RELEASE_NOTES

/*
 * Copyright (C) 2002-2022 FlyMine
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  See the LICENSE file for more
 * information or http://www.gnu.org/copyleft/lesser.html.
 *
 */
InterMine 5.1.0 (August 2022)

#2025 - FAIR: PURLs come from config file
#2183 - Improve external links using Identifiers.org
#2287 - Export query result in RDF format
#2365 - Setting a property to postprocess in project.xml does not work
#2366 - Generating intermine R2RML mapping
#2378 - Update SolrKeywordSearchHandler (thanks @sammyjava)
#2379 - RDF representation for single entity
#2381 - Add a new webservice to allow BG to RDF representation
#2382 - Add reccomended properties to Gene and Protein Bioschemas profiles
#2389 - Improve term assigned to the intermine entity
#2390 - Apply ontology terms to the attributes too
#2391 - Missing term applied to the additions file after merging

InterMine 5.0.8 (June 2022)

- Improved user input checks

InterMine 5.0.7 (April 2022)

#2419 - Updated the WS /templates to return dataTypes
#2425 - Fix XSS issue
#2427 - Create a WS returning all the templates
#2428 - Superuser can run whatever template
#2027 - Added a new generic TSV data source
      - Completly removed dependencies on jcenter
      - Added pombe organims to the taxon id to be ingnored by the idresolver
      - Copyright updated
	  - Fixed typo in the go evidence code

InterMine 5.0.6 (Dicember 2021)

#2414 - Upgraded psi lib version (thanks @asherpasha)
#2416 - Log4j upgraded to 2.17.1 (thanks @asherpasha)

InterMine 5.0.5 (Dicember 2021)

#2411 - Log4j-1x compatibility upgrade (thanks @asherpasha)

InterMine 5.0.4 (Dicember 2021)

#2324 - Remove dependency from EBI maven nexus repo
#2377 - Updated GFF3Record (thanks @sammyjava)
#2396 - Biogrid extension
#2392 - Public name can be taken by deleted account
#2397 - Implement a new WS to summarise templates
#2398 - Implement a new WS to precompute templates
#2399 - Update the GET /templates WS to show which templates user can make change
#2400 - Update the PUT /bluegenes-properties WS to use body
#2402 - WebProperties WS returns blugenes properties too
#2404 - Update CI to use Python 3.7

InterMine 5.0.3 (June 2021)

#2375 - Update interpro_keys.properties
#2376 - Update interpro-go_keys.properties
#2384 - Enrichment widget not working when changing background population

InterMine 5.0.2 (May 2021)

#2335 - BioGrid data change causing loader to throw Exception
#2344 - Why feature.setAttribute("scoreType", record.getSource()) in  GFF3Converter.java?
#2352 - Enrichment web service fails if using ids and background population 
#2356 - Graph and table windgets WSs do not work when passing IDs
#2358 - Check the type in the bag upload form
#2367 - preparation release 5.0.1

InterMine 5.0.1 (May 2021) - Broken
Due to a sync issue, the bio-webapp 5.0.1 artifact has been built wrapping intermine-webapp 5.0.0 instead of 5.0.1 and as a consequence, it doesn't contains some of the following fixes.
Please use 5.0.2 instead.
#2344 - Why feature.setAttribute("scoreType", record.getSource()) in  GFF3Converter.java?
#2352 - Enrichment web service fails if using ids and background population 
#2356 - Graph and table windgets WSs do not work when passing IDs
#2358 - Check the type in the bag upload form
#2367 - preparation release 5.0.1

InterMine 5.0.0 (April 2021)

#1720 - Need Google OAuth2 authentication web service end points
#1835 - When trying to create a list with the same name as another list via api, give informative error
#2173 - Password reset / I forgot my password service
#2177 - Include bgpath: prefixed tags in responses to lists webservice
#2201 - Include creation/last modified date in saved queries webservice
#2263 - Fixed UniprotFastaLoaderTaskTest see #2259
#2269 - Add externalLink webservice
#2280 - Webservice for sending feedback
#2288 - 200 OK response when deleting unauthorized list (instead of 400)
#2290 - Add appropriate error message when renaming a list to something existing
#2295 - Webservice as key-value store for Bluegenes properties
#2315 - Upgrade List: new webservice for bluegenes
#2325 - Disallow adding tags for unauthorized lists
#2327 - Frictionless
#2328 - DataRecord (bioscehmas profile) deprecated 
#2337 - Support passing project.credits in web-properties ws
#2345 - Remove dependency on jcenter

InterMine 4.3.1 (March 2021)

#2311 - Continuos Integration with githubactions
#2317 - Update build.gradle
#2331 - Remove invalid draw options, fixing geneExpressionAtlas displayers
#2338 - Update copyright
#2339 - Migrate from Travis to Actions

InterMine 4.3.0 (December 2020)

#2308 - Enabling bioschemas markup with JAVA 11 throws an error
#2274 - Obo: added a new generic obo file source that is configured in project.xml so that it can be used for any ontology (thanks @sammyjava)
#2276 - Removed gretty plugin (from testmine) which does't work with gradle 4.9
#2279 - NullPointerException in report page caused by generating permanent url link (Share button)
#2281 - Npe report page
#2282 - Google Charts API broke various things, including the humanmine expression viewers. 
#2296 - Update google auth and userinfo endopoints
#2305 - Fix format=jsonobjects queries for simple root classes (thanks @sammyjava)
      - The so.obo file has been removed from the bio-source-so to avoid duplication 

InterMine 4.2.0 (June 2020)

#1650 - Need way to upgrade anonymous sessions via web service
#1969 - FAIR: add profile Gene and Protein markup to the report page
#2099 - Need webservice endpoint that identifies if superuser
#2142 - Create a new logout service
#2144 - Update the /user endpoint to allow to change password
#2148 - Add PUT method to the /lists webservice to update the description
#2149 - Update the /users endpoint to attach to the user just created the lists created anonymously
#2155 - FAIR: adopt DataRecord type in the report page
#2199 - Invalid JSON response to POST /user/queries
#2205 - Update change password webservice to require current password
#2207 - Add clearLocation() to removeFeature() (thanks @sammyjava)
#2215 - Fix organism short name formation (thanks @ahmedihafez)
#2236 - Remove BioEntity.ontologyAnnotations because redundant (thanks @sammyjava)
#2237 - Editing  a Date filter on the results table shows Service failed message
#2239 - BAR ThaleMine - 6: Fixed a minor bug in reports page long fields (thanks @asherpasha)
#2240 - BAR ThaleMine - 7: go-annotation loader (thanks @asherpasha)
#2242 - /service/templates is missing optional constraint if format=json
#2246 - Issues related to fields with type Date
#2252 - Added a new bio source to load ISA files in json format
#2253 - src.data.dir.includes and src.data.dir in project.xml not always work as expected
#2255 - Added BioChemEntity (via configuration) markup
#2259 - UniProtFastaLoader doesn't extract the organism name composed by more than 2 words
#2264 - Add licence to the OboConverter

InterMine 4.1.3 (March 2020)

#2208 Delete a template -> it's still displayed on the Templates tab
#2203 Public template creation broken
#2204 vcf bio source does not work
#2190 Fix invalid response to /service/web-properties
#2212 In the report page, links to HumanMine/FlyMine are empty 

 
InterMine 4.1.2 (January 2020)

#2045 - DataSet URLs do not appear in tables; do show in report heading
#2053 - LOOP query in webapp does not work!
#2107 - Remove "upload to GenomeSpace" export
#2112 - Remove im.js, imtables.js, imtables-dep.js from intermine-webapp
#2120 - The operation was a success, but the patient died: creating solr index fails but gradlew reports success.
#2127 - Update to Java11
#2129 - Catch runtime exception in BagManager.getBags
#2145 - Complex Displayer fixed
#2151 - ThaleMine Updates to psi BioSource
#2152 - ThaleMine Updates to BioGrid
#2154 - Update json-ld home page
#2158 - Use info stored in the registry to set provider/support in the home page markup
#2159 - Travis fails - could not GET jami-interactionviewer-json
#2160 - Update chebiWS-client (psi-complexes bio-source)
#2161 - Licence dataset display null 
#2164 - Add gff source to the bio/source multi gradle project
#2172 - WebservicePythonCodeGenerator updated according to Python's code styling PEP8
#2178 - Improve permanet URI configuration
#2184 - Minor bug fix
Update copyright notice with 2002-2020

InterMine 4.1.1 (October 2019)

#2128 - ThaleMine: Gradle 4.9 / Java 11 migration.
#2135 - data change in ncbi-gff 
#2136 - Add code of conduct
#2137 - ThaleMine issues

InterMine 4.1.0 (September 2019)

#1770 - Default query config should be in json
#1819 - Galaxy plugin - InterMine
#1915 - Gradle 4.1 is to old for Java 11
#1947 - YeastMine: gradle migration
#2015 - FASTA query result: CDS translation option
#2016 - Fasta query results: extra view parameters not showing up in header correctly
#2040 - Can we remove flymine dependencies from core IM?
#2044 - ONE OF contraint not working in template form
#2051 - Seems that css path is wrong in keywordSearchResults.jsp
#2052 - apply fix to TemplateAction to im 4.0?
#2054 - Docs: Add instructions on how to make a Mine.
#2055 - Put galaxy URL in global properties
#2056 - Project script: update to handle release param correctly
#2070 - NCBI gene data
#2073 - GO error - obsolete term
#2074 - Complexes - duplicate protein accessions
#2102 - add elixir-login image to the login page
#2103 - Fix google-login button in the login page
#2108 - Move ELIXIR oauth2 configuration to global.web.properties file

InterMine 4.0.1 (July 2019)

#2060 - Restore Strains to core data model

InterMine 4.0.0 (May 2019)

#1935 - Decorate the model with ontology terms (where possible)
#1939 - Store data licences for integrated sources
#1940 - Provide data licences for integrated sources
#1941 - GO Annotation - data set is where we get the data file
#1968 - FAIR: add schemas.org (both schemas can be used)
#1969 - FAIR: add profile Gene and Protein markup to the report page
#1978 - Check if lists created overlap with other public lists (and user's lists)
#2030 - Null pointer exception when user doesn't have any lists. 

InterMine 3.1.2 (April 2019)

#704 - Keyword search - fail gracefully if there is no search index
#1497 - Docs: links in search results drop .html extension, only on index pages.
#1766 - Web services: Add tags to templates
#1773 - Gradle: when installing bio project, intermine-bio-test.properties SHOULD NOT be mandatory
#1909 - Gradle: logs need sorting out
#1952 - GAF 1.0 - remove this code
#1965 - bio and bio/sources: java.lang.ClassCastException on org.apache.xerces.parsers
#1980 - Gradle: model isn't merging correctly on postprocess on large InterMine items XML file
#1984 - Set converter.class in the right place
#1988 - Fix protein atlas displayer in humanmine
#2001 - NCBI web services = error with NULL values
#2002 - modify SolrIndexHandler to support newer Solr versions (thanks @arunans23!!)
#2007 - Gretty plugin - remove from bio-webapp?
#2008 - Error using CHEBI web services
#2009 - Publication abstract is longer than postgres index
#2013 - Remove Phenotype, it's not in the core model and has conflicting key (thanks @sammyjava)
#2017 - Gretty plugin - remove from mine-webapp
#2020 - Fix the protein atlas expression viewer
#2036 - ObjectStoreSummary does not handle ignored fields consistently. (thanks @JoeCarlson )

InterMine 3.1.1 (Feb 2019)

#1726 - Add system templates end point for converter templates.
#1732 - Web service bug in /templates?format=json
#1770 - Default query config should be in json
#1786 - GFF3: add header to record
#1796 - GFF3SequenceHandler - add docs and pass in feature object
#1811 - webservice xml queries failing with greater and less than operators
#1828 - DNaseI_hypersensitive_site (SO:0000685) misspelled
#1833 - Data types in NCBI GFF that are not in the sequence ontology
#1847 - Error parsing DOES NOT CONTAIN constraint
#1887 - OMIM: fix link outs
#1902 - Gradle: need /themes directory to merge correctly
#1906 - Enrichment widget: update link to GO (humanmine and flymine)
#1914 - InterPro DTD version
#1956 - Autocomplete fails to build: missing content stream
#1977 - publication with null title 
#1982 - Need upgrade path for biojava
#1983 - Fix log library dependency conflict
#1989 - Spelling fix on genomicRegionSearchOptionsBase.jsp 
#1992 - Remove Yahoo login link
#1994 - HumanMine - gene summaries from NCBI
#1995 - Panther - Entry only has protein accession and the taxon id in place of the gene identifier.
#1996 - OMIM - failed on bad line
#1999 - HPO errors - can't handle "created_by" metadata
#2000 - Add UniProt xref file to data download script
#2006 - Updated gretty.plugin URL

InterMine 3.1 (late November 2018)

#1596 - InterMine Core Data model - Annotation, assembly and variety
#1948 - PSI Complexes - remove bad key
#1950 - Remove ecnumbers String from Protein, it's an object now.

InterMine 3.0.0 (November 2018)

#517 - Improve Lucene search
#562 - Keyword search - speed up initial search
#871 - Replace bobo with Lucene facets
#1632 - Add search facets webservice

InterMine 2.1.1 (late October 2018)

#1916 - Adds versions to postprocesses

InterMine 2.1 (October 2018)

#1583 - Update InterMIne code generation to be Python 3 compatible
#1803 - Discontiguous CDS sequences and lengths not set properly
#1844 - FASTA query web service: times out when extensions are used
#1881 - Regions bug: trying to leave extended region field blank results in error message that takes over the page
#1892 - Update publications: POST instead of GET
#1895 - Some SO terms were not updated in 2.0 release

InterMine 2.0 (Summer 2018)

#39 - Keyword search autocomplete enabled
#83 - BioJava - update library
#160 - Create ECO data parser and add descriptions to GO evidence codes
#397 - Spin out the java webservice client from the server code
#412 - Process xrefs correctly in OBO files, e.g. alt_ids
#464 - Remove dependency on tomcat
#482 - Make filter edit / delete icons more clear
#600 - Write up tutorial on how to write a Java source
#611 - Upgrade ant jar
#612 - Maven - try using Gradle instead of Ant for dependency management
#767 - Move sub-projects to their own repo
#831 - Organism config - needs updating
#836 - OrthDB - fail if invalid config
#861 - postprocessing 'do-sources' with many sources fails
#917 - JBrowse - update config
#940 - Need public registry for friendly mines.
#941 - im-ant-tasks JAR can't be created
#971 - PSI Interactions - taxon ID is strain 
#983 - Layout.jsp - remove old variable
#1030 - Data sets should have more details - descriptions and pubs
#1093 - Add to list: does not see there other relevant lists when picking items from the table
#1099 - UniprotKB now uses evidence codes from the Evidence Ontology (ECO)
#1109 - Bioseg error messages in postgres on webapp deploy
#1168 - PSI-Complexes -- allow for more data types 
#1177 - Genome browser
#1215 - Web services: make template popularity available
#1278 - Checkstyle 6 
#1312 - Interactions widget not displaying correctly in live humanMine
#1327 - Query web services should accept JSON queries.
#1343 - Java 8 - Duplicate default methods 
#1351 - Postprocess for datasource with multiple entries in the project file
#1358 - Protein molecular weight - change to be a float instead of integer
#1405 - Replace iharder and apache.commons Base64 impls with Base64 in Java 8 SDK
#1450 - org.json jar file is old and lacks some JSON spec methods
#1477 - Update PathQueryHandler deleting code related to the node tag
#1483 - Migrate to gradle
#1510 - Split post-processors out the way data sources are
#1525 - Add SyntenicRegion and SyntenyBlock to core data model
#1531 - Remove legacy code for upgrading 
#1602 - FASTA source - make sure biojava.jar is in main/lib
#1604 - Footer broken
#1608 - Java client - requires genomic model
#1620 - Ontology Annotations: Annotate all the things!
#1655 - JSON and XML queries are different
#1656 - Loop constraints are implemented incorrectly in JSON
#1657 - Remove legacy registry code.
#1669 - Add list id to the result of query/tolist service
#1674 - Remove legacy flymine/doc
#1675 - We are using sets and lists interchangably
#1676 - End points have an attribute for queries called "XML". We accept JSON queries so this attribute name is becoming increasingly inaccurate.
#1677 - Delete HintManager
#1684 - Clients - update to use registry
#1689 - Move GO annotation evidence to Ontology annotation
#1694 - UniProt - loading retracted papers
#1697 - Update JSON jar
#1707 - Genomic Intervals as GFF3 - needs strandSpecific parameter
#1719 - NCBI web services - new API rules (3 requests per second)
#1723 - Intermine Registry: please set Access-Control-Allow-Origin
#1734 - Update Chebi JAR
#1738 - Update so.obo to latest version
#1747 - Asking for non-expiring API token should generate one if doesn't exist
#1751 - Registry - add organisation and URL
#1754 - OMIM: not loading a gene-disease relationship
#1759 - BioJava - update JAR 
#1761 - HumanMine: External Links broken
#1765 - Update URLGenerator.java to handle HTTPS sites 
#1774 - GO: data load now takes 3 hours instead of 10 minutes
#1777 - Region search: update API to include strandSpecific
#1790 - Need old integrate/resources/organism_config.properties functionality
#1792 - Galaxy: export failed - update URL
#1798 - Model change: move HPO annotations to be annotable
#1804 - Panther: bad data
#1812 - Update Postgres and Hikari driver
#1821 - Change taxon ID to be a String
#1831 - GO annotation - new evidence code HDA
#1838 - Update version of Postgres JDBC driver?
#1839 - Galaxy: fix bug that required user to retype the Galaxy URL
#1850 - HumanMine: Some genes don't have Ensembl identifier

InterMine 1.8.5 (2017 August)

#1661 - Anonymous session tokens are not authenticating

InterMine 1.8.4 (2017 August)

#961 - Need way of referring to lists stably
#1494 - LOOKUP and List upload use BagQueryRunner. Need different "match" behaviour
#1555 - Add cytological data to humanMine
#1600 - Need web service endpoint to generate permanent API tokens
#1606 - Portal - go to disambiguation page if there are issues
#1607 - Add GTEx data
#1611 - remove obsolete constraint operators
#1613 - OBO files have terms without names
#1614 - HumanMine: missing exons
#1621 - HumanMine: add cytolocation
#1626 - Remove intermine/scripts
#1631 - Add defaults web service for each mine
#1636 - Only look in public schema when counting rows in a table
#1648 - Templates export in JSON format causes deadlock.
#1652 - Add user ID to web service output

InterMine 1.8.3 (2017 July 12)

#1623 Add branding parameters for external apps. 

InterMine 1.8.2 (2017 July)

#205 - add 4 numbers used to calculate enrichment to web services
#1603 - revert logo changes on footer (temporarily)

InterMine 1.8.1 (2017 June)

Update copyright notice

InterMine 1.8 (2017 June)

#288 - List actions (set operations) greyed out but active
#439 - Sharing lists -- need better message when owner hasn't upgraded lists
#702 - Add "Show Tags" option to Lists page
#739 - filter encoding property in Database.java
#786 - Query with outer join does not validate
#789 - services.json should contain mine appropriate defaults
#802 - Region search file upload doesn't handle blank lines
#812 - Issues with Date data type
#820 - Documentation on date formats (Items XML)
#910 - Usernames containing upper-case letters created via the web service can never log in.
#942 - Allow superclass lists in template list constraints
#964 - quicksearch service should report total hits
#966 - add db parameter for schema
#1174 - Can't share lists with google logins
#1181 - Transfer sequences - not processing transcript sequences correctly
#1212 - Web service: list union - resulting type is NULL
#1269 - GFF parser - ignoring parents leaves children orphans
#1296 - List converter with subtype constraint fails
#1309 - Provide a template's popularity score in /service/templates
#1325 - GFF parser - gff config should be source-specific
#1328 - Cannot change LOOKUP filter in results table
#1382 - Templates page - my mine - add summarise all link
#1455 - Don't add ORDER BY clause to count(*) queries
#1458 - Queries page only shows the last saved query
#1471 - Drop LOOKUP constraint if value is *
#1486 - Allow the name attribute to be missing 
#1495 - Fix a caching bug in strand specific region search
#1505 - InterMine webservices are not compatible with Python3
#1507 - Unescaped pipes in the trail break tomcat 8
#1515 - GFF3 export - not adding columns
#1516 - support for DOES_NOT_CONTAIN in query xml 
#1523 - Userprofile backup script - more improvements
#1526 - Post build updating with SQL triggers
#1551 - handle the case where isoforms have multiple accessions. 
#1557 - Correctly save lists after logging in
#1569 - Update FASTA text on region search
#1572 - We've lost the trail

InterMine 1.7.3 (2017 May)

#582 - Remove partially implemented GAF export
#1052 - FlyMine: Stop loading Golden Path Fragments
#1086 - FlyMine: handle NCBI transcripts correctly
#1286 - Enable making a list from mRNA lists
#1410 - Make display names for collections and references available as JSON model
#1418 - Add UniProt accession as Xrefs.
#1444 - FlyMine: Don't load protein locations.
#1493 - Update URL for OMIM download script
#1496 - Load OMIM disease for Human Phenotypes
#1502 - Gene length correction missing from GO widget
#1532 - update-publications job fails if using UTF8 encoding
#1536 - Add link to ToxyGates
#1537 - MGI alleles file had an extra tab causing havoc. Always check for valid pubmed id.
#1538 - Add Signor data source - signalling data
#1539 - Tomcat 9 errors
#1545 - OBO Source loader to handle multiple crossReferences

InterMine 1.7.2 (2017 April)

#1533 - Update code to adapt to google API changes

InterMine 1.7.1 (2017 January)

#1482 - Error when creating a list and accessing via the web service via tablerows method.

InterMine 1.7 (2016 Xmas)

#1480 - Check interaction count on client not server side. Works for proteins and genes now.
#1462 - Removed old style path queries
#1469 - Error when creating a list and accessing via the web service
#1473 - Strand specific search off by default
#1475 - Update postgresql JDBC driver to fix error with postgres 9.6 

InterMine 1.6.9 (2016 November)

#1422 - Constrain widget results. 
#1425 - Region Search: allow strand-specific search
#1431 - GFF source: ScoreType is required to parse the file but not required in GFF3 specs 
#1441 - Region Search: Fix integer truncation bug for Extended Regions
#1443 - HTTPS - web services using hardcoded HTTP 
#1451 - The copy of a list by an un-logged user, saves the new list into db with the same name
#1456 - HPO source: doesn't capture publication if there is more than one

InterMine 1.6.8 (2016 September 20)

Fix for Region search [595e786]
Fix for FlyAtlas expression widget [#1141]
Fix for mail update [9211ab7]

InterMine 1.6.7 (2016 September 7)

#421 - Results table forgetting toggle state
#593 - cdn.intermine.org in generated JavaScript
#845 - Some tests fail occasionally
#1204 - Cytoscape: clean up
#1226 - Userprofile backup script - improvements
#1364 - Web service: for enrichment, gene length correction requires list
#1369 - Deleting templates doesn't really delete them
#1370 - Issues with https
#1372 - Human data: add ClinVar data parser
#1375 - Mail: add replyto param
#1376 - HTTPS - still not working as expected
#1378 - OMIM script fails
#1381 - InterPro - added a new database
#1383 - Bootstrap fails
#1384 - NCBI moving to HTTPS
#1385 - HPO - too many diseases
#1386 - Disease - add data set
#1387 - Disease - add Orphanet source
#1388 - Docker: tomcat uses a different port
#1396 - template.do XSS vulnerability
#1398 - Travis tests failing
#1402 - Refactor Mail
#1404 - Lists endpoint returns bad lists (Lists that need to be upgraded)


InterMine 1.6.6 (2016 13 May, Friday the 13th)

#1361 - Correct Panther homologue labels
#1322 - HumanMine keyword search is returning atomic coordinates of protein structures
#1318 - Inconsistent session expiration
#1301 - Enabled/disabled styling on template forms
#1297 - Template generates bad web service URL
#1293 - GO parser: missing additional publication IDs
#1292 - IntAct: resolve all Ensembl identifier not just the ones in NCBI file
#1284 - App gene report page kills HumanMine
#1283 - Region search: not returning SNPs
#1282 - stepZ - working with results sets
#1277 - Complex - interacting region has two locations
#1276 - Footer - make like YeastMine
#1274 - Publication Enrichment - download fails on NULL pubmed ID
#1270 - GFF parser - allow for multiple locations
#1267 - GFF parser - removeFeature() leaves synonyms
#1260 - Web services: add an intermine version web service
#1259 - NCBI GFF - create parser
#1258 - Enrichment widget: accept identifiers instead of just the list
#1252 - ID resolver - update human IDs file.
#1251 - NCBI parser - for synonyms
#1250 - Add synonyms to Ensembl XML generating script
#1249 - HGNC parser
#1248 - List upload: error
#1245 - Hardcoded CDN values
#1239 - errorMessages tile missing?
#1225 - Cytoscape: less mean error message
#1202 - UniProt: comments not capturing disease
#1201 - Results tables - external link outs don't work on objects without organism, e.g. Pubs
#1200 - HumanMine: load synonyms
#1191 - PubMed: remove obsolete classes
#1189 - HumanMine - add illumina body map.
#1180 - Postgres warning - connection closed
#1160 - 'Contact Us' link not working
#1104 - PFam data loader
#1082 - PDB - use restful API instead of manual download
#1073 - cannot change default file name in imtable export 
#1046 - XenMine - list creation error
#1015 - Panther and Homologene - Mouse genes are not being merged correctly
#986 - JS tests failing 
#984 - oAuth2 error text needs updating
#930 - Blog for InterMine / human InterMine
#925 - CHEBI data source
#918 - GOAnnotation has an empty publications collection
#764 - cytoscape display export: error #3769
#763 - cytoscape diagram not right in yeastmine
#717 - Export broken in cytoscape viewer
#624 - wrapping of java errors, contact us form
#601 - Keyword search - organism facet not being returned for some genes
#586 - FlyMine - make the childFeatures correct
#566 - Keyword search - don't index IDs
#500 - Code generation needs platform specific line endings
#449 - Quick search results only retrieving first 100 rows
#426 - Web service URL for templates constrained to a list doesn't work.
#414 - Reword error message
#206 - GO enrichment widget - accessed via webservice
#148 - Add more orthologue data sets to mastermine
#78 - Save changes to query results as new query



InterMine 1.6.5

#1255 - Restore missing template counts
#1253 - Web service: error running template to list
#1244 - MyMine: export tags fails
#1240 - Keyword search: remove link to entire index
#1232 - uniprot-fasta loading problem
#1222 - Web service: /list/tags doesn't work
#1202 - UniProt: comments not capturing disease
#1194 - Add human data to KEGG unit test
#1188 - Properly generate sequences based on type
#1080 - BioGRID config doesn't work correctly for symbols
#929 - PDB hardcoded for FlyMine
#565 - OMIM - add unit test

InterMine 1.6.4

#1221 - Template queries in my mine: can't export 

InterMine 1.6.3

#1236 - Keyword Search: don't show entire index if no keyword provided. 
#1179 - PDB failing 
#1190 - Atlas express source 

InterMine 1.6.2

#1228 - Fix tutorial, remove interpro
#1184 - Keyword search: first search takes you to home page
#1168 - PSI-Complexes -- allow for more data types
#1154 - Web services: tags for templates

InterMine 1.6.1

#1216 - Make region.start and end integers instead of strings
#1209 - Fix Panther for Drosophila
#1205 - Cytoscape fix for protein report page

InterMine 1.6 (Halloween 2015)

#1187 - GO enrichment widget -- gene length normalisation error
#1164 - GO enrichment widget -- background change error
#1163 - QueryBuilder: error querying for NULL relationships
#1153 - FlyMine: create-utr-references is failing
#1150 - IntegrationWriterDataTrackingImplTest failing tests, sometimes.
#1147 - Web service: speed up requests
#1142 - List Analysis - doesn't show the list contents for SNVs
#1136 - Problem with SNV list analysis page on upload
#1135 - FlyMine: postprocess failed on UTR references
#1125 - UniProt: add publications to genes too
#1124 - CORS issues
#1121 - Query Builder: cannot query for disease names because of trailing whitespace
#1116 - Make protein isoforms collection
#1114 - YeastMine: serial number not being reset
#1108 - Point Mutations: new index doesn't seem to handle features of size = 1;
#1105 - HumanMine - add UniProt fasta
#1103 - FlyMine: bad locations being created when there are no gaps between features
#1102 - Result table preview with many collections overflows off screen.
#1095 - FlyMine: Queries using overlaps are failing
#1094 - Code generation not updating in result tables in Safari 8
#1079 - Panther not parsing homologues parameter correctly
#1072 - Counts missing from templates on report / list pages
#1071 - Complexes - fails for human
#1067 - More queries link in summary area on http://www.flymine.org/ fails
#1065 - FlyMine: flyfish failed on dull pointer exception
#1063 - FASTA: error loading locations
#1058 - Esyn: change to use pipe delimiter
#1053 - Simple objects fail to show in results tables with outer joins
#1051 - Cytoscape network viewer - upgrade
#1049 - Add a nicer error if EsyN network to large to load.
#1035 - VCF data parser for InterMine
#1032 - CORS issue - www.humanmine.org and humanmine.org
#1024 - HumanMine config - remove bad paths
#1019 - Duplicate BioGrid interaction data
#992 - InterMineObjectFetcher.run() does not report a configuration error
#968 - Reduce tracker table size
#962 - Interaction region not a Bioentity causing problems in located features collection
#919 - Unhelpful error when no database connections available
#912 - Better error message for running out of connections
#896 - keyword search task aborts silently if it encounters an error
#834 - Fresh install on beta has issues with java 8
#804 - Add complex interaction data to InterMine
#745 - Tomcat 8
#652 - Add class keys for sequence feature
#420 - Save XML button gives "Bad URL" in Safari
#210 - VCF data parser to load data into Intermine. 
#169 - Load locations of protein domains

InterMine 1.5.6

#1075 -  Fix mising template row counts. 

InterMine 1.5.5

Minor fixes, plus new esyN displayer.

#1027 - Outer joins break the results table
#1020 - Manage columns labels gone
#1017 - Panther - didn't load yeast orthologues
#1000 - GeneLenghtCorrectionCoefficient misspelled
#996 - Inheritance in webconfig-model.xml is inconsistant
#988 - Download script failed on a few sources
#986 - JS tests failing
#980 - FlyMine: genes not being merged correctly
#978 - template with lookup failing if selecting the organism
#967 - Java client code gen errors
#957 - Homologues need to merge


InterMine 1.5.4

#1021 - View on widgets opens a blank window
#1013 - OBO converter - fails on creating synonyms. 
#967 - Java client code gen errors
#948 - Error during ant build-db on bio/test-all/dbmodel
#931 - Logo for human InterMine
#866 - Panther - rat genes
#865 - Delete mystery properties
#846 - InterPro - description text is too long for index
#824 - Duplicate human genes in data file
#722 - Table cell previews display too many fields
#591 - Links to FlyMine contain release number
#152 - Use ontology for data sources

InterMine 1.5.3

#1022 - Widget download fix

InterMine 1.5.2

#996 - Inheritance in webconfig-model.xml is inconsistant
#976 - Portal doesn't correctly process homologues
#963 - Download link for Java client is broken
#958 - improve error message when creating list from set operation
#957 - Homologues need to merge
#955 - UniProt fails to parse multiple Ensembl genes 
#937 - Travis isn't checking bio packages.
#851 - Adding numerical constraint in results filter does not accept minus values

InterMine 1.5.1

#978 - template with lookup failing if selecting the organism
#950 - Escape list description
#943 - results table no longer supports removing a filter
#935 - Query results - popups don't work after paging
#800 - Angle bracket issue in column summary dialog
#799 - Allow editing logic expression
#796 - Support one/none of operator
#795 - Support option lists in 'add filter' dialog
#794 - Allow subtype constraints in results table dialogs
#779 - Export correct strand on FASTA output with extension
#778 - Manage Columns needs to allow addition of multiple columns 
#753 - Query results - onhover the cell embiggens
#744 - expand/collapse-all sub-tables does not work in 1.6.x
#679 - Tomcat reports a memory leak on stopping a webapp
#641 - Results table - Boolean column not filterable if it contains NULLs
#628 - Results tables - column summary disappears on second click
#521 - results tables default code option
#436 - Query results - add link to query builder
#420 - Save XML button gives "Bad URL" in Safari
#374 - Result table download modifications
#311 - Filter dialogue - list of fields overlaps cancel button
#200 - Safari bug - mouseovers on results tables not working correctly
#167 - Need a 'Creating list..' warning when creating large lists from results tables.
#141 - Column headers for download

InterMine 1.5

#854 - Google is shutting down OpenID 

InterMine 1.4.2

#938 - Add HumanMine to list of mines in global properties.
#927 - Reactome - assigning too many pathways
#913 - Biogrid throws a NullPointerException when organism (Genus,Species) is unknown
#901 - OBO file contains different ontologies
#869 - ERROR: function bioseg_create(integer, integer) does not exist
#706 - Transfer sequences shouldn't query for SNPs
#187 - Format decimal places better

InterMine 1.4.1

#922 - List upload: exception thrown when it can't find default organism

InterMine 1.4 (Xmas 2014)

#848 - Report page: templates expanded by default
#841 - List upload fails in metabolicMine
#837 - keyword search results: now limited to 100 items
#832 - Build failing on wrong classes
#830 - Throw exception with helpful error message on finding ontology term without a name
#829 - BioPAX file name change
#827 - Hikari docs
#811 - "No simple name for class" error
#809 - BioGRID: append MGI prefix
#800 - Angle bracket issue in column summary dialog
#786 - Query with outer join does not validate
#782 - Entrez gene resolver changed MGI ID format, ID resolver failing
#781 - Publications: Process consortiums as authors correctly.
#777 - List conversion - config ignored, all fields displayed
#772 - Friendly mines repeating
#765 - list upload: cannot create a list of authors, for example
#752 - Change model to be SequenceFeature.homologue instead of Gene.homologue
#742 - FlyMine: Panther human homologues didn't merge
#728 - GenomicRegionSequence web service missing
#727 - Webapp - Users can't login or create lists
#721 - Allow adding of collections to top summary section of report
#720 - Collections don't appear in summary section when tagged
#718 - Use Postgres built-in ranges as an alternative to BioSeg
#716 - Biopax data download - script broken
#714 - PrecomputedTableManager fails with SimpleObjects
#712 - Prevent precomputed tables being generated unneccesarily
#696 - Add identifier to widget download
#686 - Portal - add optional organism constraint
#681 - Error with Java 8
#676 - Duplicate queries being run with LOOKUP constraints and wildcards
#664 - auto-generated python code from List analysis page when logged in
#653 - Error precomputing objectstore queries containing COUNT(*)
#648 - Write parser for GVF files
#635 - List Analysis -> any table/GO widget -> View -> 'Create list'
#632 - Adding X basepairs as extension when downloading FASTA throws an exception
#631 - Remove modmine from core code
#626 - Results tables - Integer values appear in results table but not in summary popup
#625 - choosing either ruby or python in the API tag logs an error
#618 - Selenium - automated browser tests
#617 - URL for docs is wrong in generated code
#614 - Report page - if bad ID don't throw exception
#604 - Move model out of OS package
#603 - Keyword search - memory not freed when removing webapp
#584 - Generated JSON omitting optional constraints
#580 - make sure users don't need our CDN
#575 - Export to galaxy fails
#574 - Galaxy export failing
#570 - Keyword search - select all checkbox doesn't work
#568 - Precompute fails with outer joins
#567 - Update to new file format - FlyBase expression
#558 - Update connection pool library
#538 - icons on results not working in firefox / IE 11
#529 - Label decoration of faceItem.value in keywordSearchResults.jsp
#516 - JMOL displayer not working
#517 - Improve Lucene search
#504 - results tables: Item check boxes not updated correctly
#470 - OAuth2 authentication
#465 - Use equals instead of LIKE when user has selected EQUALS
#452 - LOOKUP query with wildcard is slow
#415 - Too many segments in a range query kills the webapp
#273 - Some Permalinks are only temporary
#54 - Query for empty collections / references

1.3.10

#740 - dataCategories.jsp missing tag library includes

1.3.9

#756 - Fix GFF3 export in region search.

1.3.8

#692 - Parse the UniProt config correctly.

1.3.7

#665 - Fix for python code generator. Now produces code for logged in users which is actually correct.

1.3.6

#593 - If you have a local CDN, this will make sure your CDN is correct in generated JavaScript code.

1.3.5

#633 - GFF3Converter can skip (exclude) a defined list of GFF3 terms. Thanks to @vivekkrish!

1.3.4

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

1.3.3

#584 - Generated JSON omitting optional constraints

1.3.2

#607 - Added the ability to generate configuration for JBrowse

1.3.1

#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

1.3 (Xmas 2013)

#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
#272 - new Pathway Tool
#285 - Export is failing when removing columns
#314 - Add "getting started" tutorial for webapp config
#355 - 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
#400 - Better UI for list upload resolve identifiers step (+ #489, #494, #497, #505)
#424 - Removing particular columns from templates results in Oops!
#431 - Show templates in summary section of report page
#432 - AnnotationExtension should be in evidence
#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

1.2.2 (7 August 2013)

#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

1.2.1 (fixes for C. elegans meeting)

#359 - Allow Inline Refs & Colls on Report pages to be displayed using Results Tables JS library
#113 - NULL URLs not handled
#138 - Scroll to top after list creation on List Analysis page
#192 - Links to external sites should always open in a new window enhancement please-test
#213 - Do not get actual count of matches on identifier resolution page
#279 - Updated jQuery UI to be compatible with newer jQuery
#289 - Results table column summary fails to display when toggling between them 
#292 - missing icon font stylesheet for Results Tables on Report pages
#293 - network viewer toggle not working (flymine) 
#294 - expression graph is blue in flymine
#299 - remove publication displayer
#306 - ref #279
#307 - ref #279
#309 - Enable working FASTA exporter
#312 - Upgraded Backbone.js
#313 - YeastMine GFF3 and FASTA not working
#315 - Friendly mine links to mousemine fail
#317 - icons on results table not showing up
#318 - Creating lists with invidual objects doesn't work anymore 
#319 - Downloading query XML generates an error 
#320 - tables struggle with outerjoined queries and counts
#321 - Reordering columns in download doesn't work
#325 - Summary incorrect on numerical column 
#326 - Export dialogue is purple in wormmine
#327 - Can't filter on organism name in query results 
#328 - Can't delete tags
#329 - Do nothing if nothing is entered in search boxes on Home page
#330 - p-values greater than 1 when adjusting for gene length 
#331 - can't download GO widget data in Safari 
#334 - Add filter button broken 
#335 - Submit event not suppressed in dropdown summary form bug please-test
#336 - "Max value" ignored when correcting by gene length 
#337 - Correct query not being generated when using portal
#340 - PathQuery#verifyQuery() returns incorrect status with many OJs
#341 - Make homepage boxes work with any length of text
#343 - Homepage boxes use CSS3 not background images
#347 - opening a Results Table from List Widget should preserve a Query back link or hide it
#348 - Results tables dropdown menus theme colors
#350 - Use debug mode in List Widgets
#351 - Cross references not linking out automatically
#352 - Use labels in keyword search results 
#354 - Cell formatters - make optional
#356 - Fix Results Tables not opening from List Widgets in Firefox
#357 - Color for MouseMine links
#363 - Fix List Widgets failing with expecting JSONP by asking for JSON
#367 - Limited space when renaming lists
#368 - Inheritance not being handled correctly for list widgets 
#371 - multiple formatters per class, based on path 
#378 - Show a button instead of a checkbox in List Widgets cull by gene length
#384 - Select all items in a widget list if none are selected

1.2 (27 March 2013)

#  9 - Import templates/queries from file
# 44 - Special characters escaped correctly
# 45 - List operations: asymmetric difference 
# 93 - Keyword search: redirects work as expected
# 95 - Can create outer joins in 'summary' views in the query builder
#137 - Enrichment widgets: added option to 'normalize by gene length' 
#152 - Data source ontology
#173 - Keyword search: can create a list with over 100 members
#176 - Convert links on list analysis working
#179 - 'make_source' script creates all needed directories
#181 - Templates handling inheritance correctly now
#190 - Default fields displayed on list analysis page now include references
#196 - Template form: hide complicated logic from user
#233 - Transfer-sequences postprocess correctly creating sequences for CDSs and transcripts
#234 - Link in enrichment widgets displays identifier instead of [link], as before
#236 - Graph widgets: clicking on expected bar is disabled