From dtolmie at fhcrc.org  Thu Jul 25 12:37:50 2013
From: dtolmie at fhcrc.org (Tolmie, David A)
Date: Thu, 25 Jul 2013 16:37:50 +0000
Subject: [Eagle-i-admins] 2.0-MS2.14 or 2.0-MS2.15?
Message-ID: <CE16A26D.79FC%dtolmie@fhcrc.org>

Hi folks,

After I ran into issues with my first go of upgrading from 2.0-MS2.13 to 2.0-MS2.14, I rolled back to my pre-upgrade checkpoint.  I'm now going to make another go at upgrading, but I see a version 2.0-MS2.15 was released last week (7/18) and it's what's running on Central right now.

Does the data migration script handle skipping a version (i.e. Jumping from 2.0-MS2.13 to 2.0-MS2.15) cleanly?  Or, do I need to apply 2.0-MS2.14 before I can move to 2.0-MS2.15?

Thanks,

-Dave

________________________________
David Tolmie
Systems Librarian
Arnold Library | Fred Hutchinson Cancer Research Center | Seattle, WA
dtolmie at fhcrc.org<mailto:dtolmie at fhcrc.org>  |  tel 206.667.6852 |  fax 206.667.4737
[Description: Description: Description: Description: AL-Logo-color]<http://library.fhcrc.org/>

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From dtolmie at fhcrc.org  Thu Jul 25 13:21:16 2013
From: dtolmie at fhcrc.org (Tolmie, David A)
Date: Thu, 25 Jul 2013 17:21:16 +0000
Subject: [Eagle-i-admins] 2.0-MS2.14 or 2.0-MS2.15?
In-Reply-To: <3180_1374770281_51F15468_3180_8554_1_CE16A26D.79FC%dtolmie@fhcrc.org>
Message-ID: <CE16ABC9.7A0B%dtolmie@fhcrc.org>

Actually? On further inspection, I realized we're running 2.0-MS1.11.  So, is it safe to jump from 2.0-MS1.11 to 2.0-MS1.15?

If not, I can always treat it as a fresh install.  Since we populate our eagle-I node via the Drupal integration module, it's not terribly painful to repush all our content.  Though, it does mean our URIs would all change.

-d


From: <Tolmie>, David Tolmie <dtolmie at fhcrc.org<mailto:dtolmie at fhcrc.org>>
Date: Thursday, July 25, 2013 9:37 AM
To: "eagle-i-admins at open.med.harvard.edu<mailto:eagle-i-admins at open.med.harvard.edu>" <eagle-i-admins at open.med.harvard.edu<mailto:eagle-i-admins at open.med.harvard.edu>>
Subject: [Eagle-i-admins] 2.0-MS2.14 or 2.0-MS2.15?

Hi folks,

After I ran into issues with my first go of upgrading from 2.0-MS2.13 to 2.0-MS2.14, I rolled back to my pre-upgrade checkpoint.  I'm now going to make another go at upgrading, but I see a version 2.0-MS2.15 was released last week (7/18) and it's what's running on Central right now.

Does the data migration script handle skipping a version (i.e. Jumping from 2.0-MS2.13 to 2.0-MS2.15) cleanly?  Or, do I need to apply 2.0-MS2.14 before I can move to 2.0-MS2.15?

Thanks,

-Dave

________________________________
David Tolmie
Systems Librarian
Arnold Library | Fred Hutchinson Cancer Research Center | Seattle, WA
dtolmie at fhcrc.org<mailto:dtolmie at fhcrc.org>  |  tel 206.667.6852 |  fax 206.667.4737
[Description: Description: Description: Description: AL-Logo-color]<http://library.fhcrc.org/>

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From Daniela_Bourges at hms.harvard.edu  Thu Jul 25 13:23:32 2013
From: Daniela_Bourges at hms.harvard.edu (Bourges, Daniela)
Date: Thu, 25 Jul 2013 13:23:32 -0400
Subject: [Eagle-i-admins] 2.0-MS2.14 or 2.0-MS2.15?
In-Reply-To: <CE16A26D.79FC%dtolmie@fhcrc.org>
Message-ID: <CE16D6B1.151C7%daniela_bourges@hms.harvard.edu>

Hi Dave,
In general data migration does not handle skipping a version ? you need to get aggregate migration tables (which we usually prepare when people ask).

However, 2.15 is only a minor patch to 2.14 to correct a bug in central search. So in this particular case it doesn't matter ? feel free to go from 2.13 to 2.15

Cheers
Daniela



Dr. Daniela Bourges-Waldegg
Lead Architect, Harvard Catalyst
Harvard Medical School

Daniela_Bourges at hms.harvard.edu<mailto:Daniela_Bourges at hms.harvard.edu>
skype: dbourgesw
phone: 617-432-3126


From: <Tolmie>, David A <dtolmie at fhcrc.org<mailto:dtolmie at fhcrc.org>>
Date: Thursday, July 25, 2013 12:37
To: "eagle-i-admins at open.med.harvard.edu<mailto:eagle-i-admins at open.med.harvard.edu>" <eagle-i-admins at open.med.harvard.edu<mailto:eagle-i-admins at open.med.harvard.edu>>
Subject: [Eagle-i-admins] 2.0-MS2.14 or 2.0-MS2.15?

Hi folks,

After I ran into issues with my first go of upgrading from 2.0-MS2.13 to 2.0-MS2.14, I rolled back to my pre-upgrade checkpoint.  I'm now going to make another go at upgrading, but I see a version 2.0-MS2.15 was released last week (7/18) and it's what's running on Central right now.

Does the data migration script handle skipping a version (i.e. Jumping from 2.0-MS2.13 to 2.0-MS2.15) cleanly?  Or, do I need to apply 2.0-MS2.14 before I can move to 2.0-MS2.15?

Thanks,

-Dave

________________________________
David Tolmie
Systems Librarian
Arnold Library | Fred Hutchinson Cancer Research Center | Seattle, WA
dtolmie at fhcrc.org<mailto:dtolmie at fhcrc.org>  |  tel 206.667.6852 |  fax 206.667.4737
[cid:201775A1-6BE7-41A8-BD6A-E4F3A151CA19]<http://library.fhcrc.org/>

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From dtolmie at fhcrc.org  Thu Jul 25 13:36:17 2013
From: dtolmie at fhcrc.org (Tolmie, David A)
Date: Thu, 25 Jul 2013 17:36:17 +0000
Subject: [Eagle-i-admins] 2.0-MS2.14 or 2.0-MS2.15?
In-Reply-To: <CE16D6B1.151C7%daniela_bourges@hms.harvard.edu>
Message-ID: <CE16AF19.7A17%dtolmie@fhcrc.org>

Thanks, Daniella.  So?  It turns out we're running 1.11, not 2.13.  So, I need to upgrade to 2.04, then 2.13, then 2.15.

Do I need to upgrade the repository at each step, or can I leapfrog the repository to 2.15, and just run the data migration from each incremental step?

If I were to treat this as a new install, with the URIs for all of our content changing, old ones vanishing, new ones appearing, would that break things on the Central side of things?

I'm just trying to wrap my brain around what I can and can't safely do.

Thanks!!

-Dave


From: <Bourges>, "Bourges, Daniela" <Daniela_Bourges at hms.harvard.edu<mailto:Daniela_Bourges at hms.harvard.edu>>
Date: Thursday, July 25, 2013 10:23 AM
To: David Tolmie <dtolmie at fhcrc.org<mailto:dtolmie at fhcrc.org>>, "eagle-i-admins at open.med.harvard.edu<mailto:eagle-i-admins at open.med.harvard.edu>" <eagle-i-admins at open.med.harvard.edu<mailto:eagle-i-admins at open.med.harvard.edu>>
Subject: Re: [Eagle-i-admins] 2.0-MS2.14 or 2.0-MS2.15?

Hi Dave,
In general data migration does not handle skipping a version ? you need to get aggregate migration tables (which we usually prepare when people ask).

However, 2.15 is only a minor patch to 2.14 to correct a bug in central search. So in this particular case it doesn't matter ? feel free to go from 2.13 to 2.15

Cheers
Daniela



Dr. Daniela Bourges-Waldegg
Lead Architect, Harvard Catalyst
Harvard Medical School

Daniela_Bourges at hms.harvard.edu<mailto:Daniela_Bourges at hms.harvard.edu>
skype: dbourgesw
phone: 617-432-3126


From: <Tolmie>, David A <dtolmie at fhcrc.org<mailto:dtolmie at fhcrc.org>>
Date: Thursday, July 25, 2013 12:37
To: "eagle-i-admins at open.med.harvard.edu<mailto:eagle-i-admins at open.med.harvard.edu>" <eagle-i-admins at open.med.harvard.edu<mailto:eagle-i-admins at open.med.harvard.edu>>
Subject: [Eagle-i-admins] 2.0-MS2.14 or 2.0-MS2.15?

Hi folks,

After I ran into issues with my first go of upgrading from 2.0-MS2.13 to 2.0-MS2.14, I rolled back to my pre-upgrade checkpoint.  I'm now going to make another go at upgrading, but I see a version 2.0-MS2.15 was released last week (7/18) and it's what's running on Central right now.

Does the data migration script handle skipping a version (i.e. Jumping from 2.0-MS2.13 to 2.0-MS2.15) cleanly?  Or, do I need to apply 2.0-MS2.14 before I can move to 2.0-MS2.15?

Thanks,

-Dave

________________________________
David Tolmie
Systems Librarian
Arnold Library | Fred Hutchinson Cancer Research Center | Seattle, WA
dtolmie at fhcrc.org<mailto:dtolmie at fhcrc.org>  |  tel 206.667.6852 |  fax 206.667.4737
[Description: Description: Description: Description: AL-Logo-color]<http://library.fhcrc.org/>

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From Daniela_Bourges at hms.harvard.edu  Thu Jul 25 14:10:17 2013
From: Daniela_Bourges at hms.harvard.edu (Bourges, Daniela)
Date: Thu, 25 Jul 2013 14:10:17 -0400
Subject: [Eagle-i-admins] 2.0-MS2.14 or 2.0-MS2.15?
In-Reply-To: <CE16AF19.7A17%dtolmie@fhcrc.org>
Message-ID: <CE16E00A.15213%daniela_bourges@hms.harvard.edu>

Dave,
It's better not to change URIs once they have been published ? it's good semantic web ettiquette ;-)

You can go straight (with all your components, i.e. SWEET and repository) to 2.0-MS2.15, and then run the data migration script with cumulative tables ? the tables are tied to the ontology version, so first you need to know what your origin ontology is and what the target ontology is. I can tell you that the target ontology is 1.8.3. The footer of your SWEET indicates you currently have ontology Version 1.7.7 :
Application Version: 2.0-MS1.11 14885 2013-04-08 09:55:33
 /
Ontology Version: 1.7.7 14849 2013-04-03 16:41:44

In the following directory you will find a few cumulative tables:

https://open.med.harvard.edu/svn/eagle-i-dev/apps/trunk/dev-resources/ontology-migration-tables/

You can use the 1.6.1-1.8.3 zip (I doesn't matter that the origin ontology is older, just that your origin ontology is contained in that range).
The directory contains a README that sort of explains what to do (if you get stuck, other people in this list who have done this successfully might be able to help)

Cheers
Daniela



From: <Tolmie>, David A <dtolmie at fhcrc.org<mailto:dtolmie at fhcrc.org>>
Date: Thursday, July 25, 2013 13:36
To: Daniela Bourges Waldegg <daniela_bourges at hms.harvard.edu<mailto:daniela_bourges at hms.harvard.edu>>, "eagle-i-admins at open.med.harvard.edu<mailto:eagle-i-admins at open.med.harvard.edu>" <eagle-i-admins at open.med.harvard.edu<mailto:eagle-i-admins at open.med.harvard.edu>>
Subject: Re: [Eagle-i-admins] 2.0-MS2.14 or 2.0-MS2.15?

Thanks, Daniella.  So?  It turns out we're running 1.11, not 2.13.  So, I need to upgrade to 2.04, then 2.13, then 2.15.

Do I need to upgrade the repository at each step, or can I leapfrog the repository to 2.15, and just run the data migration from each incremental step?

If I were to treat this as a new install, with the URIs for all of our content changing, old ones vanishing, new ones appearing, would that break things on the Central side of things?

I'm just trying to wrap my brain around what I can and can't safely do.

Thanks!!

-Dave


From: <Bourges>, "Bourges, Daniela" <Daniela_Bourges at hms.harvard.edu<mailto:Daniela_Bourges at hms.harvard.edu>>
Date: Thursday, July 25, 2013 10:23 AM
To: David Tolmie <dtolmie at fhcrc.org<mailto:dtolmie at fhcrc.org>>, "eagle-i-admins at open.med.harvard.edu<mailto:eagle-i-admins at open.med.harvard.edu>" <eagle-i-admins at open.med.harvard.edu<mailto:eagle-i-admins at open.med.harvard.edu>>
Subject: Re: [Eagle-i-admins] 2.0-MS2.14 or 2.0-MS2.15?

Hi Dave,
In general data migration does not handle skipping a version ? you need to get aggregate migration tables (which we usually prepare when people ask).

However, 2.15 is only a minor patch to 2.14 to correct a bug in central search. So in this particular case it doesn't matter ? feel free to go from 2.13 to 2.15

Cheers
Daniela



Dr. Daniela Bourges-Waldegg
Lead Architect, Harvard Catalyst
Harvard Medical School

Daniela_Bourges at hms.harvard.edu<mailto:Daniela_Bourges at hms.harvard.edu>
skype: dbourgesw
phone: 617-432-3126


From: <Tolmie>, David A <dtolmie at fhcrc.org<mailto:dtolmie at fhcrc.org>>
Date: Thursday, July 25, 2013 12:37
To: "eagle-i-admins at open.med.harvard.edu<mailto:eagle-i-admins at open.med.harvard.edu>" <eagle-i-admins at open.med.harvard.edu<mailto:eagle-i-admins at open.med.harvard.edu>>
Subject: [Eagle-i-admins] 2.0-MS2.14 or 2.0-MS2.15?

Hi folks,

After I ran into issues with my first go of upgrading from 2.0-MS2.13 to 2.0-MS2.14, I rolled back to my pre-upgrade checkpoint.  I'm now going to make another go at upgrading, but I see a version 2.0-MS2.15 was released last week (7/18) and it's what's running on Central right now.

Does the data migration script handle skipping a version (i.e. Jumping from 2.0-MS2.13 to 2.0-MS2.15) cleanly?  Or, do I need to apply 2.0-MS2.14 before I can move to 2.0-MS2.15?

Thanks,

-Dave

________________________________
David Tolmie
Systems Librarian
Arnold Library | Fred Hutchinson Cancer Research Center | Seattle, WA
dtolmie at fhcrc.org<mailto:dtolmie at fhcrc.org>  |  tel 206.667.6852 |  fax 206.667.4737
[cid:201775A1-6BE7-41A8-BD6A-E4F3A151CA19]<http://library.fhcrc.org/>

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From Sophia_Cheng at hms.harvard.edu  Tue Jul 23 19:51:33 2013
From: Sophia_Cheng at hms.harvard.edu (Cheng, Sophia)
Date: Tue, 23 Jul 2013 19:51:33 -0400
Subject: [Eagle-i-admins] New process and data migration issues &
 clarification of properties [2.0-MS2.14]
Message-ID: <692B855F-D4C0-4297-9EDB-6D7A9F89A8C7@hms.harvard.edu>

Dear wonderful early adopters,

We have realized with this release that we have reached a tipping point with the number of external eagle-i system administrators and our ability to respond to each of you in an efficient manner.  Particularly, we have seen with this release that several people have run into similar issues.  To be more efficient, we would like to begin using a mailing list to handle system administration questions, e.g. stale documentation on our part regarding data migration.  The entire eagle-i software development team will also be subscribed to this email, in addition to Daniela, Marc and myself.  We hope that in this way, we can respond to any issues in a more timely matter. We truly appreciate all of your patience and want to be able to work with you in the most efficient manner for everyone.

Also, please note that in addition to general system administration questions, we will be using this mailing list to communicate other important information for early adopters, such as upcoming releases, patches, etc.

To this end, going forward, we would like to request that all system administration questions be directed to the mailing list: eagle-i-admins at open.med.harvard.edu<mailto:eagle-i-admins at open.med.harvard.edu>.  For the sake of consistency, I have also copied the list with this email to maintain a record. You can subscribe to the list here: https://open.med.harvard.edu/mailman/listinfo/eagle-i-admins.

Now, regarding some of the issues that have been encountered:
(1) Some of you have reported having issues running the data-migration.sh for the latest release, 2.0-MS2.14.  This issue manifests with notification of incorrect/missing parameters during the execution of the script, but the script does not fail.  The output looks similar to the attached file.  I have been unable to reproduce the error using the files that were mentioned in the initial email:
Datamangement Toolkit -  http://infra.search.eagle-i.net:8081/nexus/content/repositories/releases/org/eagle-i/eagle-i-datatools-datamanagement/
Repository -  http://infra.search.eagle-i.net:8081/nexus/content/repositories/releases/org/eagle-i/eagle-i-repository-dist/

Not everyone has run into this problem, so I'm wondering if I could ask those of you who have had problems to remove your existing eagle-i-datatools-datamanagement.jar, re-download the jar and try the script again.

(2) Another issue that has been reported has been due to misconfigured property files.  Going forward, the definitive example for properties for any release (2.0-MS2.13 and future) can be found here: http://infra.search.eagle-i.net:8081/nexus/content/repositories/releases/org/eagle-i/eagle-i-configuration/.  For this release (2.0-MS2.14), you may find the examples, after unzipping the file, in this path: [..]/installer/opt/eaglei/. The examples have reasonable default values where possible. Properties that require your institution specific information can be found with in double braces, e.g. {{ some_value }}.  Notable changes with this release for the properties files are:

- Configuration.properties for the properties
+-- The logo can now also be specified using a url, e.g. http://www.wizard.of.oz/rainbow.jpg
+-- Two (2) new required properties:
+==== eaglei.repository.searchBar.javascript.url - Base URL path to location of stand-alone javascript for creating the search bar. Javascript is expected to be in a directory named ?standalone? at the location of this property.
+==== eaglei.repository.centralSearch.url -  Full URL path to application where searches from the search bar will be performed.

- eagle-i-apps.properties
+-- Two (2) new required properties:
+==== eaglei.repository.searchBar.javascript.url - Base URL path to location of stand-alone javascript for creating the search bar. Javascript is expected to be in a directory named ?standalone? at the location of this property.
+==== eaglei.repository.centralSearch.url -  Full URL path to application where searches from the search bar will be performed.

(3) With this release, we have moved the configuration of the logging out of the .war and into the conf folder.  You will find in the sample configuration folder mentioned above two new files, sweet.log4j.properties and institution.log4j.properties.  If you would like to increase the level of logging to your log files, you may edit these files and then restart your tomcat for the applications to pick up the new settings.

(4) There is a known bug in the current release regarding how urls are specified in the property file.  If the property takes a url, you must explicit define it in the file with http or https, depending on whether or not the end point uses SSL. In the case of the urls pointing to www.eagle-I.net<http://www.eagle-I.net> or search.eagle-I.net<http://search.eagle-I.net>, please be sure to use https.

We strongly encourage for everyone's benefit to sign up for this mailing list (https://open.med.harvard.edu/mailman/listinfo/eagle-i-admins) and to direct future questions (including replies to this email) to eagle-i-admins at open.med.harvard.edu<mailto:eagle-i-admins at open.med.harvard.edu>.  Thank you for your patience.

Sincerely,
Sophia

Sophia K. Cheng
Software Technical Lead
eagle-i @ Harvard University
Vanderbilt Hall, 019
107 Avenue Louis Pasteur
Boston MA 02115
Skype: sophia.k.cheng
Web: www.eagle-i.net<http://www.eagle-i.net>

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