3.1.1 Release Notes

Introduction

A new version of the eagle-i applications is now available for download. The release notes documented on this page apply specifically to version 3.1.1. Please see the Upgrade Checklist for information on how to perform an upgrade.

How to use this document

Notes for this release are broken up into four categories: New Features, Improvements and/or Bug-fixes, Known Issues, Prerequisites for Upgrading & Deprecated Properties.  Within each category, notes are further divided into the application that is affected. Known issues will be cumulative of known issues that have not yet been resolved. If you are unsure what applications are applicable for your installation, please refer to this page.

Most institutions will be interested primarily in the General (affects across multiple applications) and SWEET sections within each category.

Institutions that have installed the optional SPARQLer application will be interested in the SPARQLer section within each category.

Institutions that have installed the optional Institutional Search will be interested as well in items that have been tagged INSTITUTION in the Search Application section within each category.

For those who have chosen to administer their own network of nodes, the sections of interest are General, items that have been tagged CENTRAL in Search Application  and Network Administration (Central Search Only) sections within each category.

New Features, Improvements and/or Bug-fixes

General

• NEW FEATURE Advanced query for induced pluripotent stem cells (iPSC), developed as part of the collaboration with NYSCF.

  • New search application which takes advantage of the semantic nature of our data and exploits the linkages for a more powerful querying experience, made available through NYSCF in this release, 3.1.1.
  • This application executes a SPARQL query directly against the sparqler (aka. public SPARQL endpoint) rather than searching against a solr index.

• NEW FEATURE Ontology version 1.10.2 includes new in depth modeling to describe cell lines, developed as part of the collaboration with NYSCF.  Detailed release notes about the ontology can be found here: 1.10.2 Ontology Release Notes.

• NEW FEATURE Support for integration with Profiles RNS. The base URL for profiles can be specified with the property eaglei.datatools.profilesBase.

• IMPROVEMENT Jena library upgraded from 2.6.4 to 2.10..0

• IMPROVEMENT Error pages from the repository have been styled and the messaging improved. An example page is an unresolvable eagle-i resource, https://global.eagle-i.net/i/resource-not-exist.

Search application

Applies to both central and institutional search, unless otherwise specified.

• NEW FEATURE Indexing for searches and auto-suggest now support more complex data relationships. For example, in the case of induced pluripotent stem cells (iPS cells), the ability to have an iPS cell returned as a result when the result is not directly in the iPS instance.
  • Searching for Diabetes
  • Get a match on a Human Subject (i.e. Ima Hooman) that has a diagnosis of Diabetes
  • Get a match on a Biospecimen who has the source human subject (i.e. Ima Hooman's biospecimen)
  • Get a match on an iPS Cell Line created from the biospecimen (i.e. iPS cell line from Ima Hooman's biospecimen)
• NEW FEATURE CENTRAL Hyperlink for the eagle-i logo in the banner is now configurable by adding a new property to the eagle-i-apps.properties file: eaglei.ui.search.logoLink

SWEET application

• IMPROVEMENT Ontology autosuggest and resource drop-down in forms are now wider.

SPARQLer

Also known as the public SPARQL endpoint.

• IMPROVEMENT Changed background color of workbench to avoid confusion with private SPARQL endpoint.
• IMPROVEMENT Improved robustness in synchronization with main repository..
  • Synchronization no longer dependent on eagle-i-sparqler.last-sync-date.properties file.

• IMPROVEMENT Refactoring resulted in a slimmer footprint of memory.

Network Administration

Available in Central Search only.

• BUG With Release 3.1.1, the central search index now tolerates accidentally entering multiple nodes with the same URI. In releases prior to 3.1.1, this was allowed and then subsequent indexing did not perform as expected.
  • • In Release 3.1.1, if a duplicate a URI is used in the node registry admin UI, the action will be disallowed
    • In Release 3.1.1, if a duplicate occurs in the node-registry.xml file, only the first institution will be added and a message will be logged.

Repository

• IMPROVEMENT In Release 3.1.1, a resource's metadata is included in the data harvested into the sparqler.

Known Issues

Current Release

None known at this time.

3.0.4 Release

General

• Incomplete records may be displayed in central search if no upgrade is done. Extensive work has gone into our ontology for this release to bring eagle-i to ISF compliance, in addition to enhancing the modeling for induced pluripotent stem cell types.  If existing data is not migrated to the new ontology, the central search application may not be able to interpret/recognize obsolete ontological properties and will not display them.

Network Administration

Available in central search only.

• We have seen an issue with how strictly different versions of tomcat parses local-node.xml file.  One version insisted on case sensitivity for the tag, and one version was fine. For example, tomcat version 7.0.42 does not have same parsing as version 7.0.41.  In other words, using <node url="https://some.institution.edu"> in the local-node.xml file was acceptable in one version, while the same exact line caused a parsing error (note the lower case 'url' instead of the documented 'URL').

2.0 MS 3.07 Release

General

• When using drop down boxes in Chrome, it is not possible to jump to an entry by typing the first few letters. (No workaround)

SWEET

• It is possible to save records with unnamed embedded instances. Doing so results in losing any information entered for the embedded instances. (No workaround)
• If more than one organization record has the same exact name, only one of them will be displayed in the "Work With My Organizations" dropdown. (No workaround)

Search application

Applies to both central and institutional search, unless otherwise specified.

• Entering text with square brackets, [ & ], in the search box will execute a blank search, rather than searching for the text. (No workaround)
• "Cite This Resource" - The keyboard shortcut for copying does not work in Firefox or Chrome. Workaround:
  1. Use the Copy from the browser's menu bar or from the popup while right clicking.

Network Administration

Available in central search only.

• In the network administration UI (at <myNode>/central/admin), there is no direct way to remove a node (institution) from a group. Workaround:
  1. Use central/admin to edit the node:
  2. Take the node out of service (a check-box near the bottom of the form)
  3. Save
  4. Edit the node again, removing the value from the field "Belongs to group"
  5. Put the node back into service (the same check-box)
  6. Save
• In the network administration UI (at <myNode>/central/admin), there is no direct way to change the group a node belongs to. Workaround:
  1. Use central/admin to edit the node:
  2. Take the node out of service (a check-box near the bottom of the form)
  3. Save
  4. Edit the node again
  5. Enter a new name in the field "Belongs to group"
  6. Put the node back into service (the same checkbox)
  7. Save

Prerequisites for Upgrading

SPARQLer

Also known as the public SPARQL endpoint.

• Remove eagle-i-sparqler.last-sync-date.properties file from [eagle-i home]/conf directory.

Deprecated Properties

eagle-i-apps.properties

• eaglei.feedback.method
• eaglei.datatools.uses.globals
  • Use eaglei.uses.globals instead.
• eaglei.datatools.central.coexist.filename