.harvard.edu Subject: i2b2 shrine - v1.17 - i2b2 virtual machine - shrine-webclient - ERROR Hi, I have attempted to shrinify the i2b2 VM, both vm v1.7.3, and v1.7.3a per the automated install instructions. The only difference from the v1.16.x install, is the subversion checkout, where I'm trying to use the shrine version 1.17 branch: svn co https://open.med.harvard.edu/svn/shrine/releases/1.17.0/code/install/i2b2-1.7/ quick_install I was able to use the VM webclient and run a query in both cases. However, when accessing the shrine-webclient: {URL}:6060\shrine-webclient When a query is run, there is an ERROR. In the tomcat opt/shrine/tomcat/logs/shrine.log, I see the following line: 2014-Oct-01-13:55:42.090 DEBUG [SHRINE][BufferingMultiplexer][ForkJoinPool-1-worker-1] Latest result count: 1; handled response Result(NodeId(Harvard),9 milliseconds,ErrorResponse(Exception while executing statement : Table 'shrine_query_history.SHRINE_QUERY' doesn't exist There is only an audit_entry table in mysql::shrine_query_history: AUDIT_ENTRY But in v1.16.2, there are other tables like shrine_query. Please advise. Sorry if I missed something. Mysqld is running. Thanks. _ Peter Beninato - OCTRI DW Developer Oregon Health & Science University 503-494-9985 beninato at ohsu.edu _ The information contained in this EMAIL message is confidential and protected by law. The information is intended only for the person or business identified in the document. If you are not the intended recipient, a sharing or copying the information will result in a violation of the law. If you have received this EMAIL by mistake, please notify the sender of this EMAIL and copy the Office of Information Privacy & Security at oips at ohsu.edu. Please remember to cite the NCRR/NCATS-funded CTSA grant (UL1RR024140) in any publications resulting from OCTRI funding, support services or consultations, and to submit your publication to PubMed Central. -------------- next part -------------- An HTML attachment was scrubbed... URL: From milnes at pitt.edu Thu Oct 2 10:54:18 2014 From: milnes at pitt.edu (Milnes, John T) Date: Thu, 2 Oct 2014 14:54:18 +0000 Subject: [Shrine-users] Happy Shrine page location Message-ID: Hi - Just a quick question. Is there a Happy Shrine page in the UI these days? What is the url for it? Thanks -John -------------- next part -------------- An HTML attachment was scrubbed... URL: From clint_gilbert at hms.harvard.edu Thu Oct 2 11:21:04 2014 From: clint_gilbert at hms.harvard.edu (Clint Gilbert) Date: Thu, 2 Oct 2014 11:21:04 -0400 Subject: [Shrine-users] i2b2 shrine - v1.17 - i2b2 virtual machine - shrine-webclient - ERROR --> adapter.sql In-Reply-To: <43ECC5435444BE479E03012738A1400F1514E38D@EXMB03.ohsu.edu> References: <43ECC5435444BE479E03012738A1400F1514E38D@EXMB03.ohsu.edu> Message-ID: <542D6D60.2040000@hms.harvard.edu> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Thanks Peter, good catch. That is indeed a bug; we'll get that fixed. On 10/01/2014 05:46 PM, Peter Beninato wrote: > Hi, > > > > I think the problem is here: > > https://open.med.harvard.edu/svn/shrine/releases/1.17.0/code/adapter/src/main/resources/adapter.sql > > > > > It looks like in the CTAS statement, on the first table, create > table SHRINE_QUERY, that the column in the script has a semicolon, > and not a comma at the end. > > > > I think all the tables are then not created. > > > > has_been_run boolean not null default 0; > > > > > > FYI. > > -Peter > > > > > > From:Peter Beninato Sent: Wednesday, October 01, 2014 2:09 PM > To: shrine-users at open.med.harvard.edu Subject: i2b2 shrine - > v1.17 - i2b2 virtual machine - shrine-webclient - ERROR > > > > Hi, > > > > I have attempted to shrinify the i2b2 VM, both vm v1.7.3, and > v1.7.3a per the automated install instructions. > > > > The only difference from the v1.16.x install, is the subversion > checkout, where I?m trying to use the shrine version 1.17 branch: > > svn co > https://open.med.harvard.edu/svn/shrine/releases/1.17.0/code/install/i2b2-1.7/ > > quick_install > > > > I was able to use the VM webclient and run a query in both cases. > > > > However, when accessing the shrine-webclient: > > {URL}:6060\shrine-webclient > > > > When a query is run, there is an ERROR. > > > > In the tomcat opt/shrine/tomcat/logs/shrine.log, I see the > following line: > > 2014-Oct-01-13:55:42.090 DEBUG > [SHRINE][BufferingMultiplexer][ForkJoinPool-1-worker-1] Latest > result count: 1; handled response Result(NodeId(Harvard),9 > milliseconds,ErrorResponse(Exception while executing statement : > Table 'shrine_query_history.SHRINE_QUERY' doesn't exist > > > > > > There is only an audit_entry table in mysql::shrine_query_history: > AUDIT_ENTRY > > > > But in v1.16.2, there are other tables like shrine_query. > > > > Please advise. Sorry if I missed something. > > > > Mysqld is running. > > > > Thanks. > > _ > > Peter Beninato - OCTRI DW Developer > > Oregon Health & Science University > > 503-494-9985 > > beninato at ohsu.edu > > _ > > > > The information contained in this EMAIL message is confidential > and protected by law. The information is intended only for the > person or business identified in the document. If you are not the > intended recipient, a sharing or copying the information will > result in a violation of the law. If you have received this EMAIL > by mistake, please notify the sender of this EMAIL and copy the > Office of Information Privacy & Security at oips at ohsu.edu > . > > > > /Please remember to cite the NCRR/NCATS-funded CTSA grant > (UL1RR024140) in any publications resulting /from/OCTRI funding//, > support services or consultations, and to submit your publication > to PubMed Central./ > > > > > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iEYEARECAAYFAlQtbWAACgkQ0GFaTS4nYxvrEACfYU5+/9t6xF5UX371vAjcqztU pbkAoLUp2fna+vZSXhnWGYdawaExspgv =WZwO -----END PGP SIGNATURE----- From Keith_Dwyer at hms.harvard.edu Thu Oct 2 11:22:09 2014 From: Keith_Dwyer at hms.harvard.edu (Dwyer, Keith) Date: Thu, 2 Oct 2014 11:22:09 -0400 Subject: [Shrine-users] Happy Shrine page location In-Reply-To: References: Message-ID: <49301D0A-AA44-41DC-A51A-F8B02D7C4A59@hms.harvard.edu> The Happy page is accessible at https://YOUR-SHRINE-SERVER:6443/shrine/rest/happy/all (substitute 6443 for whatever SSL port SHRINE is served on) Fair warning, the page takes a fair amount of time to load. Keith Dwyer Harvard Catalyst, SHRINE Network Operations On Oct 2, 2014, at 10:54 AM, Milnes, John T > wrote: Hi ? Just a quick question. Is there a Happy Shrine page in the UI these days? What is the url for it? Thanks -John _______________________________________________ Shrine-users mailing list Shrine-users at open.med.harvard.edu https://open.med.harvard.edu/mailman/listinfo/shrine-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From clint_gilbert at hms.harvard.edu Thu Oct 2 11:23:24 2014 From: clint_gilbert at hms.harvard.edu (Clint Gilbert) Date: Thu, 2 Oct 2014 11:23:24 -0400 Subject: [Shrine-users] Happy Shrine page location In-Reply-To: References: Message-ID: <542D6DEC.2040609@hms.harvard.edu> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 ://rest/happy/all A subset of the happy page that reports useful versions (you get this with /all too): ://rest/happy/versions Invoking both of these will take seconds or minutes, because they need to invoke i2b2 for some things, and i2b2 responds slowly. On 10/02/2014 10:54 AM, Milnes, John T wrote: > Hi ? Just a quick question. Is there a Happy Shrine page in the > UI these days? What is the url for it? > > > > Thanks > > > > -John > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iEYEARECAAYFAlQtbewACgkQ0GFaTS4nYxuKAQCcDKsT++ejHd17H2sEB9g1evrD IOEAn2PcXcT5sbQ5BE5yFY//c9mjwJ/D =UEgz -----END PGP SIGNATURE----- From michel.mansour at emory.edu Thu Oct 2 12:41:20 2014 From: michel.mansour at emory.edu (Mansour, Michel) Date: Thu, 2 Oct 2014 16:41:20 +0000 Subject: [Shrine-users] i2b2 shrine - v1.17 - i2b2 virtual machine - shrine-webclient - ERROR --> adapter.sql In-Reply-To: <43ECC5435444BE479E03012738A1400F1514E38D@EXMB03.ohsu.edu> References: <43ECC5435444BE479E03012738A1400F1514E38D@EXMB03.ohsu.edu> Message-ID: Hi Peter, I ran into this as well. I solved it the same way you did, by replacing that semicolon with a comma. Thanks, Michel -- Michel Mansour Sr. Systems Software Engineer Department of Biomedical Informatics Emory University michel.mansour at emory.edu From: Peter Beninato > Date: Wednesday, October 1, 2014 at 5:46 PM To: "shrine-users at open.med.harvard.edu" > Subject: Re: [Shrine-users] i2b2 shrine - v1.17 - i2b2 virtual machine - shrine-webclient - ERROR --> adapter.sql Hi, I think the problem is here: https://open.med.harvard.edu/svn/shrine/releases/1.17.0/code/adapter/src/main/resources/adapter.sql It looks like in the CTAS statement, on the first table, create table SHRINE_QUERY, that the column in the script has a semicolon, and not a comma at the end. I think all the tables are then not created. has_been_run boolean not null default 0; FYI. -Peter From: Peter Beninato Sent: Wednesday, October 01, 2014 2:09 PM To: shrine-users at open.med.harvard.edu Subject: i2b2 shrine - v1.17 - i2b2 virtual machine - shrine-webclient - ERROR Hi, I have attempted to shrinify the i2b2 VM, both vm v1.7.3, and v1.7.3a per the automated install instructions. The only difference from the v1.16.x install, is the subversion checkout, where I?m trying to use the shrine version 1.17 branch: svn co https://open.med.harvard.edu/svn/shrine/releases/1.17.0/code/install/i2b2-1.7/ quick_install I was able to use the VM webclient and run a query in both cases. However, when accessing the shrine-webclient: {URL}:6060\shrine-webclient When a query is run, there is an ERROR. In the tomcat opt/shrine/tomcat/logs/shrine.log, I see the following line: 2014-Oct-01-13:55:42.090 DEBUG [SHRINE][BufferingMultiplexer][ForkJoinPool-1-worker-1] Latest result count: 1; handled response Result(NodeId(Harvard),9 milliseconds,ErrorResponse(Exception while executing statement : Table 'shrine_query_history.SHRINE_QUERY' doesn't exist There is only an audit_entry table in mysql::shrine_query_history: AUDIT_ENTRY But in v1.16.2, there are other tables like shrine_query. Please advise. Sorry if I missed something. Mysqld is running. Thanks. _________________ Peter Beninato - OCTRI DW Developer Oregon Health & Science University 503-494-9985 beninato at ohsu.edu _ The information contained in this EMAIL message is confidential and protected by law. The information is intended only for the person or business identified in the document. If you are not the intended recipient, a sharing or copying the information will result in a violation of the law. If you have received this EMAIL by mistake, please notify the sender of this EMAIL and copy the Office of Information Privacy & Security at oips at ohsu.edu. Please remember to cite the NCRR/NCATS-funded CTSA grant (UL1RR024140) in any publications resulting from OCTRI funding, support services or consultations, and to submit your publication to PubMed Central. ________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). -------------- next part -------------- An HTML attachment was scrubbed... URL: From michel.mansour at emory.edu Thu Oct 2 12:46:12 2014 From: michel.mansour at emory.edu (Mansour, Michel) Date: Thu, 2 Oct 2014 16:46:12 +0000 Subject: [Shrine-users] Happy Shrine page location In-Reply-To: <542D6DEC.2040609@hms.harvard.edu> References: <542D6DEC.2040609@hms.harvard.edu> Message-ID: Hi all, Just a quick anecdote about the "Happy" page. I was getting a mapping error using the AdapterMappings_i2b2_DemoData.xml mapping file because it doesn't contain the test concept used by the happy service: \\SHRINE\SHRINE\Diagnoses\Mental Illness\Disorders usually diagnosed in infancy, childhood, or adolescence\ Instead, I plugged in the Harvard mappings (https://open.med.harvard.edu/svn/shrine/releases/1.17.0/ontology/Harvard_S hrine/i2b2_demo_data/AdapterMappings.xml), and it worked fine. Thanks, Michel -- Michel Mansour Sr. Systems Software Engineer Department of Biomedical Informatics Emory University michel.mansour at emory.edu On 10/2/14, 11:23 AM, "Clint Gilbert" wrote: >-----BEGIN PGP SIGNED MESSAGE----- >Hash: SHA1 > >://rest/happy/all > >A subset of the happy page that reports useful versions (you get this >with /all too): > >://rest/happy/versions > >Invoking both of these will take seconds or minutes, because they need >to invoke i2b2 for some things, and i2b2 responds slowly. > >On 10/02/2014 10:54 AM, Milnes, John T wrote: >> Hi ? Just a quick question. Is there a Happy Shrine page in the >> UI these days? What is the url for it? >> >> >> >> Thanks >> >> >> >> -John >> >-----BEGIN PGP SIGNATURE----- >Version: GnuPG v1 > >iEYEARECAAYFAlQtbewACgkQ0GFaTS4nYxuKAQCcDKsT++ejHd17H2sEB9g1evrD >IOEAn2PcXcT5sbQ5BE5yFY//c9mjwJ/D >=UEgz >-----END PGP SIGNATURE----- >_______________ >Shrine-users mailing list >Shrine-users at open.med.harvard.edu >https://open.med.harvard.edu/mailman/listinfo/shrine-users This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). From michel.mansour at emory.edu Thu Oct 2 12:54:43 2014 From: michel.mansour at emory.edu (Mansour, Michel) Date: Thu, 2 Oct 2014 16:54:43 +0000 Subject: [Shrine-users] [1.17.0] SHRINE_ONT database user permissions Message-ID: Hi, Our DBAs balked a little bit (though eventually relented) when they were asked to create the SHRINE_ONT database user in Oracle (i2b2/oracle/skel/ontology_create_user.sql): -- create user I2B2_DB_SHRINE_ONT_USER identified by I2B2_DB_SHRINE_ONT_PASSWORD; grant create session, connect, resource to I2B2_DB_SHRINE_ONT_USER; -- i2b2metadata.table_access grant all privileges to I2B2_DB_SHRINE_ONT_USER; -- Specifically, there were questions about granting "resource" and "all privileges" to a non-system account. I'm just curious about how these permissions are used by SHRINE and whether they are necessary post-installation. Thanks, Michel -- Michel Mansour Sr. Systems Software Engineer Department of Biomedical Informatics Emory University michel.mansour at emory.edu ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). -------------- next part -------------- An HTML attachment was scrubbed... URL: From ev2348 at columbia.edu Fri Oct 3 09:44:42 2014 From: ev2348 at columbia.edu (ev2348 at columbia.edu) Date: Fri, 03 Oct 2014 09:44:42 -0400 Subject: [Shrine-users] 1.7.0 shrine Message-ID: <20141003094442.vrpu4zpk0g80s8go@cubmail.cc.columbia.edu> Hi, I downloaded the latest version 1.7.0 of Shrine installer. You have two new columns in the Shrine table M_APPLIED_PATH VARCHAR(900), M_EXCLUSION_CD VARCHAR(900) However, for the insert statements in Shrine.sql the values are short by two columns even when the column names are included in the insert, so you get an error message. I am talking about this url https://open.med.harvard.edu/svn/shrine/releases/1.17.0/code/install/i2b2-1.7/ Is there any other changes that may affect the installation scripts and that I need to be aware of for this new version. Thanks for all your hard work. Best Elena From michel.mansour at emory.edu Fri Oct 3 12:12:37 2014 From: michel.mansour at emory.edu (Mansour, Michel) Date: Fri, 3 Oct 2014 16:12:37 +0000 Subject: [Shrine-users] Happy Shrine page location In-Reply-To: References: <542D6DEC.2040609@hms.harvard.edu> Message-ID: Follow-up question: The happy SHRINE page I see is just an unformatted XML document. Is this expected? I couldn't find an example of what we're supposed to see in the documentation. Also, the page loaded quite fast for me, while the documentation and others in this thread have said that it should take several seconds or even minutes. So I'm wondering if something has been misconfigured. There are no errors mentioned in the XML. Thanks, Michel On 10/2/14, 12:46 PM, "Mansour, Michel" wrote: >Hi all, > >Just a quick anecdote about the "Happy" page. I was getting a mapping >error using the AdapterMappings_i2b2_DemoData.xml mapping file because it >doesn't contain the test concept used by the happy service: >\\SHRINE\SHRINE\Diagnoses\Mental Illness\Disorders usually diagnosed in >infancy, childhood, or adolescence\ > >Instead, I plugged in the Harvard mappings >(https://open.med.harvard.edu/svn/shrine/releases/1.17.0/ontology/Harvard_ >S >hrine/i2b2_demo_data/AdapterMappings.xml), and it worked fine. > >Thanks, >Michel > >-- >Michel Mansour >Sr. Systems Software Engineer >Department of Biomedical Informatics >Emory University >michel.mansour at emory.edu > > >On 10/2/14, 11:23 AM, "Clint Gilbert" >wrote: > > >>-----BEGIN PGP SIGNED MESSAGE----- >>Hash: SHA1 >> >>://rest/happy/all >> >>A subset of the happy page that reports useful versions (you get this >>with /all too): >> >>://rest/happy/versions >> >>Invoking both of these will take seconds or minutes, because they need >>to invoke i2b2 for some things, and i2b2 responds slowly. >> >>On 10/02/2014 10:54 AM, Milnes, John T wrote: >>> Hi ? Just a quick question. Is there a Happy Shrine page in the >>> UI these days? What is the url for it? >>> >>> >>> >>> Thanks >>> >>> >>> >>> -John >>> >>-----BEGIN PGP SIGNATURE----- >>Version: GnuPG v1 >> >>iEYEARECAAYFAlQtbewACgkQ0GFaTS4nYxuKAQCcDKsT++ejHd17H2sEB9g1evrD >>IOEAn2PcXcT5sbQ5BE5yFY//c9mjwJ/D >>=UEgz >>-----END PGP SIGNATURE----- >>_ >>Shrine-users mailing list >>Shrine-users at open.med.harvard.edu >>https://open.med.harvard.edu/mailman/listinfo/shrine-users > > > > >This e-mail message (including any attachments) is for the sole use of >the intended recipient(s) and may contain confidential and privileged >information. If the reader of this message is not the intended >recipient, you are hereby notified that any dissemination, distribution >or copying of this message (including any attachments) is strictly >prohibited. > >If you have received this message in error, please contact >the sender by reply e-mail message and destroy all copies of the >original message (including attachments). >_ >Shrine-users mailing list >Shrine-users at open.med.harvard.edu >https://open.med.harvard.edu/mailman/listinfo/shrine-users From clint_gilbert at hms.harvard.edu Fri Oct 3 12:18:07 2014 From: clint_gilbert at hms.harvard.edu (Clint Gilbert) Date: Fri, 3 Oct 2014 12:18:07 -0400 Subject: [Shrine-users] Happy Shrine page location In-Reply-To: References: <542D6DEC.2040609@hms.harvard.edu> Message-ID: <542ECC3F.6000709@hms.harvard.edu> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Plain XML is expected. The name "happy page" is a bit misleading, since that implies an HTML page. The output is intended to be machine- and admin-readable, but not much more. A description of the output isn't present in the docs either. We'll look into adding one. On 10/03/2014 12:12 PM, Mansour, Michel wrote: > Follow-up question: The happy SHRINE page I see is just an > unformatted XML document. Is this expected? I couldn't find an > example of what we're supposed to see in the documentation. Also, > the page loaded quite fast for me, while the documentation and > others in this thread have said that it should take several seconds > or even minutes. So I'm wondering if something has been > misconfigured. There are no errors mentioned in the XML. > > Thanks, Michel > > > On 10/2/14, 12:46 PM, "Mansour, Michel" > wrote: > >> Hi all, >> >> Just a quick anecdote about the "Happy" page. I was getting a >> mapping error using the AdapterMappings_i2b2_DemoData.xml mapping >> file because it doesn't contain the test concept used by the >> happy service: \\SHRINE\SHRINE\Diagnoses\Mental Illness\Disorders >> usually diagnosed in infancy, childhood, or adolescence\ >> >> Instead, I plugged in the Harvard mappings >> (https://open.med.harvard.edu/svn/shrine/releases/1.17.0/ontology/Harvard_ >> >> S >> hrine/i2b2_demo_data/AdapterMappings.xml), and it worked fine. >> >> Thanks, Michel >> >> -- Michel Mansour Sr. Systems Software Engineer Department of >> Biomedical Informatics Emory University michel.mansour at emory.edu >> >> >> On 10/2/14, 11:23 AM, "Clint Gilbert" >> wrote: >> >> > ://rest/happy/all > > A subset of the happy page that reports useful versions (you get > this with /all too): > > ://rest/happy/versions > > Invoking both of these will take seconds or minutes, because they > need to invoke i2b2 for some things, and i2b2 responds slowly. > > On 10/02/2014 10:54 AM, Milnes, John T wrote: >>>>> Hi ? Just a quick question. Is there a Happy Shrine page >>>>> in the UI these days? What is the url for it? >>>>> >>>>> >>>>> >>>>> Thanks >>>>> >>>>> >>>>> >>>>> -John >>>>> >>> _______________________ Shrine-users >>> mailing list Shrine-users at open.med.harvard.edu >>> https://open.med.harvard.edu/mailman/listinfo/shrine-users >> >> >> >> >> This e-mail message (including any attachments) is for the sole >> use of the intended recipient(s) and may contain confidential and >> privileged information. If the reader of this message is not the >> intended recipient, you are hereby notified that any >> dissemination, distribution or copying of this message (including >> any attachments) is strictly prohibited. >> >> If you have received this message in error, please contact the >> sender by reply e-mail message and destroy all copies of the >> original message (including attachments). >> _ Shrine-users >> mailing list Shrine-users at open.med.harvard.edu >> https://open.med.harvard.edu/mailman/listinfo/shrine-users > > _________________________ Shrine-users > mailing list Shrine-users at open.med.harvard.edu > https://open.med.harvard.edu/mailman/listinfo/shrine-users > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iEYEARECAAYFAlQuzD8ACgkQ0GFaTS4nYxuNggCffXr9RTeHklJIBRZzaazT7OPD 31AAoLbCthbXslyfZrBg9WgDPvNCdfNJ =vfVv -----END PGP SIGNATURE----- From ev2348 at columbia.edu Fri Oct 3 15:57:37 2014 From: ev2348 at columbia.edu (ev2348 at columbia.edu) Date: Fri, 03 Oct 2014 15:57:37 -0400 Subject: [Shrine-users] shrine and 1.17.0 Message-ID: <20141003155737.lujn4p068g0c0ck4@cubmail.cc.columbia.edu> Hello, when downloading the adapter.sql with version 1.17.0 I also get error messages about the wrong syntax ERROR 1064 (42000): You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near '' at line 1 ERROR 1064 (42000): You have an error in your SQL syntax; check the manual that I did not get any errors with version 1.16.2 However the other file create_broadcaster_audit_table.sql works fine. Elena From Keith_Dwyer at hms.harvard.edu Fri Oct 3 16:09:34 2014 From: Keith_Dwyer at hms.harvard.edu (Dwyer, Keith) Date: Fri, 3 Oct 2014 16:09:34 -0400 Subject: [Shrine-users] shrine and 1.17.0 In-Reply-To: <20141003155737.lujn4p068g0c0ck4@cubmail.cc.columbia.edu> References: <20141003155737.lujn4p068g0c0ck4@cubmail.cc.columbia.edu> Message-ID: Yes, this seems to be a typo that slipped into that version of adapter.sql. The fix is relatively simple (change a semicolon into a comma) and will be included in the next point release. Current problematic adapter.sql: has_been_run boolean not null default 0; Fixed version: has_been_run boolean not null default 0, See also: Mailing list thread [Shrine-users] i2b2 shrine - v1.17 - i2b2 virtual machine - shrine-webclient - ERROR --> adapter.sql JIRA ticket: [SHRINE-849] Spurious semicolon in adapter db-creation script - https://open.med.harvard.edu/jira/browse/SHRINE-849 Keith Dwyer Harvard Catalyst, SHRINE Network Operations On Oct 3, 2014, at 3:57 PM, > > wrote: Hello, when downloading the adapter.sql with version 1.17.0 I also get error messages about the wrong syntax ERROR 1064 (42000): You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near '' at line 1 ERROR 1064 (42000): You have an error in your SQL syntax; check the manual that I did not get any errors with version 1.16.2 However the other file create_broadcaster_audit_table.sql works fine. Elena _______________________________________________ Shrine-users mailing list Shrine-users at open.med.harvard.edu https://open.med.harvard.edu/mailman/listinfo/shrine-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From beninato at ohsu.edu Mon Oct 6 18:59:14 2014 From: beninato at ohsu.edu (Peter Beninato) Date: Mon, 6 Oct 2014 22:59:14 +0000 Subject: [Shrine-users] i2b2 shrine - v1.17 - upgrade In-Reply-To: <2282FB3A-6177-4192-9EB7-1BBA4CD44C15@hms.harvard.edu> References: <43ECC5435444BE479E03012738A1400F1514DE2F@EXMB03.ohsu.edu> <2282FB3A-6177-4192-9EB7-1BBA4CD44C15@hms.harvard.edu> Message-ID: <43ECC5435444BE479E03012738A1400F1514FA0E@EXMB03.ohsu.edu> Hi, As described, it appears to be possible to upgrade by: 1) In Tomcat replace shrine.war 2) In Tomcat replace shrine-webclient with the proviso of safeguarding any changes to i2b2_config_data.js 3) Unless there is more to it. Truncate the SHRINE table, run an alter table for the two new modifier columns, and then run the insert script pulled out of SVN. I was able to run a simple gender/age query, without any Errors. FYI. Thanks. -Peter From: Dwyer, Keith [mailto:Keith_Dwyer at hms.harvard.edu] Sent: Tuesday, September 30, 2014 12:57 PM To: Peter Beninato Cc: shrine-users at open.med.harvard.edu Subject: Re: [Shrine-users] i2b2 shrine - v1.17 - upgrade The major changes are to: - the shrine.war application (of course) - the tables inserted into the i2b2 databases (for modifier support) - the webclient The release .war can be obtained by navigating through the open.med Sonatype Nexus repository to find the shrine-war artifact under the net.shrine group. (http://repo.open.med.harvard.edu/nexus/index.html#nexus-search;quick~net.shrine). The webclient can be obtained by running either svn co or svn export against https://open.med.harvard.edu/svn/shrine/releases/1.17.0/code/shrine-webclient/. Keep in mind that you will need to back up your old i2b2_config_data.js before installing the new webclient. Both of these items live in /opt/shrine/tomcat/webapps (or wherever your SHRINE Tomcat installation lives). Items 1 and 3 are easy enough to update, but unfortunately, item 2 requires a re-run of the database cleanup scripts and database insert scripts in the SHRINE installer. This requires setting the appropriate values in the installer's .rc files, and then manually running the i2b2 database scripts appropriate for the database engine you are using. Keith Dwyer Harvard Catalyst, SHRINE Network Operations On Sep 30, 2014, at 3:47 PM, Peter Beninato > wrote: Hi, Are there any shortcuts to implementing v1.17 from an existing shrine v.1.16.x installation? Or is it a complete re-install? _________________ Peter Beninato - OCTRI DW Developer Oregon Health & Science University 503-494-9985 beninato at ohsu.edu _ The information contained in this EMAIL message is confidential and protected by law. The information is intended only for the person or business identified in the document. If you are not the intended recipient, a sharing or copying the information will result in a violation of the law. If you have received this EMAIL by mistake, please notify the sender of this EMAIL and copy the Office of Information Privacy & Security at oips at ohsu.edu. Please remember to cite the NCRR/NCATS-funded CTSA grant (UL1RR024140) in any publications resulting from OCTRI funding, support services or consultations, and to submit your publication to PubMed Central. _______________________________ Shrine-users mailing list Shrine-users at open.med.harvard.edu https://open.med.harvard.edu/mailman/listinfo/shrine-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From beninato at ohsu.edu Mon Oct 6 19:19:50 2014 From: beninato at ohsu.edu (Peter Beninato) Date: Mon, 6 Oct 2014 23:19:50 +0000 Subject: [Shrine-users] i2b2 Shrine - v1.17 - modifier dimension ? Message-ID: <43ECC5435444BE479E03012738A1400F1514FA43@EXMB03.ohsu.edu> Hi, So, v1.17 includes support for Modifiers. In the shrine ontology table, in version v1.17 they seem to support diagnosis. There is a "separate" shrine schema for the shrine ontology. However, the modifier dimension lives in the "data" schema. Is there a shrine "DATA" schema for the modifier dimension? I have v1.17 running in a local VM, When I look at i2b2demodata.modifier_dimension, I see standard i2b2 demo data type entries. When I look at shrine_ont, there are the three tables from prior releases. The shrine ontology table has been loaded with the data for v1.17. I want to work on loading Diagnosis into our shrine install. We use the c_metadataxml field to distinguish between diagnosis types, and not Modifiers, so it'd be helpful to have a working example. Questions: Is there more to the upgrade like a modifier_dimension or a new schema for "shrine_data?" (if following i2b2 conventions, then maybe modifier_dimension would be in "shrine_data") As part of the ACT process will there be published (perhaps as csv), files that would contain the content of a few standard i2b2 tables? I think it might be advantageous if an outgrowth of the ACT process, if there were csv files for the i2b2 table, the concept_dimension, and the modifier_dimension. This is in addition to the SHRINE ontology, and maps. Why? I could load these standard tables into the SHRINE production system, and then just have to mangle/wrangle my local data to make observations with the correct concept_cd, instance_num, nval_num etc. _ Peter Beninato - OCTRI DW Developer Oregon Health & Science University 503-494-9985 beninato at ohsu.edu _ The information contained in this EMAIL message is confidential and protected by law. The information is intended only for the person or business identified in the document. If you are not the intended recipient, a sharing or copying the information will result in a violation of the law. If you have received this EMAIL by mistake, please notify the sender of this EMAIL and copy the Office of Information Privacy & Security at oips at ohsu.edu. Please remember to cite the NCRR/NCATS-funded CTSA grant (UL1RR024140) in any publications resulting from OCTRI funding, support services or consultations, and to submit your publication to PubMed Central. -------------- next part -------------- An HTML attachment was scrubbed... URL: From beninato at ohsu.edu Tue Oct 7 18:25:00 2014 From: beninato at ohsu.edu (Peter Beninato) Date: Tue, 7 Oct 2014 22:25:00 +0000 Subject: [Shrine-users] i2b2 shrine - v1.17 - upgrade --> AdapterMapping.xml Message-ID: <43ECC5435444BE479E03012738A1400F1514FD3C@EXMB03.ohsu.edu> Hi, Regarding upgrading... Is there a step missing about updating the AdapterMapping.xml file in tomcat\lib? None of the below steps seem to impact that. -Peter From: Peter Beninato Sent: Monday, October 06, 2014 3:59 PM To: 'Dwyer, Keith' Cc: shrine-users at open.med.harvard.edu Subject: RE: [Shrine-users] i2b2 shrine - v1.17 - upgrade Hi, As described, it appears to be possible to upgrade by: 1) In Tomcat replace shrine.war 2) In Tomcat replace shrine-webclient with the proviso of safeguarding any changes to i2b2_config_data.js 3) Unless there is more to it. Truncate the SHRINE table, run an alter table for the two new modifier columns, and then run the insert script pulled out of SVN. I was able to run a simple gender/age query, without any Errors. FYI. Thanks. -Peter From: Dwyer, Keith [mailto:Keith_Dwyer at hms.harvard.edu] Sent: Tuesday, September 30, 2014 12:57 PM To: Peter Beninato Cc: shrine-users at open.med.harvard.edu Subject: Re: [Shrine-users] i2b2 shrine - v1.17 - upgrade The major changes are to: - the shrine.war application (of course) - the tables inserted into the i2b2 databases (for modifier support) - the webclient The release .war can be obtained by navigating through the open.med Sonatype Nexus repository to find the shrine-war artifact under the net.shrine group. (http://repo.open.med.harvard.edu/nexus/index.html#nexus-search;quick~net.shrine). The webclient can be obtained by running either svn co or svn export against https://open.med.harvard.edu/svn/shrine/releases/1.17.0/code/shrine-webclient/. Keep in mind that you will need to back up your old i2b2_config_data.js before installing the new webclient. Both of these items live in /opt/shrine/tomcat/webapps (or wherever your SHRINE Tomcat installation lives). Items 1 and 3 are easy enough to update, but unfortunately, item 2 requires a re-run of the database cleanup scripts and database insert scripts in the SHRINE installer. This requires setting the appropriate values in the installer's .rc files, and then manually running the i2b2 database scripts appropriate for the database engine you are using. Keith Dwyer Harvard Catalyst, SHRINE Network Operations On Sep 30, 2014, at 3:47 PM, Peter Beninato > wrote: Hi, Are there any shortcuts to implementing v1.17 from an existing shrine v.1.16.x installation? Or is it a complete re-install? _________________ Peter Beninato - OCTRI DW Developer Oregon Health & Science University 503-494-9985 beninato at ohsu.edu _ The information contained in this EMAIL message is confidential and protected by law. The information is intended only for the person or business identified in the document. If you are not the intended recipient, a sharing or copying the information will result in a violation of the law. If you have received this EMAIL by mistake, please notify the sender of this EMAIL and copy the Office of Information Privacy & Security at oips at ohsu.edu. Please remember to cite the NCRR/NCATS-funded CTSA grant (UL1RR024140) in any publications resulting from OCTRI funding, support services or consultations, and to submit your publication to PubMed Central. _______________________________ Shrine-users mailing list Shrine-users at open.med.harvard.edu https://open.med.harvard.edu/mailman/listinfo/shrine-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeff.lunt at northwestern.edu Wed Oct 8 17:00:58 2014 From: jeff.lunt at northwestern.edu (Jeff Mark Lunt) Date: Wed, 8 Oct 2014 21:00:58 +0000 Subject: [Shrine-users] Trouble with "Missing Concept in Ontology Cell" Message-ID: I ran through the manual install for SHRINE, I have and I have a working i2b2 demo instance that works in terms of running queries. I ran a query in i2b2 asking the number of males in the demo data, and I got back 82. When I run the same query in SHRINE (talking to that i2b2 instance), I get back the following error: Missing Concept in Ontology Cell : [\\i2b2_DEMO\i2b2\Demographics\Gender\Male\] panel#-1 I've confirmed that the AdapterMappings.xml file is in /opt/shrine/tomcat/lib/ I've looked in my i2b2 ontology in the database on the i2b2 server, and I don't have anything that starts with i2b2_DEMO, just i2b2 (if I understand it correctly). On a hunch I tried replacing "i2b2_DEMO" in my AdapterMappings.xml file with "i2b2", so that the mapping becomes: \\i2b2\i2b2\Demographics\Gender\Male\ ...and I restarted SHRINE. However, I'm still getting the same error message about the missing concept from the Ontology. I feel like I'm not understanding the proper use of the AdapterMappings.xml file, because even if my change was incorrect I would have expected the error message to reflect the change in the naming that I did., but it didn't. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeff.lunt at northwestern.edu Wed Oct 8 17:03:14 2014 From: jeff.lunt at northwestern.edu (Jeff Mark Lunt) Date: Wed, 8 Oct 2014 21:03:14 +0000 Subject: [Shrine-users] Trouble with "Missing Concept in Ontology Cell" In-Reply-To: References: Message-ID: Sorry, I should have included that I got this error when inspecting the XML Message History for the "Previous Queries" pane in SHRINE, and that it was under the "getQueryInstanceList_fromQueryMasterId" message. From: Jeff Lunt > Date: Wednesday, October 8, 2014 at 4:00 PM To: "shrine-users at open.med.harvard.edu" > Subject: Trouble with "Missing Concept in Ontology Cell" I ran through the manual install for SHRINE, I have and I have a working i2b2 demo instance that works in terms of running queries. I ran a query in i2b2 asking the number of males in the demo data, and I got back 82. When I run the same query in SHRINE (talking to that i2b2 instance), I get back the following error: Missing Concept in Ontology Cell : [\\i2b2_DEMO\i2b2\Demographics\Gender\Male\] panel#-1 I've confirmed that the AdapterMappings.xml file is in /opt/shrine/tomcat/lib/ I've looked in my i2b2 ontology in the database on the i2b2 server, and I don't have anything that starts with i2b2_DEMO, just i2b2 (if I understand it correctly). On a hunch I tried replacing "i2b2_DEMO" in my AdapterMappings.xml file with "i2b2", so that the mapping becomes: \\i2b2\i2b2\Demographics\Gender\Male\ ...and I restarted SHRINE. However, I'm still getting the same error message about the missing concept from the Ontology. I feel like I'm not understanding the proper use of the AdapterMappings.xml file, because even if my change was incorrect I would have expected the error message to reflect the change in the naming that I did., but it didn't. -------------- next part -------------- An HTML attachment was scrubbed... URL: From beninato at ohsu.edu Wed Oct 8 17:09:55 2014 From: beninato at ohsu.edu (Peter Beninato) Date: Wed, 8 Oct 2014 21:09:55 +0000 Subject: [Shrine-users] Trouble with "Missing Concept in Ontology Cell" -- table_access.c_table_cd Message-ID: <43ECC5435444BE479E03012738A1400F151500B0@EXMB03.ohsu.edu> Hi, The \\i2b2_DEMO part comes for the ?META_DATA?.table_access.c_table_cd. I don?t use the underscore suffixes, my table only has one entry, with both the c_table_cd and c_table_name set to ?i2b2.? So, I do go in and find and replace in the AdapterMappings.xml. Do you see any errors in the tomcat shrine.log? -Peter From: shrine-users-bounces at open.med.harvard.edu [mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of Jeff Mark Lunt Sent: Wednesday, October 08, 2014 2:03 PM To: shrine-users at open.med.harvard.edu Subject: Re: [Shrine-users] Trouble with "Missing Concept in Ontology Cell" Sorry, I should have included that I got this error when inspecting the XML Message History for the "Previous Queries" pane in SHRINE, and that it was under the "getQueryInstanceList_fromQueryMasterId" message. From: Jeff Lunt > Date: Wednesday, October 8, 2014 at 4:00 PM To: "shrine-users at open.med.harvard.edu" > Subject: Trouble with "Missing Concept in Ontology Cell" I ran through the manual install for SHRINE, I have and I have a working i2b2 demo instance that works in terms of running queries. I ran a query in i2b2 asking the number of males in the demo data, and I got back 82. When I run the same query in SHRINE (talking to that i2b2 instance), I get back the following error: Missing Concept in Ontology Cell : [\\i2b2_DEMO\i2b2\Demographics\Gender\Male\] panel#-1 I've confirmed that the AdapterMappings.xml file is in /opt/shrine/tomcat/lib/ I've looked in my i2b2 ontology in the database on the i2b2 server, and I don't have anything that starts with i2b2_DEMO, just i2b2 (if I understand it correctly). On a hunch I tried replacing "i2b2_DEMO" in my AdapterMappings.xml file with "i2b2", so that the mapping becomes: \\i2b2\i2b2\Demographics\Gender\Male\ ...and I restarted SHRINE. However, I'm still getting the same error message about the missing concept from the Ontology. I feel like I'm not understanding the proper use of the AdapterMappings.xml file, because even if my change was incorrect I would have expected the error message to reflect the change in the naming that I did., but it didn't. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeff.lunt at northwestern.edu Wed Oct 8 17:48:01 2014 From: jeff.lunt at northwestern.edu (Jeff Mark Lunt) Date: Wed, 8 Oct 2014 21:48:01 +0000 Subject: [Shrine-users] Trouble with "Missing Concept in Ontology Cell" -- table_access.c_table_cd In-Reply-To: <43ECC5435444BE479E03012738A1400F151500B0@EXMB03.ohsu.edu> References: <43ECC5435444BE479E03012738A1400F151500B0@EXMB03.ohsu.edu> Message-ID: Thanks, Peter and Sushma, for the tip. I did check that, and it answers my question in terms of the mapping ? thank you! I did have a big error in my log which I've fixed by making sure that my shrine.conf was setup (it was completely missing ? don't know how I missed that), but that hasn't change the error message I'm getting in the message log. I'm still getting the same "Missing Concept in Ontology Cell" message. No more errors in my /opt/shrine/tomcat/log/shrine.log anymore, or any errors in any of the logs in that same folder. Best I can guess now is that I have a mistake somewhere in the config where SHRINE looks to do i2b2 ontology lookups. Somethings that might be relevant: * I'm doing a standalone (separate from i2b2 server) install of SHRINE, meaning that SHRINE runs on its own VM and is configured to talk to another VM * The only DB that's on the SHRINE server is the mysql instance with the query audit history ? I was trying to avoid having to install Oracle or Postgres on the SHRINE server by re-using my i2b2 DB, and pointing its data sources at that DB in the ont-ds.xml file From: Peter Beninato > Date: Wednesday, October 8, 2014 at 4:09 PM To: Jeff Lunt >, "shrine-users at open.med.harvard.edu" > Subject: RE: Trouble with "Missing Concept in Ontology Cell" -- table_access.c_table_cd Hi, The \\i2b2_DEMO part comes for the ?META_DATA?.table_access.c_table_cd. I don?t use the underscore suffixes, my table only has one entry, with both the c_table_cd and c_table_name set to ?i2b2.? So, I do go in and find and replace in the AdapterMappings.xml. Do you see any errors in the tomcat shrine.log? -Peter From: shrine-users-bounces at open.med.harvard.edu [mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of Jeff Mark Lunt Sent: Wednesday, October 08, 2014 2:03 PM To: shrine-users at open.med.harvard.edu Subject: Re: [Shrine-users] Trouble with "Missing Concept in Ontology Cell" Sorry, I should have included that I got this error when inspecting the XML Message History for the "Previous Queries" pane in SHRINE, and that it was under the "getQueryInstanceList_fromQueryMasterId" message. From: Jeff Lunt > Date: Wednesday, October 8, 2014 at 4:00 PM To: "shrine-users at open.med.harvard.edu" > Subject: Trouble with "Missing Concept in Ontology Cell" I ran through the manual install for SHRINE, I have and I have a working i2b2 demo instance that works in terms of running queries. I ran a query in i2b2 asking the number of males in the demo data, and I got back 82. When I run the same query in SHRINE (talking to that i2b2 instance), I get back the following error: Missing Concept in Ontology Cell : [\\i2b2_DEMO\i2b2\Demographics\Gender\Male\] panel#-1 I've confirmed that the AdapterMappings.xml file is in /opt/shrine/tomcat/lib/ I've looked in my i2b2 ontology in the database on the i2b2 server, and I don't have anything that starts with i2b2_DEMO, just i2b2 (if I understand it correctly). On a hunch I tried replacing "i2b2_DEMO" in my AdapterMappings.xml file with "i2b2", so that the mapping becomes: \\i2b2\i2b2\Demographics\Gender\Male\ ...and I restarted SHRINE. However, I'm still getting the same error message about the missing concept from the Ontology. I feel like I'm not understanding the proper use of the AdapterMappings.xml file, because even if my change was incorrect I would have expected the error message to reflect the change in the naming that I did., but it didn't. -------------- next part -------------- An HTML attachment was scrubbed... URL: From beninato at ohsu.edu Wed Oct 8 17:54:38 2014 From: beninato at ohsu.edu (Peter Beninato) Date: Wed, 8 Oct 2014 21:54:38 +0000 Subject: [Shrine-users] Trouble with "Missing Concept in Ontology Cell" -- table_access.c_table_cd In-Reply-To: References: <43ECC5435444BE479E03012738A1400F151500B0@EXMB03.ohsu.edu> Message-ID: <43ECC5435444BE479E03012738A1400F151500CE@EXMB03.ohsu.edu> Hi, On the VM that is running shrine, can you check that you have connectivity to the server that is hosting your ontology? These setting should also be in the shrine.rc, i2b2.rc, and common.rc. Without a db client, I guess you at least ping. How about the JBOSS server.log? Are there any errors there? -Peter From: Jeff Mark Lunt [mailto:jeff.lunt at northwestern.edu] Sent: Wednesday, October 08, 2014 2:48 PM To: Peter Beninato; shrine-users at open.med.harvard.edu; Sushma Patil Subject: Re: Trouble with "Missing Concept in Ontology Cell" -- table_access.c_table_cd Thanks, Peter and Sushma, for the tip. I did check that, and it answers my question in terms of the mapping ? thank you! I did have a big error in my log which I've fixed by making sure that my shrine.conf was setup (it was completely missing ? don't know how I missed that), but that hasn't change the error message I'm getting in the message log. I'm still getting the same "Missing Concept in Ontology Cell" message. No more errors in my /opt/shrine/tomcat/log/shrine.log anymore, or any errors in any of the logs in that same folder. Best I can guess now is that I have a mistake somewhere in the config where SHRINE looks to do i2b2 ontology lookups. Somethings that might be relevant: * I'm doing a standalone (separate from i2b2 server) install of SHRINE, meaning that SHRINE runs on its own VM and is configured to talk to another VM * The only DB that's on the SHRINE server is the mysql instance with the query audit history ? I was trying to avoid having to install Oracle or Postgres on the SHRINE server by re-using my i2b2 DB, and pointing its data sources at that DB in the ont-ds.xml file From: Peter Beninato > Date: Wednesday, October 8, 2014 at 4:09 PM To: Jeff Lunt >, "shrine-users at open.med.harvard.edu" > Subject: RE: Trouble with "Missing Concept in Ontology Cell" -- table_access.c_table_cd Hi, The \\i2b2_DEMO part comes for the ?META_DATA?.table_access.c_table_cd. I don?t use the underscore suffixes, my table only has one entry, with both the c_table_cd and c_table_name set to ?i2b2.? So, I do go in and find and replace in the AdapterMappings.xml. Do you see any errors in the tomcat shrine.log? -Peter From: shrine-users-bounces at open.med.harvard.edu [mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of Jeff Mark Lunt Sent: Wednesday, October 08, 2014 2:03 PM To: shrine-users at open.med.harvard.edu Subject: Re: [Shrine-users] Trouble with "Missing Concept in Ontology Cell" Sorry, I should have included that I got this error when inspecting the XML Message History for the "Previous Queries" pane in SHRINE, and that it was under the "getQueryInstanceList_fromQueryMasterId" message. From: Jeff Lunt > Date: Wednesday, October 8, 2014 at 4:00 PM To: "shrine-users at open.med.harvard.edu" > Subject: Trouble with "Missing Concept in Ontology Cell" I ran through the manual install for SHRINE, I have and I have a working i2b2 demo instance that works in terms of running queries. I ran a query in i2b2 asking the number of males in the demo data, and I got back 82. When I run the same query in SHRINE (talking to that i2b2 instance), I get back the following error: Missing Concept in Ontology Cell : [\\i2b2_DEMO\i2b2\Demographics\Gender\Male\] panel#-1 I've confirmed that the AdapterMappings.xml file is in /opt/shrine/tomcat/lib/ I've looked in my i2b2 ontology in the database on the i2b2 server, and I don't have anything that starts with i2b2_DEMO, just i2b2 (if I understand it correctly). On a hunch I tried replacing "i2b2_DEMO" in my AdapterMappings.xml file with "i2b2", so that the mapping becomes: \\i2b2\i2b2\Demographics\Gender\Male\ ...and I restarted SHRINE. However, I'm still getting the same error message about the missing concept from the Ontology. I feel like I'm not understanding the proper use of the AdapterMappings.xml file, because even if my change was incorrect I would have expected the error message to reflect the change in the naming that I did., but it didn't. -------------- next part -------------- An HTML attachment was scrubbed... URL: From beninato at ohsu.edu Wed Oct 8 18:11:43 2014 From: beninato at ohsu.edu (Peter Beninato) Date: Wed, 8 Oct 2014 22:11:43 +0000 Subject: [Shrine-users] Trouble with "Missing Concept in Ontology Cell" -- AdapterMappings.csv ? Message-ID: <43ECC5435444BE479E03012738A1400F151500EA@EXMB03.ohsu.edu> Hi Nich, I see from tomcat.sh to determine-adpater-mapping-url.pl it seems the source for AdapterMappings.xml for v1.17 is: https://open.med.harvard.edu/svn/shrine/releases/1.17.0/ontology/SHRINE_Demo_Downloads/AdapterMappings_i2b2_DemoData.xml Where are/is the AdapterMappings.csv file in source_control? Thanks. -Peter From: Wattanasin, Nich [mailto:NWATTANASIN at mgh.harvard.edu] Sent: Wednesday, October 08, 2014 2:58 PM To: 'Jeff Mark Lunt'; Peter Beninato; shrine-users at open.med.harvard.edu; Sushma Patil Subject: RE: [Shrine-users] Trouble with "Missing Concept in Ontology Cell" -- table_access.c_table_cd Hi Jeff, It seems your understanding of the AdapterMappings is correct. It maps SHRINE Ontology paths (e.g. \\SHRINE\) to Local Ontology paths (e.g. \\i2b2_Demo\ or whatever your local path is), and then sends those Local Paths to the CRC. If your SHRINE is setup correctly, then your hunch would also be my approach for a quick verification test since it would be the SHRINE cell that sends \\i2b2_DEMO\i2b2\Demographics\Male to the CRC. Since you?ve changed it to \\i2b2\i2b2\... , and it is still sending \\i2b2_Demo\i2b2... my first thought is to check the SHRINE log to make sure that the correct AdapterMappings.xml is being loaded from the correct path. The latest version of SHRINE can also use an AdapterMappings.csv file?I?m not sure if you have one of those loaded in addition to the .xml. Thanks, Nich ______________________________________ Nich Wattanasin Research Computing | Partners Healthcare E-mail: nwattanasin at partners.org [partnershealthcare] From: shrine-users-bounces at open.med.harvard.edu [mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of Jeff Mark Lunt Sent: Wednesday, October 08, 2014 5:48 PM To: Peter Beninato; shrine-users at open.med.harvard.edu; Sushma Patil Subject: Re: [Shrine-users] Trouble with "Missing Concept in Ontology Cell" -- table_access.c_table_cd Thanks, Peter and Sushma, for the tip. I did check that, and it answers my question in terms of the mapping ? thank you! I did have a big error in my log which I've fixed by making sure that my shrine.conf was setup (it was completely missing ? don't know how I missed that), but that hasn't change the error message I'm getting in the message log. I'm still getting the same "Missing Concept in Ontology Cell" message. No more errors in my /opt/shrine/tomcat/log/shrine.log anymore, or any errors in any of the logs in that same folder. Best I can guess now is that I have a mistake somewhere in the config where SHRINE looks to do i2b2 ontology lookups. Somethings that might be relevant: * I'm doing a standalone (separate from i2b2 server) install of SHRINE, meaning that SHRINE runs on its own VM and is configured to talk to another VM * The only DB that's on the SHRINE server is the mysql instance with the query audit history ? I was trying to avoid having to install Oracle or Postgres on the SHRINE server by re-using my i2b2 DB, and pointing its data sources at that DB in the ont-ds.xml file From: Peter Beninato > Date: Wednesday, October 8, 2014 at 4:09 PM To: Jeff Lunt >, "shrine-users at open.med.harvard.edu" > Subject: RE: Trouble with "Missing Concept in Ontology Cell" -- table_access.c_table_cd Hi, The \\i2b2_DEMO part comes for the ?META_DATA?.table_access.c_table_cd. I don?t use the underscore suffixes, my table only has one entry, with both the c_table_cd and c_table_name set to ?i2b2.? So, I do go in and find and replace in the AdapterMappings.xml. Do you see any errors in the tomcat shrine.log? -Peter From: shrine-users-bounces at open.med.harvard.edu [mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of Jeff Mark Lunt Sent: Wednesday, October 08, 2014 2:03 PM To: shrine-users at open.med.harvard.edu Subject: Re: [Shrine-users] Trouble with "Missing Concept in Ontology Cell" Sorry, I should have included that I got this error when inspecting the XML Message History for the "Previous Queries" pane in SHRINE, and that it was under the "getQueryInstanceList_fromQueryMasterId" message. From: Jeff Lunt > Date: Wednesday, October 8, 2014 at 4:00 PM To: "shrine-users at open.med.harvard.edu" > Subject: Trouble with "Missing Concept in Ontology Cell" I ran through the manual install for SHRINE, I have and I have a working i2b2 demo instance that works in terms of running queries. I ran a query in i2b2 asking the number of males in the demo data, and I got back 82. When I run the same query in SHRINE (talking to that i2b2 instance), I get back the following error: Missing Concept in Ontology Cell : [\\i2b2_DEMO\i2b2\Demographics\Gender\Male\] panel#-1 I've confirmed that the AdapterMappings.xml file is in /opt/shrine/tomcat/lib/ I've looked in my i2b2 ontology in the database on the i2b2 server, and I don't have anything that starts with i2b2_DEMO, just i2b2 (if I understand it correctly). On a hunch I tried replacing "i2b2_DEMO" in my AdapterMappings.xml file with "i2b2", so that the mapping becomes: \\i2b2\i2b2\Demographics\Gender\Male\ ...and I restarted SHRINE. However, I'm still getting the same error message about the missing concept from the Ontology. I feel like I'm not understanding the proper use of the AdapterMappings.xml file, because even if my change was incorrect I would have expected the error message to reflect the change in the naming that I did., but it didn't. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.gif Type: image/gif Size: 2674 bytes Desc: image001.gif URL: From beninato at ohsu.edu Wed Oct 8 19:16:05 2014 From: beninato at ohsu.edu (Peter Beninato) Date: Wed, 8 Oct 2014 23:16:05 +0000 Subject: [Shrine-users] SHRINE ontology - modifiers - m_applied_path / c_fullname - case of text Message-ID: <43ECC5435444BE479E03012738A1400F15150109@EXMB03.ohsu.edu> Hi, I get an error when running a SHRINE query for Diagnoses. I'm using ICD9 441.5. I have loaded Admit and Primary DX's so far. I added the "modifiers" to the i2b2 ontology via: i2b2_metadata_modifiers_insert_data.sql I loaded the modifier_dimension for the the three DX modifiers: Admit, Primary, Secondary. I can run for "ADMIT" DX via the i2b2 webclient with NO ERRORs, and get a count. Via the shrine-webclient, I get an ERROR. It is just a hunch, but there seems to be a disconnect on case. The m_applied_path for an i2b2 modifier ontology item might look like: \SHRINE\Diagnoses\Diseases of the circulatory system (390-459.99)\% But the third tuple of the entry in the DX ontology looks like: \SHRINE\Diagnoses\DISEASES OF THE CIRCULATORY SYSTEM (390-459.99)\... Could this explain why I'm not seeing the icons: Admit, Primary, Secondary in the SHRINE ontology when I expand the tree? And why the shrine query is going ERROR? Thanks. _ Peter Beninato - OCTRI DW Developer Oregon Health & Science University 503-494-9985 beninato at ohsu.edu _ The information contained in this EMAIL message is confidential and protected by law. The information is intended only for the person or business identified in the document. If you are not the intended recipient, a sharing or copying the information will result in a violation of the law. If you have received this EMAIL by mistake, please notify the sender of this EMAIL and copy the Office of Information Privacy & Security at oips at ohsu.edu. Please remember to cite the NCRR/NCATS-funded CTSA grant (UL1RR024140) in any publications resulting from OCTRI funding, support services or consultations, and to submit your publication to PubMed Central. -------------- next part -------------- An HTML attachment was scrubbed... URL: From beninato at ohsu.edu Wed Oct 8 19:30:38 2014 From: beninato at ohsu.edu (Peter Beninato) Date: Wed, 8 Oct 2014 23:30:38 +0000 Subject: [Shrine-users] SHRINE ontology - modifiers - m_applied_path / c_fullname - case of text Message-ID: <43ECC5435444BE479E03012738A1400F15150120@EXMB03.ohsu.edu> Hi, Yes. There is an impact due to CASE. I changed the ADMIT Modifier ontology m_applied_path entry to use UPPER CASE as in: \SHRINE\Diagnoses\ DISEASES OF THE CIRCULATORY SYSTEM (390-459.99)\% And the ADMIT ICON now appears. Still getting an ERROR, but making progress. Fyi. -Peter From: Peter Beninato Sent: Wednesday, October 08, 2014 4:16 PM To: shrine-users at open.med.harvard.edu Subject: SHRINE ontology - modifiers - m_applied_path / c_fullname - case of text Hi, I get an error when running a SHRINE query for Diagnoses. I'm using ICD9 441.5. I have loaded Admit and Primary DX's so far. I added the "modifiers" to the i2b2 ontology via: i2b2_metadata_modifiers_insert_data.sql I loaded the modifier_dimension for the the three DX modifiers: Admit, Primary, Secondary. I can run for "ADMIT" DX via the i2b2 webclient with NO ERRORs, and get a count. Via the shrine-webclient, I get an ERROR. It is just a hunch, but there seems to be a disconnect on case. The m_applied_path for an i2b2 modifier ontology item might look like: \SHRINE\Diagnoses\Diseases of the circulatory system (390-459.99)\% But the third tuple of the entry in the DX ontology looks like: \SHRINE\Diagnoses\DISEASES OF THE CIRCULATORY SYSTEM (390-459.99)\... Could this explain why I'm not seeing the icons: Admit, Primary, Secondary in the SHRINE ontology when I expand the tree? And why the shrine query is going ERROR? Thanks. _ Peter Beninato - OCTRI DW Developer Oregon Health & Science University 503-494-9985 beninato at ohsu.edu _ The information contained in this EMAIL message is confidential and protected by law. The information is intended only for the person or business identified in the document. If you are not the intended recipient, a sharing or copying the information will result in a violation of the law. If you have received this EMAIL by mistake, please notify the sender of this EMAIL and copy the Office of Information Privacy & Security at oips at ohsu.edu. Please remember to cite the NCRR/NCATS-funded CTSA grant (UL1RR024140) in any publications resulting from OCTRI funding, support services or consultations, and to submit your publication to PubMed Central. -------------- next part -------------- An HTML attachment was scrubbed... URL: From NWATTANASIN at mgh.harvard.edu Wed Oct 8 17:58:10 2014 From: NWATTANASIN at mgh.harvard.edu (Wattanasin, Nich) Date: Wed, 8 Oct 2014 21:58:10 +0000 Subject: [Shrine-users] Trouble with "Missing Concept in Ontology Cell" -- table_access.c_table_cd In-Reply-To: References: <43ECC5435444BE479E03012738A1400F151500B0@EXMB03.ohsu.edu> Message-ID: Hi Jeff, It seems your understanding of the AdapterMappings is correct. It maps SHRINE Ontology paths (e.g. \\SHRINE\) to Local Ontology paths (e.g. \\i2b2_Demo\ or whatever your local path is), and then sends those Local Paths to the CRC. If your SHRINE is setup correctly, then your hunch would also be my approach for a quick verification test since it would be the SHRINE cell that sends \\i2b2_DEMO\i2b2\Demographics\Male to the CRC. Since you?ve changed it to \\i2b2\i2b2\... , and it is still sending \\i2b2_Demo\i2b2... my first thought is to check the SHRINE log to make sure that the correct AdapterMappings.xml is being loaded from the correct path. The latest version of SHRINE can also use an AdapterMappings.csv file?I?m not sure if you have one of those loaded in addition to the .xml. Thanks, Nich ______________________________________ Nich Wattanasin Research Computing | Partners Healthcare E-mail: nwattanasin at partners.org [partnershealthcare] From: shrine-users-bounces at open.med.harvard.edu [mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of Jeff Mark Lunt Sent: Wednesday, October 08, 2014 5:48 PM To: Peter Beninato; shrine-users at open.med.harvard.edu; Sushma Patil Subject: Re: [Shrine-users] Trouble with "Missing Concept in Ontology Cell" -- table_access.c_table_cd Thanks, Peter and Sushma, for the tip. I did check that, and it answers my question in terms of the mapping ? thank you! I did have a big error in my log which I've fixed by making sure that my shrine.conf was setup (it was completely missing ? don't know how I missed that), but that hasn't change the error message I'm getting in the message log. I'm still getting the same "Missing Concept in Ontology Cell" message. No more errors in my /opt/shrine/tomcat/log/shrine.log anymore, or any errors in any of the logs in that same folder. Best I can guess now is that I have a mistake somewhere in the config where SHRINE looks to do i2b2 ontology lookups. Somethings that might be relevant: * I'm doing a standalone (separate from i2b2 server) install of SHRINE, meaning that SHRINE runs on its own VM and is configured to talk to another VM * The only DB that's on the SHRINE server is the mysql instance with the query audit history ? I was trying to avoid having to install Oracle or Postgres on the SHRINE server by re-using my i2b2 DB, and pointing its data sources at that DB in the ont-ds.xml file From: Peter Beninato > Date: Wednesday, October 8, 2014 at 4:09 PM To: Jeff Lunt >, "shrine-users at open.med.harvard.edu" > Subject: RE: Trouble with "Missing Concept in Ontology Cell" -- table_access.c_table_cd Hi, The \\i2b2_DEMO part comes for the ?META_DATA?.table_access.c_table_cd. I don?t use the underscore suffixes, my table only has one entry, with both the c_table_cd and c_table_name set to ?i2b2.? So, I do go in and find and replace in the AdapterMappings.xml. Do you see any errors in the tomcat shrine.log? -Peter From: shrine-users-bounces at open.med.harvard.edu [mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of Jeff Mark Lunt Sent: Wednesday, October 08, 2014 2:03 PM To: shrine-users at open.med.harvard.edu Subject: Re: [Shrine-users] Trouble with "Missing Concept in Ontology Cell" Sorry, I should have included that I got this error when inspecting the XML Message History for the "Previous Queries" pane in SHRINE, and that it was under the "getQueryInstanceList_fromQueryMasterId" message. From: Jeff Lunt > Date: Wednesday, October 8, 2014 at 4:00 PM To: "shrine-users at open.med.harvard.edu" > Subject: Trouble with "Missing Concept in Ontology Cell" I ran through the manual install for SHRINE, I have and I have a working i2b2 demo instance that works in terms of running queries. I ran a query in i2b2 asking the number of males in the demo data, and I got back 82. When I run the same query in SHRINE (talking to that i2b2 instance), I get back the following error: Missing Concept in Ontology Cell : [\\i2b2_DEMO\i2b2\Demographics\Gender\Male\] panel#-1 I've confirmed that the AdapterMappings.xml file is in /opt/shrine/tomcat/lib/ I've looked in my i2b2 ontology in the database on the i2b2 server, and I don't have anything that starts with i2b2_DEMO, just i2b2 (if I understand it correctly). On a hunch I tried replacing "i2b2_DEMO" in my AdapterMappings.xml file with "i2b2", so that the mapping becomes: \\i2b2\i2b2\Demographics\Gender\Male\ ...and I restarted SHRINE. However, I'm still getting the same error message about the missing concept from the Ontology. I feel like I'm not understanding the proper use of the AdapterMappings.xml file, because even if my change was incorrect I would have expected the error message to reflect the change in the naming that I did., but it didn't. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.gif Type: image/gif Size: 2674 bytes Desc: image001.gif URL: From NWATTANASIN at mgh.harvard.edu Wed Oct 8 18:14:59 2014 From: NWATTANASIN at mgh.harvard.edu (Wattanasin, Nich) Date: Wed, 8 Oct 2014 22:14:59 +0000 Subject: [Shrine-users] Trouble with "Missing Concept in Ontology Cell" -- AdapterMappings.csv ? In-Reply-To: <43ECC5435444BE479E03012738A1400F151500EA@EXMB03.ohsu.edu> References: <43ECC5435444BE479E03012738A1400F151500EA@EXMB03.ohsu.edu> Message-ID: Sorry for the confusion. I see that a CSV version for the i2b2 demo data is not available. SHRINE 1.17 introduced support for a CSV mapping file, but it looks like it is currently only being used in the PCORI project.. Thanks, Nich From: Peter Beninato [mailto:beninato at ohsu.edu] Sent: Wednesday, October 08, 2014 6:12 PM To: Wattanasin, Nich; 'Jeff Mark Lunt'; shrine-users at open.med.harvard.edu; Sushma Patil Subject: RE: [Shrine-users] Trouble with "Missing Concept in Ontology Cell" -- AdapterMappings.csv ? Hi Nich, I see from tomcat.sh to determine-adpater-mapping-url.pl it seems the source for AdapterMappings.xml for v1.17 is: https://open.med.harvard.edu/svn/shrine/releases/1.17.0/ontology/SHRINE_Demo_Downloads/AdapterMappings_i2b2_DemoData.xml Where are/is the AdapterMappings.csv file in source_control? Thanks. -Peter From: Wattanasin, Nich [mailto:NWATTANASIN at mgh.harvard.edu] Sent: Wednesday, October 08, 2014 2:58 PM To: 'Jeff Mark Lunt'; Peter Beninato; shrine-users at open.med.harvard.edu; Sushma Patil Subject: RE: [Shrine-users] Trouble with "Missing Concept in Ontology Cell" -- table_access.c_table_cd Hi Jeff, It seems your understanding of the AdapterMappings is correct. It maps SHRINE Ontology paths (e.g. \\SHRINE\) to Local Ontology paths (e.g. \\i2b2_Demo\ or whatever your local path is), and then sends those Local Paths to the CRC. If your SHRINE is setup correctly, then your hunch would also be my approach for a quick verification test since it would be the SHRINE cell that sends \\i2b2_DEMO\i2b2\Demographics\Male to the CRC. Since you?ve changed it to \\i2b2\i2b2\... , and it is still sending \\i2b2_Demo\i2b2... my first thought is to check the SHRINE log to make sure that the correct AdapterMappings.xml is being loaded from the correct path. The latest version of SHRINE can also use an AdapterMappings.csv file?I?m not sure if you have one of those loaded in addition to the .xml. Thanks, Nich ______________________________________ Nich Wattanasin Research Computing | Partners Healthcare E-mail: nwattanasin at partners.org [partnershealthcare] From: shrine-users-bounces at open.med.harvard.edu [mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of Jeff Mark Lunt Sent: Wednesday, October 08, 2014 5:48 PM To: Peter Beninato; shrine-users at open.med.harvard.edu; Sushma Patil Subject: Re: [Shrine-users] Trouble with "Missing Concept in Ontology Cell" -- table_access.c_table_cd Thanks, Peter and Sushma, for the tip. I did check that, and it answers my question in terms of the mapping ? thank you! I did have a big error in my log which I've fixed by making sure that my shrine.conf was setup (it was completely missing ? don't know how I missed that), but that hasn't change the error message I'm getting in the message log. I'm still getting the same "Missing Concept in Ontology Cell" message. No more errors in my /opt/shrine/tomcat/log/shrine.log anymore, or any errors in any of the logs in that same folder. Best I can guess now is that I have a mistake somewhere in the config where SHRINE looks to do i2b2 ontology lookups. Somethings that might be relevant: * I'm doing a standalone (separate from i2b2 server) install of SHRINE, meaning that SHRINE runs on its own VM and is configured to talk to another VM * The only DB that's on the SHRINE server is the mysql instance with the query audit history ? I was trying to avoid having to install Oracle or Postgres on the SHRINE server by re-using my i2b2 DB, and pointing its data sources at that DB in the ont-ds.xml file From: Peter Beninato > Date: Wednesday, October 8, 2014 at 4:09 PM To: Jeff Lunt >, "shrine-users at open.med.harvard.edu" > Subject: RE: Trouble with "Missing Concept in Ontology Cell" -- table_access.c_table_cd Hi, The \\i2b2_DEMO part comes for the ?META_DATA?.table_access.c_table_cd. I don?t use the underscore suffixes, my table only has one entry, with both the c_table_cd and c_table_name set to ?i2b2.? So, I do go in and find and replace in the AdapterMappings.xml. Do you see any errors in the tomcat shrine.log? -Peter From: shrine-users-bounces at open.med.harvard.edu [mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of Jeff Mark Lunt Sent: Wednesday, October 08, 2014 2:03 PM To: shrine-users at open.med.harvard.edu Subject: Re: [Shrine-users] Trouble with "Missing Concept in Ontology Cell" Sorry, I should have included that I got this error when inspecting the XML Message History for the "Previous Queries" pane in SHRINE, and that it was under the "getQueryInstanceList_fromQueryMasterId" message. From: Jeff Lunt > Date: Wednesday, October 8, 2014 at 4:00 PM To: "shrine-users at open.med.harvard.edu" > Subject: Trouble with "Missing Concept in Ontology Cell" I ran through the manual install for SHRINE, I have and I have a working i2b2 demo instance that works in terms of running queries. I ran a query in i2b2 asking the number of males in the demo data, and I got back 82. When I run the same query in SHRINE (talking to that i2b2 instance), I get back the following error: Missing Concept in Ontology Cell : [\\i2b2_DEMO\i2b2\Demographics\Gender\Male\] panel#-1 I've confirmed that the AdapterMappings.xml file is in /opt/shrine/tomcat/lib/ I've looked in my i2b2 ontology in the database on the i2b2 server, and I don't have anything that starts with i2b2_DEMO, just i2b2 (if I understand it correctly). On a hunch I tried replacing "i2b2_DEMO" in my AdapterMappings.xml file with "i2b2", so that the mapping becomes: \\i2b2\i2b2\Demographics\Gender\Male\ ...and I restarted SHRINE. However, I'm still getting the same error message about the missing concept from the Ontology. I feel like I'm not understanding the proper use of the AdapterMappings.xml file, because even if my change was incorrect I would have expected the error message to reflect the change in the naming that I did., but it didn't. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.gif Type: image/gif Size: 2674 bytes Desc: image001.gif URL: From jeff.lunt at northwestern.edu Thu Oct 9 15:51:56 2014 From: jeff.lunt at northwestern.edu (Jeff Mark Lunt) Date: Thu, 9 Oct 2014 19:51:56 +0000 Subject: [Shrine-users] Trouble with "Missing Concept in Ontology Cell" -- table_access.c_table_cd In-Reply-To: <43ECC5435444BE479E03012738A1400F151500CE@EXMB03.ohsu.edu> References: <43ECC5435444BE479E03012738A1400F151500B0@EXMB03.ohsu.edu> <43ECC5435444BE479E03012738A1400F151500CE@EXMB03.ohsu.edu> Message-ID: No errors in the JBOSS log, but, something interesting: * If I run a query in i2b2, the query gets output into the JBOSS log * When I run the identical query in SHRINE, using the SHRINE Ontology, I get only the following on the Jboss side: * 14:42:07,977 INFO [stdout] (Thread-165) * 14:42:07,977 INFO [stdout] (Thread-165) <> 14:42:07,978 INFO [stdout] (Thread-165) insert into #dx ( patient_num ) select * from ( select distinct patient_num from #global_temp_table where panel_count = 0 ) q I can definitely access the i2b2 server from SHRINE. The PM cell is on the i2b2 server, and if I close the requisite ports on the i2b2 server, login into SHRINE stops working. I'm also able to curl from SHRINE to i2b2 and get the HTML/XML results. So, that much is working. Did I mention that we're using MSSQL (instead of Oracle or PostgreSQL), so when going through the install scripts for SHRINE, and the settings in i2b2.rc, shrine.rc, etc., I modified the settings to try to make them work with MSSQL. For example, for i2b2hive.ONT_DB_LOOKUP.C_DB_SERVERTYPE, this is a non-standard setting: [cid:0A9A5FE8-2C9D-48B1-BE71-83E9E250EBE6] From: Peter Beninato > Date: Wednesday, October 8, 2014 at 4:54 PM To: Jeff Lunt >, "shrine-users at open.med.harvard.edu" >, Sushma Patil > Subject: RE: Trouble with "Missing Concept in Ontology Cell" -- table_access.c_table_cd Hi, On the VM that is running shrine, can you check that you have connectivity to the server that is hosting your ontology? These setting should also be in the shrine.rc, i2b2.rc, and common.rc. Without a db client, I guess you at least ping. How about the JBOSS server.log? Are there any errors there? -Peter From: Jeff Mark Lunt [mailto:jeff.lunt at northwestern.edu] Sent: Wednesday, October 08, 2014 2:48 PM To: Peter Beninato; shrine-users at open.med.harvard.edu; Sushma Patil Subject: Re: Trouble with "Missing Concept in Ontology Cell" -- table_access.c_table_cd Thanks, Peter and Sushma, for the tip. I did check that, and it answers my question in terms of the mapping ? thank you! I did have a big error in my log which I've fixed by making sure that my shrine.conf was setup (it was completely missing ? don't know how I missed that), but that hasn't change the error message I'm getting in the message log. I'm still getting the same "Missing Concept in Ontology Cell" message. No more errors in my /opt/shrine/tomcat/log/shrine.log anymore, or any errors in any of the logs in that same folder. Best I can guess now is that I have a mistake somewhere in the config where SHRINE looks to do i2b2 ontology lookups. Somethings that might be relevant: * I'm doing a standalone (separate from i2b2 server) install of SHRINE, meaning that SHRINE runs on its own VM and is configured to talk to another VM * The only DB that's on the SHRINE server is the mysql instance with the query audit history ? I was trying to avoid having to install Oracle or Postgres on the SHRINE server by re-using my i2b2 DB, and pointing its data sources at that DB in the ont-ds.xml file From: Peter Beninato > Date: Wednesday, October 8, 2014 at 4:09 PM To: Jeff Lunt >, "shrine-users at open.med.harvard.edu" > Subject: RE: Trouble with "Missing Concept in Ontology Cell" -- table_access.c_table_cd Hi, The \\i2b2_DEMO part comes for the ?META_DATA?.table_access.c_table_cd. I don?t use the underscore suffixes, my table only has one entry, with both the c_table_cd and c_table_name set to ?i2b2.? So, I do go in and find and replace in the AdapterMappings.xml. Do you see any errors in the tomcat shrine.log? -Peter From:shrine-users-bounces at open.med.harvard.edu [mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of Jeff Mark Lunt Sent: Wednesday, October 08, 2014 2:03 PM To: shrine-users at open.med.harvard.edu Subject: Re: [Shrine-users] Trouble with "Missing Concept in Ontology Cell" Sorry, I should have included that I got this error when inspecting the XML Message History for the "Previous Queries" pane in SHRINE, and that it was under the "getQueryInstanceList_fromQueryMasterId" message. From: Jeff Lunt > Date: Wednesday, October 8, 2014 at 4:00 PM To: "shrine-users at open.med.harvard.edu" > Subject: Trouble with "Missing Concept in Ontology Cell" I ran through the manual install for SHRINE, I have and I have a working i2b2 demo instance that works in terms of running queries. I ran a query in i2b2 asking the number of males in the demo data, and I got back 82. When I run the same query in SHRINE (talking to that i2b2 instance), I get back the following error: Missing Concept in Ontology Cell : [\\i2b2_DEMO\i2b2\Demographics\Gender\Male\] panel#-1 I've confirmed that the AdapterMappings.xml file is in /opt/shrine/tomcat/lib/ I've looked in my i2b2 ontology in the database on the i2b2 server, and I don't have anything that starts with i2b2_DEMO, just i2b2 (if I understand it correctly). On a hunch I tried replacing "i2b2_DEMO" in my AdapterMappings.xml file with "i2b2", so that the mapping becomes: \\i2b2\i2b2\Demographics\Gender\Male\ ...and I restarted SHRINE. However, I'm still getting the same error message about the missing concept from the Ontology. I feel like I'm not understanding the proper use of the AdapterMappings.xml file, because even if my change was incorrect I would have expected the error message to reflect the change in the naming that I did., but it didn't. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2014-10-09 at 2.50.36 PM.png Type: image/png Size: 15390 bytes Desc: Screen Shot 2014-10-09 at 2.50.36 PM.png URL: From jeff.lunt at northwestern.edu Thu Oct 9 15:58:12 2014 From: jeff.lunt at northwestern.edu (Jeff Mark Lunt) Date: Thu, 9 Oct 2014 19:58:12 +0000 Subject: [Shrine-users] Trouble with "Missing Concept in Ontology Cell" -- AdapterMappings.csv ? In-Reply-To: References: <43ECC5435444BE479E03012738A1400F151500EA@EXMB03.ohsu.edu> Message-ID: Thanks Nich, Sushma was able to help me answer the 'i2b2_DEMO' question. I wound up: 1. Changing it to 'i2b2' in the DB, confirming that the query changed to '\\i2b2\i2b2', and then changed everything back to defaults since I know understood how it worked 2. The path to the AdapterMappings.xml file appears to be correct, as I see it loaded in the SHIRNE startup log. I verified this with the following steps: * Shutdown shrine * Renamed AdapterMappings.xml to AdapterMappings.xml.bak * Started shrine ? the log threw errors saying that the file was missing * Shutdown shrine * Renamed the file back to its original name * Started shrine ? errors went away From: , Nich > Date: Wednesday, October 8, 2014 at 5:14 PM To: 'Peter Beninato' >, Jeff Lunt >, "shrine-users at open.med.harvard.edu" >, Sushma Patil > Subject: RE: [Shrine-users] Trouble with "Missing Concept in Ontology Cell" -- AdapterMappings.csv ? Sorry for the confusion. I see that a CSV version for the i2b2 demo data is not available. SHRINE 1.17 introduced support for a CSV mapping file, but it looks like it is currently only being used in the PCORI project.. Thanks, Nich From: Peter Beninato [mailto:beninato at ohsu.edu] Sent: Wednesday, October 08, 2014 6:12 PM To: Wattanasin, Nich; 'Jeff Mark Lunt'; shrine-users at open.med.harvard.edu; Sushma Patil Subject: RE: [Shrine-users] Trouble with "Missing Concept in Ontology Cell" -- AdapterMappings.csv ? Hi Nich, I see from tomcat.sh to determine-adpater-mapping-url.pl it seems the source for AdapterMappings.xml for v1.17 is: https://open.med.harvard.edu/svn/shrine/releases/1.17.0/ontology/SHRINE_Demo_Downloads/AdapterMappings_i2b2_DemoData.xml Where are/is the AdapterMappings.csv file in source_control? Thanks. -Peter From: Wattanasin, Nich [mailto:NWATTANASIN at mgh.harvard.edu] Sent: Wednesday, October 08, 2014 2:58 PM To: 'Jeff Mark Lunt'; Peter Beninato; shrine-users at open.med.harvard.edu; Sushma Patil Subject: RE: [Shrine-users] Trouble with "Missing Concept in Ontology Cell" -- table_access.c_table_cd Hi Jeff, It seems your understanding of the AdapterMappings is correct. It maps SHRINE Ontology paths (e.g. \\SHRINE\) to Local Ontology paths (e.g. \\i2b2_Demo\ or whatever your local path is), and then sends those Local Paths to the CRC. If your SHRINE is setup correctly, then your hunch would also be my approach for a quick verification test since it would be the SHRINE cell that sends \\i2b2_DEMO\i2b2\Demographics\Male to the CRC. Since you?ve changed it to \\i2b2\i2b2\... , and it is still sending \\i2b2_Demo\i2b2... my first thought is to check the SHRINE log to make sure that the correct AdapterMappings.xml is being loaded from the correct path. The latest version of SHRINE can also use an AdapterMappings.csv file?I?m not sure if you have one of those loaded in addition to the .xml. Thanks, Nich ______________________________________ Nich Wattanasin Research Computing | Partners Healthcare E-mail: nwattanasin at partners.org [partnershealthcare] From:shrine-users-bounces at open.med.harvard.edu [mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of Jeff Mark Lunt Sent: Wednesday, October 08, 2014 5:48 PM To: Peter Beninato; shrine-users at open.med.harvard.edu; Sushma Patil Subject: Re: [Shrine-users] Trouble with "Missing Concept in Ontology Cell" -- table_access.c_table_cd Thanks, Peter and Sushma, for the tip. I did check that, and it answers my question in terms of the mapping ? thank you! I did have a big error in my log which I've fixed by making sure that my shrine.conf was setup (it was completely missing ? don't know how I missed that), but that hasn't change the error message I'm getting in the message log. I'm still getting the same "Missing Concept in Ontology Cell" message. No more errors in my /opt/shrine/tomcat/log/shrine.log anymore, or any errors in any of the logs in that same folder. Best I can guess now is that I have a mistake somewhere in the config where SHRINE looks to do i2b2 ontology lookups. Somethings that might be relevant: * I'm doing a standalone (separate from i2b2 server) install of SHRINE, meaning that SHRINE runs on its own VM and is configured to talk to another VM * The only DB that's on the SHRINE server is the mysql instance with the query audit history ? I was trying to avoid having to install Oracle or Postgres on the SHRINE server by re-using my i2b2 DB, and pointing its data sources at that DB in the ont-ds.xml file From: Peter Beninato > Date: Wednesday, October 8, 2014 at 4:09 PM To: Jeff Lunt >, "shrine-users at open.med.harvard.edu" > Subject: RE: Trouble with "Missing Concept in Ontology Cell" -- table_access.c_table_cd Hi, The \\i2b2_DEMO part comes for the ?META_DATA?.table_access.c_table_cd. I don?t use the underscore suffixes, my table only has one entry, with both the c_table_cd and c_table_name set to ?i2b2.? So, I do go in and find and replace in the AdapterMappings.xml. Do you see any errors in the tomcat shrine.log? -Peter From:shrine-users-bounces at open.med.harvard.edu [mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of Jeff Mark Lunt Sent: Wednesday, October 08, 2014 2:03 PM To: shrine-users at open.med.harvard.edu Subject: Re: [Shrine-users] Trouble with "Missing Concept in Ontology Cell" Sorry, I should have included that I got this error when inspecting the XML Message History for the "Previous Queries" pane in SHRINE, and that it was under the "getQueryInstanceList_fromQueryMasterId" message. From: Jeff Lunt > Date: Wednesday, October 8, 2014 at 4:00 PM To: "shrine-users at open.med.harvard.edu" > Subject: Trouble with "Missing Concept in Ontology Cell" I ran through the manual install for SHRINE, I have and I have a working i2b2 demo instance that works in terms of running queries. I ran a query in i2b2 asking the number of males in the demo data, and I got back 82. When I run the same query in SHRINE (talking to that i2b2 instance), I get back the following error: Missing Concept in Ontology Cell : [\\i2b2_DEMO\i2b2\Demographics\Gender\Male\] panel#-1 I've confirmed that the AdapterMappings.xml file is in /opt/shrine/tomcat/lib/ I've looked in my i2b2 ontology in the database on the i2b2 server, and I don't have anything that starts with i2b2_DEMO, just i2b2 (if I understand it correctly). On a hunch I tried replacing "i2b2_DEMO" in my AdapterMappings.xml file with "i2b2", so that the mapping becomes: \\i2b2\i2b2\Demographics\Gender\Male\ ...and I restarted SHRINE. However, I'm still getting the same error message about the missing concept from the Ontology. I feel like I'm not understanding the proper use of the AdapterMappings.xml file, because even if my change was incorrect I would have expected the error message to reflect the change in the naming that I did., but it didn't. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.gif Type: image/gif Size: 2674 bytes Desc: image001.gif URL: From jeff.lunt at northwestern.edu Thu Oct 9 16:00:30 2014 From: jeff.lunt at northwestern.edu (Jeff Mark Lunt) Date: Thu, 9 Oct 2014 20:00:30 +0000 Subject: [Shrine-users] Trouble with "Missing Concept in Ontology Cell" -- table_access.c_table_cd In-Reply-To: References: <43ECC5435444BE479E03012738A1400F151500B0@EXMB03.ohsu.edu> <43ECC5435444BE479E03012738A1400F151500CE@EXMB03.ohsu.edu> Message-ID: Perhaps it's folly to try to make SHRINE use MSSQL, as the queries might only "happen" to work in some cases because of similarity in syntax. Perhaps instead I should put an isolated Postgres instance on the SHRINE server since queries to the CRC are just XML. Maybe I just made this way more complicated than was necessary. Was trying to be "clever"? From: Jeff Lunt > Date: Thursday, October 9, 2014 at 2:51 PM To: Peter Beninato >, "shrine-users at open.med.harvard.edu" >, Sushma Patil > Subject: Re: [Shrine-users] Trouble with "Missing Concept in Ontology Cell" -- table_access.c_table_cd No errors in the JBOSS log, but, something interesting: * If I run a query in i2b2, the query gets output into the JBOSS log * When I run the identical query in SHRINE, using the SHRINE Ontology, I get only the following on the Jboss side: * 14:42:07,977 INFO [stdout] (Thread-165) * 14:42:07,977 INFO [stdout] (Thread-165) <> 14:42:07,978 INFO [stdout] (Thread-165) insert into #dx ( patient_num ) select * from ( select distinct patient_num from #global_temp_table where panel_count = 0 ) q I can definitely access the i2b2 server from SHRINE. The PM cell is on the i2b2 server, and if I close the requisite ports on the i2b2 server, login into SHRINE stops working. I'm also able to curl from SHRINE to i2b2 and get the HTML/XML results. So, that much is working. Did I mention that we're using MSSQL (instead of Oracle or PostgreSQL), so when going through the install scripts for SHRINE, and the settings in i2b2.rc, shrine.rc, etc., I modified the settings to try to make them work with MSSQL. For example, for i2b2hive.ONT_DB_LOOKUP.C_DB_SERVERTYPE, this is a non-standard setting: [cid:0A9A5FE8-2C9D-48B1-BE71-83E9E250EBE6] From: Peter Beninato > Date: Wednesday, October 8, 2014 at 4:54 PM To: Jeff Lunt >, "shrine-users at open.med.harvard.edu" >, Sushma Patil > Subject: RE: Trouble with "Missing Concept in Ontology Cell" -- table_access.c_table_cd Hi, On the VM that is running shrine, can you check that you have connectivity to the server that is hosting your ontology? These setting should also be in the shrine.rc, i2b2.rc, and common.rc. Without a db client, I guess you at least ping. How about the JBOSS server.log? Are there any errors there? -Peter From: Jeff Mark Lunt [mailto:jeff.lunt at northwestern.edu] Sent: Wednesday, October 08, 2014 2:48 PM To: Peter Beninato; shrine-users at open.med.harvard.edu; Sushma Patil Subject: Re: Trouble with "Missing Concept in Ontology Cell" -- table_access.c_table_cd Thanks, Peter and Sushma, for the tip. I did check that, and it answers my question in terms of the mapping ? thank you! I did have a big error in my log which I've fixed by making sure that my shrine.conf was setup (it was completely missing ? don't know how I missed that), but that hasn't change the error message I'm getting in the message log. I'm still getting the same "Missing Concept in Ontology Cell" message. No more errors in my /opt/shrine/tomcat/log/shrine.log anymore, or any errors in any of the logs in that same folder. Best I can guess now is that I have a mistake somewhere in the config where SHRINE looks to do i2b2 ontology lookups. Somethings that might be relevant: * I'm doing a standalone (separate from i2b2 server) install of SHRINE, meaning that SHRINE runs on its own VM and is configured to talk to another VM * The only DB that's on the SHRINE server is the mysql instance with the query audit history ? I was trying to avoid having to install Oracle or Postgres on the SHRINE server by re-using my i2b2 DB, and pointing its data sources at that DB in the ont-ds.xml file From: Peter Beninato > Date: Wednesday, October 8, 2014 at 4:09 PM To: Jeff Lunt >, "shrine-users at open.med.harvard.edu" > Subject: RE: Trouble with "Missing Concept in Ontology Cell" -- table_access.c_table_cd Hi, The \\i2b2_DEMO part comes for the ?META_DATA?.table_access.c_table_cd. I don?t use the underscore suffixes, my table only has one entry, with both the c_table_cd and c_table_name set to ?i2b2.? So, I do go in and find and replace in the AdapterMappings.xml. Do you see any errors in the tomcat shrine.log? -Peter From:shrine-users-bounces at open.med.harvard.edu [mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of Jeff Mark Lunt Sent: Wednesday, October 08, 2014 2:03 PM To: shrine-users at open.med.harvard.edu Subject: Re: [Shrine-users] Trouble with "Missing Concept in Ontology Cell" Sorry, I should have included that I got this error when inspecting the XML Message History for the "Previous Queries" pane in SHRINE, and that it was under the "getQueryInstanceList_fromQueryMasterId" message. From: Jeff Lunt > Date: Wednesday, October 8, 2014 at 4:00 PM To: "shrine-users at open.med.harvard.edu" > Subject: Trouble with "Missing Concept in Ontology Cell" I ran through the manual install for SHRINE, I have and I have a working i2b2 demo instance that works in terms of running queries. I ran a query in i2b2 asking the number of males in the demo data, and I got back 82. When I run the same query in SHRINE (talking to that i2b2 instance), I get back the following error: Missing Concept in Ontology Cell : [\\i2b2_DEMO\i2b2\Demographics\Gender\Male\] panel#-1 I've confirmed that the AdapterMappings.xml file is in /opt/shrine/tomcat/lib/ I've looked in my i2b2 ontology in the database on the i2b2 server, and I don't have anything that starts with i2b2_DEMO, just i2b2 (if I understand it correctly). On a hunch I tried replacing "i2b2_DEMO" in my AdapterMappings.xml file with "i2b2", so that the mapping becomes: \\i2b2\i2b2\Demographics\Gender\Male\ ...and I restarted SHRINE. However, I'm still getting the same error message about the missing concept from the Ontology. I feel like I'm not understanding the proper use of the AdapterMappings.xml file, because even if my change was incorrect I would have expected the error message to reflect the change in the naming that I did., but it didn't. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2014-10-09 at 2.50.36 PM.png Type: image/png Size: 15390 bytes Desc: Screen Shot 2014-10-09 at 2.50.36 PM.png URL: From ev2348 at columbia.edu Thu Oct 9 16:37:16 2014 From: ev2348 at columbia.edu (ev2348 at columbia.edu) Date: Thu, 09 Oct 2014 16:37:16 -0400 Subject: [Shrine-users] new data Message-ID: <20141009163716.0zbcsm64cgcok00o@cubmail.cc.columbia.edu> Hi, I have installed SHRINE with real de-identified data from our Server I2B2. This is not the domain i2b2demo any longer but cdwdemo domain id. The installation works and I get the Shrine webpage with the SHRINE Ontology Node. I have also modified AdapterMappings.xml according to the i2b2metadata.TABLE_ACCESS first Column C_TABLE_CD, but this is all I have done with AdapterMappings.xml When I try to run a query I get the message "The cell's status message could not be understood", and keeps going and going forever without turning any results or quitting. Could you please let me know what is wrong because with i2b2demo I had none of these problems. Best Regards Elena From jeff.lunt at northwestern.edu Thu Oct 9 16:58:22 2014 From: jeff.lunt at northwestern.edu (Jeff Mark Lunt) Date: Thu, 9 Oct 2014 20:58:22 +0000 Subject: [Shrine-users] Trouble with "Missing Concept in Ontology Cell" -- table_access.c_table_cd In-Reply-To: References: <43ECC5435444BE479E03012738A1400F151500B0@EXMB03.ohsu.edu> <43ECC5435444BE479E03012738A1400F151500CE@EXMB03.ohsu.edu> Message-ID: Let me state some assumptions to make sure I understand, because a fundamental misunderstanding is probably at the root of my issues. What I thought when I did the manual/split server install: * SHRINE uses MySQL to store query history locally (in fact, this is the only db data stored on the shrine server, in a split-server setup) * SHRINE sends/receives messages to i2b2 via RESTful services: * Authentication/authorization come via a combination of the PMCell/PMService, and TABLE_ACCESS data entries * Ontology terms come via a combination of the Ontology Cell/OntologyService, and the SHRINE table in the database referenced by the OntologyShrineDS in ont-ds.xml * Data queries come via a combination of the CRC Cell/QueryToolService, and the data that's stored in i2b2demodata database (or in a production table, it would probably be called something else) * The SHRINE ontology lives on the i2b2 server, and is accessed over the RESTful OntologyService Some more assumptions/things I'm cloudy on: * There doesn't seem to be any SHRINE support for MSSQL, but since the only thing that SHRINE stores locally in a split setup is the query audit history, shrine shouldn?t care what DBMS i2b2 uses, because that's abstracted away via the RESTful services * In a split setup, the only DBMS that should be required is MySQL on the SHRINE server * The only "reason" SHRINE doesn?t support MSSQL out of the box is because no one has written MSSQL scripts. * The environment variables that are DBMS specific in the SHRINE setup scripts are just to make the installation scripts work. They aren't used by SHRINE after the fact * Just like the workbench client doesn?t require a local DBMS to talk to i2b2, and since SHRINE is basically a thin web-based client to i2b2, the DBMS that i2b2 uses is irrelevant to getting SHRINE to work properly, assuming the i2b2 server is already working properly. See any assumptions that I have wrong in there? From: Jeff Lunt > Date: Thursday, October 9, 2014 at 3:00 PM To: Jeff Lunt >, Peter Beninato >, "shrine-users at open.med.harvard.edu" >, Sushma Patil > Subject: Re: [Shrine-users] Trouble with "Missing Concept in Ontology Cell" -- table_access.c_table_cd Perhaps it's folly to try to make SHRINE use MSSQL, as the queries might only "happen" to work in some cases because of similarity in syntax. Perhaps instead I should put an isolated Postgres instance on the SHRINE server since queries to the CRC are just XML. Maybe I just made this way more complicated than was necessary. Was trying to be "clever"? From: Jeff Lunt > Date: Thursday, October 9, 2014 at 2:51 PM To: Peter Beninato >, "shrine-users at open.med.harvard.edu" >, Sushma Patil > Subject: Re: [Shrine-users] Trouble with "Missing Concept in Ontology Cell" -- table_access.c_table_cd No errors in the JBOSS log, but, something interesting: * If I run a query in i2b2, the query gets output into the JBOSS log * When I run the identical query in SHRINE, using the SHRINE Ontology, I get only the following on the Jboss side: * 14:42:07,977 INFO [stdout] (Thread-165) * 14:42:07,977 INFO [stdout] (Thread-165) <> 14:42:07,978 INFO [stdout] (Thread-165) insert into #dx ( patient_num ) select * from ( select distinct patient_num from #global_temp_table where panel_count = 0 ) q I can definitely access the i2b2 server from SHRINE. The PM cell is on the i2b2 server, and if I close the requisite ports on the i2b2 server, login into SHRINE stops working. I'm also able to curl from SHRINE to i2b2 and get the HTML/XML results. So, that much is working. Did I mention that we're using MSSQL (instead of Oracle or PostgreSQL), so when going through the install scripts for SHRINE, and the settings in i2b2.rc, shrine.rc, etc., I modified the settings to try to make them work with MSSQL. For example, for i2b2hive.ONT_DB_LOOKUP.C_DB_SERVERTYPE, this is a non-standard setting: [cid:0A9A5FE8-2C9D-48B1-BE71-83E9E250EBE6] From: Peter Beninato > Date: Wednesday, October 8, 2014 at 4:54 PM To: Jeff Lunt >, "shrine-users at open.med.harvard.edu" >, Sushma Patil > Subject: RE: Trouble with "Missing Concept in Ontology Cell" -- table_access.c_table_cd Hi, On the VM that is running shrine, can you check that you have connectivity to the server that is hosting your ontology? These setting should also be in the shrine.rc, i2b2.rc, and common.rc. Without a db client, I guess you at least ping. How about the JBOSS server.log? Are there any errors there? -Peter From: Jeff Mark Lunt [mailto:jeff.lunt at northwestern.edu] Sent: Wednesday, October 08, 2014 2:48 PM To: Peter Beninato; shrine-users at open.med.harvard.edu; Sushma Patil Subject: Re: Trouble with "Missing Concept in Ontology Cell" -- table_access.c_table_cd Thanks, Peter and Sushma, for the tip. I did check that, and it answers my question in terms of the mapping ? thank you! I did have a big error in my log which I've fixed by making sure that my shrine.conf was setup (it was completely missing ? don't know how I missed that), but that hasn't change the error message I'm getting in the message log. I'm still getting the same "Missing Concept in Ontology Cell" message. No more errors in my /opt/shrine/tomcat/log/shrine.log anymore, or any errors in any of the logs in that same folder. Best I can guess now is that I have a mistake somewhere in the config where SHRINE looks to do i2b2 ontology lookups. Somethings that might be relevant: * I'm doing a standalone (separate from i2b2 server) install of SHRINE, meaning that SHRINE runs on its own VM and is configured to talk to another VM * The only DB that's on the SHRINE server is the mysql instance with the query audit history ? I was trying to avoid having to install Oracle or Postgres on the SHRINE server by re-using my i2b2 DB, and pointing its data sources at that DB in the ont-ds.xml file From: Peter Beninato > Date: Wednesday, October 8, 2014 at 4:09 PM To: Jeff Lunt >, "shrine-users at open.med.harvard.edu" > Subject: RE: Trouble with "Missing Concept in Ontology Cell" -- table_access.c_table_cd Hi, The \\i2b2_DEMO part comes for the ?META_DATA?.table_access.c_table_cd. I don?t use the underscore suffixes, my table only has one entry, with both the c_table_cd and c_table_name set to ?i2b2.? So, I do go in and find and replace in the AdapterMappings.xml. Do you see any errors in the tomcat shrine.log? -Peter From:shrine-users-bounces at open.med.harvard.edu [mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of Jeff Mark Lunt Sent: Wednesday, October 08, 2014 2:03 PM To: shrine-users at open.med.harvard.edu Subject: Re: [Shrine-users] Trouble with "Missing Concept in Ontology Cell" Sorry, I should have included that I got this error when inspecting the XML Message History for the "Previous Queries" pane in SHRINE, and that it was under the "getQueryInstanceList_fromQueryMasterId" message. From: Jeff Lunt > Date: Wednesday, October 8, 2014 at 4:00 PM To: "shrine-users at open.med.harvard.edu" > Subject: Trouble with "Missing Concept in Ontology Cell" I ran through the manual install for SHRINE, I have and I have a working i2b2 demo instance that works in terms of running queries. I ran a query in i2b2 asking the number of males in the demo data, and I got back 82. When I run the same query in SHRINE (talking to that i2b2 instance), I get back the following error: Missing Concept in Ontology Cell : [\\i2b2_DEMO\i2b2\Demographics\Gender\Male\] panel#-1 I've confirmed that the AdapterMappings.xml file is in /opt/shrine/tomcat/lib/ I've looked in my i2b2 ontology in the database on the i2b2 server, and I don't have anything that starts with i2b2_DEMO, just i2b2 (if I understand it correctly). On a hunch I tried replacing "i2b2_DEMO" in my AdapterMappings.xml file with "i2b2", so that the mapping becomes: \\i2b2\i2b2\Demographics\Gender\Male\ ...and I restarted SHRINE. However, I'm still getting the same error message about the missing concept from the Ontology. I feel like I'm not understanding the proper use of the AdapterMappings.xml file, because even if my change was incorrect I would have expected the error message to reflect the change in the naming that I did., but it didn't. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2014-10-09 at 2.50.36 PM.png Type: image/png Size: 15390 bytes Desc: Screen Shot 2014-10-09 at 2.50.36 PM.png URL: From ev2348 at columbia.edu Fri Oct 10 14:42:53 2014 From: ev2348 at columbia.edu (ev2348 at columbia.edu) Date: Fri, 10 Oct 2014 14:42:53 -0400 Subject: [Shrine-users] adapter prpoblems Message-ID: <20141010144253.wikhw3434ss804sg@cubmail.cc.columbia.edu> Hi, I did solve some of the issues installing shrine with real data from NYPH at Columbia. I had some misconfiguration going from i2b2demo to i2b2cdw, which is our domain name here, that I needed to resolve. For the hospital i2b2 instance, the project id is CDW and the user is cdwuser. Now I can count Demographics and connect to the local (NYPH) i2b2 instance with no issues for the real data from the hospital. Anyway, my questions are about the AdapterMappings.xml. I have made some changes to the original file that I downloaded from Harvard for i2b2demo according to the terminology in table i2b2metadata.table_access. I replaced some of the terminology according to the names for columns C_table_cd and C_fullname. We use MED here for diagnosis and when I run some of the queries (anything that is not Demographics) I get error messages in Tomcat/logs/shrine. Please see some of the output below. It looks as it does not understand the terminology we use here. It goes on and on complaining about the mapping. Could you please let me know how I can get this to work. Best Elena 2014-Oct-10-12:43:05.364 DEBUG [SHRINE][SquerylAdapterDao][ForkJoinPool-1-worker-3] User i2b2CDW:shrine locked out? false 2014-Oct-10-12:43:05.364 DEBUG [SHRINE][RunQueryAdapter][ForkJoinPool-1-worker-3] Performing query from user i2b2CDW:shrine 2014-Oct-10-12:43:05.364 DEBUG [SHRINE][ExpressionTranslator][ForkJoinPool-1-worker-3] Translated: Term(\\SHRINE\SHRINE\Labs\LP32651-9\LP67162-5\) to Failure(net.shrine.adapter.AdapterMappingException: No local terms mapped to '\\SHRINE\SHRINE\Labs\LP32651-9\LP67162-5\') 2014-Oct-10-12:43:05.365 WARN [SHRINE][RunQueryAdapter][ForkJoinPool-1-worker-3] Error mapping query terms: Error mapping query terms from network to local forms. request: RunQueryRequest(CDW,180000 milliseconds,AuthenticationInfo(***,,Credential(,false)),2519699543816905284,None,Set(PATIENT_COUNT_XML),QueryDefinition(Blood group ant at 12:43:03,Term(\\SHRINE\SHRINE\Labs\LP32651-9\LP67162-5\))) net.shrine.adapter.AdapterMappingException: Error mapping query terms from network to local forms. request: RunQueryRequest(CDW,180000 milliseconds,AuthenticationInfo(,,Credential(,false)),2519699543816905284,None,Set(PATIENT_COUNT_XML),QueryDefinition(Blood group ant at 12:43:03,Term(\\SHRINE\SHRINE\Labs\LP32651-9\LP67162-5\))) at net.shrine.adapter.RunQueryAdapter.translateNetworkToLocal(RunQueryAdapter.scala:60) at net.shrine.adapter.RunQueryAdapter.translateNetworkToLocal(RunQueryAdapter.scala:42) at net.shrine.adapter.CrcAdapter.translateRequest(CrcAdapter.scala:95) at net.shrine.adapter.CrcAdapter.processRequest(CrcAdapter.scala:60) at net.shrine.adapter.RunQueryAdapter.runQuery(RunQueryAdapter.scala:121) at net.shrine.adapter.RunQueryAdapter.processRequest(RunQueryAdapter.scala:85) at net.shrine.adapter.RunQueryAdapter.processRequest(RunQueryAdapter.scala:42) at net.shrine.adapter.Adapter.perform(Adapter.scala:26) at net.shr From William.Shuman at cchmc.org Fri Oct 10 15:21:31 2014 From: William.Shuman at cchmc.org (Shuman, William (Billy)) Date: Fri, 10 Oct 2014 19:21:31 +0000 Subject: [Shrine-users] adapter prpoblems In-Reply-To: <20141010144253.wikhw3434ss804sg@cubmail.cc.columbia.edu> References: <20141010144253.wikhw3434ss804sg@cubmail.cc.columbia.edu> Message-ID: <1412968891.2590.8.camel@cchmc.org> It seems like it can not map the key \\SHRINE\SHRINE\Labs\LP32651-9 \LP67162-5\ to any local key. Is that key located in your adapter mappings file? Billy -- William Shuman Cincinnati Children's Hospital Medical Center On Fri, 2014-10-10 at 14:42 -0400, ev2348 at columbia.edu wrote: > \\SHRINE\SHRINE\Labs\LP32651-9\LP67162-5\ From beninato at ohsu.edu Fri Oct 10 15:53:04 2014 From: beninato at ohsu.edu (Peter Beninato) Date: Fri, 10 Oct 2014 19:53:04 +0000 Subject: [Shrine-users] adapter problems --> modifiers? Message-ID: <43ECC5435444BE479E03012738A1400F151505D6@EXMB03.ohsu.edu> Hi, I'm experiencing some issues with AdapterMappings.xml and modifiers. I have loaded up the shrine ontology corrected for the disconnect between c_fullname and m_applied_path (m_applied_path case, does not match i2b2 demo ontology c_fullname case). That got the modifier icons to appear. When I chose the Admit DX for 441.5. When I look in the shrine log I see: 2014-Oct-09-10:32:09.353 DEBUG [SHRINE][ExpressionTranslator][ForkJoinPool-1-worker-7] Translated: Term(\\SHRINE\SHRINE\Diagnoses\DISEASES OF THE CIRCULATORY SYSTEM (390-459.99)\DISEASES OF ARTERIES, ARTERIOLES, AND CAPILLARIES (440-449.99)\Aortic aneurysm and dissection (441)$441.5) Aortic aneurysm of unspecified site, ruptured$ to None 2014-Oct-09-10:32:09.356 WARN [SHRINE][RunQueryAdapter][ForkJoinPool-1-worker-7] Error mapping query terms: Error mapping query terms from network to local forms I see the term in AdapterMappings.xml and I can find the local term in the local i2b2 ontology, so I'm not sure why it is mapping to none. This might be related? Fyi. -Peter -----Original Message----- From: shrine-users-bounces at open.med.harvard.edu [mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of Shuman, William (Billy) Sent: Friday, October 10, 2014 12:22 PM To: ev2348 at columbia.edu Cc: shrine-users at open.med.harvard.edu Subject: Re: [Shrine-users] adapter prpoblems It seems like it can not map the key \\SHRINE\SHRINE\Labs\LP32651-9 \LP67162-5\ to any local key. Is that key located in your adapter mappings file? Billy -- William Shuman Cincinnati Children's Hospital Medical Center On Fri, 2014-10-10 at 14:42 -0400, ev2348 at columbia.edu wrote: > \\SHRINE\SHRINE\Labs\LP32651-9\LP67162-5\ _______________________________________________ Shrine-users mailing list Shrine-users at open.med.harvard.edu https://open.med.harvard.edu/mailman/listinfo/shrine-users From jdale at umn.edu Fri Oct 10 15:45:12 2014 From: jdale at umn.edu (Justin Dale) Date: Fri, 10 Oct 2014 14:45:12 -0500 Subject: [Shrine-users] Error in SHRINE 1.17.0 demo onotolgy Message-ID: We tried to load the SHRINE demo ontology for 1.17.0 ( https://open.med.harvard.edu/svn/shrine/releases/1.17.0/ontology/SHRINE_Demo_Downloads/ShrineDemo.sql) and it appears the first insert statement has an error in it (Not enough values) INSERT INTO SHRINE ( C_HLEVEL, C_FULLNAME, C_NAME, C_SYNONYM_CD, C_VISUALATTRIBUTES, C_TOTALNUM, C_BASECODE, C_METADATAXML, C_FACTTABLECOLUMN, C_TABLENAME, C_COLUMNNAME, C_COLUMNDATATYPE, C_OPERATOR, C_DIMCODE, C_COMMENT, C_TOOLTIP, UPDATE_DATE, DOWNLOAD_DATE, IMPORT_DATE, SOURCESYSTEM_CD, VALUETYPE_CD, M_APPLIED_PATH, M_EXCLUSION_CD ) VALUES ( 0, '\SHRINE\ONTOLOGYVERSION\SHRINE_DEMO_ONTOLOGY_V-1.17_9-18-14\', 'ONTOLOGYVERSION', 'N', 'LH', NULL, NULL, '', 'concept_cd', 'concept_dimension', 'concept_path', 'T', 'LIKE', '\SHRINE\ONTOLOGYVERSION\', NULL ); It's missing values for: C_TOOLTIP, UPDATE_DATE, DOWNLOAD_DATE, IMPORT_DATE, SOURCESYSTEM_CD, VALUETYPE_CD, M_APPLIED_PATH, M_EXCLUSION_CD Regards, Justin Dale Manager - Research Development and Support University of Minnesota Academic Health Center - Office of Information Systems Phone: 612.624.9747 Fax: 612.624.7458 jdale at umn.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From ev2348 at columbia.edu Fri Oct 10 16:21:39 2014 From: ev2348 at columbia.edu (ev2348 at columbia.edu) Date: Fri, 10 Oct 2014 16:21:39 -0400 Subject: [Shrine-users] adapter problems --> modifiers? In-Reply-To: <43ECC5435444BE479E03012738A1400F151505D6@EXMB03.ohsu.edu> References: <43ECC5435444BE479E03012738A1400F151505D6@EXMB03.ohsu.edu> Message-ID: <20141010162139.ezkaz9ac080kw88o@cubmail.cc.columbia.edu> Hi, I certainly downloaded the AdapterMappings.xml from Harvard SHRINE_SVN_URL_BASE=https://open.med.harvard.edu/svn/shrine/releases/${SHRINE_VERSION}/ nad made some changes according to table i2b2metadata.table_access. Attached is the copy I am using. I see some of the terms with different words but just the same for instance I have for Appendicitis I2B2 NODE: Diagnosis/ICD9 Disease/Disorder of Digestive Tract/other and unspecified Diseases of Appendix/Appendicitis SHRINE Node: Diseases anfd Injuries (001-999.99)/Diseases of Digestive System (520-579.99)/Appendicitis (540-543.99) and I get the message 2014-Oct-10-15:32:22.484 DEBUG [SHRINE][SquerylAdapterDao][ForkJoinPool-1-worker-3] User i2b2CDW:shrine locked out? false 2014-Oct-10-15:32:22.484 DEBUG [SHRINE][RunQueryAdapter][ForkJoinPool-1-worker-3] Performing query from user i2b2CDW:shrine 2014-Oct-10-15:32:22.485 DEBUG [SHRINE][ExpressionTranslator][ForkJoinPool-1-worker-3] Translated: Term(\\SHRINE\SHRINE\Diagnoses\DISEASES OF THE DIGESTIVE SYSTEM (520-579.99)\APPENDICITIS (540-543.99)\) to Failure(net.shrine.adapter.AdapterMappingException: No local terms mapped to '\\SHRINE\SHRINE\Diagnoses\DISEASES OF THE DIGESTIVE SYSTEM (520-579.99)\APPENDICITIS (540-543.99)\') 2014-Oct-10-15:32:22.485 WARN [SHRINE][RunQueryAdapter][ForkJoinPool-1-worker-3] Error mapping query terms: Error mapping query terms from network to local forms. request: RunQueryRequest(CDW,180000 milliseconds,AuthenticationInfo(,,Credential(,false)),7718049720240791039,None,Set(PATIENT_COUNT_XML),QueryDefinition(APPENDICITIS (5 at 15:32:20,Term(\\SHRINE\SHRINE\Diagnoses\DISEASES OF THE DIGESTIVE SYSTEM (520-579.99)\APPENDICITIS (540-543.99)\))) net.shrine.adapter.AdapterMappingException: Error mapping query terms from network to local forms. request: RunQueryRequest(CDW,180000 milliseconds,AuthenticationInfo(,,Credential(***,false)),7718049720240791039,None,Set(PATIENT_COUNT_XML),QueryDefinition(APPENDICITIS (5 at 15:32:20,Term(\\SHRINE\SHRINE\Diagnoses\DISEASES OF THE DIGESTIVE SYSTEM (520-579.99)\APPENDICITIS (540-543.99)\))) at net.shrine.adapter.RunQueryAdapter.translateNetworkToLocal(RunQueryAdapter.scala:60) at net.shrine.adapter.RunQueryAdapter.translateNetworkToLocal(RunQueryAdapter.scala:42) at net.shrine.adapter.CrcAdapter.translateRequest(CrcAdapter.scala:95) at net.shrine.adapter.CrcAdapter.processRequest(CrcAdapter.scala:60) at net.shrine.adapter.RunQueryAdapter.runQuery(RunQueryAdapter.scala:121) at net.shrine.adapter.RunQueryAdapter.processRequest(RunQueryAdapter.scala:85) at net.shrine.adapter.RunQueryAdapter.processRequest(RunQueryAdapter.scala:42) at net.shrine.adapter.Adapter.perform(Adapter.scala:26) at net.shrine.adapter.service.AdapterService$$anonfun$1$$anonfun$apply$1.apply(AdapterService.scala:36) at net.shrine.adapter.service.AdapterService$$anonfun$1$$anonfun$apply$1.apply(AdapterService.scala:36) at net.shrine.adapter.service.AdapterService$.time(AdapterService.scala:68) at net.shrine.adapter.service.AdapterService$$anonfun$1.apply(AdapterService.scala:35) at net.shrine.a Beninato : > Hi, > > I'm experiencing some issues with AdapterMappings.xml and modifiers. > > I have loaded up the shrine ontology corrected for the disconnect > between c_fullname and m_applied_path (m_applied_path case, does not > match i2b2 demo ontology c_fullname case). > > That got the modifier icons to appear. When I chose the Admit DX for 441.5. > > When I look in the shrine log I see: > 2014-Oct-09-10:32:09.353 DEBUG > [SHRINE][ExpressionTranslator][ForkJoinPool-1-worker-7] Translated: > Term(\\SHRINE\SHRINE\Diagnoses\DISEASES OF THE CIRCULATORY SYSTEM > (390-459.99)\DISEASES OF ARTERIES, ARTERIOLES, AND CAPILLARIES > (440-449.99)\Aortic aneurysm and dissection (441)$441.5) Aortic > aneurysm of unspecified site, ruptured$ to None > 2014-Oct-09-10:32:09.356 WARN > [SHRINE][RunQueryAdapter][ForkJoinPool-1-worker-7] Error mapping > query terms: Error mapping query terms from network to local forms > > I see the term in AdapterMappings.xml and I can find the local term > in the local i2b2 ontology, so I'm not sure why it is mapping to none. > > This might be related? > > Fyi. > -Peter > > -----Original Message----- > From: shrine-users-bounces at open.med.harvard.edu > [mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of > Shuman, William (Billy) > Sent: Friday, October 10, 2014 12:22 PM > To: ev2348 at columbia.edu > Cc: shrine-users at open.med.harvard.edu > Subject: Re: [Shrine-users] adapter prpoblems > > It seems like it can not map the Quoting Peter Beninato : > Hi, > > I'm experiencing some issues with AdapterMappings.xml and modifiers. > > I have loaded up the shrine ontology corrected for the disconnect > between c_fullname and m_applied_path (m_applied_path case, does not > match i2b2 demo ontology c_fullname case). > > That got the modifier icons to appear. When I chose the Admit DX for 441.5. > > When I look in the shrine log I see: > 2014-Oct-09-10:32:09.353 DEBUG > [SHRINE][ExpressionTranslator][ForkJoinPool-1-worker-7] Translated: > Term(\\SHRINE\SHRINE\Diagnoses\DISEASES OF THE CIRCULATORY SYSTEM > (390-459.99)\DISEASES OF ARTERIES, ARTERIOLES, AND CAPILLARIES > (440-449.99)\Aortic aneurysm and dissection (441)$441.5) Aortic > aneurysm of unspecified site, ruptured$ to None > 2014-Oct-09-10:32:09.356 WARN > [SHRINE][RunQueryAdapter][ForkJoinPool-1-worker-7] Error mapping > query terms: Error mapping query terms from network to local forms > > I see the term in AdapterMappings.xml and I can find the local term > in the local i2b2 ontology, so I'm not sure why it is mapping to none. > > This might be related? > > Fyi. > -Peter > > -----Original Message----- > From: shrine-users-bounces at open.med.harvard.edu > [mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of > Shuman, William (Billy) > Sent: Friday, October 10, 2014 12:22 PM > To: ev2348 at columbia.edu > Cc: shrine-users at open.med.harvard.edu > Subject: Re: [Shrine-users] adapter prpoblems > > It seems like it can not map the key \\SHRINE\SHRINE\Labs\LP32651-9 > \LP67162-5\ to any local key. Is that key located in your adapter > mappings file? > > Billy > -- > William Shuman Cincinnati Children's > Hospital Medical Center > > On Fri, 2014-10-10 at 14:42 -0400, ev2348 at columbia.edu wrote: >> \\SHRINE\SHRINE\Labs\LP32651-9\LP67162-5\ > _______________________________________________ > Shrine-users mailing list > Shrine-users at open.med.harvard.edu > https://open.med.harvard.edu/mailman/listinfo/shrine-users > > -------------- next part -------------- A non-text attachment was scrubbed... Name: AdapterMappings.zip Type: application/zip Size: 780197 bytes Desc: not available URL: From jeff.lunt at northwestern.edu Fri Oct 10 16:22:20 2014 From: jeff.lunt at northwestern.edu (Jeff Mark Lunt) Date: Fri, 10 Oct 2014 20:22:20 +0000 Subject: [Shrine-users] Error in SHRINE 1.17.0 demo onotolgy In-Reply-To: References: Message-ID: You could import it from a CSV. Attached is a version I exported a few days ago from a 1.15 server that I think will work on a 1.17 server. From: Justin Dale > Date: Friday, October 10, 2014 at 2:45 PM To: "shrine-users at open.med.harvard.edu" > Subject: [Shrine-users] Error in SHRINE 1.17.0 demo onotolgy We tried to load the SHRINE demo ontology for 1.17.0 (https://open.med.harvard.edu/svn/shrine/releases/1.17.0/ontology/SHRINE_Demo_Downloads/ShrineDemo.sql) and it appears the first insert statement has an error in it (Not enough values) INSERT INTO SHRINE ( C_HLEVEL, C_FULLNAME, C_NAME, C_SYNONYM_CD, C_VISUALATTRIBUTES, C_TOTALNUM, C_BASECODE, C_METADATAXML, C_FACTTABLECOLUMN, C_TABLENAME, C_COLUMNNAME, C_COLUMNDATATYPE, C_OPERATOR, C_DIMCODE, C_COMMENT, C_TOOLTIP, UPDATE_DATE, DOWNLOAD_DATE, IMPORT_DATE, SOURCESYSTEM_CD, VALUETYPE_CD, M_APPLIED_PATH, M_EXCLUSION_CD ) VALUES ( 0, '\SHRINE\ONTOLOGYVERSION\SHRINE_DEMO_ONTOLOGY_V-1.17_9-18-14\', 'ONTOLOGYVERSION', 'N', 'LH', NULL, NULL, '', 'concept_cd', 'concept_dimension', 'concept_path', 'T', 'LIKE', '\SHRINE\ONTOLOGYVERSION\', NULL ); It's missing values for: C_TOOLTIP, UPDATE_DATE, DOWNLOAD_DATE, IMPORT_DATE, SOURCESYSTEM_CD, VALUETYPE_CD, M_APPLIED_PATH, M_EXCLUSION_CD Regards, Justin Dale Manager - Research Development and Support University of Minnesota Academic Health Center - Office of Information Systems Phone: 612.624.9747 Fax: 612.624.7458 jdale at umn.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: shrine-ontology-from-demo-vm.csv Type: text/csv Size: 108352 bytes Desc: shrine-ontology-from-demo-vm.csv URL: From jdale at umn.edu Fri Oct 10 16:39:22 2014 From: jdale at umn.edu (Justin Dale) Date: Fri, 10 Oct 2014 15:39:22 -0500 Subject: [Shrine-users] Error in SHRINE 1.17.0 demo onotolgy In-Reply-To: References: Message-ID: Thanks Jeff. I noticed in your csv the following columns are missing: M_APPLIED_PATH M_EXCLUSION_CD Do you (or anyone else) know if these are required for version 1.17.0 to work? Another question related to this, is there SQL/DDL our there for the creation of the SHRINE table, preferable for version 1.17.0? Would be good to know data types, lengths, and NULL or NOT NULL. Regards, Justin Dale Manager - Research Development and Support University of Minnesota Academic Health Center - Office of Information Systems Phone: 612.624.9747 Fax: 612.624.7458 jdale at umn.edu On Fri, Oct 10, 2014 at 3:22 PM, Jeff Mark Lunt wrote: > You could import it from a CSV. Attached is a version I exported a few > days ago from a 1.15 server that I think will work on a 1.17 server. > > > > From: Justin Dale > Date: Friday, October 10, 2014 at 2:45 PM > To: "shrine-users at open.med.harvard.edu" > > Subject: [Shrine-users] Error in SHRINE 1.17.0 demo onotolgy > > We tried to load the SHRINE demo ontology for 1.17.0 ( > https://open.med.harvard.edu/svn/shrine/releases/1.17.0/ontology/SHRINE_Demo_Downloads/ShrineDemo.sql) > and it appears the first insert statement has an error in it (Not enough > values) > > INSERT INTO SHRINE ( > C_HLEVEL, > C_FULLNAME, > C_NAME, > C_SYNONYM_CD, > C_VISUALATTRIBUTES, > C_TOTALNUM, > C_BASECODE, > C_METADATAXML, > C_FACTTABLECOLUMN, > C_TABLENAME, > C_COLUMNNAME, > C_COLUMNDATATYPE, > C_OPERATOR, > C_DIMCODE, > C_COMMENT, > C_TOOLTIP, > UPDATE_DATE, > DOWNLOAD_DATE, > IMPORT_DATE, > SOURCESYSTEM_CD, > VALUETYPE_CD, > M_APPLIED_PATH, > M_EXCLUSION_CD ) > > VALUES ( > 0, > '\SHRINE\ONTOLOGYVERSION\SHRINE_DEMO_ONTOLOGY_V-1.17_9-18-14\', > 'ONTOLOGYVERSION', > 'N', > 'LH', > NULL, > NULL, '', > 'concept_cd', > 'concept_dimension', > 'concept_path', > 'T', > 'LIKE', > '\SHRINE\ONTOLOGYVERSION\', > NULL ); > > > It's missing values for: > C_TOOLTIP, > UPDATE_DATE, > DOWNLOAD_DATE, > IMPORT_DATE, > SOURCESYSTEM_CD, > VALUETYPE_CD, > M_APPLIED_PATH, > M_EXCLUSION_CD > > > Regards, > > Justin Dale > Manager - Research Development and Support > University of Minnesota > Academic Health Center - Office of Information Systems > Phone: 612.624.9747 > Fax: 612.624.7458 > jdale at umn.edu > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeff.lunt at northwestern.edu Fri Oct 10 16:49:05 2014 From: jeff.lunt at northwestern.edu (Jeff Mark Lunt) Date: Fri, 10 Oct 2014 20:49:05 +0000 Subject: [Shrine-users] Error in SHRINE 1.17.0 demo onotolgy In-Reply-To: References: Message-ID: Hm, I'm not sure on those columns. Maybe required. For the creation of the SHRINE table, it's included in the SHRINE download/SVN checkout under: * i2b2/oracle/ontology_create_tables.sql You can modify this .sql file to your specific DBMS's column types if you're not using Oracle. For MSSQL I just copied this .sql file over and changed (for example): * (oracle type) -> (MSSQL type) * NUMBER -> INT * VARCHAR2 -> VARCHAR * CLOB -> TEXT I don't remember having to change anything else, but your mileage may vary. From: Justin Dale > Date: Friday, October 10, 2014 at 3:39 PM To: Jeff Lunt > Cc: "shrine-users at open.med.harvard.edu" > Subject: Re: [Shrine-users] Error in SHRINE 1.17.0 demo onotolgy Thanks Jeff. I noticed in your csv the following columns are missing: M_APPLIED_PATH M_EXCLUSION_CD Do you (or anyone else) know if these are required for version 1.17.0 to work? Another question related to this, is there SQL/DDL our there for the creation of the SHRINE table, preferable for version 1.17.0? Would be good to know data types, lengths, and NULL or NOT NULL. Regards, Justin Dale Manager - Research Development and Support University of Minnesota Academic Health Center - Office of Information Systems Phone: 612.624.9747 Fax: 612.624.7458 jdale at umn.edu On Fri, Oct 10, 2014 at 3:22 PM, Jeff Mark Lunt > wrote: You could import it from a CSV. Attached is a version I exported a few days ago from a 1.15 server that I think will work on a 1.17 server. From: Justin Dale > Date: Friday, October 10, 2014 at 2:45 PM To: "shrine-users at open.med.harvard.edu" > Subject: [Shrine-users] Error in SHRINE 1.17.0 demo onotolgy We tried to load the SHRINE demo ontology for 1.17.0 (https://open.med.harvard.edu/svn/shrine/releases/1.17.0/ontology/SHRINE_Demo_Downloads/ShrineDemo.sql) and it appears the first insert statement has an error in it (Not enough values) INSERT INTO SHRINE ( C_HLEVEL, C_FULLNAME, C_NAME, C_SYNONYM_CD, C_VISUALATTRIBUTES, C_TOTALNUM, C_BASECODE, C_METADATAXML, C_FACTTABLECOLUMN, C_TABLENAME, C_COLUMNNAME, C_COLUMNDATATYPE, C_OPERATOR, C_DIMCODE, C_COMMENT, C_TOOLTIP, UPDATE_DATE, DOWNLOAD_DATE, IMPORT_DATE, SOURCESYSTEM_CD, VALUETYPE_CD, M_APPLIED_PATH, M_EXCLUSION_CD ) VALUES ( 0, '\SHRINE\ONTOLOGYVERSION\SHRINE_DEMO_ONTOLOGY_V-1.17_9-18-14\', 'ONTOLOGYVERSION', 'N', 'LH', NULL, NULL, '', 'concept_cd', 'concept_dimension', 'concept_path', 'T', 'LIKE', '\SHRINE\ONTOLOGYVERSION\', NULL ); It's missing values for: C_TOOLTIP, UPDATE_DATE, DOWNLOAD_DATE, IMPORT_DATE, SOURCESYSTEM_CD, VALUETYPE_CD, M_APPLIED_PATH, M_EXCLUSION_CD Regards, Justin Dale Manager - Research Development and Support University of Minnesota Academic Health Center - Office of Information Systems Phone: 612.624.9747 Fax: 612.624.7458 jdale at umn.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From mhorvath at wakehealth.edu Fri Oct 10 16:58:08 2014 From: mhorvath at wakehealth.edu (Michael Horvath) Date: Fri, 10 Oct 2014 20:58:08 +0000 Subject: [Shrine-users] Error in SHRINE 1.17.0 demo onotolgy In-Reply-To: References: Message-ID: <96E1AA641D2EDE49A7A43FE98067A3E93B42FE39@EXCHDB1.medctr.ad.wfubmc.edu> Those table affect modifiers, which weren?t present in Shrine 1.15. I believe one or both of them might have been non-nullable in i2b2, in which case you fill in ?@? symbols as a replacement. Michael Horvath Programmer / Analyst [Wake Forest School of Medicine] Biomedical Research Services & Administration Medical Center Boulevard \ Winston-Salem, NC 27157 p 336.716.9755 \ f 336.716.5055 From: shrine-users-bounces at open.med.harvard.edu [mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of Justin Dale Sent: Friday, October 10, 2014 4:39 PM To: Jeff Mark Lunt Cc: shrine-users at open.med.harvard.edu Subject: Re: [Shrine-users] Error in SHRINE 1.17.0 demo onotolgy Thanks Jeff. I noticed in your csv the following columns are missing: M_APPLIED_PATH M_EXCLUSION_CD Do you (or anyone else) know if these are required for version 1.17.0 to work? Another question related to this, is there SQL/DDL our there for the creation of the SHRINE table, preferable for version 1.17.0? Would be good to know data types, lengths, and NULL or NOT NULL. Regards, Justin Dale Manager - Research Development and Support University of Minnesota Academic Health Center - Office of Information Systems Phone: 612.624.9747 Fax: 612.624.7458 jdale at umn.edu On Fri, Oct 10, 2014 at 3:22 PM, Jeff Mark Lunt > wrote: You could import it from a CSV. Attached is a version I exported a few days ago from a 1.15 server that I think will work on a 1.17 server. From: Justin Dale > Date: Friday, October 10, 2014 at 2:45 PM To: "shrine-users at open.med.harvard.edu" > Subject: [Shrine-users] Error in SHRINE 1.17.0 demo onotolgy We tried to load the SHRINE demo ontology for 1.17.0 (https://open.med.harvard.edu/svn/shrine/releases/1.17.0/ontology/SHRINE_Demo_Downloads/ShrineDemo.sql) and it appears the first insert statement has an error in it (Not enough values) INSERT INTO SHRINE ( C_HLEVEL, C_FULLNAME, C_NAME, C_SYNONYM_CD, C_VISUALATTRIBUTES, C_TOTALNUM, C_BASECODE, C_METADATAXML, C_FACTTABLECOLUMN, C_TABLENAME, C_COLUMNNAME, C_COLUMNDATATYPE, C_OPERATOR, C_DIMCODE, C_COMMENT, C_TOOLTIP, UPDATE_DATE, DOWNLOAD_DATE, IMPORT_DATE, SOURCESYSTEM_CD, VALUETYPE_CD, M_APPLIED_PATH, M_EXCLUSION_CD ) VALUES ( 0, '\SHRINE\ONTOLOGYVERSION\SHRINE_DEMO_ONTOLOGY_V-1.17_9-18-14\', 'ONTOLOGYVERSION', 'N', 'LH', NULL, NULL, '', 'concept_cd', 'concept_dimension', 'concept_path', 'T', 'LIKE', '\SHRINE\ONTOLOGYVERSION\', NULL ); It's missing values for: C_TOOLTIP, UPDATE_DATE, DOWNLOAD_DATE, IMPORT_DATE, SOURCESYSTEM_CD, VALUETYPE_CD, M_APPLIED_PATH, M_EXCLUSION_CD Regards, Justin Dale Manager - Research Development and Support University of Minnesota Academic Health Center - Office of Information Systems Phone: 612.624.9747 Fax: 612.624.7458 jdale at umn.edu -------------- next part -------------- An HTML attachment was scrubbed... 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Name: image001.gif Type: image/gif Size: 3242 bytes Desc: image001.gif URL: From jeff.lunt at northwestern.edu Fri Oct 10 17:21:20 2014 From: jeff.lunt at northwestern.edu (Jeff Mark Lunt) Date: Fri, 10 Oct 2014 21:21:20 +0000 Subject: [Shrine-users] SHRINE PM_CELL_DATA question Message-ID: The SHRINE PM_CELL_DATA entry for the SHRINE Federated query on a demo server (the last line here): EDIT CELL_ID PROJECT_PATH NAME METHOD_CD URL CAN_OVERRIDE CHANGE_DATE ENTRY_DATE CHANGEBY_CHAR STATUS_CD [Edit] CRC / Data Repository REST http://192.168.56.101:9090/i2b2/services/QueryToolService/ 1 - - - A [Edit] FRC / File Repository SOAP http://192.168.56.101:9090/i2b2/services/FRService/ 1 - - - A [Edit] ONT / Ontology Cell REST http://192.168.56.101:9090/i2b2/services/OntologyService/ 1 - - - A [Edit] WORK / Workplace Cell REST http://192.168.56.101:9090/i2b2/services/WorkplaceService/ 1 - - - A [Edit] IM / IM Cell REST http://192.168.56.101:9090/i2b2/services/IMService/ 1 - - - A [Edit] CRC /SHRINE SHRINE Federated Query REST https://192.168.56.101:6443/shrine/rest/i2b2/ 1 - - - A ...is the purpose of this entry to allow a SHRINE instance to query itself and receive federated queries from other SHRINE instances? If so is this is the RESTful service the does the ontology concept translation via whatever's in AdapterMappings.xml? -------------- next part -------------- An HTML attachment was scrubbed... URL: From beninato at ohsu.edu Fri Oct 10 17:29:19 2014 From: beninato at ohsu.edu (Peter Beninato) Date: Fri, 10 Oct 2014 21:29:19 +0000 Subject: [Shrine-users] Error in SHRINE 1.17.0 demo onotolgy In-Reply-To: <96E1AA641D2EDE49A7A43FE98067A3E93B42FE39@EXCHDB1.medctr.ad.wfubmc.edu> References: <96E1AA641D2EDE49A7A43FE98067A3E93B42FE39@EXCHDB1.medctr.ad.wfubmc.edu> Message-ID: <43ECC5435444BE479E03012738A1400F15150660@EXMB03.ohsu.edu> Hi, Yes, those columns are needed to support modifiers. I?m not sure if there were other changes to the insert script for the SHRINE table, but I just truncated and then loaded from the v1.17 repository. TRUNCATE TABLE SHRINE DROP STORAGE; ALTER TABLE SHRINE add ( M_APPLIED_PATH VARCHAR2(900), M_EXCLUSION_CD VARCHAR2(900) ); . From: shrine-users-bounces at open.med.harvard.edu [mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of Michael Horvath Sent: Friday, October 10, 2014 1:58 PM To: shrine-users at open.med.harvard.edu Subject: Re: [Shrine-users] Error in SHRINE 1.17.0 demo onotolgy Those table affect modifiers, which weren?t present in Shrine 1.15. I believe one or both of them might have been non-nullable in i2b2, in which case you fill in ?@? symbols as a replacement. Michael Horvath Programmer / Analyst [Wake Forest School of Medicine] Biomedical Research Services & Administration Medical Center Boulevard \ Winston-Salem, NC 27157 p 336.716.9755 \ f 336.716.5055 From: shrine-users-bounces at open.med.harvard.edu [mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of Justin Dale Sent: Friday, October 10, 2014 4:39 PM To: Jeff Mark Lunt Cc: shrine-users at open.med.harvard.edu Subject: Re: [Shrine-users] Error in SHRINE 1.17.0 demo onotolgy Thanks Jeff. I noticed in your csv the following columns are missing: M_APPLIED_PATH M_EXCLUSION_CD Do you (or anyone else) know if these are required for version 1.17.0 to work? Another question related to this, is there SQL/DDL our there for the creation of the SHRINE table, preferable for version 1.17.0? Would be good to know data types, lengths, and NULL or NOT NULL. Regards, Justin Dale Manager - Research Development and Support University of Minnesota Academic Health Center - Office of Information Systems Phone: 612.624.9747 Fax: 612.624.7458 jdale at umn.edu On Fri, Oct 10, 2014 at 3:22 PM, Jeff Mark Lunt > wrote: You could import it from a CSV. Attached is a version I exported a few days ago from a 1.15 server that I think will work on a 1.17 server. From: Justin Dale > Date: Friday, October 10, 2014 at 2:45 PM To: "shrine-users at open.med.harvard.edu" > Subject: [Shrine-users] Error in SHRINE 1.17.0 demo onotolgy We tried to load the SHRINE demo ontology for 1.17.0 (https://open.med.harvard.edu/svn/shrine/releases/1.17.0/ontology/SHRINE_Demo_Downloads/ShrineDemo.sql) and it appears the first insert statement has an error in it (Not enough values) INSERT INTO SHRINE ( C_HLEVEL, C_FULLNAME, C_NAME, C_SYNONYM_CD, C_VISUALATTRIBUTES, C_TOTALNUM, C_BASECODE, C_METADATAXML, C_FACTTABLECOLUMN, C_TABLENAME, C_COLUMNNAME, C_COLUMNDATATYPE, C_OPERATOR, C_DIMCODE, C_COMMENT, C_TOOLTIP, UPDATE_DATE, DOWNLOAD_DATE, IMPORT_DATE, SOURCESYSTEM_CD, VALUETYPE_CD, M_APPLIED_PATH, M_EXCLUSION_CD ) VALUES ( 0, '\SHRINE\ONTOLOGYVERSION\SHRINE_DEMO_ONTOLOGY_V-1.17_9-18-14\', 'ONTOLOGYVERSION', 'N', 'LH', NULL, NULL, '', 'concept_cd', 'concept_dimension', 'concept_path', 'T', 'LIKE', '\SHRINE\ONTOLOGYVERSION\', NULL ); It's missing values for: C_TOOLTIP, UPDATE_DATE, DOWNLOAD_DATE, IMPORT_DATE, SOURCESYSTEM_CD, VALUETYPE_CD, M_APPLIED_PATH, M_EXCLUSION_CD Regards, Justin Dale Manager - Research Development and Support University of Minnesota Academic Health Center - Office of Information Systems Phone: 612.624.9747 Fax: 612.624.7458 jdale at umn.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.gif Type: image/gif Size: 3242 bytes Desc: image001.gif URL: From beninato at ohsu.edu Fri Oct 10 17:37:46 2014 From: beninato at ohsu.edu (Peter Beninato) Date: Fri, 10 Oct 2014 21:37:46 +0000 Subject: [Shrine-users] adapter problems --> modifiers? In-Reply-To: <20141010162139.ezkaz9ac080kw88o@cubmail.cc.columbia.edu> References: <43ECC5435444BE479E03012738A1400F151505D6@EXMB03.ohsu.edu> <20141010162139.ezkaz9ac080kw88o@cubmail.cc.columbia.edu> Message-ID: <43ECC5435444BE479E03012738A1400F15150688@EXMB03.ohsu.edu> Hi, When you expand the SHRINE ontology to, Diseases anfd Injuries (001-999.99)/Diseases of Digestive System (520-579.99)/Appendicitis (540-543.99), Do you see icons for: Admit, Principal, Secondary? If you don't see those icons then... Since this deals with Diagnoses. Please look at the m_applied_path in an entry in SHRINE where the c_fullname = ' \Admit Diagnosis\' (or principal or secondar) Take the m_applied_path, and use it as the criteria: Select * >From shrine Where c_fullname = {my_m_applied_path from Admit DX} You may get no rows. My experience is that the third tuple in the m_applied_path needs to be capitalized to match the c_fullname that you want to add the modifiers too. Once I made that change, I got past an error condition. And on to another... Fyi. -Peter -----Original Message----- From: ev2348 at columbia.edu [mailto:ev2348 at columbia.edu] Sent: Friday, October 10, 2014 1:22 PM To: Peter Beninato Cc: Shuman, William (Billy); shrine-users at open.med.harvard.edu Subject: RE: [Shrine-users] adapter problems --> modifiers? Hi, I certainly downloaded the AdapterMappings.xml from Harvard SHRINE_SVN_URL_BASE=https://open.med.harvard.edu/svn/shrine/releases/${SHRINE_VERSION}/ nad made some changes according to table i2b2metadata.table_access. Attached is the copy I am using. I see some of the terms with different words but just the same for instance I have for Appendicitis I2B2 NODE: Diagnosis/ICD9 Disease/Disorder of Digestive Tract/other and unspecified Diseases of Appendix/Appendicitis SHRINE Node: Diseases anfd Injuries (001-999.99)/Diseases of Digestive System (520-579.99)/Appendicitis (540-543.99) and I get the message 2014-Oct-10-15:32:22.484 DEBUG [SHRINE][SquerylAdapterDao][ForkJoinPool-1-worker-3] User i2b2CDW:shrine locked out? false 2014-Oct-10-15:32:22.484 DEBUG [SHRINE][RunQueryAdapter][ForkJoinPool-1-worker-3] Performing query from user i2b2CDW:shrine 2014-Oct-10-15:32:22.485 DEBUG [SHRINE][ExpressionTranslator][ForkJoinPool-1-worker-3] Translated: Term(\\SHRINE\SHRINE\Diagnoses\DISEASES OF THE DIGESTIVE SYSTEM (520-579.99)\APPENDICITIS (540-543.99)\) to Failure(net.shrine.adapter.AdapterMappingException: No local terms mapped to '\\SHRINE\SHRINE\Diagnoses\DISEASES OF THE DIGESTIVE SYSTEM (520-579.99)\APPENDICITIS (540-543.99)\') 2014-Oct-10-15:32:22.485 WARN [SHRINE][RunQueryAdapter][ForkJoinPool-1-worker-3] Error mapping query terms: Error mapping query terms from network to local forms. request: RunQueryRequest(CDW,180000 milliseconds,AuthenticationInfo(***,,Credential(,false)),7718049720240791039,None,Set(PATIENT_COUNT_XML),QueryDefinition(APPENDICITIS (5 at 15:32:20,Term(\\SHRINE\SHRINE\Diagnoses\DISEASES OF THE DIGESTIVE SYSTEM (520-579.99)\APPENDICITIS (540-543.99)\))) net.shrine.adapter.AdapterMappingException: Error mapping query terms from network to local forms. request: RunQueryRequest(CDW,180000 milliseconds,AuthenticationInfo(,,Credential(***,false)),7718049720240791039,None,Set(PATIENT_COUNT_XML),QueryDefinition(APPENDICITIS (5 at 15:32:20,Term(\\SHRINE\SHRINE\Diagnoses\DISEASES OF THE DIGESTIVE SYSTEM (520-579.99)\APPENDICITIS (540-543.99)\))) at net.shrine.adapter.RunQueryAdapter.translateNetworkToLocal(RunQueryAdapter.scala:60) at net.shrine.adapter.RunQueryAdapter.translateNetworkToLocal(RunQueryAdapter.scala:42) at net.shrine.adapter.CrcAdapter.translateRequest(CrcAdapter.scala:95) at net.shrine.adapter.CrcAdapter.processRequest(CrcAdapter.scala:60) at net.shrine.adapter.RunQueryAdapter.runQuery(RunQueryAdapter.scala:121) at net.shrine.adapter.RunQueryAdapter.processRequest(RunQueryAdapter.scala:85) at net.shrine.adapter.RunQueryAdapter.processRequest(RunQueryAdapter.scala:42) at net.shrine.adapter.Adapter.perform(Adapter.scala:26) at net.shrine.adapter.service.AdapterService$$anonfun$1$$anonfun$apply$1.apply(AdapterService.scala:36) at net.shrine.adapter.service.AdapterService$$anonfun$1$$anonfun$apply$1.apply(AdapterService.scala:36) at net.shrine.adapter.service.AdapterService$.time(AdapterService.scala:68) at net.shrine.adapter.service.AdapterService$$anonfun$1.apply(AdapterService.scala:35) at net.shrine.a Beninato : > Hi, > > I'm experiencing some issues with AdapterMappings.xml and modifiers. > > I have loaded up the shrine ontology corrected for the disconnect > between c_fullname and m_applied_path (m_applied_path case, does not > match i2b2 demo ontology c_fullname case). > > That got the modifier icons to appear. When I chose the Admit DX for 441.5. > > When I look in the shrine log I see: > 2014-Oct-09-10:32:09.353 DEBUG > [SHRINE][ExpressionTranslator][ForkJoinPool-1-worker-7] Translated: > Term(\\SHRINE\SHRINE\Diagnoses\DISEASES OF THE CIRCULATORY SYSTEM > (390-459.99)\DISEASES OF ARTERIES, ARTERIOLES, AND CAPILLARIES > (440-449.99)\Aortic aneurysm and dissection (441)$441.5) Aortic > aneurysm of unspecified site, ruptured$ to None > 2014-Oct-09-10:32:09.356 WARN > [SHRINE][RunQueryAdapter][ForkJoinPool-1-worker-7] Error mapping > query terms: Error mapping query terms from network to local forms > > I see the term in AdapterMappings.xml and I can find the local term > in the local i2b2 ontology, so I'm not sure why it is mapping to none. > > This might be related? > > Fyi. > -Peter > > -----Original Message----- > From: shrine-users-bounces at open.med.harvard.edu > [mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of > Shuman, William (Billy) > Sent: Friday, October 10, 2014 12:22 PM > To: ev2348 at columbia.edu > Cc: shrine-users at open.med.harvard.edu > Subject: Re: [Shrine-users] adapter prpoblems > > It seems like it can not map the Quoting Peter Beninato : > Hi, > > I'm experiencing some issues with AdapterMappings.xml and modifiers. > > I have loaded up the shrine ontology corrected for the disconnect > between c_fullname and m_applied_path (m_applied_path case, does not > match i2b2 demo ontology c_fullname case). > > That got the modifier icons to appear. When I chose the Admit DX for 441.5. > > When I look in the shrine log I see: > 2014-Oct-09-10:32:09.353 DEBUG > [SHRINE][ExpressionTranslator][ForkJoinPool-1-worker-7] Translated: > Term(\\SHRINE\SHRINE\Diagnoses\DISEASES OF THE CIRCULATORY SYSTEM > (390-459.99)\DISEASES OF ARTERIES, ARTERIOLES, AND CAPILLARIES > (440-449.99)\Aortic aneurysm and dissection (441)$441.5) Aortic > aneurysm of unspecified site, ruptured$ to None > 2014-Oct-09-10:32:09.356 WARN > [SHRINE][RunQueryAdapter][ForkJoinPool-1-worker-7] Error mapping > query terms: Error mapping query terms from network to local forms > > I see the term in AdapterMappings.xml and I can find the local term > in the local i2b2 ontology, so I'm not sure why it is mapping to none. > > This might be related? > > Fyi. > -Peter > > -----Original Message----- > From: shrine-users-bounces at open.med.harvard.edu > [mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of > Shuman, William (Billy) > Sent: Friday, October 10, 2014 12:22 PM > To: ev2348 at columbia.edu > Cc: shrine-users at open.med.harvard.edu > Subject: Re: [Shrine-users] adapter prpoblems > > It seems like it can not map the key \\SHRINE\SHRINE\Labs\LP32651-9 > \LP67162-5\ to any local key. Is that key located in your adapter > mappings file? > > Billy > -- > William Shuman Cincinnati Children's > Hospital Medical Center > > On Fri, 2014-10-10 at 14:42 -0400, ev2348 at columbia.edu wrote: >> \\SHRINE\SHRINE\Labs\LP32651-9\LP67162-5\ > _______________________________________________ > Shrine-users mailing list > Shrine-users at open.med.harvard.edu > https://open.med.harvard.edu/mailman/listinfo/shrine-users > > From ev2348 at columbia.edu Mon Oct 13 12:14:29 2014 From: ev2348 at columbia.edu (ev2348 at columbia.edu) Date: Mon, 13 Oct 2014 12:14:29 -0400 Subject: [Shrine-users] Shrine-users Digest, Vol 26, Issue 24 In-Reply-To: References: Message-ID: <20141013121429.e108xfforkgso8k4@cubmail.cc.columbia.edu> Hello I see the three icons Admit, Principal, Secondary? The only thing I can count is Demographics with or without ERROR. The rest it does not work. Elena > Quoting shrine-users-request at open.med.harvard.edu: > Send Shrine-users mailing list submissions to > shrine-users at open.med.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://open.med.harvard.edu/mailman/listinfo/shrine-users > or, via email, send a message with subject or body 'help' to > shrine-users-request at open.med.harvard.edu > > You can reach the person managing the list at > shrine-users-owner at open.med.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Shrine-users digest..." > > > Today's Topics: > > 1. Re: adapter problems --> modifiers? (Peter Beninato) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 10 Oct 2014 21:37:46 +0000 > From: Peter Beninato > To: "ev2348 at columbia.edu" > Cc: "shrine-users at open.med.harvard.edu" > > Subject: Re: [Shrine-users] adapter problems --> modifiers? > Message-ID: <43ECC5435444BE479E03012738A1400F15150688 at EXMB03.ohsu.edu> > Content-Type: text/plain; charset="us-ascii" > > Hi, > > When you expand the SHRINE ontology to, Diseases anfd Injuries > (001-999.99)/Diseases of Digestive System (520-579.99)/Appendicitis > (540-543.99), Do you see icons for: > Admit, Principal, Secondary? > > If you don't see those icons then... > > > Since this deals with Diagnoses. Please look at the m_applied_path > in an entry in SHRINE where the c_fullname = ' \Admit Diagnosis\' > (or principal or secondar) > > Take the m_applied_path, and use it as the criteria: > Select * >> From shrine > Where c_fullname = {my_m_applied_path from Admit DX} > > You may get no rows. My experience is that the third tuple in the > m_applied_path needs to be capitalized to match the c_fullname that > you want to add the modifiers too. > > Once I made that change, I got past an error condition. > > And on to another... > > Fyi. > -Peter > > -----Original Message----- > From: ev2348 at columbia.edu [mailto:ev2348 at columbia.edu] > Sent: Friday, October 10, 2014 1:22 PM > To: Peter Beninato > Cc: Shuman, William (Billy); shrine-users at open.med.harvard.edu > Subject: RE: [Shrine-users] adapter problems --> modifiers? > > Hi, > I certainly downloaded the AdapterMappings.xml from Harvard > SHRINE_SVN_URL_BASE=https://open.med.harvard.edu/svn/shrine/releases/${SHRINE_VERSION}/ > nad made some changes according to table i2b2metadata.table_access. > Attached is the copy I am using. I see some of the terms with > different words but just the same for instance I have for Appendicitis > > I2B2 NODE: > Diagnosis/ICD9 Disease/Disorder of Digestive Tract/other and > unspecified Diseases of Appendix/Appendicitis > > SHRINE Node: > Diseases anfd Injuries (001-999.99)/Diseases of Digestive System > (520-579.99)/Appendicitis (540-543.99) > > and I get the message > > 2014-Oct-10-15:32:22.484 DEBUG > [SHRINE][SquerylAdapterDao][ForkJoinPool-1-worker-3] User > i2b2CDW:shrine locked out? false > 2014-Oct-10-15:32:22.484 DEBUG > [SHRINE][RunQueryAdapter][ForkJoinPool-1-worker-3] Performing query > from user i2b2CDW:shrine > 2014-Oct-10-15:32:22.485 DEBUG > [SHRINE][ExpressionTranslator][ForkJoinPool-1-worker-3] Translated: > Term(\\SHRINE\SHRINE\Diagnoses\DISEASES OF THE DIGESTIVE SYSTEM > (520-579.99)\APPENDICITIS (540-543.99)\) to > Failure(net.shrine.adapter.AdapterMappingException: No local terms > mapped to '\\SHRINE\SHRINE\Diagnoses\DISEASES OF THE DIGESTIVE > SYSTEM (520-579.99)\APPENDICITIS (540-543.99)\') > 2014-Oct-10-15:32:22.485 WARN > [SHRINE][RunQueryAdapter][ForkJoinPool-1-worker-3] Error mapping query > terms: Error mapping query terms from network to local forms. request: > RunQueryRequest(CDW,180000 > milliseconds,AuthenticationInfo(***,,Credential(,false)),7718049720240791039,None,Set(PATIENT_COUNT_XML),QueryDefinition(APPENDICITIS (5 at 15:32:20,Term(\\SHRINE\SHRINE\Diagnoses\DISEASES OF THE DIGESTIVE SYSTEM > (520-579.99)\APPENDICITIS > (540-543.99)\))) > net.shrine.adapter.AdapterMappingException: Error mapping query > terms from network to local forms. request: > RunQueryRequest(CDW,180000 > milliseconds,AuthenticationInfo(,,Credential(*,false)),7718049720240791039,None,Set(PATIENT_COUNT_XML),QueryDefinition(APPENDICITIS (5 at 15:32:20,Term(\\SHRINE\SHRINE\Diagnoses\DISEASES OF THE DIGESTIVE SYSTEM > (520-579.99)\APPENDICITIS > (540-543.99)\))) > at > net.shrine.adapter.RunQueryAdapter.translateNetworkToLocal(RunQueryAdapter.scala:60) > at > net.shrine.adapter.RunQueryAdapter.translateNetworkToLocal(RunQueryAdapter.scala:42) > at net.shrine.adapter.CrcAdapter.translateRequest(CrcAdapter.scala:95) > at net.shrine.adapter.CrcAdapter.processRequest(CrcAdapter.scala:60) > at net.shrine.adapter.RunQueryAdapter.runQuery(RunQueryAdapter.scala:121) > at > net.shrine.adapter.RunQueryAdapter.processRequest(RunQueryAdapter.scala:85) > at > net.shrine.adapter.RunQueryAdapter.processRequest(RunQueryAdapter.scala:42) > at net.shrine.adapter.Adapter.perform(Adapter.scala:26) > at > net.shrine.adapter.service.AdapterService$$anonfun$1$$anonfun$apply$1.apply(AdapterService.scala:36) > at > net.shrine.adapter.service.AdapterService$$anonfun$1$$anonfun$apply$1.apply(AdapterService.scala:36) > at net.shrine.adapter.service.AdapterService$.time(AdapterService.scala:68) > at > net.shrine.adapter.service.AdapterService$$anonfun$1.apply(AdapterService.scala:35) > at net.shrine.a > > Beninato : > >> Hi, >> >> I'm experiencing some issues with AdapterMappings.xml and modifiers. >> >> I have loaded up the shrine ontology corrected for the disconnect >> between c_fullname and m_applied_path (m_applied_path case, does not >> match i2b2 demo ontology c_fullname case). >> >> That got the modifier icons to appear. When I chose the Admit DX for 441.5. >> >> When I look in the shrine log I see: >> 2014-Oct-09-10:32:09.353 DEBUG >> [SHRINE][ExpressionTranslator][ForkJoinPool-1-worker-7] Translated: >> Term(\\SHRINE\SHRINE\Diagnoses\DISEASES OF THE CIRCULATORY SYSTEM >> (390-459.99)\DISEASES OF ARTERIES, ARTERIOLES, AND CAPILLARIES >> (440-449.99)\Aortic aneurysm and dissection (441)$441.5) Aortic >> aneurysm of unspecified site, ruptured$ to None >> 2014-Oct-09-10:32:09.356 WARN >> [SHRINE][RunQueryAdapter][ForkJoinPool-1-worker-7] Error mapping >> query terms: Error mapping query terms from network to local forms >> >> I see the term in AdapterMappings.xml and I can find the local term >> in the local i2b2 ontology, so I'm not sure why it is mapping to none. >> >> This might be related? >> >> Fyi. >> -Peter >> >> -----Original Message----- >> From: shrine-users-bounces at open.med.harvard.edu >> [mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of >> Shuman, William (Billy) >> Sent: Friday, October 10, 2014 12:22 PM >> To: ev2348 at columbia.edu >> Cc: shrine-users at open.med.harvard.edu >> Subject: Re: [Shrine-users] adapter prpoblems >> >> It seems like it can not map the > > Quoting Peter Beninato : > >> Hi, >> >> I'm experiencing some issues with AdapterMappings.xml and modifiers. >> >> I have loaded up the shrine ontology corrected for the disconnect >> between c_fullname and m_applied_path (m_applied_path case, does not >> match i2b2 demo ontology c_fullname case). >> >> That got the modifier icons to appear. When I chose the Admit DX for 441.5. >> >> When I look in the shrine log I see: >> 2014-Oct-09-10:32:09.353 DEBUG >> [SHRINE][ExpressionTranslator][ForkJoinPool-1-worker-7] Translated: >> Term(\\SHRINE\SHRINE\Diagnoses\DISEASES OF THE CIRCULATORY SYSTEM >> (390-459.99)\DISEASES OF ARTERIES, ARTERIOLES, AND CAPILLARIES >> (440-449.99)\Aortic aneurysm and dissection (441)$441.5) Aortic >> aneurysm of unspecified site, ruptured$ to None >> 2014-Oct-09-10:32:09.356 WARN >> [SHRINE][RunQueryAdapter][ForkJoinPool-1-worker-7] Error mapping >> query terms: Error mapping query terms from network to local forms >> >> I see the term in AdapterMappings.xml and I can find the local term >> in the local i2b2 ontology, so I'm not sure why it is mapping to none. >> >> This might be related? >> >> Fyi. >> -Peter >> >> -----Original Message----- >> From: shrine-users-bounces at open.med.harvard.edu >> [mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of >> Shuman, William (Billy) >> Sent: Friday, October 10, 2014 12:22 PM >> To: ev2348 at columbia.edu >> Cc: shrine-users at open.med.harvard.edu >> Subject: Re: [Shrine-users] adapter prpoblems >> >> It seems like it can not map the key \\SHRINE\SHRINE\Labs\LP32651-9 >> \LP67162-5\ to any local key. Is that key located in your adapter >> mappings file? >> >> Billy >> -- >> William Shuman Cincinnati Children's >> Hospital Medical Center >> >> On Fri, 2014-10-10 at 14:42 -0400, ev2348 at columbia.edu wrote: >>> \\SHRINE\SHRINE\Labs\LP32651-9\LP67162-5\ >> _ >> Shrine-users mailing list >> Shrine-users at open.med.harvard.edu >> https://open.med.harvard.edu/mailman/listinfo/shrine-users >> >> > > > > > ------------------------------ > > _ > Shrine-users mailing list > Shrine-users at open.med.harvard.edu > https://open.med.harvard.edu/mailman/listinfo/shrine-users > > > End of Shrine-users Digest, Vol 26, Issue 24 > ****************************************** > > From beninato at ohsu.edu Mon Oct 13 12:20:34 2014 From: beninato at ohsu.edu (Peter Beninato) Date: Mon, 13 Oct 2014 16:20:34 +0000 Subject: [Shrine-users] : Error mapping query terms from network to local forms Message-ID: <43ECC5435444BE479E03012738A1400F15150A9D@EXMB03.ohsu.edu> Hi, Thanks Elena for confirming icons, and sharing your experiences. That describes the behavior I'm experiencing too. Can run a query against gender/age on i2b2 and Shrine without error. After correcting SHRINE ontology for Diagnosis Modifiers, can run query against i2b2, but SHRINE query throws Error. The shrine log indicates there is some issues with term mapping. >> 2014-Oct-09-10:32:09.353 DEBUG >> [SHRINE][ExpressionTranslator][ForkJoinPool-1-worker-7] Translated: >> Term(\\SHRINE\SHRINE\Diagnoses\DISEASES OF THE CIRCULATORY SYSTEM >> (390-459.99)\DISEASES OF ARTERIES, ARTERIOLES, AND CAPILLARIES >> (440-449.99)\Aortic aneurysm and dissection (441)$441.5) Aortic >> aneurysm of unspecified site, ruptured$ to None >> 2014-Oct-09-10:32:09.356 WARN >> [SHRINE][RunQueryAdapter][ForkJoinPool-1-worker-7] Error mapping >> query terms: Error mapping query terms from network to local forms Not sure what corrective action to take. -Peter -----Original Message----- From: shrine-users-bounces at open.med.harvard.edu [mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of ev2348 at columbia.edu Sent: Monday, October 13, 2014 9:14 AM To: shrine-users at open.med.harvard.edu; shrine-users-request at open.med.harvard.edu Subject: Re: [Shrine-users] Shrine-users Digest, Vol 26, Issue 24 Hello I see the three icons Admit, Principal, Secondary? The only thing I can count is Demographics with or without ERROR. The rest it does not work. Elena > Quoting shrine-users-request at open.med.harvard.edu: > Send Shrine-users mailing list submissions to > shrine-users at open.med.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://open.med.harvard.edu/mailman/listinfo/shrine-users > or, via email, send a message with subject or body 'help' to > shrine-users-request at open.med.harvard.edu > > You can reach the person managing the list at > shrine-users-owner at open.med.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Shrine-users digest..." > > > Today's Topics: > > 1. Re: adapter problems --> modifiers? (Peter Beninato) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 10 Oct 2014 21:37:46 +0000 > From: Peter Beninato > To: "ev2348 at columbia.edu" > Cc: "shrine-users at open.med.harvard.edu" > > Subject: Re: [Shrine-users] adapter problems --> modifiers? > Message-ID: <43ECC5435444BE479E03012738A1400F15150688 at EXMB03.ohsu.edu> > Content-Type: text/plain; charset="us-ascii" > > Hi, > > When you expand the SHRINE ontology to, Diseases anfd Injuries > (001-999.99)/Diseases of Digestive System (520-579.99)/Appendicitis > (540-543.99), Do you see icons for: > Admit, Principal, Secondary? > > If you don't see those icons then... > > > Since this deals with Diagnoses. Please look at the m_applied_path > in an entry in SHRINE where the c_fullname = ' \Admit Diagnosis\' > (or principal or secondar) > > Take the m_applied_path, and use it as the criteria: > Select * >> From shrine > Where c_fullname = {my_m_applied_path from Admit DX} > > You may get no rows. My experience is that the third tuple in the > m_applied_path needs to be capitalized to match the c_fullname that > you want to add the modifiers too. > > Once I made that change, I got past an error condition. > > And on to another... > > Fyi. > -Peter > > -----Original Message----- > From: ev2348 at columbia.edu [mailto:ev2348 at columbia.edu] > Sent: Friday, October 10, 2014 1:22 PM > To: Peter Beninato > Cc: Shuman, William (Billy); shrine-users at open.med.harvard.edu > Subject: RE: [Shrine-users] adapter problems --> modifiers? > > Hi, > I certainly downloaded the AdapterMappings.xml from Harvard > SHRINE_SVN_URL_BASE=https://open.med.harvard.edu/svn/shrine/releases/$ > {SHRINE_VERSION}/ nad made some changes according to table > i2b2metadata.table_access. > Attached is the copy I am using. I see some of the terms with > different words but just the same for instance I have for Appendicitis > > I2B2 NODE: > Diagnosis/ICD9 Disease/Disorder of Digestive Tract/other and > unspecified Diseases of Appendix/Appendicitis > > SHRINE Node: > Diseases anfd Injuries (001-999.99)/Diseases of Digestive System > (520-579.99)/Appendicitis (540-543.99) > > and I get the message > > 2014-Oct-10-15:32:22.484 DEBUG > [SHRINE][SquerylAdapterDao][ForkJoinPool-1-worker-3] User > i2b2CDW:shrine locked out? false > 2014-Oct-10-15:32:22.484 DEBUG > [SHRINE][RunQueryAdapter][ForkJoinPool-1-worker-3] Performing query > from user i2b2CDW:shrine > 2014-Oct-10-15:32:22.485 DEBUG > [SHRINE][ExpressionTranslator][ForkJoinPool-1-worker-3] Translated: > Term(\\SHRINE\SHRINE\Diagnoses\DISEASES OF THE DIGESTIVE SYSTEM > (520-579.99)\APPENDICITIS (540-543.99)\) to > Failure(net.shrine.adapter.AdapterMappingException: No local terms > mapped to '\\SHRINE\SHRINE\Diagnoses\DISEASES OF THE DIGESTIVE > SYSTEM (520-579.99)\APPENDICITIS (540-543.99)\') > 2014-Oct-10-15:32:22.485 WARN > [SHRINE][RunQueryAdapter][ForkJoinPool-1-worker-3] Error mapping query > terms: Error mapping query terms from network to local forms. request: > RunQueryRequest(CDW,180000 > milliseconds,AuthenticationInfo(***,,Credential(,false)),7718049720240791039,None,Set(PATIENT_COUNT_XML),QueryDefinition(APPENDICITIS (5 at 15:32:20,Term(\\SHRINE\SHRINE\Diagnoses\DISEASES OF THE DIGESTIVE SYSTEM > (520-579.99)\APPENDICITIS > (540-543.99)\))) > net.shrine.adapter.AdapterMappingException: Error mapping query > terms from network to local forms. request: > RunQueryRequest(CDW,180000 > milliseconds,AuthenticationInfo(,,Credential(*,false)),7718049720240791039,None,Set(PATIENT_COUNT_XML),QueryDefinition(APPENDICITIS (5 at 15:32:20,Term(\\SHRINE\SHRINE\Diagnoses\DISEASES OF THE DIGESTIVE SYSTEM > (520-579.99)\APPENDICITIS > (540-543.99)\))) > at > net.shrine.adapter.RunQueryAdapter.translateNetworkToLocal(RunQueryAdapter.scala:60) > at > net.shrine.adapter.RunQueryAdapter.translateNetworkToLocal(RunQueryAdapter.scala:42) > at net.shrine.adapter.CrcAdapter.translateRequest(CrcAdapter.scala:95) > at net.shrine.adapter.CrcAdapter.processRequest(CrcAdapter.scala:60) > at net.shrine.adapter.RunQueryAdapter.runQuery(RunQueryAdapter.scala:121) > at > net.shrine.adapter.RunQueryAdapter.processRequest(RunQueryAdapter.scala:85) > at > net.shrine.adapter.RunQueryAdapter.processRequest(RunQueryAdapter.scala:42) > at net.shrine.adapter.Adapter.perform(Adapter.scala:26) > at > net.shrine.adapter.service.AdapterService$$anonfun$1$$anonfun$apply$1.apply(AdapterService.scala:36) > at > net.shrine.adapter.service.AdapterService$$anonfun$1$$anonfun$apply$1.apply(AdapterService.scala:36) > at net.shrine.adapter.service.AdapterService$.time(AdapterService.scala:68) > at > net.shrine.adapter.service.AdapterService$$anonfun$1.apply(AdapterService.scala:35) > at net.shrine.a > > Beninato : > >> Hi, >> >> I'm experiencing some issues with AdapterMappings.xml and modifiers. >> >> I have loaded up the shrine ontology corrected for the disconnect >> between c_fullname and m_applied_path (m_applied_path case, does not >> match i2b2 demo ontology c_fullname case). >> >> That got the modifier icons to appear. When I chose the Admit DX for 441.5. >> >> When I look in the shrine log I see: >> 2014-Oct-09-10:32:09.353 DEBUG >> [SHRINE][ExpressionTranslator][ForkJoinPool-1-worker-7] Translated: >> Term(\\SHRINE\SHRINE\Diagnoses\DISEASES OF THE CIRCULATORY SYSTEM >> (390-459.99)\DISEASES OF ARTERIES, ARTERIOLES, AND CAPILLARIES >> (440-449.99)\Aortic aneurysm and dissection (441)$441.5) Aortic >> aneurysm of unspecified site, ruptured$ to None >> 2014-Oct-09-10:32:09.356 WARN >> [SHRINE][RunQueryAdapter][ForkJoinPool-1-worker-7] Error mapping >> query terms: Error mapping query terms from network to local forms >> >> I see the term in AdapterMappings.xml and I can find the local term >> in the local i2b2 ontology, so I'm not sure why it is mapping to none. >> >> This might be related? >> >> Fyi. >> -Peter >> >> -----Original Message----- >> From: shrine-users-bounces at open.med.harvard.edu >> [mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of >> Shuman, William (Billy) >> Sent: Friday, October 10, 2014 12:22 PM >> To: ev2348 at columbia.edu >> Cc: shrine-users at open.med.harvard.edu >> Subject: Re: [Shrine-users] adapter prpoblems >> >> It seems like it can not map the > > Quoting Peter Beninato : > >> Hi, >> >> I'm experiencing some issues with AdapterMappings.xml and modifiers. >> >> I have loaded up the shrine ontology corrected for the disconnect >> between c_fullname and m_applied_path (m_applied_path case, does not >> match i2b2 demo ontology c_fullname case). >> >> That got the modifier icons to appear. When I chose the Admit DX for 441.5. >> >> When I look in the shrine log I see: >> 2014-Oct-09-10:32:09.353 DEBUG >> [SHRINE][ExpressionTranslator][ForkJoinPool-1-worker-7] Translated: >> Term(\\SHRINE\SHRINE\Diagnoses\DISEASES OF THE CIRCULATORY SYSTEM >> (390-459.99)\DISEASES OF ARTERIES, ARTERIOLES, AND CAPILLARIES >> (440-449.99)\Aortic aneurysm and dissection (441)$441.5) Aortic >> aneurysm of unspecified site, ruptured$ to None >> 2014-Oct-09-10:32:09.356 WARN >> [SHRINE][RunQueryAdapter][ForkJoinPool-1-worker-7] Error mapping >> query terms: Error mapping query terms from network to local forms >> >> I see the term in AdapterMappings.xml and I can find the local term >> in the local i2b2 ontology, so I'm not sure why it is mapping to none. >> >> This might be related? >> >> Fyi. >> -Peter >> >> -----Original Message----- >> From: shrine-users-bounces at open.med.harvard.edu >> [mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of >> Shuman, William (Billy) >> Sent: Friday, October 10, 2014 12:22 PM >> To: ev2348 at columbia.edu >> Cc: shrine-users at open.med.harvard.edu >> Subject: Re: [Shrine-users] adapter prpoblems >> >> It seems like it can not map the key \\SHRINE\SHRINE\Labs\LP32651-9 >> \LP67162-5\ to any local key. Is that key located in your adapter >> mappings file? >> >> Billy >> -- >> William Shuman Cincinnati Children's >> Hospital Medical Center >> >> On Fri, 2014-10-10 at 14:42 -0400, ev2348 at columbia.edu wrote: >>> \\SHRINE\SHRINE\Labs\LP32651-9\LP67162-5\ >> _______________________ >> Shrine-users mailing list >> Shrine-users at open.med.harvard.edu >> https://open.med.harvard.edu/mailman/listinfo/shrine-users >> >> > > > > > ------------------------------ > > _ > Shrine-users mailing list > Shrine-users at open.med.harvard.edu > https://open.med.harvard.edu/mailman/listinfo/shrine-users > > > End of Shrine-users Digest, Vol 26, Issue 24 > ****************************************** > > _________________________ Shrine-users mailing list Shrine-users at open.med.harvard.edu https://open.med.harvard.edu/mailman/listinfo/shrine-users From ev2348 at columbia.edu Mon Oct 13 12:41:37 2014 From: ev2348 at columbia.edu (ev2348 at columbia.edu) Date: Mon, 13 Oct 2014 12:41:37 -0400 Subject: [Shrine-users] : Error mapping query terms from network to local forms In-Reply-To: <43ECC5435444BE479E03012738A1400F15150A9D@EXMB03.ohsu.edu> References: <43ECC5435444BE479E03012738A1400F15150A9D@EXMB03.ohsu.edu> Message-ID: <20141013124137.jxyjnqg7k80c84ks@cubmail.cc.columbia.edu> Hi, When I had 1.16.2 installed I could not see the three icons but I could see the errors in Tomcat/lib/shrine.log that I sent last week. When I substituted Shrine.sql and populated the Shrine table with version 1.17.0, then I can see the tree icons you mentioned Admit, Principal, Secondary?, but it does not help because the queries return ERROR Harvard issue and the logs are empty as shrine.log does not give me any messages which is even worst because you have no clue. Elena Quoting Peter Beninato : > Hi, > > Thanks Elena for confirming icons, and sharing your experiences. > > That describes the behavior I'm experiencing too. Can run a query > against gender/age on i2b2 and Shrine without error. > > After correcting SHRINE ontology for Diagnosis Modifiers, can run > query against i2b2, but SHRINE query throws Error. > > > The shrine log indicates there is some issues with term mapping. > >>> 2014-Oct-09-10:32:09.353 DEBUG >>> [SHRINE][ExpressionTranslator][ForkJoinPool-1-worker-7] Translated: >>> Term(\\SHRINE\SHRINE\Diagnoses\DISEASES OF THE CIRCULATORY SYSTEM >>> (390-459.99)\DISEASES OF ARTERIES, ARTERIOLES, AND CAPILLARIES >>> (440-449.99)\Aortic aneurysm and dissection (441)$441.5) Aortic >>> aneurysm of unspecified site, ruptured$ to None >>> 2014-Oct-09-10:32:09.356 WARN >>> [SHRINE][RunQueryAdapter][ForkJoinPool-1-worker-7] Error mapping >>> query terms: Error mapping query terms from network to local forms > > Not sure what corrective action to take. > > -Peter > > > -----Original Message----- > From: shrine-users-bounces at open.med.harvard.edu > [mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of > ev2348 at columbia.edu > Sent: Monday, October 13, 2014 9:14 AM > To: shrine-users at open.med.harvard.edu; > shrine-users-request at open.med.harvard.edu > Subject: Re: [Shrine-users] Shrine-users Digest, Vol 26, Issue 24 > > Hello I see the three icons > Admit, Principal, Secondary? > > The only thing I can count is Demographics with or without ERROR. > The rest it does not work. > Elena >> > Quoting shrine-users-request at open.med.harvard.edu: > >> Send Shrine-users mailing list submissions to >> shrine-users at open.med.harvard.edu >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://open.med.harvard.edu/mailman/listinfo/shrine-users >> or, via email, send a message with subject or body 'help' to >> shrine-users-request at open.med.harvard.edu >> >> You can reach the person managing the list at >> shrine-users-owner at open.med.harvard.edu >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Shrine-users digest..." >> >> >> Today's Topics: >> >> 1. Re: adapter problems --> modifiers? (Peter Beninato) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Fri, 10 Oct 2014 21:37:46 +0000 >> From: Peter Beninato >> To: "ev2348 at columbia.edu" >> Cc: "shrine-users at open.med.harvard.edu" >> >> Subject: Re: [Shrine-users] adapter problems --> modifiers? >> Message-ID: <43ECC5435444BE479E03012738A1400F15150688 at EXMB03.ohsu.edu> >> Content-Type: text/plain; charset="us-ascii" >> >> Hi, >> >> When you expand the SHRINE ontology to, Diseases anfd Injuries >> (001-999.99)/Diseases of Digestive System (520-579.99)/Appendicitis >> (540-543.99), Do you see icons for: >> Admit, Principal, Secondary? >> >> If you don't see those icons then... >> >> >> Since this deals with Diagnoses. Please look at the m_applied_path >> in an entry in SHRINE where the c_fullname = ' \Admit Diagnosis\' >> (or principal or secondar) >> >> Take the m_applied_path, and use it as the criteria: >> Select * >>> From shrine >> Where c_fullname = {my_m_applied_path from Admit DX} >> >> You may get no rows. My experience is that the third tuple in the >> m_applied_path needs to be capitalized to match the c_fullname that >> you want to add the modifiers too. >> >> Once I made that change, I got past an error condition. >> >> And on to another... >> >> Fyi. >> -Peter >> >> -----Original Message----- >> From: ev2348 at columbia.edu [mailto:ev2348 at columbia.edu] >> Sent: Friday, October 10, 2014 1:22 PM >> To: Peter Beninato >> Cc: Shuman, William (Billy); shrine-users at open.med.harvard.edu >> Subject: RE: [Shrine-users] adapter problems --> modifiers? >> >> Hi, >> I certainly downloaded the AdapterMappings.xml from Harvard >> SHRINE_SVN_URL_BASE=https://open.med.harvard.edu/svn/shrine/releases/$ >> {SHRINE_VERSION}/ nad made some changes according to table >> i2b2metadata.table_access. >> Attached is the copy I am using. I see some of the terms with >> different words but just the same for instance I have for Appendicitis >> >> I2B2 NODE: >> Diagnosis/ICD9 Disease/Disorder of Digestive Tract/other and >> unspecified Diseases of Appendix/Appendicitis >> >> SHRINE Node: >> Diseases anfd Injuries (001-999.99)/Diseases of Digestive System >> (520-579.99)/Appendicitis (540-543.99) >> >> and I get the message >> >> 2014-Oct-10-15:32:22.484 DEBUG >> [SHRINE][SquerylAdapterDao][ForkJoinPool-1-worker-3] User >> i2b2CDW:shrine locked out? false >> 2014-Oct-10-15:32:22.484 DEBUG >> [SHRINE][RunQueryAdapter][ForkJoinPool-1-worker-3] Performing query >> from user i2b2CDW:shrine >> 2014-Oct-10-15:32:22.485 DEBUG >> [SHRINE][ExpressionTranslator][ForkJoinPool-1-worker-3] Translated: >> Term(\\SHRINE\SHRINE\Diagnoses\DISEASES OF THE DIGESTIVE SYSTEM >> (520-579.99)\APPENDICITIS (540-543.99)\) to >> Failure(net.shrine.adapter.AdapterMappingException: No local terms >> mapped to '\\SHRINE\SHRINE\Diagnoses\DISEASES OF THE DIGESTIVE >> SYSTEM (520-579.99)\APPENDICITIS (540-543.99)\') >> 2014-Oct-10-15:32:22.485 WARN >> [SHRINE][RunQueryAdapter][ForkJoinPool-1-worker-3] Error mapping query >> terms: Error mapping query terms from network to local forms. request: >> RunQueryRequest(CDW,180000 >> milliseconds,AuthenticationInfo(***,,Credential(,false)),7718049720240791039,None,Set(PATIENT_COUNT_XML),QueryDefinition(APPENDICITIS (5 at 15:32:20,Term(\\SHRINE\SHRINE\Diagnoses\DISEASES OF THE DIGESTIVE >> SYSTEM >> (520-579.99)\APPENDICITIS >> (540-543.99)\))) >> net.shrine.adapter.AdapterMappingException: Error mapping query >> terms from network to local forms. request: >> RunQueryRequest(CDW,180000 >> milliseconds,AuthenticationInfo(,,Credential(*,false)),7718049720240791039,None,Set(PATIENT_COUNT_XML),QueryDefinition(APPENDICITIS (5 at 15:32:20,Term(\\SHRINE\SHRINE\Diagnoses\DISEASES OF THE DIGESTIVE >> SYSTEM >> (520-579.99)\APPENDICITIS >> (540-543.99)\))) >> at >> net.shrine.adapter.RunQueryAdapter.translateNetworkToLocal(RunQueryAdapter.scala:60) >> at >> net.shrine.adapter.RunQueryAdapter.translateNetworkToLocal(RunQueryAdapter.scala:42) >> at net.shrine.adapter.CrcAdapter.translateRequest(CrcAdapter.scala:95) >> at net.shrine.adapter.CrcAdapter.processRequest(CrcAdapter.scala:60) >> at net.shrine.adapter.RunQueryAdapter.runQuery(RunQueryAdapter.scala:121) >> at >> net.shrine.adapter.RunQueryAdapter.processRequest(RunQueryAdapter.scala:85) >> at >> net.shrine.adapter.RunQueryAdapter.processRequest(RunQueryAdapter.scala:42) >> at net.shrine.adapter.Adapter.perform(Adapter.scala:26) >> at >> net.shrine.adapter.service.AdapterService$$anonfun$1$$anonfun$apply$1.apply(AdapterService.scala:36) >> at >> net.shrine.adapter.service.AdapterService$$anonfun$1$$anonfun$apply$1.apply(AdapterService.scala:36) >> at net.shrine.adapter.service.AdapterService$.time(AdapterService.scala:68) >> at >> net.shrine.adapter.service.AdapterService$$anonfun$1.apply(AdapterService.scala:35) >> at net.shrine.a >> >> Beninato : >> >>> Hi, >>> >>> I'm experiencing some issues with AdapterMappings.xml and modifiers. >>> >>> I have loaded up the shrine ontology corrected for the disconnect >>> between c_fullname and m_applied_path (m_applied_path case, does not >>> match i2b2 demo ontology c_fullname case). >>> >>> That got the modifier icons to appear. When I chose the Admit DX for 441.5. >>> >>> When I look in the shrine log I see: >>> 2014-Oct-09-10:32:09.353 DEBUG >>> [SHRINE][ExpressionTranslator][ForkJoinPool-1-worker-7] Translated: >>> Term(\\SHRINE\SHRINE\Diagnoses\DISEASES OF THE CIRCULATORY SYSTEM >>> (390-459.99)\DISEASES OF ARTERIES, ARTERIOLES, AND CAPILLARIES >>> (440-449.99)\Aortic aneurysm and dissection (441)$441.5) Aortic >>> aneurysm of unspecified site, ruptured$ to None >>> 2014-Oct-09-10:32:09.356 WARN >>> [SHRINE][RunQueryAdapter][ForkJoinPool-1-worker-7] Error mapping >>> query terms: Error mapping query terms from network to local forms >>> >>> I see the term in AdapterMappings.xml and I can find the local term >>> in the local i2b2 ontology, so I'm not sure why it is mapping to none. >>> >>> This might be related? >>> >>> Fyi. >>> -Peter >>> >>> -----Original Message----- >>> From: shrine-users-bounces at open.med.harvard.edu >>> [mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of >>> Shuman, William (Billy) >>> Sent: Friday, October 10, 2014 12:22 PM >>> To: ev2348 at columbia.edu >>> Cc: shrine-users at open.med.harvard.edu >>> Subject: Re: [Shrine-users] adapter prpoblems >>> >>> It seems like it can not map the >> >> Quoting Peter Beninato : >> >>> Hi, >>> >>> I'm experiencing some issues with AdapterMappings.xml and modifiers. >>> >>> I have loaded up the shrine ontology corrected for the disconnect >>> between c_fullname and m_applied_path (m_applied_path case, does not >>> match i2b2 demo ontology c_fullname case). >>> >>> That got the modifier icons to appear. When I chose the Admit DX for 441.5. >>> >>> When I look in the shrine log I see: >>> 2014-Oct-09-10:32:09.353 DEBUG >>> [SHRINE][ExpressionTranslator][ForkJoinPool-1-worker-7] Translated: >>> Term(\\SHRINE\SHRINE\Diagnoses\DISEASES OF THE CIRCULATORY SYSTEM >>> (390-459.99)\DISEASES OF ARTERIES, ARTERIOLES, AND CAPILLARIES >>> (440-449.99)\Aortic aneurysm and dissection (441)$441.5) Aortic >>> aneurysm of unspecified site, ruptured$ to None >>> 2014-Oct-09-10:32:09.356 WARN >>> [SHRINE][RunQueryAdapter][ForkJoinPool-1-worker-7] Error mapping >>> query terms: Error mapping query terms from network to local forms >>> >>> I see the term in AdapterMappings.xml and I can find the local term >>> in the local i2b2 ontology, so I'm not sure why it is mapping to none. >>> >>> This might be related? >>> >>> Fyi. >>> -Peter >>> >>> -----Original Message----- >>> From: shrine-users-bounces at open.med.harvard.edu >>> [mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of >>> Shuman, William (Billy) >>> Sent: Friday, October 10, 2014 12:22 PM >>> To: ev2348 at columbia.edu >>> Cc: shrine-users at open.med.harvard.edu >>> Subject: Re: [Shrine-users] adapter prpoblems >>> >>> It seems like it can not map the key \\SHRINE\SHRINE\Labs\LP32651-9 >>> \LP67162-5\ to any local key. Is that key located in your adapter >>> mappings file? >>> >>> Billy >>> -- >>> William Shuman Cincinnati Children's >>> Hospital Medical Center >>> >>> On Fri, 2014-10-10 at 14:42 -0400, ev2348 at columbia.edu wrote: >>>> \\SHRINE\SHRINE\Labs\LP32651-9\LP67162-5\ >>> _______________________ >>> Shrine-users mailing list >>> Shrine-users at open.med.harvard.edu >>> https://open.med.harvard.edu/mailman/listinfo/shrine-users >>> >>> >> >> >> >> >> ------------------------------ >> >> _ >> Shrine-users mailing list >> Shrine-users at open.med.harvard.edu >> https://open.med.harvard.edu/mailman/listinfo/shrine-users >> >> >> End of Shrine-users Digest, Vol 26, Issue 24 >> ****************************************** >> >> > > > > _________________________ > Shrine-users mailing list > Shrine-users at open.med.harvard.edu > https://open.med.harvard.edu/mailman/listinfo/shrine-users > > From Philip_Trevvett at hms.harvard.edu Tue Oct 14 08:58:33 2014 From: Philip_Trevvett at hms.harvard.edu (Trevvett, Philip) Date: Tue, 14 Oct 2014 08:58:33 -0400 Subject: [Shrine-users] Error in SHRINE 1.17.0 demo onotolgy In-Reply-To: References: Message-ID: The first row should now have the correct values and is checked in: https://open.med.harvard.edu/svn/shrine/releases/1.17.0/ontology/SHRINE_Demo_Downloads/ShrineDemo.sql Thanks, philip ________________________________________ From: shrine-users-bounces at open.med.harvard.edu [shrine-users-bounces at open.med.harvard.edu] On Behalf Of Justin Dale [jdale at umn.edu] Sent: Friday, October 10, 2014 3:45 PM To: shrine-users at open.med.harvard.edu Subject: [Shrine-users] Error in SHRINE 1.17.0 demo onotolgy We tried to load the SHRINE demo ontology for 1.17.0 (https://open.med.harvard.edu/svn/shrine/releases/1.17.0/ontology/SHRINE_Demo_Downloads/ShrineDemo.sql) and it appears the first insert statement has an error in it (Not enough values) INSERT INTO SHRINE ( C_HLEVEL, C_FULLNAME, C_NAME, C_SYNONYM_CD, C_VISUALATTRIBUTES, C_TOTALNUM, C_BASECODE, C_METADATAXML, C_FACTTABLECOLUMN, C_TABLENAME, C_COLUMNNAME, C_COLUMNDATATYPE, C_OPERATOR, C_DIMCODE, C_COMMENT, C_TOOLTIP, UPDATE_DATE, DOWNLOAD_DATE, IMPORT_DATE, SOURCESYSTEM_CD, VALUETYPE_CD, M_APPLIED_PATH, M_EXCLUSION_CD ) VALUES ( 0, '\SHRINE\ONTOLOGYVERSION\SHRINE_DEMO_ONTOLOGY_V-1.17_9-18-14\', 'ONTOLOGYVERSION', 'N', 'LH', NULL, NULL, '', 'concept_cd', 'concept_dimension', 'concept_path', 'T', 'LIKE', '\SHRINE\ONTOLOGYVERSION\', NULL ); It's missing values for: C_TOOLTIP, UPDATE_DATE, DOWNLOAD_DATE, IMPORT_DATE, SOURCESYSTEM_CD, VALUETYPE_CD, M_APPLIED_PATH, M_EXCLUSION_CD Regards, Justin Dale Manager - Research Development and Support University of Minnesota Academic Health Center - Office of Information Systems Phone: 612.624.9747 Fax: 612.624.7458 jdale at umn.edu From jeff.lunt at northwestern.edu Tue Oct 14 10:23:15 2014 From: jeff.lunt at northwestern.edu (Jeff Mark Lunt) Date: Tue, 14 Oct 2014 14:23:15 +0000 Subject: [Shrine-users] Error in SHRINE 1.17.0 demo onotolgy In-Reply-To: References: Message-ID: That link still points to a version that has the same number of values as was originally reported. Did you intend to post a different link? On 10/14/14, 7:58 AM, "Trevvett, Philip" wrote: >The first row should now have the correct values and is checked in: > >https://open.med.harvard.edu/svn/shrine/releases/1.17.0/ontology/SHRINE_De >mo_Downloads/ShrineDemo.sql > >Thanks, >philip >________________________________________ >From: shrine-users-bounces at open.med.harvard.edu >[shrine-users-bounces at open.med.harvard.edu] On Behalf Of Justin Dale >[jdale at umn.edu] >Sent: Friday, October 10, 2014 3:45 PM >To: shrine-users at open.med.harvard.edu >Subject: [Shrine-users] Error in SHRINE 1.17.0 demo onotolgy > >We tried to load the SHRINE demo ontology for 1.17.0 >(https://open.med.harvard.edu/svn/shrine/releases/1.17.0/ontology/SHRINE_D >emo_Downloads/ShrineDemo.sql) and it appears the first insert statement >has an error in it (Not enough values) > >INSERT INTO SHRINE ( >C_HLEVEL, >C_FULLNAME, >C_NAME, >C_SYNONYM_CD, >C_VISUALATTRIBUTES, >C_TOTALNUM, >C_BASECODE, >C_METADATAXML, >C_FACTTABLECOLUMN, >C_TABLENAME, >C_COLUMNNAME, >C_COLUMNDATATYPE, >C_OPERATOR, >C_DIMCODE, >C_COMMENT, >C_TOOLTIP, >UPDATE_DATE, >DOWNLOAD_DATE, >IMPORT_DATE, >SOURCESYSTEM_CD, >VALUETYPE_CD, >M_APPLIED_PATH, >M_EXCLUSION_CD ) > >VALUES ( >0, >'\SHRINE\ONTOLOGYVERSION\SHRINE_DEMO_ONTOLOGY_V-1.17_9-18-14\', >'ONTOLOGYVERSION', >'N', >'LH', >NULL, >NULL, '', >'concept_cd', >'concept_dimension', >'concept_path', >'T', >'LIKE', >'\SHRINE\ONTOLOGYVERSION\', >NULL ); > > >It's missing values for: >C_TOOLTIP, >UPDATE_DATE, >DOWNLOAD_DATE, >IMPORT_DATE, >SOURCESYSTEM_CD, >VALUETYPE_CD, >M_APPLIED_PATH, >M_EXCLUSION_CD > > >Regards, > >Justin Dale >Manager - Research Development and Support >University of Minnesota >Academic Health Center - Office of Information Systems >Phone: 612.624.9747 >Fax: 612.624.7458 >jdale at umn.edu >_______________________________________________ >Shrine-users mailing list >Shrine-users at open.med.harvard.edu >https://open.med.harvard.edu/mailman/listinfo/shrine-users From Philip_Trevvett at hms.harvard.edu Tue Oct 14 12:22:46 2014 From: Philip_Trevvett at hms.harvard.edu (Trevvett, Philip) Date: Tue, 14 Oct 2014 12:22:46 -0400 Subject: [Shrine-users] Error in SHRINE 1.17.0 demo onotolgy In-Reply-To: References: Message-ID: The link should be fine now, was just a little slow to update. Try again now. Thanks, philip -----Original Message----- From: Jeff Mark Lunt [mailto:jeff.lunt at northwestern.edu] Sent: Tuesday, October 14, 2014 10:23 AM To: Trevvett, Philip; Justin Dale; shrine-users at open.med.harvard.edu Subject: Re: [Shrine-users] Error in SHRINE 1.17.0 demo onotolgy That link still points to a version that has the same number of values as was originally reported. Did you intend to post a different link? On 10/14/14, 7:58 AM, "Trevvett, Philip" wrote: >The first row should now have the correct values and is checked in: > >https://open.med.harvard.edu/svn/shrine/releases/1.17.0/ontology/SHRINE >_De >mo_Downloads/ShrineDemo.sql > >Thanks, >philip >________________________________________ >From: shrine-users-bounces at open.med.harvard.edu >[shrine-users-bounces at open.med.harvard.edu] On Behalf Of Justin Dale >[jdale at umn.edu] >Sent: Friday, October 10, 2014 3:45 PM >To: shrine-users at open.med.harvard.edu >Subject: [Shrine-users] Error in SHRINE 1.17.0 demo onotolgy > >We tried to load the SHRINE demo ontology for 1.17.0 >(https://open.med.harvard.edu/svn/shrine/releases/1.17.0/ontology/SHRIN >E_D >emo_Downloads/ShrineDemo.sql) and it appears the first insert statement >has an error in it (Not enough values) > >INSERT INTO SHRINE ( >C_HLEVEL, >C_FULLNAME, >C_NAME, >C_SYNONYM_CD, >C_VISUALATTRIBUTES, >C_TOTALNUM, >C_BASECODE, >C_METADATAXML, >C_FACTTABLECOLUMN, >C_TABLENAME, >C_COLUMNNAME, >C_COLUMNDATATYPE, >C_OPERATOR, >C_DIMCODE, >C_COMMENT, >C_TOOLTIP, >UPDATE_DATE, >DOWNLOAD_DATE, >IMPORT_DATE, >SOURCESYSTEM_CD, >VALUETYPE_CD, >M_APPLIED_PATH, >M_EXCLUSION_CD ) > >VALUES ( >0, >'\SHRINE\ONTOLOGYVERSION\SHRINE_DEMO_ONTOLOGY_V-1.17_9-18-14\', >'ONTOLOGYVERSION', >'N', >'LH', >NULL, >NULL, '', >'concept_cd', >'concept_dimension', >'concept_path', >'T', >'LIKE', >'\SHRINE\ONTOLOGYVERSION\', >NULL ); > > >It's missing values for: >C_TOOLTIP, >UPDATE_DATE, >DOWNLOAD_DATE, >IMPORT_DATE, >SOURCESYSTEM_CD, >VALUETYPE_CD, >M_APPLIED_PATH, >M_EXCLUSION_CD > > >Regards, > >Justin Dale >Manager - Research Development and Support University of Minnesota >Academic Health Center - Office of Information Systems >Phone: 612.624.9747 >Fax: 612.624.7458 >jdale at umn.edu >_______________________________________________ >Shrine-users mailing list >Shrine-users at open.med.harvard.edu >https://open.med.harvard.edu/mailman/listinfo/shrine-users From jeff.lunt at northwestern.edu Tue Oct 14 13:18:32 2014 From: jeff.lunt at northwestern.edu (Jeff Mark Lunt) Date: Tue, 14 Oct 2014 17:18:32 +0000 Subject: [Shrine-users] Error in SHRINE 1.17.0 demo onotolgy In-Reply-To: References: Message-ID: Thanks. Looks good. On 10/14/14, 11:22 AM, "Trevvett, Philip" wrote: >The link should be fine now, was just a little slow to update. > >Try again now. > >Thanks, >philip > >-----Original Message----- >From: Jeff Mark Lunt [mailto:jeff.lunt at northwestern.edu] >Sent: Tuesday, October 14, 2014 10:23 AM >To: Trevvett, Philip; Justin Dale; shrine-users at open.med.harvard.edu >Subject: Re: [Shrine-users] Error in SHRINE 1.17.0 demo onotolgy > >That link still points to a version that has the same number of values as >was originally reported. Did you intend to post a different link? > > >On 10/14/14, 7:58 AM, "Trevvett, Philip" >wrote: > >>The first row should now have the correct values and is checked in: >> >>https://open.med.harvard.edu/svn/shrine/releases/1.17.0/ontology/SHRINE >>_De >>mo_Downloads/ShrineDemo.sql >> >>Thanks, >>philip >>________________________________________ >>From: shrine-users-bounces at open.med.harvard.edu >>[shrine-users-bounces at open.med.harvard.edu] On Behalf Of Justin Dale >>[jdale at umn.edu] >>Sent: Friday, October 10, 2014 3:45 PM >>To: shrine-users at open.med.harvard.edu >>Subject: [Shrine-users] Error in SHRINE 1.17.0 demo onotolgy >> >>We tried to load the SHRINE demo ontology for 1.17.0 >>(https://open.med.harvard.edu/svn/shrine/releases/1.17.0/ontology/SHRIN >>E_D >>emo_Downloads/ShrineDemo.sql) and it appears the first insert statement >>has an error in it (Not enough values) >> >>INSERT INTO SHRINE ( >>C_HLEVEL, >>C_FULLNAME, >>C_NAME, >>C_SYNONYM_CD, >>C_VISUALATTRIBUTES, >>C_TOTALNUM, >>C_BASECODE, >>C_METADATAXML, >>C_FACTTABLECOLUMN, >>C_TABLENAME, >>C_COLUMNNAME, >>C_COLUMNDATATYPE, >>C_OPERATOR, >>C_DIMCODE, >>C_COMMENT, >>C_TOOLTIP, >>UPDATE_DATE, >>DOWNLOAD_DATE, >>IMPORT_DATE, >>SOURCESYSTEM_CD, >>VALUETYPE_CD, >>M_APPLIED_PATH, >>M_EXCLUSION_CD ) >> >>VALUES ( >>0, >>'\SHRINE\ONTOLOGYVERSION\SHRINE_DEMO_ONTOLOGY_V-1.17_9-18-14\', >>'ONTOLOGYVERSION', >>'N', >>'LH', >>NULL, >>NULL, '', >>'concept_cd', >>'concept_dimension', >>'concept_path', >>'T', >>'LIKE', >>'\SHRINE\ONTOLOGYVERSION\', >>NULL ); >> >> >>It's missing values for: >>C_TOOLTIP, >>UPDATE_DATE, >>DOWNLOAD_DATE, >>IMPORT_DATE, >>SOURCESYSTEM_CD, >>VALUETYPE_CD, >>M_APPLIED_PATH, >>M_EXCLUSION_CD >> >> >>Regards, >> >>Justin Dale >>Manager - Research Development and Support University of Minnesota >>Academic Health Center - Office of Information Systems >>Phone: 612.624.9747 >>Fax: 612.624.7458 >>jdale at umn.edu >>_______________________________________________ >>Shrine-users mailing list >>Shrine-users at open.med.harvard.edu >>https://open.med.harvard.edu/mailman/listinfo/shrine-users > From Philip_Trevvett at hms.harvard.edu Wed Oct 15 12:32:20 2014 From: Philip_Trevvett at hms.harvard.edu (Trevvett, Philip) Date: Wed, 15 Oct 2014 12:32:20 -0400 Subject: [Shrine-users] Update to Shrine 1.17 demoontology Message-ID: Hi all, To address recent issues with querying diagnoses against i2b2 demo data with shrine 1.17, i've checked in an updated version of the demo ontology that is available here: https://open.med.harvard.edu/svn/shrine/releases/1.17.0/ontology/SHRINE_Demo_Downloads/ This addresses issues with capitalization differences between fullname, modifier applied paths, and adaptermappings keys that were causing dx queries to fail. If you've been having issues querying for diagnoses or modifiers using the demo ontology please load this version. Thanks, Philip From ev2348 at columbia.edu Wed Oct 15 12:57:38 2014 From: ev2348 at columbia.edu (ev2348 at columbia.edu) Date: Wed, 15 Oct 2014 12:57:38 -0400 Subject: [Shrine-users] shrine ontology Message-ID: <20141015125738.olt3s7qhcc4o4gck@cubmail.cc.columbia.edu> Hello, I am trying to make Shrine to work with our data in the i2b2 Server (from Electronic Health Records) no i2b2demo domain anymore. I am able to change the AdapterMappings.xlm to reflect our domain according to the entries in the local i2b2 Server implementation of i2b2metadata.access_table. I can successfully query Demographics and Medications. However, we have MED codes for Diagnosis and the AdapterMappings has 20 icd9 codes for Diagnosis. Can anybody tell me how can I either change the AdapterMappings.xml for Diagnosis or if I need to change the i2b2 database. Is there any tools so I can map MED codes to ICD9 codes or in order to implement Shrine we just need to figure out how to change the local Ontology to make it work with Shrine. Does it need to be done manually to the best of our guests on the associations between the codes? Do we need the ETL change so that we have Diagnosis according to the 20 different ICD9 codes provided in the AdapterMappings.xml? Elena From Philip_Trevvett at hms.harvard.edu Wed Oct 15 13:20:46 2014 From: Philip_Trevvett at hms.harvard.edu (Trevvett, Philip) Date: Wed, 15 Oct 2014 13:20:46 -0400 Subject: [Shrine-users] shrine ontology In-Reply-To: <20141015125738.olt3s7qhcc4o4gck@cubmail.cc.columbia.edu> References: <20141015125738.olt3s7qhcc4o4gck@cubmail.cc.columbia.edu> Message-ID: Hi Elena, can you clarify what you mean by 20 icd9 codes? all diagnoses in the shrine demo ontology are icd9 codes, not just 20. have you been able to successfully perform queries against the demodata? I would recommend that as a first step to confirm everything is working. following that, if you do not use icd9 codes locally, you would need to map your local codes to icd9. In terms of creating mappings, if you map to icd9 leaf nodes and low level folders, you can then generate hierarchical mappings and compress redundant mappings using the tools here: https://open.med.harvard.edu/wiki/display/SHRINE/Mapping+Tools this is not an interface for manual mapping, but rather a set of simple tools that should faciliate taking a basic set of mappings and generating a clean adaptermappings.csv file, including all hierarchical mappings. (this will also make it easier to reuse mappings in the case of hierarchical changes on either side). thanks, philip ________________________________________ From: shrine-users-bounces at open.med.harvard.edu [shrine-users-bounces at open.med.harvard.edu] On Behalf Of ev2348 at columbia.edu [ev2348 at columbia.edu] Sent: Wednesday, October 15, 2014 12:57 PM To: shrine-users at open.med.harvard.edu Subject: [Shrine-users] shrine ontology Hello, I am trying to make Shrine to work with our data in the i2b2 Server (from Electronic Health Records) no i2b2demo domain anymore. I am able to change the AdapterMappings.xlm to reflect our domain according to the entries in the local i2b2 Server implementation of i2b2metadata.access_table. I can successfully query Demographics and Medications. However, we have MED codes for Diagnosis and the AdapterMappings has 20 icd9 codes for Diagnosis. Can anybody tell me how can I either change the AdapterMappings.xml for Diagnosis or if I need to change the i2b2 database. Is there any tools so I can map MED codes to ICD9 codes or in order to implement Shrine we just need to figure out how to change the local Ontology to make it work with Shrine. Does it need to be done manually to the best of our guests on the associations between the codes? Do we need the ETL change so that we have Diagnosis according to the 20 different ICD9 codes provided in the AdapterMappings.xml? Elena _______________________________________________ Shrine-users mailing list Shrine-users at open.med.harvard.edu https://open.med.harvard.edu/mailman/listinfo/shrine-users From mhorvath at wakehealth.edu Thu Oct 16 11:11:08 2014 From: mhorvath at wakehealth.edu (Michael Horvath) Date: Thu, 16 Oct 2014 15:11:08 +0000 Subject: [Shrine-users] Update to Shrine 1.17 demoontology In-Reply-To: References: Message-ID: <96E1AA641D2EDE49A7A43FE98067A3E93B4306AC@EXCHDB1.medctr.ad.wfubmc.edu> I'm seeing errors with the provided shrine ontology and adaptermappings. Shrine 1.17 running against I2B2 1.7 with the default demodata. Sample query against \\i2b2_DIAG\i2b2\Diagnoses\Respiratory system (460-519)\Chronic obstructive diseases (490-496)$493) Asthma\(493-9) Asthma, unspecified\(493-90) Asthma, unspecified type~\ returns fine (133 patients) for both I2B2 and it's equivalent in SHRINE. When I perform a query against that same entry using the Admit Diagnosis modifier, I get a good result in I2B2 (23 patients), however I get an error in SHRINE. Missing Concept in Ontology Cell : Error getting modifierinfo for modifier key [\\i2b2_DIAG\Admit Diagnosis\] and appliedPath [\SHRINE\Diagnoses\Diseases of the respiratory system (460-519.99)\%] panel#0 Elsewhere in shrine.log, I have this message when performing the query: 2014-Oct-16-10:46:24.424 DEBUG [SHRINE][ExpressionTranslator][ForkJoinPool-1-worker-1] Translated: Term(\\SHRINE\SHRINE\Diagnoses\Diseases of the respiratory system (460-519.99)\Chronic obstructive pulmonary disease and allied conditions (490-496.99)\Asthma (493)\Asthma, unspecified (493.9)\(493.90) Asthma, unspecified type, unspecified$ to Success(Term(\\i2b2_DIAG\i2b2\Diagnoses\Respiratory system (460-519)\Chronic obstructive diseases (490-496)$493) Asthma\(493-9) Asthma, unspecified\(493-90) Asthma, unspecified type~$) 2014-Oct-16-10:46:24.424 DEBUG [SHRINE][ExpressionTranslator][ForkJoinPool-1-worker-1] Translated: Term(\\SHRINE\Admit Diagnosis\) to Success(Term(\\i2b2_DIAG\Admit Diagnosis\)) 2014-Oct-16-10:46:24.432 DEBUG [SHRINE][RunQueryAdapter][ForkJoinPool-1-worker-1] Sending Shrine-formatted request to the CRC at 'http://localhost:9080/i2b2/services/QueryToolService/': RunQueryRequest(Demo,180000 milliseconds,AuthenticationInfo(i2b2demo,demo,Credential(demouser,false)),1731076943908539842,None,Set(PATIENT_COUNT_XML),QueryDefinition(Admit Diagnosis at 10:46:22,Modified(Term(\\i2b2_DIAG\i2b2\Diagnoses\Respiratory system (460-519)\Chronic obstructive diseases (490-496)$493) Asthma\(493-9) Asthma, unspecified\(493-90) Asthma, unspecified type~$,Modifiers(Admit Diagnosis,\SHRINE\Diagnoses\Diseases of the respiratory system (460-519.99)\%,\\i2b2_DIAG\Admit Diagnosis\)))) and also in shrine.log, the query sent to i2b2 is: Admit Diagnosis at 10:46:22 0 1 1 0 1 7 \\i2b2_DIAG\i2b2\Diagnoses\Respiratory system (460-519)\Chronic obstructive diseases (490-496)\(493) Asthma\(493-9) Asthma, unspecified\(493-90) Asthma, unspecified type~\ \\i2b2_DIAG\i2b2\Diagnoses\Respiratory system (460-519)\Chronic obstructive diseases (490-496)\(493) Asthma\(493-9) Asthma, unspecified\(493-90) Asthma, unspecified type~\ \\i2b2_DIAG\i2b2\Diagnoses\Respiratory system (460-519)\Chronic obstructive diseases (490-496)\(493) Asthma\(493-9) Asthma, unspecified\(493-90) Asthma, unspecified type~\ ENC Admit Diagnosis \SHRINE\Diagnoses\Diseases of the respiratory system (460-519.99)\% \\i2b2_DIAG\Admit Diagnosis\ LA false It seems like possibly the applied_path here is wrong, since it still references the \SHRINE ontology? Thanks, Michael -----Original Message----- From: shrine-users-bounces at open.med.harvard.edu [mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of Trevvett, Philip Sent: Wednesday, October 15, 2014 12:32 PM To: shrine-users at open.med.harvard.edu Subject: [Shrine-users] Update to Shrine 1.17 demoontology Hi all, To address recent issues with querying diagnoses against i2b2 demo data with shrine 1.17, i've checked in an updated version of the demo ontology that is available here: https://open.med.harvard.edu/svn/shrine/releases/1.17.0/ontology/SHRINE_Demo_Downloads/ This addresses issues with capitalization differences between fullname, modifier applied paths, and adaptermappings keys that were causing dx queries to fail. If you've been having issues querying for diagnoses or modifiers using the demo ontology please load this version. Thanks, Philip _______________________________________________ Shrine-users mailing list Shrine-users at open.med.harvard.edu https://open.med.harvard.edu/mailman/listinfo/shrine-users From Philip_Trevvett at hms.harvard.edu Thu Oct 16 12:39:46 2014 From: Philip_Trevvett at hms.harvard.edu (Trevvett, Philip) Date: Thu, 16 Oct 2014 12:39:46 -0400 Subject: [Shrine-users] Update to Shrine 1.17 demoontology In-Reply-To: <96E1AA641D2EDE49A7A43FE98067A3E93B4306AC@EXCHDB1.medctr.ad.wfubmc.edu> References: <96E1AA641D2EDE49A7A43FE98067A3E93B4306AC@EXCHDB1.medctr.ad.wfubmc.edu> Message-ID: My understanding is that the applied path in the shrine ontology is only referenced to display modifiers in the shrine webclient. Part of implementing modifiers was a change on the i2b2 side that made it not necessary for applied paths to be mapped/part of the query. So if you're using Shrine 1.17 and i2b2 1.7, applied paths should not be related to query execution issues. I'll take a look at the mappings and see if there's anything else I can find. -philip -----Original Message----- From: Michael Horvath [mailto:mhorvath at wakehealth.edu] Sent: Thursday, October 16, 2014 11:11 AM To: shrine-users at open.med.harvard.edu; Trevvett, Philip Subject: RE: Update to Shrine 1.17 demoontology I'm seeing errors with the provided shrine ontology and adaptermappings. Shrine 1.17 running against I2B2 1.7 with the default demodata. Sample query against \\i2b2_DIAG\i2b2\Diagnoses\Respiratory system (460-519)\Chronic obstructive diseases (490-496)$493) Asthma\(493-9) Asthma, unspecified\(493-90) Asthma, unspecified type~\ returns fine (133 patients) for both I2B2 and it's equivalent in SHRINE. When I perform a query against that same entry using the Admit Diagnosis modifier, I get a good result in I2B2 (23 patients), however I get an error in SHRINE. Missing Concept in Ontology Cell : Error getting modifierinfo for modifier key [\\i2b2_DIAG\Admit Diagnosis\] and appliedPath [\SHRINE\Diagnoses\Diseases of the respiratory system (460-519.99)\%] panel#0 Elsewhere in shrine.log, I have this message when performing the query: 2014-Oct-16-10:46:24.424 DEBUG [SHRINE][ExpressionTranslator][ForkJoinPool-1-worker-1] Translated: Term(\\SHRINE\SHRINE\Diagnoses\Diseases of the respiratory system (460-519.99)\Chronic obstructive pulmonary disease and allied conditions (490-496.99)\Asthma (493)\Asthma, unspecified (493.9)\(493.90) Asthma, unspecified type, unspecified$ to Success(Term(\\i2b2_DIAG\i2b2\Diagnoses\Respiratory system (460-519)\Chronic obstructive diseases (490-496)$493) Asthma\(493-9) Asthma, unspecified\(493-90) Asthma, unspecified type~$) 2014-Oct-16-10:46:24.424 DEBUG [SHRINE][ExpressionTranslator][ForkJoinPool-1-worker-1] Translated: Term(\\SHRINE\Admit Diagnosis\) to Success(Term(\\i2b2_DIAG\Admit Diagnosis\)) 2014-Oct-16-10:46:24.432 DEBUG [SHRINE][RunQueryAdapter][ForkJoinPool-1-worker-1] Sending Shrine-formatted request to the CRC at 'http://localhost:9080/i2b2/services/QueryToolService/': RunQueryRequest(Demo,180000 milliseconds,AuthenticationInfo(i2b2demo,demo,Credential(demouser,false)),1731076943908539842,None,Set(PATIENT_COUNT_XML),QueryDefinition(Admit Diagnosis at 10:46:22,Modified(Term(\\i2b2_DIAG\i2b2\Diagnoses\Respiratory system (460-519)\Chronic obstructive diseases (490-496)$493) Asthma\(493-9) Asthma, unspecified\(493-90) Asthma, unspecified type~$,Modifiers(Admit Diagnosis,\SHRINE\Diagnoses\Diseases of the respiratory system (460-519.99)\%,\\i2b2_DIAG\Admit Diagnosis\)))) and also in shrine.log, the query sent to i2b2 is: Admit Diagnosis at 10:46:22 0 1 1 0 1 7 \\i2b2_DIAG\i2b2\Diagnoses\Respiratory system (460-519)\Chronic obstructive diseases (490-496)\(493) Asthma\(493-9) Asthma, unspecified\(493-90) Asthma, unspecified type~\ \\i2b2_DIAG\i2b2\Diagnoses\Respiratory system (460-519)\Chronic obstructive diseases (490-496)\(493) Asthma\(493-9) Asthma, unspecified\(493-90) Asthma, unspecified type~\ \\i2b2_DIAG\i2b2\Diagnoses\Respiratory system (460-519)\Chronic obstructive diseases (490-496)\(493) Asthma\(493-9) Asthma, unspecified\(493-90) Asthma, unspecified type~\ ENC Admit Diagnosis \SHRINE\Diagnoses\Diseases of the respiratory system (460-519.99)\% \\i2b2_DIAG\Admit Diagnosis\ LA false It seems like possibly the applied_path here is wrong, since it still references the \SHRINE ontology? Thanks, Michael -----Original Message----- From: shrine-users-bounces at open.med.harvard.edu [mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of Trevvett, Philip Sent: Wednesday, October 15, 2014 12:32 PM To: shrine-users at open.med.harvard.edu Subject: [Shrine-users] Update to Shrine 1.17 demoontology Hi all, To address recent issues with querying diagnoses against i2b2 demo data with shrine 1.17, i've checked in an updated version of the demo ontology that is available here: https://open.med.harvard.edu/svn/shrine/releases/1.17.0/ontology/SHRINE_Demo_Downloads/ This addresses issues with capitalization differences between fullname, modifier applied paths, and adaptermappings keys that were causing dx queries to fail. If you've been having issues querying for diagnoses or modifiers using the demo ontology please load this version. Thanks, Philip _______________________________________________ Shrine-users mailing list Shrine-users at open.med.harvard.edu https://open.med.harvard.edu/mailman/listinfo/shrine-users From William_Simons at hms.harvard.edu Thu Oct 16 12:47:45 2014 From: William_Simons at hms.harvard.edu (Simons, William) Date: Thu, 16 Oct 2014 12:47:45 -0400 Subject: [Shrine-users] Update to Shrine 1.17 demoontology In-Reply-To: Message-ID: It has to be i2b2 1.7.03 in order for modifiers to work properly on the server side. The applied path should be ignored by shrine and i2b2 except in the case of the web client. On 10/16/14, 12:39 PM, "Trevvett, Philip" wrote: >My understanding is that the applied path in the shrine ontology is only >referenced to display modifiers in the shrine webclient. Part of >implementing modifiers was a change on the i2b2 side that made it not >necessary for applied paths to be mapped/part of the query. > >So if you're using Shrine 1.17 and i2b2 1.7, applied paths should not be >related to query execution issues. > >I'll take a look at the mappings and see if there's anything else I can >find. > >-philip > >-----Original Message----- >From: Michael Horvath [mailto:mhorvath at wakehealth.edu] >Sent: Thursday, October 16, 2014 11:11 AM >To: shrine-users at open.med.harvard.edu; Trevvett, Philip >Subject: RE: Update to Shrine 1.17 demoontology > >I'm seeing errors with the provided shrine ontology and adaptermappings. >Shrine 1.17 running against I2B2 1.7 with the default demodata. Sample >query against \\i2b2_DIAG\i2b2\Diagnoses\Respiratory system >(460-519)\Chronic obstructive diseases (490-496)$493) Asthma\(493-9) >Asthma, unspecified\(493-90) Asthma, unspecified type~\ returns fine (133 >patients) for both I2B2 and it's equivalent in SHRINE. > >When I perform a query against that same entry using the Admit Diagnosis >modifier, I get a good result in I2B2 (23 patients), however I get an >error in SHRINE. > > > Missing Concept in Ontology Cell : >Error getting modifierinfo for modifier key [\\i2b2_DIAG\Admit >Diagnosis\] and appliedPath [\SHRINE\Diagnoses\Diseases of the >respiratory system (460-519.99)\%] panel#0 > > >Elsewhere in shrine.log, I have this message when performing the query: > >2014-Oct-16-10:46:24.424 DEBUG >[SHRINE][ExpressionTranslator][ForkJoinPool-1-worker-1] Translated: >Term(\\SHRINE\SHRINE\Diagnoses\Diseases of the respiratory system >(460-519.99)\Chronic obstructive pulmonary disease and allied conditions >(490-496.99)\Asthma (493)\Asthma, unspecified (493.9)\(493.90) Asthma, >unspecified type, unspecified$ to >Success(Term(\\i2b2_DIAG\i2b2\Diagnoses\Respiratory system >(460-519)\Chronic obstructive diseases (490-496)$493) Asthma\(493-9) >Asthma, unspecified\(493-90) Asthma, unspecified type~$) >2014-Oct-16-10:46:24.424 DEBUG >[SHRINE][ExpressionTranslator][ForkJoinPool-1-worker-1] Translated: >Term(\\SHRINE\Admit Diagnosis\) to Success(Term(\\i2b2_DIAG\Admit >Diagnosis\)) >2014-Oct-16-10:46:24.432 DEBUG >[SHRINE][RunQueryAdapter][ForkJoinPool-1-worker-1] Sending >Shrine-formatted request to the CRC at >'http://localhost:9080/i2b2/services/QueryToolService/': >RunQueryRequest(Demo,180000 >milliseconds,AuthenticationInfo(i2b2demo,demo,Credential(demouser,false)), >1731076943908539842,None,Set(PATIENT_COUNT_XML),QueryDefinition(Admit >Diagnosis at 10:46:22,Modified(Term(\\i2b2_DIAG\i2b2\Diagnoses\Respiratory >system (460-519)\Chronic obstructive diseases (490-496)$493) >Asthma\(493-9) Asthma, unspecified\(493-90) Asthma, unspecified >type~$,Modifiers(Admit Diagnosis,\SHRINE\Diagnoses\Diseases of the >respiratory system (460-519.99)\%,\\i2b2_DIAG\Admit Diagnosis\)))) > >and also in shrine.log, the query sent to i2b2 is: > > > Admit Diagnosis at 10:46:22 > 0 > 1 > > 1 > 0 > 1 > > 7 > > \\i2b2_DIAG\i2b2\Diagnoses\Respiratory system >(460-519)\Chronic obstructive diseases (490-496)\(493) Asthma\(493-9) >Asthma, unspecified\(493-90) Asthma, unspecified type~\ > > > \\i2b2_DIAG\i2b2\Diagnoses\Respiratory system >(460-519)\Chronic obstructive diseases (490-496)\(493) Asthma\(493-9) >Asthma, unspecified\(493-90) Asthma, unspecified type~\ > > > \\i2b2_DIAG\i2b2\Diagnoses\Respiratory system >(460-519)\Chronic obstructive diseases (490-496)\(493) Asthma\(493-9) >Asthma, unspecified\(493-90) Asthma, unspecified type~\ > > ENC > > > Admit Diagnosis > \SHRINE\Diagnoses\Diseases of the respiratory >system (460-519.99)\% > \\i2b2_DIAG\Admit Diagnosis\ > > LA > false > > > > >It seems like possibly the applied_path here is wrong, since it still >references the \SHRINE ontology? > >Thanks, >Michael > >-----Original Message----- >From: shrine-users-bounces at open.med.harvard.edu >[mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of Trevvett, >Philip >Sent: Wednesday, October 15, 2014 12:32 PM >To: shrine-users at open.med.harvard.edu >Subject: [Shrine-users] Update to Shrine 1.17 demoontology > >Hi all, > >To address recent issues with querying diagnoses against i2b2 demo data >with shrine 1.17, i've checked in an updated version of the demo ontology >that is available here: >https://open.med.harvard.edu/svn/shrine/releases/1.17.0/ontology/SHRINE_De >mo_Downloads/ > >This addresses issues with capitalization differences between fullname, >modifier applied paths, and adaptermappings keys that were causing dx >queries to fail. If you've been having issues querying for diagnoses or >modifiers using the demo ontology please load this version. > >Thanks, >Philip >_ >Shrine-users mailing list >Shrine-users at open.med.harvard.edu >https://open.med.harvard.edu/mailman/listinfo/shrine-users > >_ >Shrine-users mailing list >Shrine-users at open.med.harvard.edu >https://open.med.harvard.edu/mailman/listinfo/shrine-users From mhorvath at wakehealth.edu Thu Oct 16 12:49:00 2014 From: mhorvath at wakehealth.edu (Michael Horvath) Date: Thu, 16 Oct 2014 16:49:00 +0000 Subject: [Shrine-users] Update to Shrine 1.17 demoontology In-Reply-To: References: <96E1AA641D2EDE49A7A43FE98067A3E93B4306AC@EXCHDB1.medctr.ad.wfubmc.edu>, Message-ID: <96E1AA641D2EDE49A7A43FE98067A3E93B4306FC@EXCHDB1.medctr.ad.wfubmc.edu> Oh I see. To be more specific, I was running this against i2b2 1.7.01. From the release notes on i2b2 1.7.03 (https://www.i2b2.org/software/releaseNotes_current.pdf): Change Summary - i2b2 Core Software - Version 1.7.03 Bug Fixes [CORE-143] - Do not require M_APPLIED_PATH when retrieving modifier information from the Ontology Cell I'll see about updating the i2b2 application and trying again. Thanks, -Michael ________________________________________ From: Trevvett, Philip [Philip_Trevvett at hms.harvard.edu] Sent: Thursday, October 16, 2014 12:39 PM To: Michael Horvath; shrine-users at open.med.harvard.edu Subject: RE: Update to Shrine 1.17 demoontology My understanding is that the applied path in the shrine ontology is only referenced to display modifiers in the shrine webclient. Part of implementing modifiers was a change on the i2b2 side that made it not necessary for applied paths to be mapped/part of the query. So if you're using Shrine 1.17 and i2b2 1.7, applied paths should not be related to query execution issues. I'll take a look at the mappings and see if there's anything else I can find. -philip -----Original Message----- From: Michael Horvath [mailto:mhorvath at wakehealth.edu] Sent: Thursday, October 16, 2014 11:11 AM To: shrine-users at open.med.harvard.edu; Trevvett, Philip Subject: RE: Update to Shrine 1.17 demoontology I'm seeing errors with the provided shrine ontology and adaptermappings. Shrine 1.17 running against I2B2 1.7 with the default demodata. Sample query against \\i2b2_DIAG\i2b2\Diagnoses\Respiratory system (460-519)\Chronic obstructive diseases (490-496)$493) Asthma\(493-9) Asthma, unspecified\(493-90) Asthma, unspecified type~\ returns fine (133 patients) for both I2B2 and it's equivalent in SHRINE. When I perform a query against that same entry using the Admit Diagnosis modifier, I get a good result in I2B2 (23 patients), however I get an error in SHRINE. Missing Concept in Ontology Cell : Error getting modifierinfo for modifier key [\\i2b2_DIAG\Admit Diagnosis\] and appliedPath [\SHRINE\Diagnoses\Diseases of the respiratory system (460-519.99)\%] panel#0 Elsewhere in shrine.log, I have this message when performing the query: 2014-Oct-16-10:46:24.424 DEBUG [SHRINE][ExpressionTranslator][ForkJoinPool-1-worker-1] Translated: Term(\\SHRINE\SHRINE\Diagnoses\Diseases of the respiratory system (460-519.99)\Chronic obstructive pulmonary disease and allied conditions (490-496.99)\Asthma (493)\Asthma, unspecified (493.9)\(493.90) Asthma, unspecified type, unspecified$ to Success(Term(\\i2b2_DIAG\i2b2\Diagnoses\Respiratory system (460-519)\Chronic obstructive diseases (490-496)$493) Asthma\(493-9) Asthma, unspecified\(493-90) Asthma, unspecified type~$) 2014-Oct-16-10:46:24.424 DEBUG [SHRINE][ExpressionTranslator][ForkJoinPool-1-worker-1] Translated: Term(\\SHRINE\Admit Diagnosis\) to Success(Term(\\i2b2_DIAG\Admit Diagnosis\)) 2014-Oct-16-10:46:24.432 DEBUG [SHRINE][RunQueryAdapter][ForkJoinPool-1-worker-1] Sending Shrine-formatted request to the CRC at 'http://localhost:9080/i2b2/services/QueryToolService/': RunQueryRequest(Demo,180000 milliseconds,AuthenticationInfo(i2b2demo,demo,Credential(demouser,false)),1731076943908539842,None,Set(PATIENT_COUNT_XML),QueryDefinition(Admit Diagnosis at 10:46:22,Modified(Term(\\i2b2_DIAG\i2b2\Diagnoses\Respiratory system (460-519)\Chronic obstructive diseases (490-496)$493) Asthma\(493-9) Asthma, unspecified\(493-90) Asthma, unspecified type~$,Modifiers(Admit Diagnosis,\SHRINE\Diagnoses\Diseases of the respiratory system (460-519.99)\%,\\i2b2_DIAG\Admit Diagnosis\)))) and also in shrine.log, the query sent to i2b2 is: Admit Diagnosis at 10:46:22 0 1 1 0 1 7 \\i2b2_DIAG\i2b2\Diagnoses\Respiratory system (460-519)\Chronic obstructive diseases (490-496)\(493) Asthma\(493-9) Asthma, unspecified\(493-90) Asthma, unspecified type~\ \\i2b2_DIAG\i2b2\Diagnoses\Respiratory system (460-519)\Chronic obstructive diseases (490-496)\(493) Asthma\(493-9) Asthma, unspecified\(493-90) Asthma, unspecified type~\ \\i2b2_DIAG\i2b2\Diagnoses\Respiratory system (460-519)\Chronic obstructive diseases (490-496)\(493) Asthma\(493-9) Asthma, unspecified\(493-90) Asthma, unspecified type~\ ENC Admit Diagnosis \SHRINE\Diagnoses\Diseases of the respiratory system (460-519.99)\% \\i2b2_DIAG\Admit Diagnosis\ LA false It seems like possibly the applied_path here is wrong, since it still references the \SHRINE ontology? Thanks, Michael -----Original Message----- From: shrine-users-bounces at open.med.harvard.edu [mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of Trevvett, Philip Sent: Wednesday, October 15, 2014 12:32 PM To: shrine-users at open.med.harvard.edu Subject: [Shrine-users] Update to Shrine 1.17 demoontology Hi all, To address recent issues with querying diagnoses against i2b2 demo data with shrine 1.17, i've checked in an updated version of the demo ontology that is available here: https://open.med.harvard.edu/svn/shrine/releases/1.17.0/ontology/SHRINE_Demo_Downloads/ This addresses issues with capitalization differences between fullname, modifier applied paths, and adaptermappings keys that were causing dx queries to fail. If you've been having issues querying for diagnoses or modifiers using the demo ontology please load this version. Thanks, Philip _______________________________________________ Shrine-users mailing list Shrine-users at open.med.harvard.edu https://open.med.harvard.edu/mailman/listinfo/shrine-users From mhorvath at wakehealth.edu Thu Oct 16 15:22:21 2014 From: mhorvath at wakehealth.edu (Michael Horvath) Date: Thu, 16 Oct 2014 19:22:21 +0000 Subject: [Shrine-users] Update to Shrine 1.17 demoontology In-Reply-To: References: Message-ID: <96E1AA641D2EDE49A7A43FE98067A3E93B4307A9@EXCHDB1.medctr.ad.wfubmc.edu> Upgrading to i2b2 1.7.03 did the trick, thanks. -mrh -----Original Message----- From: Simons, William [mailto:William_Simons at hms.harvard.edu] Sent: Thursday, October 16, 2014 12:48 PM To: Trevvett, Philip; Michael Horvath; shrine-users at open.med.harvard.edu Subject: Re: [Shrine-users] Update to Shrine 1.17 demoontology It has to be i2b2 1.7.03 in order for modifiers to work properly on the server side. The applied path should be ignored by shrine and i2b2 except in the case of the web client. On 10/16/14, 12:39 PM, "Trevvett, Philip" wrote: >My understanding is that the applied path in the shrine ontology is only >referenced to display modifiers in the shrine webclient. Part of >implementing modifiers was a change on the i2b2 side that made it not >necessary for applied paths to be mapped/part of the query. > >So if you're using Shrine 1.17 and i2b2 1.7, applied paths should not >be related to query execution issues. > >I'll take a look at the mappings and see if there's anything else I can >find. > >-philip > >-----Original Message----- >From: Michael Horvath [mailto:mhorvath at wakehealth.edu] >Sent: Thursday, October 16, 2014 11:11 AM >To: shrine-users at open.med.harvard.edu; Trevvett, Philip >Subject: RE: Update to Shrine 1.17 demoontology > >I'm seeing errors with the provided shrine ontology and adaptermappings. >Shrine 1.17 running against I2B2 1.7 with the default demodata. Sample >query against \\i2b2_DIAG\i2b2\Diagnoses\Respiratory system >(460-519)\Chronic obstructive diseases (490-496)$493) Asthma\(493-9) >Asthma, unspecified\(493-90) Asthma, unspecified type~\ returns fine >(133 >patients) for both I2B2 and it's equivalent in SHRINE. > >When I perform a query against that same entry using the Admit >Diagnosis modifier, I get a good result in I2B2 (23 patients), however >I get an error in SHRINE. > > > Missing Concept in Ontology Cell : >Error getting modifierinfo for modifier key [\\i2b2_DIAG\Admit >Diagnosis\] and appliedPath [\SHRINE\Diagnoses\Diseases of the >respiratory system (460-519.99)\%] panel#0 > > >Elsewhere in shrine.log, I have this message when performing the query: > >2014-Oct-16-10:46:24.424 DEBUG >[SHRINE][ExpressionTranslator][ForkJoinPool-1-worker-1] Translated: >Term(\\SHRINE\SHRINE\Diagnoses\Diseases of the respiratory system >(460-519.99)\Chronic obstructive pulmonary disease and allied >conditions (490-496.99)\Asthma (493)\Asthma, unspecified >(493.9)\(493.90) Asthma, unspecified type, unspecified$ to >Success(Term(\\i2b2_DIAG\i2b2\Diagnoses\Respiratory system >(460-519)\Chronic obstructive diseases (490-496)$493) Asthma\(493-9) >Asthma, unspecified\(493-90) Asthma, unspecified type~$) >2014-Oct-16-10:46:24.424 DEBUG >[SHRINE][ExpressionTranslator][ForkJoinPool-1-worker-1] Translated: >Term(\\SHRINE\Admit Diagnosis\) to Success(Term(\\i2b2_DIAG\Admit >Diagnosis\)) >2014-Oct-16-10:46:24.432 DEBUG >[SHRINE][RunQueryAdapter][ForkJoinPool-1-worker-1] Sending >Shrine-formatted request to the CRC at >'http://localhost:9080/i2b2/services/QueryToolService/': >RunQueryRequest(Demo,180000 >milliseconds,AuthenticationInfo(i2b2demo,demo,Credential(demouser,false >)), >1731076943908539842,None,Set(PATIENT_COUNT_XML),QueryDefinition(Admit >Diagnosis at 10:46:22,Modified(Term(\\i2b2_DIAG\i2b2\Diagnoses\Respiratory >system (460-519)\Chronic obstructive diseases (490-496)$493) >Asthma\(493-9) Asthma, unspecified\(493-90) Asthma, unspecified >type~$,Modifiers(Admit Diagnosis,\SHRINE\Diagnoses\Diseases of the >respiratory system (460-519.99)\%,\\i2b2_DIAG\Admit Diagnosis\)))) > >and also in shrine.log, the query sent to i2b2 is: > > > Admit Diagnosis at 10:46:22 > 0 > 1 > > 1 > 0 > 1 > > 7 > > \\i2b2_DIAG\i2b2\Diagnoses\Respiratory system >(460-519)\Chronic obstructive diseases (490-496)\(493) Asthma\(493-9) >Asthma, unspecified\(493-90) Asthma, unspecified type~\ > > > \\i2b2_DIAG\i2b2\Diagnoses\Respiratory system >(460-519)\Chronic obstructive diseases (490-496)\(493) Asthma\(493-9) >Asthma, unspecified\(493-90) Asthma, unspecified type~\ > > > \\i2b2_DIAG\i2b2\Diagnoses\Respiratory system >(460-519)\Chronic obstructive diseases (490-496)\(493) Asthma\(493-9) >Asthma, unspecified\(493-90) Asthma, unspecified type~\ > > ENC > > > Admit Diagnosis > \SHRINE\Diagnoses\Diseases of the >respiratory system (460-519.99)\% > \\i2b2_DIAG\Admit Diagnosis\ > > LA > false > > > > >It seems like possibly the applied_path here is wrong, since it still >references the \SHRINE ontology? > >Thanks, >Michael > >-----Original Message----- >From: shrine-users-bounces at open.med.harvard.edu >[mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of >Trevvett, Philip >Sent: Wednesday, October 15, 2014 12:32 PM >To: shrine-users at open.med.harvard.edu >Subject: [Shrine-users] Update to Shrine 1.17 demoontology > >Hi all, > >To address recent issues with querying diagnoses against i2b2 demo data >with shrine 1.17, i've checked in an updated version of the demo >ontology that is available here: >https://open.med.harvard.edu/svn/shrine/releases/1.17.0/ontology/SHRINE >_De >mo_Downloads/ > >This addresses issues with capitalization differences between fullname, >modifier applied paths, and adaptermappings keys that were causing dx >queries to fail. If you've been having issues querying for diagnoses >or modifiers using the demo ontology please load this version. > >Thanks, >Philip >_________________ >Shrine-users mailing list >Shrine-users at open.med.harvard.edu >https://open.med.harvard.edu/mailman/listinfo/shrine-users > >_ >Shrine-users mailing list >Shrine-users at open.med.harvard.edu >https://open.med.harvard.edu/mailman/listinfo/shrine-users From beninato at ohsu.edu Thu Oct 16 17:41:53 2014 From: beninato at ohsu.edu (Peter Beninato) Date: Thu, 16 Oct 2014 21:41:53 +0000 Subject: [Shrine-users] Shrine - Happy Page - Message-ID: <43ECC5435444BE479E03012738A1400F15151529@EXMB03.ohsu.edu> Hi, Where does the shrine happy page get the information ? Did the upgraded as outlined in another email, drop war, shrine-webclient, update shrine ontology, AdapterMappings. But the happy page shows shrine version of 1.16.2. Common.rc was edited for shrine version, 1.17.0 and tomcat was bounced Please advise on how/where to correct. Thanks. _ Peter Beninato - OCTRI DW Developer Oregon Health & Science University 503-494-9985 beninato at ohsu.edu _ The information contained in this EMAIL message is confidential and protected by law. The information is intended only for the person or business identified in the document. If you are not the intended recipient, a sharing or copying the information will result in a violation of the law. If you have received this EMAIL by mistake, please notify the sender of this EMAIL and copy the Office of Information Privacy & Security at oips at ohsu.edu. Please remember to cite the NCRR/NCATS-funded CTSA grant (UL1RR024140) in any publications resulting from OCTRI funding, support services or consultations, and to submit your publication to PubMed Central. -------------- next part -------------- An HTML attachment was scrubbed... URL: From beninato at ohsu.edu Fri Oct 17 11:15:55 2014 From: beninato at ohsu.edu (Peter Beninato) Date: Fri, 17 Oct 2014 15:15:55 +0000 Subject: [Shrine-users] Shrine - Happy Page - -- > war not deployed Message-ID: <43ECC5435444BE479E03012738A1400F1515164C@EXMB03.ohsu.edu> Hi, Needed to remove the deployed web app, then tomcat deployed the war, which was version 1.17.x. Fyi. -Peter From: Peter Beninato Sent: Thursday, October 16, 2014 2:42 PM To: shrine-users at open.med.harvard.edu Subject: Shrine - Happy Page - Hi, Where does the shrine happy page get the information ? Did the upgraded as outlined in another email, drop war, shrine-webclient, update shrine ontology, AdapterMappings. But the happy page shows shrine version of 1.16.2. Common.rc was edited for shrine version, 1.17.0 and tomcat was bounced Please advise on how/where to correct. Thanks. _ Peter Beninato - OCTRI DW Developer Oregon Health & Science University 503-494-9985 beninato at ohsu.edu _________________ The information contained in this EMAIL message is confidential and protected by law. The information is intended only for the person or business identified in the document. If you are not the intended recipient, a sharing or copying the information will result in a violation of the law. If you have received this EMAIL by mistake, please notify the sender of this EMAIL and copy the Office of Information Privacy & Security at oips at ohsu.edu. Please remember to cite the NCRR/NCATS-funded CTSA grant (UL1RR024140) in any publications resulting from OCTRI funding, support services or consultations, and to submit your publication to PubMed Central. -------------- next part -------------- An HTML attachment was scrubbed... URL: From William_Simons at hms.harvard.edu Fri Oct 17 16:07:16 2014 From: William_Simons at hms.harvard.edu (Simons, William) Date: Fri, 17 Oct 2014 16:07:16 -0400 Subject: [Shrine-users] Shrine-users Digest, Vol 26, Issue 24 In-Reply-To: <20141013121429.e108xfforkgso8k4@cubmail.cc.columbia.edu> Message-ID: Have you checked your AdapterMappings file for the presence of that term? The ?Error mapping query terms from network to local forms.? indicates that there is no mapping present for that term. On 10/13/14, 12:14 PM, "ev2348 at columbia.edu" wrote: >Hello I see the three icons > Admit, Principal, Secondary? > >The only thing I can count is Demographics with or without ERROR. The >rest it does not work. >Elena >> >Quoting shrine-users-request at open.med.harvard.edu: > >> Send Shrine-users mailing list submissions to >> shrine-users at open.med.harvard.edu >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://open.med.harvard.edu/mailman/listinfo/shrine-users >> or, via email, send a message with subject or body 'help' to >> shrine-users-request at open.med.harvard.edu >> >> You can reach the person managing the list at >> shrine-users-owner at open.med.harvard.edu >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Shrine-users digest..." >> >> >> Today's Topics: >> >> 1. Re: adapter problems --> modifiers? (Peter Beninato) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Fri, 10 Oct 2014 21:37:46 +0000 >> From: Peter Beninato >> To: "ev2348 at columbia.edu" >> Cc: "shrine-users at open.med.harvard.edu" >> >> Subject: Re: [Shrine-users] adapter problems --> modifiers? >> Message-ID: <43ECC5435444BE479E03012738A1400F15150688 at EXMB03.ohsu.edu> >> Content-Type: text/plain; charset="us-ascii" >> >> Hi, >> >> When you expand the SHRINE ontology to, Diseases anfd Injuries >> (001-999.99)/Diseases of Digestive System (520-579.99)/Appendicitis >> (540-543.99), Do you see icons for: >> Admit, Principal, Secondary? >> >> If you don't see those icons then... >> >> >> Since this deals with Diagnoses. Please look at the m_applied_path >> in an entry in SHRINE where the c_fullname = ' \Admit Diagnosis\' >> (or principal or secondar) >> >> Take the m_applied_path, and use it as the criteria: >> Select * >>> From shrine >> Where c_fullname = {my_m_applied_path from Admit DX} >> >> You may get no rows. My experience is that the third tuple in the >> m_applied_path needs to be capitalized to match the c_fullname that >> you want to add the modifiers too. >> >> Once I made that change, I got past an error condition. >> >> And on to another... >> >> Fyi. >> -Peter >> >> -----Original Message----- >> From: ev2348 at columbia.edu [mailto:ev2348 at columbia.edu] >> Sent: Friday, October 10, 2014 1:22 PM >> To: Peter Beninato >> Cc: Shuman, William (Billy); shrine-users at open.med.harvard.edu >> Subject: RE: [Shrine-users] adapter problems --> modifiers? >> >> Hi, >> I certainly downloaded the AdapterMappings.xml from Harvard >> >>SHRINE_SVN_URL_BASE=https://open.med.harvard.edu/svn/shrine/releases/${SH >>RINE_VERSION}/ >> nad made some changes according to table i2b2metadata.table_access. >> Attached is the copy I am using. I see some of the terms with >> different words but just the same for instance I have for Appendicitis >> >> I2B2 NODE: >> Diagnosis/ICD9 Disease/Disorder of Digestive Tract/other and >> unspecified Diseases of Appendix/Appendicitis >> >> SHRINE Node: >> Diseases anfd Injuries (001-999.99)/Diseases of Digestive System >> (520-579.99)/Appendicitis (540-543.99) >> >> and I get the message >> >> 2014-Oct-10-15:32:22.484 DEBUG >> [SHRINE][SquerylAdapterDao][ForkJoinPool-1-worker-3] User >> i2b2CDW:shrine locked out? false >> 2014-Oct-10-15:32:22.484 DEBUG >> [SHRINE][RunQueryAdapter][ForkJoinPool-1-worker-3] Performing query >> from user i2b2CDW:shrine >> 2014-Oct-10-15:32:22.485 DEBUG >> [SHRINE][ExpressionTranslator][ForkJoinPool-1-worker-3] Translated: >> Term(\\SHRINE\SHRINE\Diagnoses\DISEASES OF THE DIGESTIVE SYSTEM >> (520-579.99)\APPENDICITIS (540-543.99)\) to >> Failure(net.shrine.adapter.AdapterMappingException: No local terms >> mapped to '\\SHRINE\SHRINE\Diagnoses\DISEASES OF THE DIGESTIVE >> SYSTEM (520-579.99)\APPENDICITIS (540-543.99)\') >> 2014-Oct-10-15:32:22.485 WARN >> [SHRINE][RunQueryAdapter][ForkJoinPool-1-worker-3] Error mapping query >> terms: Error mapping query terms from network to local forms. request: >> RunQueryRequest(CDW,180000 >> >>milliseconds,AuthenticationInfo(***,,Credential(,false) >>),7718049720240791039,None,Set(PATIENT_COUNT_XML),QueryDefinition(APPENDI >>CITIS (5 at 15:32:20,Term(\\SHRINE\SHRINE\Diagnoses\DISEASES OF THE >>DIGESTIVE SYSTEM >> (520-579.99)\APPENDICITIS >> (540-543.99)\))) >> net.shrine.adapter.AdapterMappingException: Error mapping query >> terms from network to local forms. request: >> RunQueryRequest(CDW,180000 >> >>milliseconds,AuthenticationInfo(,,Credential(*,false) >>),7718049720240791039,None,Set(PATIENT_COUNT_XML),QueryDefinition(APPENDI >>CITIS (5 at 15:32:20,Term(\\SHRINE\SHRINE\Diagnoses\DISEASES OF THE >>DIGESTIVE SYSTEM >> (520-579.99)\APPENDICITIS >> (540-543.99)\))) >> at >> >>net.shrine.adapter.RunQueryAdapter.translateNetworkToLocal(RunQueryAdapte >>r.scala:60) >> at >> >>net.shrine.adapter.RunQueryAdapter.translateNetworkToLocal(RunQueryAdapte >>r.scala:42) >> at net.shrine.adapter.CrcAdapter.translateRequest(CrcAdapter.scala:95) >> at net.shrine.adapter.CrcAdapter.processRequest(CrcAdapter.scala:60) >> at >>net.shrine.adapter.RunQueryAdapter.runQuery(RunQueryAdapter.scala:121) >> at >> >>net.shrine.adapter.RunQueryAdapter.processRequest(RunQueryAdapter.scala:8 >>5) >> at >> >>net.shrine.adapter.RunQueryAdapter.processRequest(RunQueryAdapter.scala:4 >>2) >> at net.shrine.adapter.Adapter.perform(Adapter.scala:26) >> at >> >>net.shrine.adapter.service.AdapterService$$anonfun$1$$anonfun$apply$1.app >>ly(AdapterService.scala:36) >> at >> >>net.shrine.adapter.service.AdapterService$$anonfun$1$$anonfun$apply$1.app >>ly(AdapterService.scala:36) >> at >>net.shrine.adapter.service.AdapterService$.time(AdapterService.scala:68) >> at >> >>net.shrine.adapter.service.AdapterService$$anonfun$1.apply(AdapterService >>.scala:35) >> at net.shrine.a >> >> Beninato : >> >>> Hi, >>> >>> I'm experiencing some issues with AdapterMappings.xml and modifiers. >>> >>> I have loaded up the shrine ontology corrected for the disconnect >>> between c_fullname and m_applied_path (m_applied_path case, does not >>> match i2b2 demo ontology c_fullname case). >>> >>> That got the modifier icons to appear. When I chose the Admit DX for >>>441.5. >>> >>> When I look in the shrine log I see: >>> 2014-Oct-09-10:32:09.353 DEBUG >>> [SHRINE][ExpressionTranslator][ForkJoinPool-1-worker-7] Translated: >>> Term(\\SHRINE\SHRINE\Diagnoses\DISEASES OF THE CIRCULATORY SYSTEM >>> (390-459.99)\DISEASES OF ARTERIES, ARTERIOLES, AND CAPILLARIES >>> (440-449.99)\Aortic aneurysm and dissection (441)$441.5) Aortic >>> aneurysm of unspecified site, ruptured$ to None >>> 2014-Oct-09-10:32:09.356 WARN >>> [SHRINE][RunQueryAdapter][ForkJoinPool-1-worker-7] Error mapping >>> query terms: Error mapping query terms from network to local forms >>> >>> I see the term in AdapterMappings.xml and I can find the local term >>> in the local i2b2 ontology, so I'm not sure why it is mapping to none. >>> >>> This might be related? >>> >>> Fyi. >>> -Peter >>> >>> -----Original Message----- >>> From: shrine-users-bounces at open.med.harvard.edu >>> [mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of >>> Shuman, William (Billy) >>> Sent: Friday, October 10, 2014 12:22 PM >>> To: ev2348 at columbia.edu >>> Cc: shrine-users at open.med.harvard.edu >>> Subject: Re: [Shrine-users] adapter prpoblems >>> >>> It seems like it can not map the >> >> Quoting Peter Beninato : >> >>> Hi, >>> >>> I'm experiencing some issues with AdapterMappings.xml and modifiers. >>> >>> I have loaded up the shrine ontology corrected for the disconnect >>> between c_fullname and m_applied_path (m_applied_path case, does not >>> match i2b2 demo ontology c_fullname case). >>> >>> That got the modifier icons to appear. When I chose the Admit DX for >>>441.5. >>> >>> When I look in the shrine log I see: >>> 2014-Oct-09-10:32:09.353 DEBUG >>> [SHRINE][ExpressionTranslator][ForkJoinPool-1-worker-7] Translated: >>> Term(\\SHRINE\SHRINE\Diagnoses\DISEASES OF THE CIRCULATORY SYSTEM >>> (390-459.99)\DISEASES OF ARTERIES, ARTERIOLES, AND CAPILLARIES >>> (440-449.99)\Aortic aneurysm and dissection (441)$441.5) Aortic >>> aneurysm of unspecified site, ruptured$ to None >>> 2014-Oct-09-10:32:09.356 WARN >>> [SHRINE][RunQueryAdapter][ForkJoinPool-1-worker-7] Error mapping >>> query terms: Error mapping query terms from network to local forms >>> >>> I see the term in AdapterMappings.xml and I can find the local term >>> in the local i2b2 ontology, so I'm not sure why it is mapping to none. >>> >>> This might be related? >>> >>> Fyi. >>> -Peter >>> >>> -----Original Message----- >>> From: shrine-users-bounces at open.med.harvard.edu >>> [mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of >>> Shuman, William (Billy) >>> Sent: Friday, October 10, 2014 12:22 PM >>> To: ev2348 at columbia.edu >>> Cc: shrine-users at open.med.harvard.edu >>> Subject: Re: [Shrine-users] adapter prpoblems >>> >>> It seems like it can not map the key \\SHRINE\SHRINE\Labs\LP32651-9 >>> \LP67162-5\ to any local key. Is that key located in your adapter >>> mappings file? >>> >>> Billy >>> -- >>> William Shuman Cincinnati Children's >>> Hospital Medical Center >>> >>> On Fri, 2014-10-10 at 14:42 -0400, ev2348 at columbia.edu wrote: >>>> \\SHRINE\SHRINE\Labs\LP32651-9\LP67162-5\ >>> _______________________ >>> Shrine-users mailing list >>> Shrine-users at open.med.harvard.edu >>> https://open.med.harvard.edu/mailman/listinfo/shrine-users >>> >>> >> >> >> >> >> ------------------------------ >> >> _ >> Shrine-users mailing list >> Shrine-users at open.med.harvard.edu >> https://open.med.harvard.edu/mailman/listinfo/shrine-users >> >> >> End of Shrine-users Digest, Vol 26, Issue 24 >> ****************************************** >> >> > > > >_________________________ >Shrine-users mailing list >Shrine-users at open.med.harvard.edu >https://open.med.harvard.edu/mailman/listinfo/shrine-users From ev2348 at columbia.edu Mon Oct 20 12:17:19 2014 From: ev2348 at columbia.edu (ev2348 at columbia.edu) Date: Mon, 20 Oct 2014 12:17:19 -0400 Subject: [Shrine-users] act Message-ID: <20141020121719.gnlb143340o0o8s8@cubmail.cc.columbia.edu> Hello, thanks for all your help. I need to follow the milestones for ACT and now I am in Phase B. Milestone 4 Install ACT hub node and provide documentation for connecting a site to the ACT hub. Dependencies Systems and staff at Harvard Medical School. I have to follow the milestones even when around here they just want the local EMR. Can you tell me what is ACT hub node. Best Regards Elena From Keith_Dwyer at hms.harvard.edu Mon Oct 20 12:21:12 2014 From: Keith_Dwyer at hms.harvard.edu (Dwyer, Keith) Date: Mon, 20 Oct 2014 12:21:12 -0400 Subject: [Shrine-users] act In-Reply-To: <20141020121719.gnlb143340o0o8s8@cubmail.cc.columbia.edu> References: <20141020121719.gnlb143340o0o8s8@cubmail.cc.columbia.edu> Message-ID: Milestone 4 has already been handled by HMS, who is hosting the hub node. The instructions that all other have to follow to connect to the hub can be found here: https://open.med.harvard.edu/wiki/display/SHRINE/Post-Install+Configuration+and+Tasks#Post-InstallConfigurationandTasks-hub-connect Keith Dwyer Harvard Catalyst, SHRINE Network Operations On Oct 20, 2014, at 12:17 PM, > > wrote: Hello, thanks for all your help. I need to follow the milestones for ACT and now I am in Phase B. Milestone 4 Install ACT hub node and provide documentation for connecting a site to the ACT hub. Dependencies Systems and staff at Harvard Medical School. I have to follow the milestones even when around here they just want the local EMR. Can you tell me what is ACT hub node. Best Regards Elena _______________________________________________ Shrine-users mailing list Shrine-users at open.med.harvard.edu https://open.med.harvard.edu/mailman/listinfo/shrine-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From Phillip.Reeder at UTSouthwestern.edu Mon Oct 20 12:35:52 2014 From: Phillip.Reeder at UTSouthwestern.edu (Phillip Reeder) Date: Mon, 20 Oct 2014 16:35:52 +0000 Subject: [Shrine-users] Error running Happy Page Message-ID: I?m able to run queries through the shrine-webclient, but when I access https://[host]/shrine/rest/happy/version, I?m getting an http 500 error message. Does anyone know what to do to fix this error? The Tomcat log shows the following: Oct 20, 2014 11:26:12 AM com.sun.jersey.spi.container.ContainerResponse mapMappableContainerException SEVERE: The exception contained within MappableContainerException could not be mapped to a response, re-throwing to the HTTP container java.net.ConnectException: Connection timed out at java.net.PlainSocketImpl.socketConnect(Native Method) at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:339) at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:200) at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:182) at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392) at java.net.Socket.connect(Socket.java:579) at java.net.Socket.connect(Socket.java:528) at sun.net.NetworkClient.doConnect(NetworkClient.java:180) at sun.net.www.http.HttpClient.openServer(HttpClient.java:432) at sun.net.www.http.HttpClient.openServer(HttpClient.java:527) at sun.net.www.http.HttpClient.(HttpClient.java:211) at sun.net.www.http.HttpClient.New(HttpClient.java:308) at sun.net.www.http.HttpClient.New(HttpClient.java:326) at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:996) at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:932) at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:850) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1300) at com.sun.org.apache.xerces.internal.impl.XMLEntityManager.setupCurrentEntity(XMLEntityManager.java:643) at com.sun.org.apache.xerces.internal.impl.XMLEntityManager.startEntity(XMLEntityManager.java:1297) at com.sun.org.apache.xerces.internal.impl.XMLEntityManager.startDTDEntity(XMLEntityManager.java:1264) at com.sun.org.apache.xerces.internal.impl.XMLDTDScannerImpl.setInputSource(XMLDTDScannerImpl.java:263) at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$DTDDriver.dispatch(XMLDocumentScannerImpl.java:1164) at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$DTDDriver.next(XMLDocumentScannerImpl.java:1050) at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(XMLDocumentScannerImpl.java:964) at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:606) at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:510) at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:848) at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:777) at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:141) at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1213) at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:648) at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl.parse(SAXParserImpl.java:332) at scala.xml.factory.XMLLoader$class.loadXML(XMLLoader.scala:41) at scala.xml.XML$.loadXML(XML.scala:60) at scala.xml.factory.XMLLoader$class.loadString(XMLLoader.scala:60) at scala.xml.XML$.loadString(XML.scala:60) at net.shrine.client.PosterOntClient.childrenOf(PosterOntClient.scala:44) at net.shrine.ont.data.OntClientOntologyMetadata.ontologyVersion(OntClientOntologyMetadata.scala:19) at net.shrine.service.HappyShrineService.versionReport(HappyShrineService.scala:308) at net.shrine.service.HappyShrineResource.versionReport(HappyShrineResource.scala:51) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at com.sun.jersey.spi.container.JavaMethodInvokerFactory$1.invoke(JavaMethodInvokerFactory.java:60) at com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDispatchProvider$TypeOutInvoker._dispatch(AbstractResourceMethodDispatchProvider.java:185) at com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(ResourceJavaMethodDispatcher.java:75) at com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept(HttpMethodRule.java:302) at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147) at com.sun.jersey.server.impl.uri.rules.ResourceObjectRule.accept(ResourceObjectRule.java:100) at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147) at com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootResourceClassesRule.java:84) at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1542) at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1473) at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1419) at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1409) at com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:409) at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:540) at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:715) at javax.servlet.http.HttpServlet.service(HttpServlet.java:717) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:298) at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:859) at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:588) at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:489) at java.lang.Thread.run(Thread.java:745) Thanks, Phillip ________________________________ UT Southwestern Medical Center The future of medicine, today. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Phillip.Reeder at UTSouthwestern.edu Mon Oct 20 13:32:02 2014 From: Phillip.Reeder at UTSouthwestern.edu (Phillip Reeder) Date: Mon, 20 Oct 2014 17:32:02 +0000 Subject: [Shrine-users] Error running Happy Page Message-ID: I have further diagnosed the issue and I think it has to do with our network proxy server for accessing outside URLs. On an i2b2 VM install of shrine on my laptop, I get the timeout when I?m connected to our normal university network. We have a testing location where I can bypass the proxy server and when I do so, the same VM returns an XML response showing the version, revision, build date, etc. So, the question I have now is what url is the shrine happy page trying to access? And do I need to add the http proxy settings to Tomcat somewhere, or request that our network people allow the server to bypass the proxy? I?m just trying to determine the best plan of action. Thanks, Phillip From: Phillip Reeder > Date: Monday, October 20, 2014 at 11:35 AM To: "shrine-users at open.med.harvard.edu" > Subject: [Shrine-users] Error running Happy Page I?m able to run queries through the shrine-webclient, but when I access https://[host]/shrine/rest/happy/version, I?m getting an http 500 error message. Does anyone know what to do to fix this error? The Tomcat log shows the following: Oct 20, 2014 11:26:12 AM com.sun.jersey.spi.container.ContainerResponse mapMappableContainerException SEVERE: The exception contained within MappableContainerException could not be mapped to a response, re-throwing to the HTTP container java.net.ConnectException: Connection timed out at java.net.PlainSocketImpl.socketConnect(Native Method) at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:339) at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:200) at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:182) at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392) at java.net.Socket.connect(Socket.java:579) at java.net.Socket.connect(Socket.java:528) at sun.net.NetworkClient.doConnect(NetworkClient.java:180) at sun.net.www.http.HttpClient.openServer(HttpClient.java:432) at sun.net.www.http.HttpClient.openServer(HttpClient.java:527) at sun.net.www.http.HttpClient.(HttpClient.java:211) at sun.net.www.http.HttpClient.New(HttpClient.java:308) at sun.net.www.http.HttpClient.New(HttpClient.java:326) at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:996) at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:932) at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:850) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1300) at com.sun.org.apache.xerces.internal.impl.XMLEntityManager.setupCurrentEntity(XMLEntityManager.java:643) at com.sun.org.apache.xerces.internal.impl.XMLEntityManager.startEntity(XMLEntityManager.java:1297) at com.sun.org.apache.xerces.internal.impl.XMLEntityManager.startDTDEntity(XMLEntityManager.java:1264) at com.sun.org.apache.xerces.internal.impl.XMLDTDScannerImpl.setInputSource(XMLDTDScannerImpl.java:263) at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$DTDDriver.dispatch(XMLDocumentScannerImpl.java:1164) at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$DTDDriver.next(XMLDocumentScannerImpl.java:1050) at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(XMLDocumentScannerImpl.java:964) at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:606) at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:510) at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:848) at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:777) at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:141) at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1213) at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:648) at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl.parse(SAXParserImpl.java:332) at scala.xml.factory.XMLLoader$class.loadXML(XMLLoader.scala:41) at scala.xml.XML$.loadXML(XML.scala:60) at scala.xml.factory.XMLLoader$class.loadString(XMLLoader.scala:60) at scala.xml.XML$.loadString(XML.scala:60) at net.shrine.client.PosterOntClient.childrenOf(PosterOntClient.scala:44) at net.shrine.ont.data.OntClientOntologyMetadata.ontologyVersion(OntClientOntologyMetadata.scala:19) at net.shrine.service.HappyShrineService.versionReport(HappyShrineService.scala:308) at net.shrine.service.HappyShrineResource.versionReport(HappyShrineResource.scala:51) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at com.sun.jersey.spi.container.JavaMethodInvokerFactory$1.invoke(JavaMethodInvokerFactory.java:60) at com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDispatchProvider$TypeOutInvoker._dispatch(AbstractResourceMethodDispatchProvider.java:185) at com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(ResourceJavaMethodDispatcher.java:75) at com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept(HttpMethodRule.java:302) at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147) at com.sun.jersey.server.impl.uri.rules.ResourceObjectRule.accept(ResourceObjectRule.java:100) at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147) at com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootResourceClassesRule.java:84) at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1542) at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1473) at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1419) at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1409) at com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:409) at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:540) at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:715) at javax.servlet.http.HttpServlet.service(HttpServlet.java:717) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:298) at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:859) at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:588) at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:489) at java.lang.Thread.run(Thread.java:745) Thanks, Phillip ________________________________ UT Southwestern Medical Center The future of medicine, today. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Phillip.Reeder at UTSouthwestern.edu Tue Oct 21 16:23:22 2014 From: Phillip.Reeder at UTSouthwestern.edu (Phillip Reeder) Date: Tue, 21 Oct 2014 20:23:22 +0000 Subject: [Shrine-users] Error running Happy Page In-Reply-To: References: Message-ID: I ran a tcpdump on the i2b2/shrine vm while hitting the happy/version page and I?m seeing a bunch of traffic to hans-moleman.w3.org. See below for a few of the lines from the tcpdump. I?m guessing this is what is causing the page to timeout on me. Any suggestions? 18:59:47.654017 IP hans-moleman.w3.org.http > 192.168.199.135.59582: Flags [P.], seq 30984:31262, ack 666, win 64240, length 278 18:59:47.654021 IP 192.168.199.135.59582 > hans-moleman.w3.org.http: Flags [.], ack 31262, win 62780, length 0 18:59:52.661256 IP 192.168.199.135.59582 > hans-moleman.w3.org.http: Flags [F.], seq 666, ack 31262, win 62780, length 0 18:59:52.661640 IP hans-moleman.w3.org.http > 192.168.199.135.59582: Flags [.], ack 667, win 64239, length 0 18:59:52.661962 IP 192.168.199.135.59581 > hans-moleman.w3.org.http: Flags [F.], seq 224, ack 25974, win 58400, length 0 18:59:52.662111 IP hans-moleman.w3.org.http > 192.168.199.135.59581: Flags [.], ack 225, win 64239, length 0 18:59:52.712055 IP hans-moleman.w3.org.http > 192.168.199.135.59582: Flags [FP.], seq 31262, ack 667, win 64239, length 0 18:59:52.712103 IP 192.168.199.135.59582 > hans-moleman.w3.org.http: Flags [.], ack 31263, win 62780, length 0 Phillip From: Phillip Reeder > Date: Monday, October 20, 2014 at 12:32 PM To: "shrine-users at open.med.harvard.edu" > Subject: Re: [Shrine-users] Error running Happy Page I have further diagnosed the issue and I think it has to do with our network proxy server for accessing outside URLs. On an i2b2 VM install of shrine on my laptop, I get the timeout when I?m connected to our normal university network. We have a testing location where I can bypass the proxy server and when I do so, the same VM returns an XML response showing the version, revision, build date, etc. So, the question I have now is what url is the shrine happy page trying to access? And do I need to add the http proxy settings to Tomcat somewhere, or request that our network people allow the server to bypass the proxy? I?m just trying to determine the best plan of action. Thanks, Phillip From: Phillip Reeder > Date: Monday, October 20, 2014 at 11:35 AM To: "shrine-users at open.med.harvard.edu" > Subject: [Shrine-users] Error running Happy Page I?m able to run queries through the shrine-webclient, but when I access https://[host]/shrine/rest/happy/version, I?m getting an http 500 error message. Does anyone know what to do to fix this error? The Tomcat log shows the following: Oct 20, 2014 11:26:12 AM com.sun.jersey.spi.container.ContainerResponse mapMappableContainerException SEVERE: The exception contained within MappableContainerException could not be mapped to a response, re-throwing to the HTTP container java.net.ConnectException: Connection timed out at java.net.PlainSocketImpl.socketConnect(Native Method) at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:339) at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:200) at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:182) at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392) at java.net.Socket.connect(Socket.java:579) at java.net.Socket.connect(Socket.java:528) at sun.net.NetworkClient.doConnect(NetworkClient.java:180) at sun.net.www.http.HttpClient.openServer(HttpClient.java:432) at sun.net.www.http.HttpClient.openServer(HttpClient.java:527) at sun.net.www.http.HttpClient.(HttpClient.java:211) at sun.net.www.http.HttpClient.New(HttpClient.java:308) at sun.net.www.http.HttpClient.New(HttpClient.java:326) at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:996) at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:932) at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:850) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1300) at com.sun.org.apache.xerces.internal.impl.XMLEntityManager.setupCurrentEntity(XMLEntityManager.java:643) at com.sun.org.apache.xerces.internal.impl.XMLEntityManager.startEntity(XMLEntityManager.java:1297) at com.sun.org.apache.xerces.internal.impl.XMLEntityManager.startDTDEntity(XMLEntityManager.java:1264) at com.sun.org.apache.xerces.internal.impl.XMLDTDScannerImpl.setInputSource(XMLDTDScannerImpl.java:263) at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$DTDDriver.dispatch(XMLDocumentScannerImpl.java:1164) at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$DTDDriver.next(XMLDocumentScannerImpl.java:1050) at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(XMLDocumentScannerImpl.java:964) at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:606) at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:510) at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:848) at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:777) at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:141) at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1213) at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:648) at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl.parse(SAXParserImpl.java:332) at scala.xml.factory.XMLLoader$class.loadXML(XMLLoader.scala:41) at scala.xml.XML$.loadXML(XML.scala:60) at scala.xml.factory.XMLLoader$class.loadString(XMLLoader.scala:60) at scala.xml.XML$.loadString(XML.scala:60) at net.shrine.client.PosterOntClient.childrenOf(PosterOntClient.scala:44) at net.shrine.ont.data.OntClientOntologyMetadata.ontologyVersion(OntClientOntologyMetadata.scala:19) at net.shrine.service.HappyShrineService.versionReport(HappyShrineService.scala:308) at net.shrine.service.HappyShrineResource.versionReport(HappyShrineResource.scala:51) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at com.sun.jersey.spi.container.JavaMethodInvokerFactory$1.invoke(JavaMethodInvokerFactory.java:60) at com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDispatchProvider$TypeOutInvoker._dispatch(AbstractResourceMethodDispatchProvider.java:185) at com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(ResourceJavaMethodDispatcher.java:75) at com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept(HttpMethodRule.java:302) at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147) at com.sun.jersey.server.impl.uri.rules.ResourceObjectRule.accept(ResourceObjectRule.java:100) at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147) at com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootResourceClassesRule.java:84) at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1542) at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1473) at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1419) at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1409) at com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:409) at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:540) at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:715) at javax.servlet.http.HttpServlet.service(HttpServlet.java:717) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:298) at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:859) at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:588) at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:489) at java.lang.Thread.run(Thread.java:745) Thanks, Phillip ________________________________ UT Southwestern Medical Center The future of medicine, today. -------------- next part -------------- An HTML attachment was scrubbed... URL: From adfrench at regenstrief.org Wed Oct 22 13:56:08 2014 From: adfrench at regenstrief.org (French, Tony) Date: Wed, 22 Oct 2014 17:56:08 +0000 Subject: [Shrine-users] multiple i2b2 projects behind the same shrine node Message-ID: Is it possible to expose multiple i2b2 projects behind a single Shrine node? If so, would I have a single shrine.conf or one for each project/CRC? Are there any examples or documentation that would explain the setup? Our i2b2 setup consists of multiple institutions/health systems. We have a single PM and single Hive. However, each institution has its own project ID, CRC, ONT and Work schemas. All of which are exposed from a single webclient that that is configured to allow access to each of the institutions based on user login and project selection (if the user has access to multiple projects). Institution A: i2b2_a_data, i2b2_a_metadata, i2b2_a_workdata Institution B: i2b2_b_data, i2b2_b_metadata, i2b2_b_workdata Shared: i2b2_pm, i2b2_hive I currently have Shrine deployed with one of the institutions (project/CRC) but I'm running into a brick wall trying to figure out how to deploy the others, short of deploying each on its own node or virtual node. Thanks in advance for any assistance. Tony -------------- next part -------------- An HTML attachment was scrubbed... URL: From tseto at stanford.edu Wed Oct 22 16:55:34 2014 From: tseto at stanford.edu (Tina Seto) Date: Wed, 22 Oct 2014 13:55:34 -0700 (PDT) Subject: [Shrine-users] data steward page In-Reply-To: <000001cfee38$64ad1e00$2e075a00$@catalyst.harvard.edu> References: <1041236915.4817128.1414001931208.JavaMail.zimbra@stanford.edu> <1424153206.4823452.1414002147766.JavaMail.zimbra@stanford.edu> <000001cfee38$64ad1e00$2e075a00$@catalyst.harvard.edu> Message-ID: <568330544.5097620.1414011334498.JavaMail.zimbra@stanford.edu> A second question is, how do I configure the webclient to not use the data steward model, which seems to be activated with the automatic install? Thanks, Tina ----- Original Message ----- From: "Shrinehelp" To: "Tina Seto" Cc: shrine-users at open.med.harvard.edu Sent: Wednesday, October 22, 2014 1:40:19 PM Subject: RE: data steward page Hi Tina, I?m copying to this email the shrine mailing list which is the primary point of contact for getting technical support from the Harvard SHRINE team and the user community on how to implement SHRINE. It?s also a great resource since you can consult the archives, so I encourage you to register via the link below: https://open.med.harvard.edu/mailman/listinfo/shrine-users This email address (shrinehelp at catalyst.harvard.edu) is aimed at end-users looking for answers on how to use SHRINE, run queries etc. Best, Katia Katia Zilber-Izhar Project Coordinator Center for Biomedical Informatics / Harvard Catalyst Harvard Medical School Phone number: 617-384-8958 katia_zilber at hms.harvard.edu From: Tina Seto [mailto:tseto at stanford.edu] Sent: Wednesday, October 22, 2014 2:22 PM To: Shrine Help Subject: data steward page Hi, I'm able to bring up the happy page and the shrine-webclient, except when I try to run a query, I need an 'Approved Query Topic'. Clicking on the button 'Request New Topic' will bring up Harvard's shrine-hms-authorization page. How do I install the Data Steward pages or the webapp shrine-hms-authorization on my own system? Thanks, Tina Seto Senior Clinical Data Engineer Stanford Center for Clinical Informatics -------------- next part -------------- An HTML attachment was scrubbed... URL: From clint_gilbert at hms.harvard.edu Thu Oct 23 08:47:09 2014 From: clint_gilbert at hms.harvard.edu (Clint Gilbert) Date: Thu, 23 Oct 2014 08:47:09 -0400 Subject: [Shrine-users] Error running Happy Page In-Reply-To: References: Message-ID: <5448F8CD.8040407@hms.harvard.edu> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 At the moment, no, unfortunately. It seems some of the JVM's built-in XML-parsing code is trying too hard to resolve referenced entities in XML obtained from i2b2. I'll look into it. On 10/21/2014 04:23 PM, Phillip Reeder wrote: > I ran a tcpdump on the i2b2/shrine vm while hitting the > happy/version page and I?m seeing a bunch of traffic to > hans-moleman.w3.org. See below for a few of the lines from the > tcpdump. I?m guessing this is what is causing the page to timeout > on me. Any suggestions? > > 18:59:47.654017 IP hans-moleman.w3.org.http > > 192.168.199.135.59582: Flags [P.], seq 30984:31262, ack 666, win > 64240, length 278 > > 18:59:47.654021 IP 192.168.199.135.59582 > > hans-moleman.w3.org.http: Flags [.], ack 31262, win 62780, length > 0 > > 18:59:52.661256 IP 192.168.199.135.59582 > > hans-moleman.w3.org.http: Flags [F.], seq 666, ack 31262, win > 62780, length 0 > > 18:59:52.661640 IP hans-moleman.w3.org.http > > 192.168.199.135.59582: Flags [.], ack 667, win 64239, length 0 > > 18:59:52.661962 IP 192.168.199.135.59581 > > hans-moleman.w3.org.http: Flags [F.], seq 224, ack 25974, win > 58400, length 0 > > 18:59:52.662111 IP hans-moleman.w3.org.http > > 192.168.199.135.59581: Flags [.], ack 225, win 64239, length 0 > > 18:59:52.712055 IP hans-moleman.w3.org.http > > 192.168.199.135.59582: Flags [FP.], seq 31262, ack 667, win 64239, > length 0 > > 18:59:52.712103 IP 192.168.199.135.59582 > > hans-moleman.w3.org.http: Flags [.], ack 31263, win 62780, length > 0 > > > Phillip > > > From: Phillip Reeder > Date: Monday, October > 20, 2014 at 12:32 PM To: "shrine-users at open.med.harvard.edu > " > > Subject: Re: > [Shrine-users] Error running Happy Page > > I have further diagnosed the issue and I think it has to do with > our network proxy server for accessing outside URLs. On an i2b2 VM > install of shrine on my laptop, I get the timeout when I?m > connected to our normal university network. We have a testing > location where I can bypass the proxy server and when I do so, the > same VM returns an XML response showing the version, revision, > build date, etc. > > So, the question I have now is what url is the shrine happy page > trying to access? And do I need to add the http proxy settings to > Tomcat somewhere, or request that our network people allow the > server to bypass the proxy? I?m just trying to determine the best > plan of action. > > Thanks, Phillip > > From: Phillip Reeder > Date: Monday, October > 20, 2014 at 11:35 AM To: "shrine-users at open.med.harvard.edu > " > > Subject: [Shrine-users] > Error running Happy Page > > I?m able to run queries through the shrine-webclient, but when I > access https://[host]/shrine/rest/happy/version, I?m getting an > http 500 error message. Does anyone know what to do to fix this > error? > > > The Tomcat log shows the following: > > Oct 20, 2014 11:26:12 AM > com.sun.jersey.spi.container.ContainerResponse > mapMappableContainerException > > SEVERE: The exception contained within MappableContainerException > could not be mapped to a response, re-throwing to the HTTP > container > > java.net.ConnectException: Connection timed out > > at java.net.PlainSocketImpl.socketConnect(Native Method) > > at > java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:339) > > at > java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:200) > > at > java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:182) > > at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392) > > at java.net.Socket.connect(Socket.java:579) > > at java.net.Socket.connect(Socket.java:528) > > at sun.net.NetworkClient.doConnect(NetworkClient.java:180) > > at sun.net.www.http.HttpClient.openServer(HttpClient.java:432) > > at sun.net.www.http.HttpClient.openServer(HttpClient.java:527) > > at sun.net.www.http.HttpClient.(HttpClient.java:211) > > at sun.net.www.http.HttpClient.New(HttpClient.java:308) > > at sun.net.www.http.HttpClient.New(HttpClient.java:326) > > at > sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:996) > > at > sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:932) > > at > sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:850) > > at > sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1300) > > at > com.sun.org.apache.xerces.internal.impl.XMLEntityManager.setupCurrentEntity(XMLEntityManager.java:643) > > at > com.sun.org.apache.xerces.internal.impl.XMLEntityManager.startEntity(XMLEntityManager.java:1297) > > at > com.sun.org.apache.xerces.internal.impl.XMLEntityManager.startDTDEntity(XMLEntityManager.java:1264) > > at > com.sun.org.apache.xerces.internal.impl.XMLDTDScannerImpl.setInputSource(XMLDTDScannerImpl.java:263) > > at > com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$DTDDriver.dispatch(XMLDocumentScannerImpl.java:1164) > > at > com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$DTDDriver.next(XMLDocumentScannerImpl.java:1050) > > at > com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(XMLDocumentScannerImpl.java:964) > > at > com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:606) > > at > com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:510) > > at > com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:848) > > at > com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:777) > > at > com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:141) > > at > com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1213) > > at > com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:648) > > at > com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl.parse(SAXParserImpl.java:332) > > at scala.xml.factory.XMLLoader$class.loadXML(XMLLoader.scala:41) > > at scala.xml.XML$.loadXML(XML.scala:60) > > at > scala.xml.factory.XMLLoader$class.loadString(XMLLoader.scala:60) > > at scala.xml.XML$.loadString(XML.scala:60) > > at > net.shrine.client.PosterOntClient.childrenOf(PosterOntClient.scala:44) > > at > net.shrine.ont.data.OntClientOntologyMetadata.ontologyVersion(OntClientOntologyMetadata.scala:19) > > at > net.shrine.service.HappyShrineService.versionReport(HappyShrineService.scala:308) > > at > net.shrine.service.HappyShrineResource.versionReport(HappyShrineResource.scala:51) > > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > > at > sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) > > at > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) > > at java.lang.reflect.Method.invoke(Method.java:606) > > at > com.sun.jersey.spi.container.JavaMethodInvokerFactory$1.invoke(JavaMethodInvokerFactory.java:60) > > at > com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDispatchProvider$TypeOutInvoker._dispatch(AbstractResourceMethodDispatchProvider.java:185) > > at > com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(ResourceJavaMethodDispatcher.java:75) > > at > com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept(HttpMethodRule.java:302) > > at > com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147) > > at > com.sun.jersey.server.impl.uri.rules.ResourceObjectRule.accept(ResourceObjectRule.java:100) > > at > com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147) > > at > com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootResourceClassesRule.java:84) > > at > com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1542) > > at > com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1473) > > at > com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1419) > > at > com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1409) > > at > com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:409) > > at > com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:540) > > at > com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:715) > > at javax.servlet.http.HttpServlet.service(HttpServlet.java:717) > > at > org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290) > > at > org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) > > at > org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219) > > at > org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191) > > at > org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) > > at > org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102) > > at > org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109) > > at > org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:298) > > at > org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:859) > > at > org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:588) > > at > org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:489) > > at java.lang.Thread.run(Thread.java:745) > > > Thanks, Phillip > > ------------------------------------------------------------------------ > > UT Southwestern Medical Center The future of medicine, today. -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iEYEARECAAYFAlRI+M0ACgkQ0GFaTS4nYxvC3QCgyYBZAt0/FFaM/95GfFW3t/3S czoAoMPFty2k/c4x5lgAdVDyfKcErXCg =Ino7 -----END PGP SIGNATURE----- From Keith_Dwyer at hms.harvard.edu Thu Oct 23 14:43:32 2014 From: Keith_Dwyer at hms.harvard.edu (Dwyer, Keith) Date: Thu, 23 Oct 2014 14:43:32 -0400 Subject: [Shrine-users] data steward page In-Reply-To: <568330544.5097620.1414011334498.JavaMail.zimbra@stanford.edu> References: <1041236915.4817128.1414001931208.JavaMail.zimbra@stanford.edu> <1424153206.4823452.1414002147766.JavaMail.zimbra@stanford.edu> <000001cfee38$64ad1e00$2e075a00$@catalyst.harvard.edu> <568330544.5097620.1414011334498.JavaMail.zimbra@stanford.edu> Message-ID: <3B7CE631-6209-4E87-937A-3CF0C86FECC2@hms.harvard.edu> Yes, unfortunately it seems that the public webclient distribution still retains configuration information for the internal test networks that use a data steward. The quickest way to disable this at the moment is to comment out or unset the isSHRINE variable in i2b2_config_data.js, which should suffice if you want to prove basic functionality. Keith Dwyer Harvard Catalyst, SHRINE Network Operations On Oct 22, 2014, at 4:55 PM, Tina Seto > wrote: A second question is, how do I configure the webclient to not use the data steward model, which seems to be activated with the automatic install? Thanks, Tina ________________________________ From: "Shrinehelp" > To: "Tina Seto" > Cc: shrine-users at open.med.harvard.edu Sent: Wednesday, October 22, 2014 1:40:19 PM Subject: RE: data steward page Hi Tina, I?m copying to this email the shrine mailing list which is the primary point of contact for getting technical support from the Harvard SHRINE team and the user community on how to implement SHRINE. It?s also a great resource since you can consult the archives, so I encourage you to register via the link below: https://open.med.harvard.edu/mailman/listinfo/shrine-users This email address (shrinehelp at catalyst.harvard.edu) is aimed at end-users looking for answers on how to use SHRINE, run queries etc. Best, Katia Katia Zilber-Izhar Project Coordinator Center for Biomedical Informatics / Harvard Catalyst Harvard Medical School Phone number: 617-384-8958 katia_zilber at hms.harvard.edu From: Tina Seto [mailto:tseto at stanford.edu] Sent: Wednesday, October 22, 2014 2:22 PM To: Shrine Help Subject: data steward page Hi, I'm able to bring up the happy page and the shrine-webclient, except when I try to run a query, I need an 'Approved Query Topic'. Clicking on the button 'Request New Topic' will bring up Harvard's shrine-hms-authorization page. How do I install the Data Steward pages or the webapp shrine-hms-authorization on my own system? Thanks, Tina Seto Senior Clinical Data Engineer Stanford Center for Clinical Informatics _______________________________________________ Shrine-users mailing list Shrine-users at open.med.harvard.edu https://open.med.harvard.edu/mailman/listinfo/shrine-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From William.Shuman at cchmc.org Thu Oct 23 14:46:35 2014 From: William.Shuman at cchmc.org (Shuman, William (Billy)) Date: Thu, 23 Oct 2014 18:46:35 +0000 Subject: [Shrine-users] Error running Happy Page In-Reply-To: <5448F8CD.8040407@hms.harvard.edu> References: <5448F8CD.8040407@hms.harvard.edu> Message-ID: <1414089994.1142.16.camel@cchmc.org> If it is a xerces issue, you could just endorse a later version at the JVM. We typically endorse xerces at version 2.9.1. We are able to see the happy page with that version endorsed. Billy -- William Shuman Cincinnati Children's Hospital Medical Center On Thu, 2014-10-23 at 08:47 -0400, Clint Gilbert wrote: > At the moment, no, unfortunately. It seems some of the JVM's built-in > XML-parsing code is trying too hard to resolve referenced entities in > XML obtained from i2b2. I'll look into it. > > On 10/21/2014 04:23 PM, Phillip Reeder wrote: > > I ran a tcpdump on the i2b2/shrine vm while hitting the > > happy/version page and I?m seeing a bunch of traffic to > > hans-moleman.w3.org. See below for a few of the lines from the > > tcpdump. I?m guessing this is what is causing the page to timeout > > on me. Any suggestions? > > > > 18:59:47.654017 IP hans-moleman.w3.org.http > > > 192.168.199.135.59582: Flags [P.], seq 30984:31262, ack 666, win > > 64240, length 278 > > > > 18:59:47.654021 IP 192.168.199.135.59582 > > > hans-moleman.w3.org.http: Flags [.], ack 31262, win 62780, length > > 0 > > > > 18:59:52.661256 IP 192.168.199.135.59582 > > > hans-moleman.w3.org.http: Flags [F.], seq 666, ack 31262, win > > 62780, length 0 > > > > 18:59:52.661640 IP hans-moleman.w3.org.http > > > 192.168.199.135.59582: Flags [.], ack 667, win 64239, length 0 > > > > 18:59:52.661962 IP 192.168.199.135.59581 > > > hans-moleman.w3.org.http: Flags [F.], seq 224, ack 25974, win > > 58400, length 0 > > > > 18:59:52.662111 IP hans-moleman.w3.org.http > > > 192.168.199.135.59581: Flags [.], ack 225, win 64239, length 0 > > > > 18:59:52.712055 IP hans-moleman.w3.org.http > > > 192.168.199.135.59582: Flags [FP.], seq 31262, ack 667, win 64239, > > length 0 > > > > 18:59:52.712103 IP 192.168.199.135.59582 > > > hans-moleman.w3.org.http: Flags [.], ack 31263, win 62780, length > > 0 > > > > > > Phillip > > > > > > From: Phillip Reeder > > Date: Monday, October > > 20, 2014 at 12:32 PM To: "shrine-users at open.med.harvard.edu > > " > > > > Subject: Re: > > [Shrine-users] Error running Happy Page > > > > I have further diagnosed the issue and I think it has to do with > > our network proxy server for accessing outside URLs. On an i2b2 VM > > install of shrine on my laptop, I get the timeout when I?m > > connected to our normal university network. We have a testing > > location where I can bypass the proxy server and when I do so, the > > same VM returns an XML response showing the version, revision, > > build date, etc. > > > > So, the question I have now is what url is the shrine happy page > > trying to access? And do I need to add the http proxy settings to > > Tomcat somewhere, or request that our network people allow the > > server to bypass the proxy? I?m just trying to determine the best > > plan of action. > > > > Thanks, Phillip > > > > From: Phillip Reeder > > Date: Monday, October > > 20, 2014 at 11:35 AM To: "shrine-users at open.med.harvard.edu > > " > > > > Subject: [Shrine-users] > > Error running Happy Page > > > > I?m able to run queries through the shrine-webclient, but when I > > access https://[host]/shrine/rest/happy/version, I?m getting an > > http 500 error message. Does anyone know what to do to fix this > > error? > > > > > > The Tomcat log shows the following: > > > > Oct 20, 2014 11:26:12 AM > > com.sun.jersey.spi.container.ContainerResponse > > mapMappableContainerException > > > > SEVERE: The exception contained within MappableContainerException > > could not be mapped to a response, re-throwing to the HTTP > > container > > > > java.net.ConnectException: Connection timed out > > > > at java.net.PlainSocketImpl.socketConnect(Native Method) > > > > at > > java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:339) > > > > at > > java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:200) > > > > at > > java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:182) > > > > at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392) > > > > at java.net.Socket.connect(Socket.java:579) > > > > at java.net.Socket.connect(Socket.java:528) > > > > at sun.net.NetworkClient.doConnect(NetworkClient.java:180) > > > > at sun.net.www.http.HttpClient.openServer(HttpClient.java:432) > > > > at sun.net.www.http.HttpClient.openServer(HttpClient.java:527) > > > > at sun.net.www.http.HttpClient.(HttpClient.java:211) > > > > at sun.net.www.http.HttpClient.New(HttpClient.java:308) > > > > at sun.net.www.http.HttpClient.New(HttpClient.java:326) > > > > at > > sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:996) > > > > at > > sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:932) > > > > at > > sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:850) > > > > at > > sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1300) > > > > at > > com.sun.org.apache.xerces.internal.impl.XMLEntityManager.setupCurrentEntity(XMLEntityManager.java:643) > > > > at > > com.sun.org.apache.xerces.internal.impl.XMLEntityManager.startEntity(XMLEntityManager.java:1297) > > > > at > > com.sun.org.apache.xerces.internal.impl.XMLEntityManager.startDTDEntity(XMLEntityManager.java:1264) > > > > at > > com.sun.org.apache.xerces.internal.impl.XMLDTDScannerImpl.setInputSource(XMLDTDScannerImpl.java:263) > > > > at > > com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$DTDDriver.dispatch(XMLDocumentScannerImpl.java:1164) > > > > at > > com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$DTDDriver.next(XMLDocumentScannerImpl.java:1050) > > > > at > > com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(XMLDocumentScannerImpl.java:964) > > > > at > > com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:606) > > > > at > > com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:510) > > > > at > > com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:848) > > > > at > > com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:777) > > > > at > > com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:141) > > > > at > > com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1213) > > > > at > > com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:648) > > > > at > > com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl.parse(SAXParserImpl.java:332) > > > > at scala.xml.factory.XMLLoader$class.loadXML(XMLLoader.scala:41) > > > > at scala.xml.XML$.loadXML(XML.scala:60) > > > > at > > scala.xml.factory.XMLLoader$class.loadString(XMLLoader.scala:60) > > > > at scala.xml.XML$.loadString(XML.scala:60) > > > > at > > net.shrine.client.PosterOntClient.childrenOf(PosterOntClient.scala:44) > > > > at > > net.shrine.ont.data.OntClientOntologyMetadata.ontologyVersion(OntClientOntologyMetadata.scala:19) > > > > at > > net.shrine.service.HappyShrineService.versionReport(HappyShrineService.scala:308) > > > > at > > net.shrine.service.HappyShrineResource.versionReport(HappyShrineResource.scala:51) > > > > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > > > > at > > sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) > > > > at > > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) > > > > at java.lang.reflect.Method.invoke(Method.java:606) > > > > at > > com.sun.jersey.spi.container.JavaMethodInvokerFactory$1.invoke(JavaMethodInvokerFactory.java:60) > > > > at > > com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDispatchProvider$TypeOutInvoker._dispatch(AbstractResourceMethodDispatchProvider.java:185) > > > > at > > com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(ResourceJavaMethodDispatcher.java:75) > > > > at > > com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept(HttpMethodRule.java:302) > > > > at > > com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147) > > > > at > > com.sun.jersey.server.impl.uri.rules.ResourceObjectRule.accept(ResourceObjectRule.java:100) > > > > at > > com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147) > > > > at > > com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootResourceClassesRule.java:84) > > > > at > > com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1542) > > > > at > > com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1473) > > > > at > > com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1419) > > > > at > > com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1409) > > > > at > > com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:409) > > > > at > > com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:540) > > > > at > > com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:715) > > > > at javax.servlet.http.HttpServlet.service(HttpServlet.java:717) > > > > at > > org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290) > > > > at > > org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) > > > > at > > org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219) > > > > at > > org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191) > > > > at > > org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) > > > > at > > org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102) > > > > at > > org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109) > > > > at > > org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:298) > > > > at > > org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:859) > > > > at > > org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:588) > > > > at > > org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:489) > > > > at java.lang.Thread.run(Thread.java:745) > > > > > > Thanks, Phillip > > > > ------------------------------------------------------------------------ > > > > UT Southwestern Medical Center The future of medicine, today. > _______________________________________________ > Shrine-users mailing list > Shrine-users at open.med.harvard.edu > https://open.med.harvard.edu/mailman/listinfo/shrine-users From mhorvath at wakehealth.edu Fri Oct 24 16:19:43 2014 From: mhorvath at wakehealth.edu (Michael Horvath) Date: Fri, 24 Oct 2014 20:19:43 +0000 Subject: [Shrine-users] AdapterMapping csv support Message-ID: <96E1AA641D2EDE49A7A43FE98067A3E93B4310B9@EXCHDB1.medctr.ad.wfubmc.edu> Is there anything more that needs to be done in order to use csv files for adaptermappings in 1.17? I downloaded https://open.med.harvard.edu/svn/shrine/releases/1.17.0/ontology/PCORI/PCORI_AdapterMappings.csv, modifed $tomcat_home/lib/shrine.conf to set adapterMappingsFileName = "PCORI_AdapterMappings.csv", and reloaded the server. shrine.conf shows: 2014-Oct-24-16:01:41.699 INFO [SHRINE][ClasspathFormatDetectingAdapterMappingsSource][main] Loading adapter mappings from PCORI_AdapterMappings.csv 2014-Oct-24-16:01:49.116 WARN [SHRINE][FormatDetectingAdapterMappingsSource$][main] Couldn't load adapter mappings from PCORI_AdapterMappings.csv 2014-Oct-24-16:01:49.117 DEBUG [SHRINE][ClasspathFormatDetectingAdapterMappingsSource][main] Loading adapter mappings took 7416 milliseconds. catalina.out shows (full error not pasted): SEVERE: The provider class, class net.shrine.jersey.DefaultShrineResourceConfig, could not be instantiated. Processing will continue but the class will not be utilized scala.MatchError: [Ljava.lang.String;@577c5e (of class [Ljava.lang.String;) Thanks, Michael Horvath? ??? Programmer / Analyst?????????? Biomedical Research Services & Administration? ? Medical Center Boulevard ?\? Winston-Salem, NC 27157 p 336.716.9755 ?\? f 336.716.5055 From clint_gilbert at hms.harvard.edu Fri Oct 24 16:56:31 2014 From: clint_gilbert at hms.harvard.edu (Clint Gilbert) Date: Fri, 24 Oct 2014 16:56:31 -0400 Subject: [Shrine-users] AdapterMapping csv support In-Reply-To: <96E1AA641D2EDE49A7A43FE98067A3E93B4310B9@EXCHDB1.medctr.ad.wfubmc.edu> References: <96E1AA641D2EDE49A7A43FE98067A3E93B4310B9@EXCHDB1.medctr.ad.wfubmc.edu> Message-ID: <544ABCFF.6010603@hms.harvard.edu> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 The error reporting could be better here, and will be for 1.18. Right now all I can say is that there is an unexpected line somewhere in your CSV. All lines need to be 2-"columns", that is , More "columns", or not enough, will prevent your mapping file from loading. I generally favor strictness, but I'm open to suggestions on whether adapter mapping csv parsing should forge onward in the face of bad lines. On 10/24/2014 04:19 PM, Michael Horvath wrote: > Is there anything more that needs to be done in order to use csv > files for adaptermappings in 1.17? > > I downloaded > https://open.med.harvard.edu/svn/shrine/releases/1.17.0/ontology/PCORI/PCORI_AdapterMappings.csv, > modifed $tomcat_home/lib/shrine.conf to set > adapterMappingsFileName = "PCORI_AdapterMappings.csv", and reloaded > the server. > > shrine.conf shows: > > 2014-Oct-24-16:01:41.699 INFO > [SHRINE][ClasspathFormatDetectingAdapterMappingsSource][main] > Loading adapter mappings from PCORI_AdapterMappings.csv > 2014-Oct-24-16:01:49.116 WARN > [SHRINE][FormatDetectingAdapterMappingsSource$][main] Couldn't load > adapter mappings from PCORI_AdapterMappings.csv > 2014-Oct-24-16:01:49.117 DEBUG > [SHRINE][ClasspathFormatDetectingAdapterMappingsSource][main] > Loading adapter mappings took 7416 milliseconds. > > catalina.out shows (full error not pasted): > > SEVERE: The provider class, class > net.shrine.jersey.DefaultShrineResourceConfig, could not be > instantiated. Processing will continue but the class will not be > utilized scala.MatchError: [Ljava.lang.String;@577c5e (of class > [Ljava.lang.String;) > > Thanks, Michael Horvath Programmer / Analyst > > Biomedical Research Services & Administration Medical Center > Boulevard \ Winston-Salem, NC 27157 p 336.716.9755 \ f > 336.716.5055 > > > > _______________________________________________ Shrine-users > mailing list Shrine-users at open.med.harvard.edu > https://open.med.harvard.edu/mailman/listinfo/shrine-users > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iEYEARECAAYFAlRKvP8ACgkQ0GFaTS4nYxuT5gCfYCOE8a0YML2e9X0YctWVbVey RQEAoM6XbHyp6dlRITe6ypANM2N7ZNgm =Ua1E -----END PGP SIGNATURE----- From shrinehelp at catalyst.harvard.edu Wed Oct 22 16:40:19 2014 From: shrinehelp at catalyst.harvard.edu (Shrinehelp) Date: Wed, 22 Oct 2014 16:40:19 -0400 Subject: [Shrine-users] data steward page In-Reply-To: <1424153206.4823452.1414002147766.JavaMail.zimbra@stanford.edu> References: <1041236915.4817128.1414001931208.JavaMail.zimbra@stanford.edu> <1424153206.4823452.1414002147766.JavaMail.zimbra@stanford.edu> Message-ID: <000001cfee38$64ad1e00$2e075a00$@catalyst.harvard.edu> Hi Tina, I?m copying to this email the shrine mailing list which is the primary point of contact for getting technical support from the Harvard SHRINE team and the user community on how to implement SHRINE. It?s also a great resource since you can consult the archives, so I encourage you to register via the link below: https://open.med.harvard.edu/mailman/listinfo/shrine-users This email address (shrinehelp at catalyst.harvard.edu) is aimed at end-users looking for answers on how to use SHRINE, run queries etc. Best, Katia Katia Zilber-Izhar Project Coordinator Center for Biomedical Informatics / Harvard Catalyst Harvard Medical School Phone number: 617-384-8958 katia_zilber at hms.harvard.edu From: Tina Seto [mailto:tseto at stanford.edu] Sent: Wednesday, October 22, 2014 2:22 PM To: Shrine Help Subject: data steward page Hi, I'm able to bring up the happy page and the shrine-webclient, except when I try to run a query, I need an 'Approved Query Topic'. Clicking on the button 'Request New Topic' will bring up Harvard's shrine-hms-authorization page. How do I install the Data Steward pages or the webapp shrine-hms-authorization on my own system? Thanks, Tina Seto Senior Clinical Data Engineer Stanford Center for Clinical Informatics -------------- next part -------------- An HTML attachment was scrubbed... URL: From Ronald.Campbell at uth.tmc.edu Mon Oct 27 17:11:22 2014 From: Ronald.Campbell at uth.tmc.edu (Ronald Campbell) Date: Mon, 27 Oct 2014 21:11:22 +0000 Subject: [Shrine-users] Location of .key files for Shrine Message-ID: <941A43E9AFA0824F9F6CCE21B7B71EFB285731FF@MBX4.shis.uth.tmc.edu> Hi Everyone, I'm trying to locate the .key file for Shrine. I've found the .cer file and the keystore, but I can't find the .key. Does anyone know where it is? Thank you, Ron -------------- next part -------------- An HTML attachment was scrubbed... URL: From mhorvath at wakehealth.edu Tue Oct 28 08:28:03 2014 From: mhorvath at wakehealth.edu (Michael Horvath) Date: Tue, 28 Oct 2014 12:28:03 +0000 Subject: [Shrine-users] AdapterMapping csv support In-Reply-To: <544ABCFF.6010603@hms.harvard.edu> References: <96E1AA641D2EDE49A7A43FE98067A3E93B4310B9@EXCHDB1.medctr.ad.wfubmc.edu> <544ABCFF.6010603@hms.harvard.edu> Message-ID: <96E1AA641D2EDE49A7A43FE98067A3E93B4315BC@EXCHDB1.medctr.ad.wfubmc.edu> Is it likely that unescaped commas inside the quoted portions of each of the two columns would be causing the issue? Thanks, Michael -----Original Message----- From: shrine-users-bounces at open.med.harvard.edu [mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of Clint Gilbert Sent: Friday, October 24, 2014 4:57 PM To: shrine-users at open.med.harvard.edu Subject: Re: [Shrine-users] AdapterMapping csv support -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 The error reporting could be better here, and will be for 1.18. Right now all I can say is that there is an unexpected line somewhere in your CSV. All lines need to be 2-"columns", that is , More "columns", or not enough, will prevent your mapping file from loading. I generally favor strictness, but I'm open to suggestions on whether adapter mapping csv parsing should forge onward in the face of bad lines. On 10/24/2014 04:19 PM, Michael Horvath wrote: > Is there anything more that needs to be done in order to use csv files > for adaptermappings in 1.17? > > I downloaded > https://open.med.harvard.edu/svn/shrine/releases/1.17.0/ontology/PCORI > /PCORI_AdapterMappings.csv, modifed $tomcat_home/lib/shrine.conf to > set adapterMappingsFileName = "PCORI_AdapterMappings.csv", and > reloaded the server. > > shrine.conf shows: > > 2014-Oct-24-16:01:41.699 INFO > [SHRINE][ClasspathFormatDetectingAdapterMappingsSource][main] > Loading adapter mappings from PCORI_AdapterMappings.csv > 2014-Oct-24-16:01:49.116 WARN > [SHRINE][FormatDetectingAdapterMappingsSource$][main] Couldn't load > adapter mappings from PCORI_AdapterMappings.csv > 2014-Oct-24-16:01:49.117 DEBUG > [SHRINE][ClasspathFormatDetectingAdapterMappingsSource][main] > Loading adapter mappings took 7416 milliseconds. > > catalina.out shows (full error not pasted): > > SEVERE: The provider class, class > net.shrine.jersey.DefaultShrineResourceConfig, could not be > instantiated. Processing will continue but the class will not be > utilized scala.MatchError: [Ljava.lang.String;@577c5e (of class > [Ljava.lang.String;) > > Thanks, Michael Horvath Programmer / Analyst > > Biomedical Research Services & Administration Medical Center Boulevard > \ Winston-Salem, NC 27157 p 336.716.9755 \ f > 336.716.5055 > > > > _ Shrine-users mailing > list Shrine-users at open.med.harvard.edu > https://open.med.harvard.edu/mailman/listinfo/shrine-users > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iEYEARECAAYFAlRKvP8ACgkQ0GFaTS4nYxuT5gCfYCOE8a0YML2e9X0YctWVbVey RQEAoM6XbHyp6dlRITe6ypANM2N7ZNgm =Ua1E -----END PGP SIGNATURE----- _ Shrine-users mailing list Shrine-users at open.med.harvard.edu https://open.med.harvard.edu/mailman/listinfo/shrine-users From clint_gilbert at hms.harvard.edu Tue Oct 28 10:30:35 2014 From: clint_gilbert at hms.harvard.edu (Clint Gilbert) Date: Tue, 28 Oct 2014 10:30:35 -0400 Subject: [Shrine-users] AdapterMapping csv support In-Reply-To: <96E1AA641D2EDE49A7A43FE98067A3E93B4315BC@EXCHDB1.medctr.ad.wfubmc.edu> References: <96E1AA641D2EDE49A7A43FE98067A3E93B4310B9@EXCHDB1.medctr.ad.wfubmc.edu> <544ABCFF.6010603@hms.harvard.edu> <96E1AA641D2EDE49A7A43FE98067A3E93B4315BC@EXCHDB1.medctr.ad.wfubmc.edu> Message-ID: <544FA88B.7000104@hms.harvard.edu> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 I would think not, but can't say for sure. I'll experiment with that later today. On 10/28/2014 08:28 AM, Michael Horvath wrote: > Is it likely that unescaped commas inside the quoted portions of > each of the two columns would be causing the issue? > > Thanks, Michael > > -----Original Message----- From: > shrine-users-bounces at open.med.harvard.edu > [mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of > Clint Gilbert Sent: Friday, October 24, 2014 4:57 PM To: > shrine-users at open.med.harvard.edu Subject: Re: [Shrine-users] > AdapterMapping csv support > > The error reporting could be better here, and will be for 1.18. > Right now all I can say is that there is an unexpected line > somewhere in your CSV. All lines need to be 2-"columns", that is > > , > > More "columns", or not enough, will prevent your mapping file from > loading. > > I generally favor strictness, but I'm open to suggestions on > whether adapter mapping csv parsing should forge onward in the face > of bad lines. > > On 10/24/2014 04:19 PM, Michael Horvath wrote: >> Is there anything more that needs to be done in order to use csv >> files for adaptermappings in 1.17? > >> I downloaded >> https://open.med.harvard.edu/svn/shrine/releases/1.17.0/ontology/PCORI >> >> /PCORI_AdapterMappings.csv, modifed $tomcat_home/lib/shrine.conf to >> set adapterMappingsFileName = "PCORI_AdapterMappings.csv", and >> reloaded the server. > >> shrine.conf shows: > >> 2014-Oct-24-16:01:41.699 INFO >> [SHRINE][ClasspathFormatDetectingAdapterMappingsSource][main] >> Loading adapter mappings from PCORI_AdapterMappings.csv >> 2014-Oct-24-16:01:49.116 WARN >> [SHRINE][FormatDetectingAdapterMappingsSource$][main] Couldn't >> load adapter mappings from PCORI_AdapterMappings.csv >> 2014-Oct-24-16:01:49.117 DEBUG >> [SHRINE][ClasspathFormatDetectingAdapterMappingsSource][main] >> Loading adapter mappings took 7416 milliseconds. > >> catalina.out shows (full error not pasted): > >> SEVERE: The provider class, class >> net.shrine.jersey.DefaultShrineResourceConfig, could not be >> instantiated. Processing will continue but the class will not be >> utilized scala.MatchError: [Ljava.lang.String;@577c5e (of class >> [Ljava.lang.String;) > >> Thanks, Michael Horvath Programmer / Analyst > >> Biomedical Research Services & Administration Medical Center >> Boulevard \ Winston-Salem, NC 27157 p 336.716.9755 \ f >> 336.716.5055 > > > >> _ Shrine-users >> mailing list Shrine-users at open.med.harvard.edu >> https://open.med.harvard.edu/mailman/listinfo/shrine-users > > _ Shrine-users > mailing list Shrine-users at open.med.harvard.edu > https://open.med.harvard.edu/mailman/listinfo/shrine-users > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iEYEARECAAYFAlRPqIoACgkQ0GFaTS4nYxtO0ACghG6wqLBVouRMtBfH6YqDrwgH +M4AmwXWxygkHam8fKCEb/khIzdh9aeG =4YUR -----END PGP SIGNATURE----- From mhorvath at wakehealth.edu Tue Oct 28 10:57:34 2014 From: mhorvath at wakehealth.edu (Michael Horvath) Date: Tue, 28 Oct 2014 14:57:34 +0000 Subject: [Shrine-users] AdapterMapping csv support In-Reply-To: <544FA88B.7000104@hms.harvard.edu> References: <96E1AA641D2EDE49A7A43FE98067A3E93B4310B9@EXCHDB1.medctr.ad.wfubmc.edu> <544ABCFF.6010603@hms.harvard.edu> <96E1AA641D2EDE49A7A43FE98067A3E93B4315BC@EXCHDB1.medctr.ad.wfubmc.edu> <544FA88B.7000104@hms.harvard.edu> Message-ID: <96E1AA641D2EDE49A7A43FE98067A3E93B431694@EXCHDB1.medctr.ad.wfubmc.edu> Looks like the issue was with a trailing empty line at the end of the file. Loads fine (and much faster than the xml equivalent) now. Thanks, Michael -----Original Message----- From: Clint Gilbert [mailto:clint_gilbert at hms.harvard.edu] Sent: Tuesday, October 28, 2014 10:31 AM To: Michael Horvath; shrine-users at open.med.harvard.edu Subject: Re: [Shrine-users] AdapterMapping csv support -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 I would think not, but can't say for sure. I'll experiment with that later today. On 10/28/2014 08:28 AM, Michael Horvath wrote: > Is it likely that unescaped commas inside the quoted portions of each > of the two columns would be causing the issue? > > Thanks, Michael > > -----Original Message----- From: > shrine-users-bounces at open.med.harvard.edu > [mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of Clint > Gilbert Sent: Friday, October 24, 2014 4:57 PM To: > shrine-users at open.med.harvard.edu Subject: Re: [Shrine-users] > AdapterMapping csv support > > The error reporting could be better here, and will be for 1.18. > Right now all I can say is that there is an unexpected line somewhere > in your CSV. All lines need to be 2-"columns", that is > > , > > More "columns", or not enough, will prevent your mapping file from > loading. > > I generally favor strictness, but I'm open to suggestions on whether > adapter mapping csv parsing should forge onward in the face of bad > lines. > > On 10/24/2014 04:19 PM, Michael Horvath wrote: >> Is there anything more that needs to be done in order to use csv >> files for adaptermappings in 1.17? > >> I downloaded >> https://open.med.harvard.edu/svn/shrine/releases/1.17.0/ontology/PCOR >> I >> >> /PCORI_AdapterMappings.csv, modifed $tomcat_home/lib/shrine.conf to >> set adapterMappingsFileName = "PCORI_AdapterMappings.csv", and >> reloaded the server. > >> shrine.conf shows: > >> 2014-Oct-24-16:01:41.699 INFO >> [SHRINE][ClasspathFormatDetectingAdapterMappingsSource][main] >> Loading adapter mappings from PCORI_AdapterMappings.csv >> 2014-Oct-24-16:01:49.116 WARN >> [SHRINE][FormatDetectingAdapterMappingsSource$][main] Couldn't load >> adapter mappings from PCORI_AdapterMappings.csv >> 2014-Oct-24-16:01:49.117 DEBUG >> [SHRINE][ClasspathFormatDetectingAdapterMappingsSource][main] >> Loading adapter mappings took 7416 milliseconds. > >> catalina.out shows (full error not pasted): > >> SEVERE: The provider class, class >> net.shrine.jersey.DefaultShrineResourceConfig, could not be >> instantiated. Processing will continue but the class will not be >> utilized scala.MatchError: [Ljava.lang.String;@577c5e (of class >> [Ljava.lang.String;) > >> Thanks, Michael Horvath Programmer / Analyst > >> Biomedical Research Services & Administration Medical Center >> Boulevard \ Winston-Salem, NC 27157 p 336.716.9755 \ f >> 336.716.5055 > > > >> _______________________ Shrine-users mailing >> list Shrine-users at open.med.harvard.edu >> https://open.med.harvard.edu/mailman/listinfo/shrine-users > > _ Shrine-users mailing > list Shrine-users at open.med.harvard.edu > https://open.med.harvard.edu/mailman/listinfo/shrine-users > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iEYEARECAAYFAlRPqIoACgkQ0GFaTS4nYxtO0ACghG6wqLBVouRMtBfH6YqDrwgH +M4AmwXWxygkHam8fKCEb/khIzdh9aeG =4YUR -----END PGP SIGNATURE----- From Phillip.Reeder at UTSouthwestern.edu Tue Oct 28 11:20:16 2014 From: Phillip.Reeder at UTSouthwestern.edu (Phillip Reeder) Date: Tue, 28 Oct 2014 15:20:16 +0000 Subject: [Shrine-users] Location of .key files for Shrine Message-ID: On the latest version of shrine, the keystore is shrine.keystore in the /opt/shrine directory. The previous version I believe had the file in the /root/.spin/conf folder. The /opt/shrine/tomcat/lib/shrine.conf file specifies the location and password for the shrine.keystore so you can find the location that is being used there, or change it to a new location. The /opt/shrine/tomcat/conf/server.xml file also contains the location of the keystore so if you move the file, you would also need to change it there as well. ? Phillip Reeder UT Southwestern From: Ronald Campbell > Date: Monday, October 27, 2014 at 4:11 PM To: "shrine-users at open.med.harvard.edu" > Subject: [Shrine-users] Location of .key files for Shrine Hi Everyone, I?m trying to locate the .key file for Shrine. I?ve found the .cer file and the keystore, but I can?t find the .key. Does anyone know where it is? Thank you, Ron __________ UT Southwestern Medical Center The future of medicine, today. -------------- next part -------------- An HTML attachment was scrubbed... URL: From clint_gilbert at hms.harvard.edu Tue Oct 28 11:59:15 2014 From: clint_gilbert at hms.harvard.edu (Clint Gilbert) Date: Tue, 28 Oct 2014 11:59:15 -0400 Subject: [Shrine-users] AdapterMapping csv support In-Reply-To: <96E1AA641D2EDE49A7A43FE98067A3E93B431694@EXCHDB1.medctr.ad.wfubmc.edu> References: <96E1AA641D2EDE49A7A43FE98067A3E93B4310B9@EXCHDB1.medctr.ad.wfubmc.edu> <544ABCFF.6010603@hms.harvard.edu> <96E1AA641D2EDE49A7A43FE98067A3E93B4315BC@EXCHDB1.medctr.ad.wfubmc.edu> <544FA88B.7000104@hms.harvard.edu> <96E1AA641D2EDE49A7A43FE98067A3E93B431694@EXCHDB1.medctr.ad.wfubmc.edu> Message-ID: <544FBD53.9030902@hms.harvard.edu> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 That's good to hear. Shrine should definitely tolerate empty lines; I'll make sure it does for 1.18. On 10/28/2014 10:57 AM, Michael Horvath wrote: > Looks like the issue was with a trailing empty line at the end of > the file. Loads fine (and much faster than the xml equivalent) > now. > > Thanks, Michael > > -----Original Message----- From: Clint Gilbert > [mailto:clint_gilbert at hms.harvard.edu] Sent: Tuesday, October 28, > 2014 10:31 AM To: Michael Horvath; > shrine-users at open.med.harvard.edu Subject: Re: [Shrine-users] > AdapterMapping csv support > > I would think not, but can't say for sure. I'll experiment with > that later today. > > On 10/28/2014 08:28 AM, Michael Horvath wrote: >> Is it likely that unescaped commas inside the quoted portions of >> each of the two columns would be causing the issue? > >> Thanks, Michael > >> -----Original Message----- From: >> shrine-users-bounces at open.med.harvard.edu >> [mailto:shrine-users-bounces at open.med.harvard.edu] On Behalf Of >> Clint Gilbert Sent: Friday, October 24, 2014 4:57 PM To: >> shrine-users at open.med.harvard.edu Subject: Re: [Shrine-users] >> AdapterMapping csv support > >> The error reporting could be better here, and will be for 1.18. >> Right now all I can say is that there is an unexpected line >> somewhere in your CSV. All lines need to be 2-"columns", that >> is > >> , > >> More "columns", or not enough, will prevent your mapping file >> from loading. > >> I generally favor strictness, but I'm open to suggestions on >> whether adapter mapping csv parsing should forge onward in the >> face of bad lines. > >> On 10/24/2014 04:19 PM, Michael Horvath wrote: >>> Is there anything more that needs to be done in order to use >>> csv files for adaptermappings in 1.17? > >>> I downloaded >>> https://open.med.harvard.edu/svn/shrine/releases/1.17.0/ontology/PCOR >>> >>> I >>> >>> > /PCORI_AdapterMappings.csv, modifed $tomcat_home/lib/shrine.conf > to >>> set adapterMappingsFileName = "PCORI_AdapterMappings.csv", and >>> reloaded the server. > >>> shrine.conf shows: > >>> 2014-Oct-24-16:01:41.699 INFO >>> [SHRINE][ClasspathFormatDetectingAdapterMappingsSource][main] >>> Loading adapter mappings from PCORI_AdapterMappings.csv >>> 2014-Oct-24-16:01:49.116 WARN >>> [SHRINE][FormatDetectingAdapterMappingsSource$][main] Couldn't >>> load adapter mappings from PCORI_AdapterMappings.csv >>> 2014-Oct-24-16:01:49.117 DEBUG >>> [SHRINE][ClasspathFormatDetectingAdapterMappingsSource][main] >>> Loading adapter mappings took 7416 milliseconds. > >>> catalina.out shows (full error not pasted): > >>> SEVERE: The provider class, class >>> net.shrine.jersey.DefaultShrineResourceConfig, could not be >>> instantiated. Processing will continue but the class will not >>> be utilized scala.MatchError: [Ljava.lang.String;@577c5e (of >>> class [Ljava.lang.String;) > >>> Thanks, Michael Horvath Programmer / Analyst > >>> Biomedical Research Services & Administration Medical Center >>> Boulevard \ Winston-Salem, NC 27157 p 336.716.9755 \ f >>> 336.716.5055 > > > >>> _______________________ Shrine-users >>> mailing list Shrine-users at open.med.harvard.edu >>> https://open.med.harvard.edu/mailman/listinfo/shrine-users > >> _ Shrine-users >> mailing list Shrine-users at open.med.harvard.edu >> https://open.med.harvard.edu/mailman/listinfo/shrine-users > > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iEYEARECAAYFAlRPvVMACgkQ0GFaTS4nYxsI6QCghL8t1b5l1ta6OXcHyMmmjjsw UlUAnjPjoTnPbAkT6/Tgv3FDVoYatr4A =0Tc0 -----END PGP SIGNATURE----- From schuffr at ohsu.edu Tue Oct 28 12:43:47 2014 From: schuffr at ohsu.edu (Robert Schuff) Date: Tue, 28 Oct 2014 16:43:47 +0000 Subject: [Shrine-users] act In-Reply-To: References: <20141020121719.gnlb143340o0o8s8@cubmail.cc.columbia.edu> Message-ID: Hi all, Any new information on the ACT ontology? Keith: Does the Harvard hub implied below have the act ontology deployed then? Can it be published? Thanks! Rob Robert Schuff, MS Instructor, Dept. of Medical Informatics and Clinical Epidemiology Director, Clinical Research Informatics Oregon Clinical & Translational Research Institute Oregon Health & Science University http://www.octri.org/ From: , Keith > Date: Monday, October 20, 2014 9:21 AM To: "ev2348 at columbia.edu" > Cc: "shrine-users at open.med.harvard.edu" > Subject: Re: [Shrine-users] act Milestone 4 has already been handled by HMS, who is hosting the hub node. The instructions that all other have to follow to connect to the hub can be found here: https://open.med.harvard.edu/wiki/display/SHRINE/Post-Install+Configuration+and+Tasks#Post-InstallConfigurationandTasks-hub-connect Keith Dwyer Harvard Catalyst, SHRINE Network Operations On Oct 20, 2014, at 12:17 PM, > > wrote: Hello, thanks for all your help. I need to follow the milestones for ACT and now I am in Phase B. Milestone 4 Install ACT hub node and provide documentation for connecting a site to the ACT hub. Dependencies Systems and staff at Harvard Medical School. I have to follow the milestones even when around here they just want the local EMR. Can you tell me what is ACT hub node. Best Regards Elena _________________________ Shrine-users mailing list Shrine-users at open.med.harvard.edu https://open.med.harvard.edu/mailman/listinfo/shrine-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From Douglas_MacFadden at hms.harvard.edu Tue Oct 28 12:52:45 2014 From: Douglas_MacFadden at hms.harvard.edu (MacFadden, Douglas) Date: Tue, 28 Oct 2014 12:52:45 -0400 Subject: [Shrine-users] act In-Reply-To: References: <20141020121719.gnlb143340o0o8s8@cubmail.cc.columbia.edu> Message-ID: Rob, The ACT working group is still finalizing the ACT ontology. Mike Becich heads up this group. Shyam Visweswaran (also at Pittsburgh) is also in a leadership role and can help answer questions. Doug Douglas MacFadden Chief Informatics Officer, Harvard Catalyst Harvard Medical School douglas_macfadden at hms.harvard.edu 617-384-8960 From: Robert Schuff > Date: Tuesday, October 28, 2014 at 12:43 PM To: "shrine-users at open.med.harvard.edu" > Subject: Re: [Shrine-users] act Hi all, Any new information on the ACT ontology? Keith: Does the Harvard hub implied below have the act ontology deployed then? Can it be published? Thanks! Rob Robert Schuff, MS Instructor, Dept. of Medical Informatics and Clinical Epidemiology Director, Clinical Research Informatics Oregon Clinical & Translational Research Institute Oregon Health & Science University http://www.octri.org/ From: , Keith > Date: Monday, October 20, 2014 9:21 AM To: "ev2348 at columbia.edu" > Cc: "shrine-users at open.med.harvard.edu" > Subject: Re: [Shrine-users] act Milestone 4 has already been handled by HMS, who is hosting the hub node. The instructions that all other have to follow to connect to the hub can be found here: https://open.med.harvard.edu/wiki/display/SHRINE/Post-Install+Configuration+and+Tasks#Post-InstallConfigurationandTasks-hub-connect Keith Dwyer Harvard Catalyst, SHRINE Network Operations On Oct 20, 2014, at 12:17 PM, > > wrote: Hello, thanks for all your help. I need to follow the milestones for ACT and now I am in Phase B. Milestone 4 Install ACT hub node and provide documentation for connecting a site to the ACT hub. Dependencies Systems and staff at Harvard Medical School. I have to follow the milestones even when around here they just want the local EMR. Can you tell me what is ACT hub node. Best Regards Elena _______________________________________________ Shrine-users mailing list Shrine-users at open.med.harvard.edu https://open.med.harvard.edu/mailman/listinfo/shrine-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From William_Simons at hms.harvard.edu Wed Oct 29 10:40:12 2014 From: William_Simons at hms.harvard.edu (Simons, William) Date: Wed, 29 Oct 2014 10:40:12 -0400 Subject: [Shrine-users] Location of .key files for Shrine In-Reply-To: <941A43E9AFA0824F9F6CCE21B7B71EFB285731FF@MBX4.shis.uth.tmc.edu> Message-ID: Hi Ronald, Are you referring to the private key that SHRINE uses for SSL and signing requests? That is not a separate file and should be included in your keystore. You can generate a new self-signed cert using the -genkeypair option from keytool. Alternatively you can use certreq and importcert to generate a certificate request and get that signed by a CA. See http://docs.oracle.com/javase/6/docs/technotes/tools/solaris/keytool.html and https://open.med.harvard.edu/wiki/display/SHRINE/Manual+Server+Installation for more details. Bill From: Ronald Campbell > Date: Monday, October 27, 2014 at 5:11 PM To: "shrine-users at open.med.harvard.edu" > Subject: [Shrine-users] Location of .key files for Shrine Hi Everyone, I?m trying to locate the .key file for Shrine. I?ve found the .cer file and the keystore, but I can?t find the .key. Does anyone know where it is? Thank you, Ron -------------- next part -------------- An HTML attachment was scrubbed... URL: