Ecosyste.ms: Issues

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GitHub / biolink/biolinkml issues and pull requests

#399 - Issue 368 enhancements

Pull Request - State: closed - Opened by hsolbrig over 3 years ago - 1 comment

#398 - robot templates

Pull Request - State: closed - Opened by cmungall over 3 years ago - 2 comments

#396 - add antonymy as a meta model attribute

Pull Request - State: closed - Opened by sierra-moxon over 3 years ago - 2 comments

#393 - indent using 4 spaces as per md standard. Fixes #392

Pull Request - State: closed - Opened by cmungall over 3 years ago

#392 - indentation of class hierarchy not working in generated index.md

Issue - State: closed - Opened by cmungall over 3 years ago - 2 comments

#384 - Issue 381

Pull Request - State: closed - Opened by hsolbrig over 3 years ago - 1 comment

#383 - Update README.md - link to HOT

Pull Request - State: closed - Opened by cmungall over 3 years ago

#380 - Loaders

Pull Request - State: closed - Opened by hsolbrig over 3 years ago

#379 - Add test to document current behavior

Pull Request - State: closed - Opened by hsolbrig over 3 years ago

#377 - Biolink ML generation fails silently

Issue - State: closed - Opened by matentzn almost 4 years ago - 4 comments

#374 - JSONLD Context needs `"@container": "@set"` for multivalued entries

Issue - State: closed - Opened by hsolbrig over 3 years ago - 1 comment

#372 - Added tsv->schema inference, fixes #371

Pull Request - State: closed - Opened by cmungall almost 4 years ago - 2 comments

#371 - infer a simple data dictionary schema from a TSV

Issue - State: closed - Opened by cmungall almost 4 years ago

#369 - including enums in python imports, fixes #368

Pull Request - State: closed - Opened by cmungall almost 4 years ago

#368 - enums are not imported in generated python code

Issue - State: closed - Opened by cmungall almost 4 years ago

#365 - '@container' must be emitted for multivalued elements in JSON-LD Context

Issue - State: closed - Opened by hsolbrig almost 4 years ago - 1 comment

#357 - Fix for issue #355.

Pull Request - State: closed - Opened by hsolbrig almost 4 years ago

#354 - Improve markdowngen

Pull Request - State: closed - Opened by deepakunni3 almost 4 years ago - 1 comment

#353 - Update setup.cfg

Pull Request - State: closed - Opened by hsolbrig almost 4 years ago

#352 - YAML generator isn't a command line option

Issue - State: closed - Opened by hsolbrig almost 4 years ago - 1 comment

#345 - Issue 344

Pull Request - State: closed - Opened by deepakunni3 almost 4 years ago

#344 - missing PATO prefix

Issue - State: closed - Opened by balhoff about 4 years ago - 9 comments

#341 - Fix for issue #338

Pull Request - State: closed - Opened by hsolbrig almost 4 years ago

#340 - Issue 338

Pull Request - State: closed - Opened by hsolbrig almost 4 years ago

#339 - SchemaLoader should be monotonic

Issue - State: closed - Opened by hsolbrig almost 4 years ago

#338 - Boolean values don't include underlying python type

Issue - State: closed - Opened by hsolbrig almost 4 years ago - 1 comment

#337 - sql ddl gen

Pull Request - State: closed - Opened by cmungall almost 4 years ago - 1 comment

#336 - create gen-* modules as separate pip installs

Issue - State: closed - Opened by wdduncan almost 4 years ago - 2 comments

#334 - Issue 332

Pull Request - State: closed - Opened by hsolbrig almost 4 years ago

#333 - gen-owl error(s)

Issue - State: closed - Opened by dwinston almost 4 years ago - 6 comments

#332 - gen-jsonld generates an incorrect @context

Issue - State: closed - Opened by cmungall almost 4 years ago - 1 comment

#331 - gen-owl error(s)

Issue - State: closed - Opened by dwinston almost 4 years ago - 2 comments

#326 - alt_description not behaving as expected

Issue - State: closed - Opened by hsolbrig almost 4 years ago

#325 - Is `repr` property used?

Issue - State: closed - Opened by hsolbrig almost 4 years ago - 1 comment

#324 - Enumerations

Pull Request - State: closed - Opened by hsolbrig almost 4 years ago

#323 - Issue 319 mixins in domain and range

Pull Request - State: closed - Opened by RichardBruskiewich almost 4 years ago - 2 comments

#322 - Should `slot_usage` be allowed in `mixin` definitions?

Issue - State: closed - Opened by RichardBruskiewich almost 4 years ago - 1 comment

#321 - Issue 320 mixin abstract as default

Pull Request - State: closed - Opened by RichardBruskiewich almost 4 years ago - 1 comment

#318 - SPARQL queries for models and instance data #229

Pull Request - State: closed - Opened by cmungall almost 4 years ago - 1 comment

#314 - more rdf examples

Pull Request - State: closed - Opened by cmungall almost 4 years ago

#313 - Adding more docs about generating RDF and JSON-LD contexts

Pull Request - State: closed - Opened by cmungall almost 4 years ago

#312 - Add decimal to types.yaml

Pull Request - State: closed - Opened by cmungall almost 4 years ago - 2 comments

#307 - incremental documentation improvements

Pull Request - State: closed - Opened by cmungall about 4 years ago

#304 - Latest version of PyShEx causes an exception in biolinkml.

Issue - State: closed - Opened by PhillipsOwen about 4 years ago - 5 comments

#301 - Proposed changes for issue #159

Pull Request - State: closed - Opened by hsolbrig about 4 years ago - 1 comment

#299 - Prefixcase

Pull Request - State: closed - Opened by hsolbrig about 4 years ago

#297 - biolinkml None slots populated in object

Issue - State: closed - Opened by wdduncan about 4 years ago - 3 comments

#296 - biolinkml optional slots populated in object

Issue - State: closed - Opened by wdduncan about 4 years ago - 3 comments

#295 - Pattern

Pull Request - State: closed - Opened by hsolbrig about 4 years ago

#292 - issue 290 - generate symmetry and inverse in OWL

Pull Request - State: closed - Opened by cmungall about 4 years ago

#290 - symmetry and inverse characteristics are not translated in OWL

Issue - State: closed - Opened by cmungall about 4 years ago

#284 - INFO log prefix source

Pull Request - State: closed - Opened by RichardBruskiewich about 4 years ago - 2 comments

#283 - Fixes for issues #281 and #282

Pull Request - State: closed - Opened by hsolbrig about 4 years ago

#282 - Mappings aren't listed in markdown

Issue - State: closed - Opened by hsolbrig about 4 years ago

#281 - Markdown not generating output for non-owned slots

Issue - State: closed - Opened by hsolbrig about 4 years ago

#278 - Namespace gen revisions

Pull Request - State: closed - Opened by RichardBruskiewich about 4 years ago

#277 - Fixed issue #276. Tightened up the YAML importer to fail on empty li…

Pull Request - State: closed - Opened by hsolbrig about 4 years ago

#276 - Empty list element not reported well

Issue - State: closed - Opened by hsolbrig about 4 years ago

#264 - Slots, slot_usage and attributes

Issue - State: closed - Opened by hsolbrig about 4 years ago - 6 comments
Labels: question, Underway, Close Pending

#262 - Create prefixmapgen and update jsonldcontextgen

Pull Request - State: closed - Opened by rajshruti18 about 4 years ago - 10 comments

#260 - Relative import paths have one too many dots

Issue - State: closed - Opened by hsolbrig about 4 years ago - 1 comment
Labels: Underway

#221 - Should mappings.yaml include/be more SKOS-like?

Issue - State: closed - Opened by RichardBruskiewich over 4 years ago

#198 - Update `__post_init__` signatures to match PyCharm IDE fix

Issue - State: closed - Opened by hsolbrig over 4 years ago - 1 comment

#186 - Clarify semantics of inlined: True - dicts vs lists

Issue - State: closed - Opened by cmungall over 4 years ago - 6 comments

#168 - WIP: add additional metadata in owlgen

Pull Request - State: closed - Opened by cmungall over 4 years ago - 4 comments

#167 - Add a generic annotations pattern

Issue - State: closed - Opened by cmungall over 4 years ago - 3 comments
Labels: metamodel extension, Underway

#164 - change owlgen to use default_prefix for namespace

Pull Request - State: closed - Opened by cmungall over 4 years ago - 1 comment

#159 - Design patterns for handling measurement properties

Issue - State: closed - Opened by cmungall over 4 years ago - 5 comments

#149 - makefile targets

Pull Request - State: closed - Opened by cmungall over 4 years ago - 3 comments

#140 - tests are too fragile

Issue - State: closed - Opened by cmungall over 4 years ago - 6 comments
Labels: Documentation Needed, Underway

#137 - temp disable 103

Pull Request - State: closed - Opened by cmungall over 4 years ago

#130 - JSON-Schema generation fixes

Pull Request - State: closed - Opened by cmungall over 4 years ago

#127 - Add ability to constrain by regexes

Issue - State: closed - Opened by cmungall over 4 years ago - 1 comment

#126 - Dynamically extending meta.yaml

Issue - State: closed - Opened by cmungall over 4 years ago
Labels: question

#123 - Issue 121: merge imports

Pull Request - State: closed - Opened by cmungall over 4 years ago

#119 - adding details to docs

Pull Request - State: closed - Opened by cmungall over 4 years ago

#114 - WIP: fix for missing slots in python generation

Pull Request - State: closed - Opened by cmungall over 4 years ago

#102 - SchemaLoader doesn't raise error for slots with both a key and identifier

Issue - State: closed - Opened by jiaola almost 5 years ago - 2 comments

#86 - why are inline slots multivalued?

Issue - State: closed - Opened by cmungall almost 5 years ago

#85 - gen-py-classes emits warnings on stdout

Issue - State: closed - Opened by cmungall almost 5 years ago

#82 - Model CEDAR templates

Issue - State: closed - Opened by wdduncan almost 5 years ago - 2 comments

#80 - Specifying a class uri

Issue - State: closed - Opened by wdduncan almost 5 years ago - 6 comments

#65 - Automatic generation of own-slots causes markdown to be weird

Issue - State: closed - Opened by cmungall about 5 years ago

#63 - ShEx validation error in test_mappings_generators

Issue - State: closed - Opened by hsolbrig about 5 years ago

#60 - Lists in single values should result in an error

Issue - State: closed - Opened by hsolbrig about 5 years ago

#58 - Name attribute cannot have spaces

Issue - State: closed - Opened by hsolbrig about 5 years ago

#56 - Domain of slot should match any declaring subclass

Issue - State: closed - Opened by hsolbrig about 5 years ago

#39 - Python generator doesn't know how to map an imported URL to a python import

Issue - State: closed - Opened by hsolbrig over 5 years ago - 1 comment
Labels: Defer

#36 - Implement a biolink model tagger, to add categories to nodes in a set of triples

Issue - State: closed - Opened by cmungall over 5 years ago - 5 comments
Labels: Low Priority

#33 - json-schema should unfold properties of superclasses

Issue - State: closed - Opened by cmungall over 5 years ago - 1 comment

#30 - Adding mapping subtypes. Fixes https://github.com/biolink/biolink-mod…

Pull Request - State: closed - Opened by cmungall over 5 years ago - 2 comments

#18 - Inverse should be symmetric

Issue - State: closed - Opened by hsolbrig over 5 years ago

#16 - Generated OWL uses iriType rather than classes in equivalence axiom

Issue - State: closed - Opened by cmungall over 5 years ago - 1 comment

#7 - compare biolinkml with grakn schema language

Issue - State: closed - Opened by cmungall over 5 years ago
Labels: question, Low Priority