Release 0.6.2

What's Changed

• Fix for failure for reasoner to update after undo by @balhoff in #114
• Remove evidence requirements for annotation extensions in GPAD output. by @balhoff in #120
• Adds an export service to get explanations for all inferred relations. by @balhoff in #123
• Remove has-part from whitelist by @cmungall in #122
• attempt to add xenbase to jsonld context by @kltm in #125
• Allow passing of custom JSON-LD context to StartUpTool. by @balhoff in #129
• Only allow root annotations in GPAD export if ND evidence. by @balhoff in #130
• Remove regulation_of qualifiers from GPAD. Fixes #126. by @balhoff in #128
• Additional tests for expansion of class IDs to class IRIs by @cmungall in #133
• Added additional tests to clarify behavior of parsing class IDs pa… by @cmungall in #134
• Testing ComplementOf expressions by @cmungall in #135
• Testing ComplementOf-SomeValuesFrom expressions by @cmungall in #136
• Getting rid of unused utility class with weird catalog use by @cmungall in #137
• Add regulates_o_occurs_in to whitelist by @cmungall in #138
• Changed model import to load RDF direct into Blazegraph by @balhoff in #144
• A testcase that checks revised import and dump functions by @yy20716 in #145
• Removed constraint on available memory for test. by @balhoff in #148
• Add back annotation extension filtering based on evidence. by @balhoff in #147
• Compact test ontology file (go-lego-module.omn.gz) by @yy20716 in #146
• Extending BlazegraphMolecularModelManagerTest to test the full processing cycle of Blazegraph by @yy20716 in #150
• Extend GPAD generation codes to support negations in the qualifier field of GPAD. by @yy20716 in #153
• Add model production status to GPAD. by @balhoff in #157
• Use providedBy annotation for 'assigned by' column by @balhoff in #158
• Return contributor labels in meta response. by @balhoff in #159
• Concatenate multiple sources on a single evidence. by @balhoff in #161
• Update arachne version by @balhoff in #163
• Use group shorthand for assigned-by. by @balhoff in #165
• Throw exception rather than create a GPAD for an inconsistent ontology. by @balhoff in #169
• Add new annotation relations to GPAD export. Fixes #170. by @balhoff in #171
• Filter out PR:000000001 as subject of GPAD annotations. by @balhoff in #176
• Molecular function annotations in GPAD must only use 'enables' or 'contributes to'. by @balhoff in #177
• Disallow GPAD annotations to terms in do_not_annotate subsets. by @balhoff in #182
• Exclude CARO terms from annotation extensions. by @balhoff in #184
• Remove commas from underscore property names. by @balhoff in #183
• Disallow equivalent conjunctive expressions in sets. by @balhoff in #189
• Don't load models with 'delete' modelstate. by @balhoff in #193
• Switch to new JSON-LD context file for identifiers by @cmungall in #194
• regenerated, fixed issue with MGI by @cmungall in #198
• Remove “MGI:” from MGI prefix expansion. by @balhoff in #201
• Implemented SPARQL endpoint service. by @balhoff in #202
• Add instructions for creating ontology mirror. by @balhoff in #211
• Remove addition of Tbox axioms to model graphs. by @balhoff in #192
• SPARQL endpoint in batch service by @balhoff in #222
• Filter CHEBI terms from GPAD annotation subjects. by @balhoff in #224
• Update version of owl-to-rules to avoid 'indirect rules' for reflexive subclasses. by @balhoff in #232
• Update from master by @balhoff in #233
• Adding search API at /search to minerva by @goodb in #234
• Shex validation by @goodb in #237
• Shex validation - #237 - mvn fix for JNI error by @goodb in #238
• switched to maven shade plugin by @goodb in #239
• Update several dependencies to allow running on Java 11 (and also 8) by @balhoff in #240
• Issue 212 validation service response by @goodb in #241
• Added explanations for core shape failures by @goodb in #242
• Use openjdk on travis. by @balhoff in #244
• implements pattern for retrieving canonical identifiers in gpad output by @goodb in #247
• adding result count request paramater #235 and #230 by @goodb in #248
• Run command-line GPAD export in parallel. by @balhoff in #243
• Add validation framework as package an made accessible via minerva cmdline client by @goodb in #251
• update cmdrunner with defaults for shex by @goodb in #252
• provide for local go-lego in validator by @goodb in #253
• Owl cmdline issue254 by @goodb in #255
• adding parallel gpad export from master to dev by @goodb in #257
• Issue258 remove owltools by @goodb in #259
• Conversion to neo lite and golr #260 by @goodb in #261
• Search api sparql query template uri curie by @goodb in #264
• switched to isa_closure for golr query by @goodb in #263
• many additions in here - perhaps most impactful - #261 regarding #260 by @goodb in #262
• for step 4 in #260 by @goodb in #265
• adding information on the shapes that do match troublesome nodes. by @goodb in #270
• add id to order by for #235 by @goodb in #271
• fix ordering for model search by @goodb in #272
• fix search result for users and groups by @goodb in #273
• Performance go shapes199 by @goodb in #274
• addressing shape inheritance issue by @goodb in #275
• Performance go shapes199 by @goodb in #276
• fixing error running command line by @goodb in #277
• Switch to refine for validation by @goodb in #278
• Add tests for validator and search services by @goodb in #279
• implemented POST by @goodb in #280
• running command line client as part of travis. by @goodb in #281
• Status service 282 by @goodb in #284
• Add pipeline report to cmdline validation by @goodb in #285
• require golr server specification for command line run by @goodb in #287
• hopefully improved clarity of command line usage by @goodb in #288
• Blazegraph for go lego experiment by @goodb in #297
• Bugfixes on blazegraph conversion by @goodb in #299
• Testing model level shex validation by @goodb in #306
• think bug dead by @goodb in #307
• take out all super types from response. rendering took forever by @goodb in #308
• code and test for exact match text search by @goodb in #310
• changing routes for search service by @goodb in #312
• change ontojournal location by @goodb in #313
• changing all root protein to chebi reference by @goodb in #314
• have tbox in manager when loading model from blazegraph by @goodb in #316
• removing /tmp/blazegraph.jnl references by @goodb in #317
• minor update - now assumes pre-merged tbox ontology by @goodb in #320
• Add title to shex validation report 318 by @goodb in #323
• fixing title printing to file.. by @goodb in #324
• Dev by @goodb in #326
• added root-type to default m3batch response by @goodb in #327
• Shex validation model metadata by @goodb in #329
• Add cardinality to shex validation report by @goodb in #331
• add search by model id by @goodb in #334
• allow for multiple ids in search by @goodb in #336
• adding root types for partial model responses by @goodb in #340
• Model measurements by @goodb in #342
• update master with many changes on dev by @goodb in #343
• Eliminate imports by @goodb in #346
• updates to line up with molecular event by @goodb in #347
• Shex closed impl bug fix by @goodb in #351
• update to model statistics calculation by @goodb in #352
• Modification state handling ART by @goodb in #357
• Add shex explanation json to cli output by @goodb in #359
• fixes #360 by @goodb in #361
• Dev by @goodb in #354
• using git-commit-plugin that is compatible with java8 by @abessiari in #363
• Added ART API for stored model by @tmushayahama in #365
• GROUP BY only model id. by @balhoff in #372
• Fix mismatch in date variable so that ordering works. by @balhoff in #374
• added support for sonarqube by @abessiari in #373
• Close output streams when dumping files. by @balhoff in #380
• Return all matching individuals in search by @balhoff in #376
• Close output streams when dumping files. by @balhoff in #381
• add located_in and is_active_in to allowed list of relations fixes #385 by @sierra-moxon in #384
• Updating production Minerva by @tmushayahama in #386
• Align dev and master by @balhoff in #400
• Test with github actions by @balhoff in #402
• Export creation-date and modification-date annotation properties in GPAD. by @balhoff in #401
• Suppress UBERON annotation extensions when an EMAPA structure is present. by @balhoff in #405
• Don't create root MF annotation when root BP annotation is present by @balhoff in #404
• Add relations to allowed extensions by @balhoff in #407
• Merge latest by @balhoff in #416
• Tweak test to work with changed data. by @balhoff in #414
• Allow both root MF and BP if different OWL instances. by @balhoff in #409
• Retrieve created and imported dates from axiom annotations. by @balhoff in #415
• Don’t filter out GPAD annotations for 'do not annotate' violations. by @balhoff in #418
• Don’t output import-date in GPAD. by @balhoff in #423
• Update master branch from dev by @balhoff in #421
• Exclude annotations to regulated terms by @balhoff in #427
• GPAD export needs an ontojournal. by @balhoff in #429
• Add Uberon life cycle stage and PO plant structure development stage to root types list. by @balhoff in #431
• Allow skipping ShEx in --validate-go-cams when --shex is omitted by @dustine32 in #422
• Fixes for handling negations in ShEx validation by @balhoff in #433
• Filter out root MF annotations if any other MF annotation exists for the GP. by @balhoff in #436
• Retrieve creation date from evidence node. by @balhoff in #435
• Remove 'has participant' as valid extension relation by @balhoff in #438
• Log4j PR for testing on dev by @balhoff in #440
• Add log4j-core; update to log4j 2.16.0 by @balhoff in #443
• Add log4j xml config by @balhoff in #444
• Use log4j 2.16.0. by @balhoff in #439
• Update ant, junit, commons-io. by @balhoff in #441
• Update test data. by @balhoff in #450
• Bump log4j-core from 2.16.0 to 2.17.1 by @dependabot in #446
• Bring master up to date with dev by @balhoff in #452
• Temporarily suppress creation-date in GPAD. by @balhoff in #453
• Automatically load tbox into ontojournal for GPAD export command. by @balhoff in #455
• Return root type for complement classes. by @balhoff in #451
• Fix test to use correct root type for complexes. by @balhoff in #459
• Optimize imports and reformat everything with IntelliJ defaults. by @balhoff in #458
• Update closure test counts. by @balhoff in #461
• Implement command for migrating references to obsolete terms. by @balhoff in #462
• Include git revision and ontology version IRI in status service. by @balhoff in #470
• Replace obsolete GO term in test file. by @balhoff in #471
• Add PCL prefix expansion. by @balhoff in #472
• Removing code that fixes deprecations during responses (too slow). by @balhoff in #468
• Speed up JSON rendering of object property assertions by using in-memory label lookup. by @balhoff in #473
• Fix test data failure. by @balhoff in #495
• Add biological phase to root types. by @balhoff in #497
• Implement model copy operation. by @balhoff in #482
• Implement replace-terms command. by @balhoff in #478
• Add command to dump models to JSON files. by @balhoff in #501
• Dump model on each save. by @balhoff in #505
• Increment version. by @balhoff in #509

New Contributors

• @kltm made their first contribution in #125
• @yy20716 made their first contribution in #145
• @abessiari made their first contribution in #363
• @tmushayahama made their first contribution in #365
• @sierra-moxon made their first contribution in #384
• @dustine32 made their first contribution in #422
• @dependabot made their first contribution in #446

Full Changelog: v0.6.1...v0.6.2