InterMine 4.1.3

#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

flymine-49.0

fixes test for new wording

InterMine 4.1.2

#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

Updated copyright notice with 2002-2020

humanmine-7.0

updates jami-interactionviewer-json to available version

InterMine 4.1.1

#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

#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

#2060 - Restore Strains to core data model

InterMine 4.0.0

#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

#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
#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)
#2036 - ObjectStoreSummary does not handle ignored fields consistently. (thanks @JoeCarlson )

InterMine 3.1.1

A small patch release with some important bug fixes.

And a big thanks to our contributors: @sammyjava, @JoelRichardson and @nuin!!

#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