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 4.0.0. 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 (effects across multiple applications), SWEET and SPARQLer sections 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

  • IMPROVEMENT Major ontology change

    • Migrated from using MeSH terms to Disease Ontology
    • Significant ISF refactoring

  • IMPROVEMENT First pass made to clean up logging to help debugging

Search application

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

  • NEW FEATURE After executing an iPS Cell Search, there is now a summary of the search criteria above the results table.
  • BUG All bookmarked iPS Cell Searches will now redraw the form with the values selected

  • BUG Entering a double quote and/or multiple backslashes in the search bar will not throw an obscure error

  • BUG INSTITUTION The correct contact form is now used and use of the contact form should work

SWEET application

  • BUG SWEET no longer tries to start a node registry service. This was only a problem for institutions that happen to have a node-registry.xml file available for SWEET to access.

Ontology Browser

  • IMPROVEMENT Synonyms are now separated by a semi-colon for clarity

SPARQLer

Also known as the public SPARQL endpoint.

  • IMPROVEMENT A default view for queries is now selected, published-resources.

Repository

  • NEW FEATURE Passwords are now stored encrypted

    • After upgrading the repository application, passwords will automatically be encrypted the first time the new repository application starts.
    • The repository does not need to be re-installed.
    • Password encryption should be transparent to users
    • NOTE: the prepare-install.sh script that is packaged with the repository distribution is not compatible with prior versions of the user database.
  • IMPROVEMENT A default view for queries is now selected, published-resources.

Known Issues

The following are known issues that may be addressed in releases after 4.0.0. If there is a suitable workaround for a given issue, it will be listed.

Current Release

The following are known issues for institutions who do not upgrade:

  • Clicking on a disease name on a resource instance will result in an error
  • Searching for MeSH term names will not bring up results for those terms unless they appear in a field other than related disease
  • MeSH terms will not show up in autosuggest unless the same name exists in the new disease ontology
  • Filtering for diseases on the iPS Cell Search will not return cell lines that are using the old disease ontology

Prior Releases

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

Repository

The user database will no longer be compatible with older versions of the repository (pre 4.0.0).

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