InterMine 1.3.4

This patch contains a fix for #446

The Interaction Widget download only captured the first 50 rows instead of the full result set.

InterMine 1.3.3

This patch contains a fix for #584

InterMine 1.3.2

Added the ability to generate configuration for JBrowse. This means a JBrowse instance can be set up to run off an InterMine back-end with very little effort. See http://intermine.readthedocs.org/en/latest/web-services/how-do-i/#how-do-i-set-up-jbrowse-to-work-with-intermine

#607 Add JBrowse auto-configuration

InterMine 1.3.1

InterMine 1.3.1 includes several important bug fixes and lots and lots of documentation. There are no model or major changes so you should be able to pull in the updates without any issues - so we highly recommend you upgrade immediately.

• Major security issue fixed!
• Keyword search handles "quoted strings" correctly
• Race condition caused by large userprofile database fixed
• Some data fixes to UniProt, Panther and others

And please please be sure to take a look at Alex's beautiful web services documentation!

See below for the complete list of fixes included in this release.

#172 - Error when middle click on 'Show Results'
#370 - Add HTTP api docs for the bio web services
#383 - Warning messages keep popping up when navigating between lists
#407 - Favicons for mines - flymine, modmine, intermine
#446 - Interaction Widget download only capturing 50 rows
#456 - we should serve subfeatures in our jbrowse output.
#463 - Add InterMine Query Tool
#473 - MouseMine - synonyms not being indexed correctly
#503 - Add janitor thread to id resolution servlet
#515 - UniProt keywords: multi-line text loses whitespace
#524 - list enrichment web service xml output
#526 - web service documentation
#528 - Keyword search iodocs - add facet and 100 limit
#529 - Add path formatter to keyword search facets, as per @hkmoon
#530 - unmatched DIV in dataCategories.jsp
#535 - keyword search with quotes
#536 - uniprot features location
#537 - pop-up info box on mouse-over in results table..
#539 - web service (perl): "XML is not well formatted" error if field names have underscore [_]
#540 - list-widgets normalise by length does not work anymore
#543 - Add List DELETE to web.xml
#545 - Error on home page related to lists
#549 - Panther - update to allow for new codes
#550 - Webapp failing regularly
#555 - Exception when running query using Java client library
#560 - Update links on docs
#570 - Keyword search - select all checkbox doesn't work
#573 - Breadcrumbs don't make sense

InterMine 1.3

We're happy to announce the latest version of InterMine - 1.3. In this release, we've added a bunch of new tools, redesigned some of the webapp and fixed a bunch of bugs.

• The list upload has been reworked and made more user friendly with some new functionality.
• Pathways Tool - we've updated the pathways tool (docs coming soon)
• JBrowse - it's now possible to deploy JBrowse against your InterMine instance without any configuration

See below for the complete list.

#7 - Keyword search - organism facet should be on parent class
#64 - Jumpy display: new table controls on report pages
#66 - Autocomplete displays underneath autocomplete suggested by browser
#70 - Result Table popups extend beyond visible area
#151 - Use "list" instead of "bag".
#155 - beta - missing error msg "Your query would take too long"
#157 - UTF characters in imjs
#158 - im-tables css has rules for svg elements that are too broad
#163 - Column headers not displayed
#165 - Autocomplete broken in "Add new filter" dialog
#166 - Sort order drag-n-drop bug.
#184 - Error messages on results tables when user clicks before page loads.
#194 - Webapp: Oops! - Server Error
#197 - Results Table Gene Link open in a new window
#207 - Save button not working following Get XML code
#214 - Uploading lists - type issue
#215 - Query results: fixed width columns hide data
#218 - Export collection attributes to GFF/FASTA
#223 - UniProt Parser Suggestion
#224 - Results tables not appearing on IE 8
#228 - Query too long to run warning
#239 - Update the JS code generator
#285 - Export is failing when removing columns
#314 - Add "getting started" tutorial for webapp config
#355 - [ WormMine beta release ] Enable hiding specific fields from querybuilder
#381 - Templates on home page are owned by the superuser only
#382 - LOOKUP for protein ignores organism name
#383 - Warning messages keep popping up when navigating between lists
#392 - ConcurrentModificationException when adding to a list.
#399 - YeastMine - external link icon is wrong
#424 - Removing particular columns from templates results in Oops!
#431 - Show templates in summary section of report page
#438 - GFF3 Download fails on non sequence features - should be disabled
#442 - Download dialogue - suggestions
#444 - Query results - need dropdowns when adding filters
#445 - Code generation - don't use ID. never ever!
#449 - Quick search results only retrieving first 100 rows
#450 - Report page - results tables are being added to the query history
#451 - Autocomplete not scrolling all the way
#453 - ID Resolution WS update
#454 - Update sequence feature displayer
#461 - 500 error code response with empty query constraints.
#469 - Homologene - correct identifiers
#471 - Dead link to Reactome inference details on Reports Page
#472 - OrthoDB - add option to use protein ID field
#479 - move new list widgets to InterMine
#483 - $ not exported on window
#494 - List upload - download summary requires Blobs
#496 - InitialiserPlugin should start the upgrade procedure for the super users lists
#497 - bagName not populating when upgrading a list, results in NullPointerException
#500 - Code generation needs platform specific line endings
#507 - Make sure perl client is up to speed with current webservicery
#509 - Add data set to publication
#510 - "Download" window UI is malformed when invoked inside Report Displayer
#511 - doubleclicking an option on QueryBuilder type selector not worky under IE9

InterMine 1.2.2

This is a minor release containing a few small bug fixes.

#283 - Don't load MeSH terms by default when using PubMed data converter
#372 - Add UberonTerm
#373 - Fix query cancellation when using wild card with LOOKUP
#390 - A tiny gap in the header of FlyMine report pages
#405 - Fix browser detection not working with jQuery >= 1.9.1
#409 - Remove waiting page when running queries
#416 - Fixed screen black out when selecting 250 rows in query results