Intermine Versions Save

#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

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 of this, it doesn't contain some of the following fixes. Patch release including: #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

Release to power BlueGenes 1.0.0 #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

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

#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

check out for humanmine 8.0

#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