Releases: intermine/intermine
InterMine 1.8
This release of InterMine contains a bunch of bug fixes and a few small improvements.
Fixes
#288 - List actions (set operations) greyed out but active
#439 - Better message when list is not available
#739 - filter encoding property in Database.java
#786 - Query with outer join does not validate
#802 - Region search file upload doesn't handle blank lines
#812 - Issues with Date data type
#910 - Usernames containing upper-case letters created via the web service can never log in.
#942 - Allow superclass lists in template list constraints
#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
#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
#1458 - Queries page only shows the last saved query
#1471 - Drop LOOKUP constraint if value is *
#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
#1523 - Userprofile backup script - more improvements
#1551 - handle the case where isoforms have multiple accessions.
#1557 - Correctly save lists after logging in
#1572 - We've lost the trail
Improvements
#702 - Add "Show Tags" option to Lists page
#789 - services.json should contain mine appropriate defaults
#820 - Documentation on date formats (Items XML)
#964 - quicksearch service should report total hits
#966 - add db parameter for schema
#1309 - Provide a template's popularity score in /service/templates
#1455 - Don't add ORDER BY clause to count(*) queries
#1486 - Allow the name attribute to be missing - Thanks @sammyjava!
#1516 - support for DOES_NOT_CONTAIN in query xml - Thanks @JoeCarlson!
#1526 - Post build updating with SQL triggers - Thanks @JoeCarlson!
#1569 - Update FASTA text on region search
InterMine 1.7.3
#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
#1533 - Update code to adapt to google API changes
InterMine 1.7.1
#1482 - Error when creating a list and accessing via the web service via tablerows method.
InterMine 1.7
#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 (thanks @cmdcolin!)
InterMine 1.6.9
#1422 - Constrain widget results.
#1425 - Region Search: allow strand-specific search (Thanks @sammyjava!)
#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
InterMine 1.6.7
#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
This release has several important bug fixes. Please upgrade ASAP!
Enrichment Widget Web Service
A new web service allows enrichment to be performed on a list of identifiers, in addition to a saved list. See our our live web services demo for an example.
NOTE: This web service is required by the new InterMine UI currently under development. So please upgrade ASAP!
Default Footer
Most people are using their own footer, but we've added a "citation" parameter to the default footer. This is in fervent hope that users will see it and be more likely to cite our paper. To update the text to your own paper, see here. We've also added the link to the InterMine Android app.
InterMine Version
We currently have two web services that return the Web service version number and webapp release. We've added a third web service that returns the version of InterMine release version. See our live web services demo for an example.
Data Model Changes
Interaction Region now has a set of locations instead of a reference to a single location. Only relevant if you were using the IntAct interaction data source.
Human Data Sources Switch
Please see https://intermineorg.wordpress.com/2016/02/17/humanmine-identifier-switch/ for details. If you are using InterMine data parsers, the human genes will resolve to NCBI Entrez Gene IDs. If you have questions or problems, please contact us.
Complex Interaction Viewer
We've added a nice viewer for complexes. Source: http://interactionviewer.org/
See the docs for more detail.
Complete list
#1361 - Correct Panther homologue labels
#1322 - HumanMine keyword search is returning atomic coordinates of protein structures
#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
#1277 - Complex - interacting region has two locations
#1276 - Default Footer - add citation details
#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
#1249 - HGNC parser
#1225 - Cytoscape: less mean error message
#1202 - UniProt: comments not capturing disease
#1200 - HumanMine: load synonyms
#1191 - PubMed: remove obsolete classes
#1189 - HumanMine - add illumina body map.
#925 - CHEBI web services for interactions 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
#426 - Web service URL for templates constrained to a list doesn't work.
Thanks
Thank you to @deepakunni3 and @JoelRichardson for their contributions. Joel had four bug fixes!
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