From Marc_Ciriello at hms.harvard.edu Tue Jul 1 17:29:48 2014 From: Marc_Ciriello at hms.harvard.edu (Ciriello, Marc) Date: Tue, 1 Jul 2014 17:29:48 -0400 Subject: [Eagle-i-admins] release 2.0MS3.07 In-Reply-To: Message-ID: Hi Faith: Yes, the latest release uses an ontology created from the ISF. An email will go out soon giving more information about which release to use for the upgrade and other details. Thanks for asking and stay tuned, Marc From: Faith Coldren > Date: Wed, 25 Jun 2014 12:50:03 -0400 To: "eagle-i-admins at open.med.harvard.edu" > Subject: [Eagle-i-admins] release 2.0MS3.07 Hi, Does release 2.0MS3.07 use the Integrated Semantic Framework? Best, Faith -------------- next part -------------- An HTML attachment was scrubbed... URL: From Sophia_Cheng at hms.harvard.edu Fri Jul 11 18:35:37 2014 From: Sophia_Cheng at hms.harvard.edu (Cheng, Sophia) Date: Fri, 11 Jul 2014 18:35:37 -0400 Subject: [Eagle-i-admins] Coming soon ... eagle-i 3.0 (patch 1) Message-ID: <4A85FA7E1F2BF74E9C4F18748E720C88D0215AC1B3@ITCCRMAIL02.MED.HARVARD.EDU> Dear eagle-i sys admins, As some of you may already know, we have a new release of our software. We are in the process of vetting a patch for the release, which will be available on Monday, July 14. We would like to ask that you wait for the patch to be released before upgrading. More information regarding release notes, configuration changes, etc. will be forthcoming over the weekend. In the meantime, as a teaser, the eagle-i ontology is now ISF compliant. One point of confusion that has come up is that we have recently changed our version-ing convention. In the past, we were using the format: [Major version] MS [Minor Version].[Patch/Release candidate] (e.g. 2.0 MS 3.07) We have now moved to a more conventional approach of: [Major version].[Minor version].[Patch/release candidate] (e.g. 3.0.6) We, unfortunately, picked a time where our last minor version is the same number as our new major version. Stay tuned for more information. And as always, thank you for your patience. Kind regards, Sophia ---- Sophia K. Cheng Technical Lead Harvard Catalyst | eagle-i email: sophia_cheng at hms.harvard.edu skype: sophia.k.cheng Harvard Medical School Harvard Catalyst | The Harvard Clinical and Translational Science Center Landmark Center, Suite 504 West 401 Park Drive Boston, MA 02215 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Sophia_Cheng at hms.harvard.edu Thu Jul 17 17:23:07 2014 From: Sophia_Cheng at hms.harvard.edu (Cheng, Sophia) Date: Thu, 17 Jul 2014 17:23:07 -0400 Subject: [Eagle-i-admins] eagle-i version 3.0.6 release Message-ID: Dear eagle-i Sys Admins, We are pleased to announce the release of eagle-i version 3.0.6. It is now ready for download. We strongly encourage all admins to upgrade their installations as soon as possible. As part of this release, we have made significant changes to our ontology. To ensure that your resources can be properly displayed to users, your data needs to be migrated to the latest version. For the complete list of what this release contains, please see our release notes here: https://open.med.harvard.edu/wiki/display/eaglei/3.0.6+Release+Notes If you have any questions or comments regarding the documentation, please let us know. Kind Regards, Sophia ---- Sophia K. Cheng Technical Lead Harvard Catalyst | eagle-i email: sophia?_cheng at hms.harvard.edu skype: sophia.k.cheng web: www. eagle-I.net Harvard Medical School Harvard Catalyst | The Harvard Clinical and Translational Science Center Landmark Center, Suite 504 West 401 Park Drive Boston, MA 02215 -------------- next part -------------- An HTML attachment was scrubbed... URL: From halltodd at msu.edu Fri Jul 18 12:08:14 2014 From: halltodd at msu.edu (Todd Hall) Date: Fri, 18 Jul 2014 12:08:14 -0400 Subject: [Eagle-i-admins] patch Message-ID: <03f601cfa2a2$7b2a5fd0$717f1f70$@msu.edu> Hello, I was working with Sophia Cheng. She wanted me to run a patch on our local installation of Eagle-I before we tried upgrading. She wrote that it was released on Monday but I can't seem to find a link for it. Can you help me out? Best Regards, Todd E. Hall spartan Systems Administrator ----------------------------------------------------- Biomedical Research Informatics Core (BRIC) Clinical and Translational Sciences Institute (CTSI) Michigan State University - West Fee Hall 909 Fee Road, Room B510 - W1 East Lansing, Michigan 48824-1317 Phone: (517) 884-2906 BRIC Helpline: (517) 643-2075 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 554 bytes Desc: not available URL: From Michael_Cherry at hms.harvard.edu Fri Jul 18 17:00:29 2014 From: Michael_Cherry at hms.harvard.edu (Cherry, Michael) Date: Fri, 18 Jul 2014 17:00:29 -0400 Subject: [Eagle-i-admins] patch In-Reply-To: <03f601cfa2a2$7b2a5fd0$717f1f70$@msu.edu> References: <03f601cfa2a2$7b2a5fd0$717f1f70$@msu.edu> Message-ID: <2D9A56628D03E943A293017B10EFD25CFEC887C3FD@ITCCRMAIL01.MED.HARVARD.EDU> > I was working with Sophia Cheng.? She wanted me to run a patch > on our local installation of Eagle-I before we tried upgrading.? She > wrote that it was released on Monday but I can't seem to find a > link for it.? Can you help me out? Hello Todd, Sophia's message from Monday contained a typo - the latest publicly-available release is 3.0.4, not 3.0.6. It's available for download in the usual place, under https://open.med.harvard.edu/wiki/display/eaglei/Software+downloads Let us know if you have any other questions or issues, and apologies for the confusion. regards, - Michael Cherry Sr. Release Operations Engineer Harrvard Catalyst | Center for Biomedical Informatics Harvard Medical School From halltodd at msu.edu Fri Jul 18 17:57:29 2014 From: halltodd at msu.edu (Todd Hall) Date: Fri, 18 Jul 2014 17:57:29 -0400 Subject: [Eagle-i-admins] patch In-Reply-To: <2D9A56628D03E943A293017B10EFD25CFEC887C3FD@ITCCRMAIL01.MED.HARVARD.EDU> References: <03f601cfa2a2$7b2a5fd0$717f1f70$@msu.edu> <2D9A56628D03E943A293017B10EFD25CFEC887C3FD@ITCCRMAIL01.MED.HARVARD.EDU> Message-ID: <007701cfa2d3$458ad7c0$d0a08740$@msu.edu> Hello Michael, May I assume version 3.04 is the "patch" that Sophia was referring and should I just stop there or proceed to 3.07? Regards, Todd E. Hall Systems Administrator ----------------------------------------------------- Biomedical Research Informatics Core (BRIC) Clinical and Translational Sciences Institute (CTSI) Michigan State University - West Fee Hall 909 Fee Road, Room B510 ? W1 East Lansing, Michigan 48824-1317 Phone:?(517) 884-2906 BRIC Helpline:?(517) 643-2075 -----Original Message----- From: Cherry, Michael [mailto:Michael_Cherry at hms.harvard.edu] Sent: Friday, July 18, 2014 5:00 PM To: Todd Hall; eagle-i-admins at open.med.harvard.edu Subject: RE: [Eagle-i-admins] patch > I was working with Sophia Cheng.? She wanted me to run a patch on our > local installation of Eagle-I before we tried upgrading.? She wrote > that it was released on Monday but I can't seem to find a link for it.? > Can you help me out? Hello Todd, Sophia's message from Monday contained a typo - the latest publicly-available release is 3.0.4, not 3.0.6. It's available for download in the usual place, under https://open.med.harvard.edu/wiki/display/eaglei/Software+downloads Let us know if you have any other questions or issues, and apologies for the confusion. regards, - Michael Cherry Sr. Release Operations Engineer Harrvard Catalyst | Center for Biomedical Informatics Harvard Medical School From Michael_Cherry at hms.harvard.edu Fri Jul 18 18:12:45 2014 From: Michael_Cherry at hms.harvard.edu (Cherry, Michael) Date: Fri, 18 Jul 2014 18:12:45 -0400 Subject: [Eagle-i-admins] patch In-Reply-To: <007701cfa2d3$458ad7c0$d0a08740$@msu.edu> References: <03f601cfa2a2$7b2a5fd0$717f1f70$@msu.edu> <2D9A56628D03E943A293017B10EFD25CFEC887C3FD@ITCCRMAIL01.MED.HARVARD.EDU> <007701cfa2d3$458ad7c0$d0a08740$@msu.edu> Message-ID: <2D9A56628D03E943A293017B10EFD25CFEC887C3FE@ITCCRMAIL01.MED.HARVARD.EDU> > May I assume version 3.04 is the "patch" that Sophia > was referring and should I just stop there or proceed to 3.07? Hi Todd, Ahh, I fear we're running into some confusion caused by our recent change to our release numbering convention. I'm also jumping into this conversation midstream, so please allow me to ask two clarifying questions: 1) When you said (earlier today) that Sophia wanted you to run a patch, were you talking about the general announcement she sent to this list yesterday (Thursday the 17th)? Or was this a communication with you directly? 2) What version of eagle-i are you running right now? (You can see this in the footer of the SWEET application, or on the repository admin page) - Mike C From halltodd at msu.edu Fri Jul 18 18:38:56 2014 From: halltodd at msu.edu (halltodd at msu.edu) Date: Fri, 18 Jul 2014 18:38:56 -0400 Subject: [Eagle-i-admins] patch Message-ID: <2995soli29wnbc41gyw0b7j2.1405723136239@email.android.com> You are very wise to ask that question. Sophia and I were in private conversations. They were unrelated to her public statements on Eagle-i-admin.? Best Regards,? Todd
-------- Original message --------
From: "Cherry, Michael"
Date:07/18/2014 6:12 PM (GMT-05:00)
To: Todd Hall , eagle-i-admins at open.med.harvard.edu
Subject: RE: [Eagle-i-admins] patch
> May I assume version 3.04 is the "patch" that Sophia > was referring and should I just stop there or proceed to 3.07? Hi Todd, Ahh, I fear we're running into some confusion caused by our recent change to our release numbering convention. I'm also jumping into this conversation midstream, so please allow me to ask two clarifying questions: 1) When you said (earlier today) that Sophia wanted you to run a patch, were you talking about the general announcement she sent to this list yesterday (Thursday the 17th)? Or was this a communication with you directly? 2) What version of eagle-i are you running right now? (You can see this in the footer of the SWEET application, or on the repository admin page) - Mike C -------------- next part -------------- An HTML attachment was scrubbed... URL: From Michael_Cherry at hms.harvard.edu Fri Jul 18 19:32:07 2014 From: Michael_Cherry at hms.harvard.edu (Cherry, Michael) Date: Fri, 18 Jul 2014 19:32:07 -0400 Subject: [Eagle-i-admins] patch In-Reply-To: <2995soli29wnbc41gyw0b7j2.1405723136239@email.android.com> References: <2995soli29wnbc41gyw0b7j2.1405723136239@email.android.com> Message-ID: <2D9A56628D03E943A293017B10EFD25CFEC887C400@ITCCRMAIL01.MED.HARVARD.EDU> > ... Sophia and I were in private conversations. They were > unrelated to her public statements on Eagle-i-admin. Ah good - light is beginning to break. :-) So back to my question #2 - what version are you on right now? (That should let me figure out what you need to patch to, so I can point you to where to get it.) Also, if you want to forward me her message(s) to you (off-list please) that might get us there sooner. regards, - Mike C From jlease at hmc.psu.edu Mon Jul 21 16:06:39 2014 From: jlease at hmc.psu.edu (Lease, Joshua) Date: Mon, 21 Jul 2014 20:06:39 +0000 Subject: [Eagle-i-admins] ETL Multiple Affiliations Message-ID: Admins, I am attempting to import data via the ETL, but cannot figure out how to import an item with multiple affiliations. Separating the affiliations via a semi-colon (like most fields with multiple entries) does not work. Has anyone figured this out already? Thanks, Joshua Lease *****E-Mail Confidentiality Notice***** This message (including any attachments) contains information intended for a specific individual(s) and purpose that may be privileged, confidential or otherwise protected from disclosure pursuant to applicable law. Any inappropriate use, distribution or copying of the message is strictly prohibited and may subject you to criminal or civil penalty. If you have received this transmission in error, please reply to the sender indicating this error and delete the transmission from your system immediately. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Marc_Ciriello at hms.harvard.edu Mon Jul 21 17:14:23 2014 From: Marc_Ciriello at hms.harvard.edu (Ciriello, Marc) Date: Mon, 21 Jul 2014 17:14:23 -0400 Subject: [Eagle-i-admins] patch In-Reply-To: <2D9A56628D03E943A293017B10EFD25CFEC887C400@ITCCRMAIL01.MED.HARVARD.EDU> Message-ID: Hi All: The word "patch" might be causing some confusion, so let's set it aside and just talk versions. The goal is to get all of the nodes onto 3.0.4 Depending on what version of the software you are on, you might have a 1-step or a 2-step upgrade process for the repository only. Other applications can be upgraded in one step, from whatever version you are on, to 3.0.4. Read on, however, for some important detail. First, check to see what version of the ontology and software (application version) you are on - you can check the footer of your SWEET login page for this information if you can't find it elsewhere. If you have an ontology version OLDER than 1.8.3.1 (regardless of software version), please contact me so we can get you back up to speed offline. For the rest of you, let's look at the application version and see what steps you need to take to upgrade your repository. Nodes running? 2.0 MS 2.14 2.0 MS 2.15 2.0 MS 2.16, all originally packaged with ontology version 1.8.3.1 have a 2-step repository upgrade. They should? ?upgrade to 2.0 MS3.07 (comes packaged with ontology version 1.8.4), then? ?upgrade to 3.0.4 (comes packaged with ontology version 1.9.3) Summary: 2.0 MS 2.1X --> 2.0 MS 3.07 --> 3.0.4 Nodes running? 2.0 MS 3.07, originally packaged with ontology version 1.8.4 have a 1-step repository upgrade. They should? ?upgrade to 3.0.4 (comes packaged with ontology version 1.9.3) Summary: 2.0 MS 3.07 --> 3.0.4 Note that you need to check for configuration changes in versions you are skipping - those are not made for you automatically in the upgrade process. Remember, this is only for the REPOSITORY. All other applications can be upgraded in one step. Why (maybe) 2 steps? Data migration. The repository upgrade process also makes necessary adjustments to your data to keep it compliant with the latest ontology. Data migration happens at the time of repository upgrade and is not cumulative, so you might need to take a little more care to keep your data in good shape and ease it through 2 sequential data migrations via repository upgrade process. I hope this helps - please let us know if you encounter any problems. Marc On 7/18/14 7:32 PM, "Cherry, Michael" wrote: > >> ... Sophia and I were in private conversations. They were >> unrelated to her public statements on Eagle-i-admin. > >Ah good - light is beginning to break. :-) > >So back to my question #2 - what version are you on right now? (That >should let me figure out what you need to patch to, so I can point you to >where to get it.) > >Also, if you want to forward me her message(s) to you (off-list please) >that might get us there sooner. > >regards, >- Mike C > >_______________________________________________ >Eagle-i-admins mailing list >Eagle-i-admins at open.med.harvard.edu >https://open.med.harvard.edu/mailman/listinfo/eagle-i-admins From Marc_Ciriello at hms.harvard.edu Tue Jul 22 11:55:27 2014 From: Marc_Ciriello at hms.harvard.edu (Ciriello, Marc) Date: Tue, 22 Jul 2014 11:55:27 -0400 Subject: [Eagle-i-admins] ETL Multiple Affiliations In-Reply-To: Message-ID: Hi Joshua: I don't have a solution for your technical question, but can suggest a work-around of sorts. You could ETL the organization (correct me if these are not organization records) and add the affiliations manually in the SWEET thereafter. It might be less trouble to do that, depending on the number of records, than to troubleshoot the ETL process. If anyone else has experience with ETL and can provide a different tip or solution, please reply. Regards, Marc From: "Lease, Joshua" > Date: Mon, 21 Jul 2014 16:06:39 -0400 To: "eagle-i-admins at open.med.harvard.edu" > Subject: [Eagle-i-admins] ETL Multiple Affiliations Admins, I am attempting to import data via the ETL, but cannot figure out how to import an item with multiple affiliations. Separating the affiliations via a semi-colon (like most fields with multiple entries) does not work. Has anyone figured this out already? Thanks, Joshua Lease *****E-Mail Confidentiality Notice***** This message (including any attachments) contains information intended for a specific individual(s) and purpose that may be privileged, confidential or otherwise protected from disclosure pursuant to applicable law. Any inappropriate use, distribution or copying of the message is strictly prohibited and may subject you to criminal or civil penalty. If you have received this transmission in error, please reply to the sender indicating this error and delete the transmission from your system immediately. -------------- next part -------------- An HTML attachment was scrubbed... URL: From halltodd at msu.edu Thu Jul 24 11:51:03 2014 From: halltodd at msu.edu (Todd Hall) Date: Thu, 24 Jul 2014 11:51:03 -0400 Subject: [Eagle-i-admins] upgrade help Message-ID: <010601cfa757$12fc1f20$38f45d60$@msu.edu> I setup a test server for Eagle-I to perform the upgrade to 3.07 and then to 3.0.4. Below is what I'm getting following the prerequisite upgrade via the release notes and the upgrade instructions. Any ideas? Regards, Todd E. Hall spartan Systems Administrator ----------------------------------------------------- Biomedical Research Informatics Core (BRIC) Clinical and Translational Sciences Institute (CTSI) Michigan State University - West Fee Hall 909 Fee Road, Room B510 - W1 East Lansing, Michigan 48824-1317 Phone: (517) 884-2906 BRIC Helpline: (517) 643-2075 [root at eagle-i-test etc]# bash $REPO_HOME/etc/upgrade.sh admin ##### http://localhost:8443 ***** Checking and Upgrading Repository's Internal Graphs curl: (7) Failed to connect to ::1: Network is unreachable /internal: HTTP request failed: HTTP status=000 cmd=0 WARNING: FAILED to get list of internal graphs, continuing.. ***** Checking and Upgrading Data Model Ontology curl: (7) Failed to connect to ::1: Network is unreachable /model: HTTP request failed: HTTP status=000 cmd=0 ERROR: Failed getting data model ontology versions. ***** Checking and Upgrading Property Group Access Control Grants curl: (7) Failed to connect to ::1: Network is unreachable Failed sending HTTP /sparql request, curl status=7 OK - Property Group Access Control grants all succeeded. ***** *S*P*E*C*I*A*L* UPGRADES for 1.6MS6, 1.7MS1 and 2.0MS1 ====>>> Step 1. Updating roles. curl: (7) Failed to connect to ::1: Network is unreachable Failed sending HTTP /sparql request, curl status=7 ERROR: Step 1 got unknown result = "" FAIL - there were failures in specials, YOU MUST RESTORE THE BACKUP. rm -rf /tmp/repo-upgrade-8124 [root at eagle-i-test etc]# -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 554 bytes Desc: not available URL: From halltodd at msu.edu Thu Jul 24 11:59:17 2014 From: halltodd at msu.edu (Todd Hall) Date: Thu, 24 Jul 2014 11:59:17 -0400 Subject: [Eagle-i-admins] disregard previous email Message-ID: <011501cfa758$39239e70$ab6adb50$@msu.edu> My previous message was premature. I forgot to start Tomcat. I have a different issue but I'll investigate before I ask for help Best Regards, Todd E. Hall spartan Systems Administrator ----------------------------------------------------- Biomedical Research Informatics Core (BRIC) Clinical and Translational Sciences Institute (CTSI) Michigan State University - West Fee Hall 909 Fee Road, Room B510 - W1 East Lansing, Michigan 48824-1317 Phone: (517) 884-2906 BRIC Helpline: (517) 643-2075 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 554 bytes Desc: not available URL: From halltodd at msu.edu Fri Jul 25 10:45:51 2014 From: halltodd at msu.edu (Todd Hall) Date: Fri, 25 Jul 2014 10:45:51 -0400 Subject: [Eagle-i-admins] data migration for 2.0-MS3.0x Message-ID: <022d01cfa817$2180d840$648288c0$@msu.edu> I successfully upgraded from 2.14 to 3.07 (I don't think this is a deal breaker since MS3.04 is the official release) on a test system. When I run the data-migration.sh file, I get the following in the log and on the screen. The ontology is version 1.8.4. When I ran the upgrade.sh shell, it gave no errors or warnings [root at eagle-i-test conf]# bash /opt/eaglei/repo/etc/data-migration.sh -u admin -p xxxxxxx -r https://lcoalhost:8443 Java info: /usr/java/jdk1.7.0_17/bin/java java version "1.7.0_17" Java(TM) SE Runtime Environment (build 1.7.0_17-b02) Java HotSpot(TM) 64-Bit Server VM (build 23.7-b01, mixed mode) using classpath : /opt/eaglei/repo/etc:/opt/eaglei/repo/etc/eagle-i-datatools-datamanagement.j ar ***** There are no special procedures for this release. ***** Standard data migration procedures 2014-07-25 10:39:41,518 WARN org.eaglei.services.repository.RepositoryHttpConfig - The url for a repository can not be null. 2014-07-25 10:39:41,520 ERROR org.eaglei.datatools.datamanagement.command.CommandUtils - Bulk command did not proceed. org.eaglei.services.repository.RepositoryProviderException: The url for the repository is invalid. at org.eaglei.services.repository.RepositoryHttpConfig.(RepositoryHttpCon fig.java:106) at org.eaglei.datatools.datamanagement.TriplesCRUDService.(TriplesCRUDSer vice.java:58) at org.eaglei.datatools.datamanagement.DataManagementProvider.(DataManage mentProvider.java:79) at org.eaglei.datatools.datamanagement.command.AbstractBulkCommand.initialize(A bstractBulkCommand.java:83) at org.eaglei.datatools.datamanagement.command.AbstractBulkCommand.setupAndExec uteCommand(AbstractBulkCommand.java:178) at org.eaglei.datatools.datamanagement.command.CommandUtils.execute(CommandUtil s.java:107) at org.eaglei.datatools.datamanagement.command.ChangePredicate.main(ChangePredi cate.java:205) ===== Command did not complete. Root cause: The url for the repository is invalid. Stack trace for diagnosis: org.eaglei.services.repository.RepositoryProviderException: The url for the repository is invalid. at org.eaglei.services.repository.RepositoryHttpConfig.(RepositoryHttpCon fig.java:106) at org.eaglei.datatools.datamanagement.TriplesCRUDService.(TriplesCRUDSer vice.java:58) at org.eaglei.datatools.datamanagement.DataManagementProvider.(DataManage mentProvider.java:79) at org.eaglei.datatools.datamanagement.command.AbstractBulkCommand.initialize(A bstractBulkCommand.java:83) at org.eaglei.datatools.datamanagement.command.AbstractBulkCommand.setupAndExec uteCommand(AbstractBulkCommand.java:178) at org.eaglei.datatools.datamanagement.command.CommandUtils.execute(CommandUtil s.java:107) at org.eaglei.datatools.datamanagement.command.ChangePredicate.main(ChangePredi cate.java:205) Best Regards, Todd E. Hall spartan Systems Administrator ----------------------------------------------------- Biomedical Research Informatics Core (BRIC) Clinical and Translational Sciences Institute (CTSI) Michigan State University - West Fee Hall 909 Fee Road, Room B510 - W1 East Lansing, Michigan 48824-1317 Phone: (517) 884-2906 BRIC Helpline: (517) 643-2075 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 554 bytes Desc: not available URL: From fcoldren at mail.med.upenn.edu Fri Jul 25 13:55:51 2014 From: fcoldren at mail.med.upenn.edu (Faith Coldren) Date: Fri, 25 Jul 2014 13:55:51 -0400 Subject: [Eagle-i-admins] installing on VM Message-ID: Hello, I have set up a VM (test environment) to install the current version of eagle-i that Penn is running (2.0 MS2.14) and test the upgrade procedure. On the VM, I installed the repo (following the installation instructions) and copied in the data from our live instance of eagle-i (using the curl commands for Restoring from make-snapshot). However, I cannot seem to correctly install SWEET (following install directions ). The repo is available on my machine at https://192.168.56.107:8443 and I can access the repository administration at https://192.168.56.107:8443/repository/admin/. However, https://192.168.56.107:8443/sweet gives a HTTP status 404. What should I do to install SWEET? Thank you, Faith Faith Coldren ITMAT University of Pennsylvania 215-573-9462 -------------- next part -------------- An HTML attachment was scrubbed... URL: From fcoldren at mail.med.upenn.edu Fri Jul 25 13:25:31 2014 From: fcoldren at mail.med.upenn.edu (Faith Coldren) Date: Fri, 25 Jul 2014 13:25:31 -0400 Subject: [Eagle-i-admins] installing on VM Message-ID: Hello, I have set up a VM (test environment) to install the current version of eagle-i that Penn is running (2.0 MS2.14) and test the upgrade procedure. On the VM, I installed the repo (following the installation instructions) and copied in the data from our live instance of eagle-i (using the curl commands for Restoring from make-snapshot). However, I cannot seem to correctly install SWEET (following install directions ). The repo is available on my machine at https://192.168.56.107:8443 and I can access the repository administration at https://192.168.56.107:8443/repository/admin/. However, https://192.168.56.107:8443/sweet gives a HTTP status 404. It looks like there are a bunch of errors in the sweet.log file. I've attached this file. What should I do to install SWEET? Thank you, Faith -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: sweet.log Type: application/octet-stream Size: 144035 bytes Desc: not available URL: From David_Neiman at hms.harvard.edu Mon Jul 28 08:28:45 2014 From: David_Neiman at hms.harvard.edu (Neiman, David) Date: Mon, 28 Jul 2014 08:28:45 -0400 Subject: [Eagle-i-admins] installing on VM In-Reply-To: References: Message-ID: Faith, The sweet log file (sweet.log) indicates an obvious and fatal problem. The application cannot find your eagle-i-apps.properties file so cannot start up. This file needs to be placed in the Tomcat classpath. This is one of the directories where Tomcat has access to eagle-i files. There is an "eagle-i home" directory which should be set in the Tomcat catalina.properties file. This file can be found in your Tomcat deployment in the conf/ directory. The value in catalina.properties: org.eaglei.home= Within that value the should also be a conf/ directory which should contain your eagle-i-apps.properties file. Thanks, Dave Neiman eagle-i team On Jul 25, 2014, at 1:25 PM, Faith Coldren > wrote: Hello, I have set up a VM (test environment) to install the current version of eagle-i that Penn is running (2.0 MS2.14) and test the upgrade procedure. On the VM, I installed the repo (following the installation instructions) and copied in the data from our live instance of eagle-i (using the curl commands for Restoring from make-snapshot). However, I cannot seem to correctly install SWEET (following install directions). The repo is available on my machine at https://192.168.56.107:8443 and I can access the repository administration at https://192.168.56.107:8443/repository/admin/. However, https://192.168.56.107:8443/sweet gives a HTTP status 404. It looks like there are a bunch of errors in the sweet.log file. I've attached this file. What should I do to install SWEET? Thank you, Faith _______________________________________________ Eagle-i-admins mailing list Eagle-i-admins at open.med.harvard.edu https://open.med.harvard.edu/mailman/listinfo/eagle-i-admins -------------- next part -------------- An HTML attachment was scrubbed... URL: From jlease at hmc.psu.edu Mon Jul 28 12:22:58 2014 From: jlease at hmc.psu.edu (Lease, Joshua) Date: Mon, 28 Jul 2014 16:22:58 +0000 Subject: [Eagle-i-admins] Request this Resource Feature Message-ID: Admins, I am attempting to use the "request this resource feature" in our local institutional search. Upon populating the form with valid information and clicking send request, a popup states ?An error occurred while trying to send a message to a contact.? I can successfully send messages to the same person using the ?Send message to resource contact? feature. I was unable to find anything in the server logs related to the issue. Is there some sort of configuration option needed to use this feature? Do we need to be connected to the eagle-i Network, before we can use this feature? Is there documentation describing the functionality of this feature? Any other ideas? Thanks Again, Joshua Lease *****E-Mail Confidentiality Notice***** This message (including any attachments) contains information intended for a specific individual(s) and purpose that may be privileged, confidential or otherwise protected from disclosure pursuant to applicable law. Any inappropriate use, distribution or copying of the message is strictly prohibited and may subject you to criminal or civil penalty. If you have received this transmission in error, please reply to the sender indicating this error and delete the transmission from your system immediately. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Michael_Cherry at hms.harvard.edu Tue Jul 29 16:06:46 2014 From: Michael_Cherry at hms.harvard.edu (Cherry, Michael) Date: Tue, 29 Jul 2014 16:06:46 -0400 Subject: [Eagle-i-admins] Eagle-i Download Message-ID: <2D9A56628D03E943A293017B10EFD25CFEC887CA2D@ITCCRMAIL01.MED.HARVARD.EDU> > On 7/23/14 12:21 PM, "Yulish, Tim" wrote: > ... I am gathering requirements now ... see that Harvard uses a virtual > machine with Cent OS. Do you have a base virtual machine with Cent OS > on it that we could test out? ... I wanted to ask just in case you have > a template VM that I could download and throw up for a quick pilot. Hello Tim, (I'm replying to this publicly in case anyone else has the same question) We do not have any template VMs. At one point we were considering making a VMWare image with eagle-i pre-installed available as part of each release, but we discovered that many insititutions' IT departments are reluctant to allow foreign VMs to be spun up in their virtualization farms. As such, we concluded that the potential audience wasn't big enough to be worth the effort. If we hear of more demand for this, we might consider making one available in the future. I don't know if this would help you, but what we DO have is a public AMI available at Amazon Web Services (AWS). It's a little bit out of date (it was created a year ago and I believe is CentOS 6.3), but if this would be useful to you, its AMI name is "eaglei-install-1.0.2-20130814" (available in all 3 US regions of AWS). I hope this is in some way helpful. If you have further questions, please don't hesitate to post them to this list. regards, - Michael Cherry Sr. Release Operations Engineer Harrvard Catalyst | Center for Biomedical Informatics Harvard Medical School From Sophia_Cheng at hms.harvard.edu Thu Jul 31 18:27:43 2014 From: Sophia_Cheng at hms.harvard.edu (Cheng, Sophia) Date: Thu, 31 Jul 2014 18:27:43 -0400 Subject: [Eagle-i-admins] Request this Resource Feature Message-ID: Hi Joshua, I suspect that you may have the wrong configurations. You shouldn?t be seeing ?Request this Resource? button at all in the institutional search application. I have just audited and updated our sample configurations that should be used for a simple node installation: https://open.med.harvard.edu/svn/eagle-i-dev/apps/trunk/configuration/src/main/resources/examples/node-simple/ These should (95% sure) be all that you need to get up and running for the most common use case. Please let me know if this doesn?t help or if you have further issues. Kind Regards, Sophia ---- Sophia K. Cheng Technical Lead Harvard Catalyst | eagle-i email: sophia?_cheng at hms.harvard.edu skype: sophia.k.cheng web: www. eagle-I.net Harvard Medical School Harvard Catalyst | The Harvard Clinical and Translational Science Center Landmark Center, Suite 504 West 401 Park Drive Boston, MA 02215 From: , Joshua > Date: Monday, July 28, 2014 at 12:22 PM To: eagle-i-admins > Subject: [Eagle-i-admins] Request this Resource Feature Admins, I am attempting to use the "request this resource feature" in our local institutional search. Upon populating the form with valid information and clicking send request, a popup states ?An error occurred while trying to send a message to a contact.? I can successfully send messages to the same person using the ?Send message to resource contact? feature. I was unable to find anything in the server logs related to the issue. Is there some sort of configuration option needed to use this feature? Do we need to be connected to the eagle-i Network, before we can use this feature? Is there documentation describing the functionality of this feature? Any other ideas? Thanks Again, Joshua Lease *****E-Mail Confidentiality Notice***** This message (including any attachments) contains information intended for a specific individual(s) and purpose that may be privileged, confidential or otherwise protected from disclosure pursuant to applicable law. Any inappropriate use, distribution or copying of the message is strictly prohibited and may subject you to criminal or civil penalty. If you have received this transmission in error, please reply to the sender indicating this error and delete the transmission from your system immediately. -------------- next part -------------- An HTML attachment was scrubbed... URL: