@julie-sullivan julie-sullivan released this Aug 6, 2018 · 5 commits to dev since this release

Assets 2

#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

@julie-sullivan julie-sullivan released this Sep 4, 2017 · 197 commits to dev since this release

Assets 2

#1661 - Anonymous session tokens are not authenticating

@julie-sullivan julie-sullivan released this Aug 9, 2017 · 203 commits to dev since this release

Assets 2

This release is a hodge podge of bug fixes, features, updates to API needed by blue genes and general tidying up.

  • The iOS app exposed a race condition in the /service/templates request. This was knocking over some mines!
  • Please note all the scripts have been moved to their own repository: intermine/intermine-scripts
  • Blue genes is going to use some attributes in web.properties, see the docs for details.
  • Special thank you to @vivekkrish and @JoeCarlson for their excellent contributions. (again!)

New features

#1494 - LOOKUP and List upload use BagQueryRunner. Need different "match" behaviour
#1606 - Portal - go to disambiguation page if there are issues
#1607 - Add GTEx data source

Needed by Blue genes

#961 - Need way of referring to lists stably
#1600 - Need web service endpoint to generate permanent API tokens
#1631 - Add defaults web service for each mine
#1652 - Add user ID to web service output

Bug fixes

#1613 - OBO files have terms without names
#1636 - Only look in public schema when counting rows in a table (@JoeCarlson)
#1647 - Enables user login tracking in LOGIN_TRACK_TABLE for OAuth2 flow (@vivekkrish)
#1648 - Templates export in JSON format causes deadlock.

Spring Summer cleaning

#1611 - remove obsolete constraint operators
#1626 - Remove intermine/scripts

Aug 8, 2017
HumanMine 4.0 release

@julie-sullivan julie-sullivan released this Jul 18, 2017 · 307 commits to dev since this release

Assets 2

#1623 Add branding parameters for external apps.

@julie-sullivan julie-sullivan released this Jul 3, 2017 · 328 commits to dev since this release

Assets 2

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