feat: Add API ontology querying module #39

nayib-jose-gloria · 2024-02-21T17:26:40Z

Reason for Change

feat(API): Implement must-haves of Generalized Ontology Querying API (based on Pablo’s prototype) + Tests #14

Changes

implement all_ontology querying functions to fetch metadata, for single term IDs and bulk IDs
reorganize file structure to store artifacts that will be packaged with the API in the python/api directory, rather than in the ontology-builder directory (which will not be packaged).
- In turn, reorganize the env.py constants + GHAs pointing to directories to read from / output generated files to.

Testing steps

unit tests

Notes for Reviewer

…y.json

# Conflicts: # tools/ontology-builder/src/ontology-references/all_ontology.json.gz

# Conflicts: # tools/ontology-builder/src/env.py

Bento007

Just make them bulk operations that can take a list of 1.

Bento007 · 2024-02-21T18:32:46Z

api/python/src/cellxgene_ontology_guide/query.py

+import gzip
+import json
+
+with gzip.open(env.ALL_ONTOLOGY_JSON, "rt") as f:


How long does this step take, and does it need to happen every time we load the library?

It loads once, on first import of this module. Python will cache the global var init after that such that, even if its imported multiple places in a program, it will only load this once.

Not sure on how long it takes, but the unit tests run in about 2 seconds

api/python/__init__.py

api/python/src/cellxgene_ontology_guide/query.py

api/python/tests/test_query.py

.github/workflows/generate_all_ontology.yml

Bento007 · 2024-02-23T20:12:16Z

api/python/__init__.py

Is this file needed?

it was removed! unless you're saying you think it should be added back in? don't think its needed

Yes remove. Sorry I thought it was just an empty file.

Bento007

one minor thing to address other wise LGTM

🤖 I have created a release *beep* *boop* --- <details><summary>python-api: 0.0.1</summary> ## 0.0.1 (2024-02-24) ### Features * Add API ontology querying module ([68f3168](68f3168)) * Add API ontology querying module ([#39](#39)) ([239ef2b](239ef2b)) * **API:** setup python library ([211a099](211a099)) * **API:** setup python library ([f60f897](f60f897)) * **API:** Setup the library for development ([1f7ce03](1f7ce03)) * implement stubbed query functions ([334deb5](334deb5)) * set version regex for pyton api ([3720dab](3720dab)) ### BugFixes * README.md ([1eae21d](1eae21d)) </details> <details><summary>ontology-assets: 0.0.1</summary> ## 0.0.1 (2024-02-24) ### Misc * moving the generated artifacts ([c03c8e3](c03c8e3)) </details> <details><summary>0.0.1</summary> ## 0.0.1 (2024-02-24) ### Features * Add API ontology querying module ([68f3168](68f3168)) * Add API ontology querying module ([#39](#39)) ([239ef2b](239ef2b)) * **API:** setup python library ([211a099](211a099)) * **API:** setup python library ([f60f897](f60f897)) * **API:** Setup the library for development ([1f7ce03](1f7ce03)) * **data release:** add hand curated_lists.py and orphans with comments and a generator s… ([#33](#33)) ([413dc23](413dc23)) * Define JSON Schemas for ontology data release artifacts ([#32](#32)) ([b23894a](b23894a)) * fix changelog ([0285ef7](0285ef7)) * implement stubbed query functions ([334deb5](334deb5)) * set version regex for pyton api ([3720dab](3720dab)) * setup Lintes for repo ([4a70384](4a70384)) * Store branch ancestors ("part_of" relationships) in all_ontology.json ([80e1f0d](80e1f0d)) * Store branch ancestors ("part_of" relationships) in all_ontology.json ([#38](#38)) ([64c2653](64c2653)) * **testing:** add testing for ontology-builder ([e087eca](e087eca)) * **testing:** add testing for ontology-builder ([e087eca](e087eca)) * upload assets on release ([81725db](81725db)) ### Misc * add ontology-assets to release ([b09c814](b09c814)) * add ontology-assets to release ([04835c0](04835c0)) * bootstrap release-please ([f32db86](f32db86)) * bootstrap release-please ([7d0554f](7d0554f)) * change bootstrap-sha ([f2571e8](f2571e8)) * check that pr titles follow conventional commit format ([#41](#41)) ([bd6d842](bd6d842)) * clean-up extract ontology term metadata parsing ([b9d2959](b9d2959)) * configure release-please ([#40](#40)) ([879ead2](879ead2)) * **deps:** bump owlready2 from 0.38 to 0.45 in /tools/ontology-builder ([5466a08](5466a08)) * **deps:** bump owlready2 from 0.38 to 0.45 in /tools/ontology-builder ([#37](#37)) ([db3e5c8](db3e5c8)) * **deps:** bump pyyaml from 6.0 to 6.0.1 in /tools/ontology-builder ([98dfba2](98dfba2)) * **deps:** bump pyyaml from 6.0 to 6.0.1 in /tools/ontology-builder ([#36](#36)) ([72e7e40](72e7e40)) * move over all_ontology.json generator script + gha to repo from single-cell-curation ([f90fb05](f90fb05)) * move over all_ontology.json generator script + gha to repo from single-cell-curation ([#27](#27)) ([49237a7](49237a7)) * moving the generated artifacts ([c03c8e3](c03c8e3)) * refactor all_ontology_generator for cleanliness and modularity ([b96c552](b96c552)) * refactor all_ontology_generator for cleanliness and modularity ([b96c552](b96c552)) * refactor all_ontology_generator for cleanliness and modularity ([4384459](4384459)) * release 0.0.2 ([4972aa2](4972aa2)) * release 0.0.2 ([#42](#42)) ([19079d4](19079d4)) * remove unused release.yml configs ([ce00bef](ce00bef)) * test-release ([5f20d18](5f20d18)) ### BugFixes * add dependabot.yml ([575f371](575f371)) * add ontology-assets ([8d51dea](8d51dea)) * add ontology-assets ([01f504d](01f504d)) * README.md ([d19efeb](d19efeb)) * README.md ([1eae21d](1eae21d)) * release pr format ([20d9d1d](20d9d1d)) * remove root from release-please-config.json ([8265b3e](8265b3e)) * test branch ([f68622a](f68622a)) * test branch ([fac02bb](fac02bb)) * test release ([aab95e8](aab95e8)) </details> --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please).

🤖 I have created a release *beep* *boop* --- <details><summary>python-api: 0.0.1</summary> ## 0.0.1 (2024-02-26) ### Features * Add API ontology querying module ([68f3168](68f3168)) * Add API ontology querying module ([#39](#39)) ([239ef2b](239ef2b)) * **API:** setup python library ([211a099](211a099)) * **API:** setup python library ([f60f897](f60f897)) * **API:** Setup the library for development ([1f7ce03](1f7ce03)) * implement stubbed query functions ([334deb5](334deb5)) * set version regex for pyton api ([3720dab](3720dab)) ### BugFixes * README.md ([1eae21d](1eae21d)) </details> <details><summary>ontology-assets: 0.0.1</summary> ## 0.0.1 (2024-02-26) ### Misc * move curated lists to ontology-assets ([#48](#48)) ([77916df](77916df)) * moving the generated artifacts ([c03c8e3](c03c8e3)) </details> <details><summary>0.0.1</summary> ## 0.0.1 (2024-02-26) ### Features * Add API ontology querying module ([68f3168](68f3168)) * Add API ontology querying module ([#39](#39)) ([239ef2b](239ef2b)) * **API:** setup python library ([211a099](211a099)) * **API:** setup python library ([f60f897](f60f897)) * **API:** Setup the library for development ([1f7ce03](1f7ce03)) * **data release:** add hand curated_lists.py and orphans with comments and a generator s… ([#33](#33)) ([413dc23](413dc23)) * Define JSON Schemas for ontology data release artifacts ([#32](#32)) ([b23894a](b23894a)) * fix changelog ([0285ef7](0285ef7)) * implement stubbed query functions ([334deb5](334deb5)) * regenerate all_ontology if the schema changes ([5f74bfb](5f74bfb)) * set version regex for pyton api ([3720dab](3720dab)) * setup Lintes for repo ([4a70384](4a70384)) * Store branch ancestors ("part_of" relationships) in all_ontology.json ([80e1f0d](80e1f0d)) * Store branch ancestors ("part_of" relationships) in all_ontology.json ([#38](#38)) ([64c2653](64c2653)) * **testing:** add testing for ontology-builder ([e087eca](e087eca)) * **testing:** add testing for ontology-builder ([e087eca](e087eca)) ### Misc * add ontology-assets to release ([b09c814](b09c814)) * add ontology-assets to release ([04835c0](04835c0)) * bootstrap release-please ([f32db86](f32db86)) * bootstrap release-please ([7d0554f](7d0554f)) * change bootstrap-sha ([f2571e8](f2571e8)) * check that pr titles follow conventional commit format ([#41](#41)) ([bd6d842](bd6d842)) * clean-up extract ontology term metadata parsing ([b9d2959](b9d2959)) * configure release-please ([#40](#40)) ([879ead2](879ead2)) * **deps:** bump owlready2 from 0.38 to 0.45 in /tools/ontology-builder ([5466a08](5466a08)) * **deps:** bump owlready2 from 0.38 to 0.45 in /tools/ontology-builder ([#37](#37)) ([db3e5c8](db3e5c8)) * **deps:** bump pyyaml from 6.0 to 6.0.1 in /tools/ontology-builder ([98dfba2](98dfba2)) * **deps:** bump pyyaml from 6.0 to 6.0.1 in /tools/ontology-builder ([#36](#36)) ([72e7e40](72e7e40)) * enable release-please for API and Assets ([#55](#55)) ([9ecda79](9ecda79)) * move curated lists to ontology-assets ([#48](#48)) ([77916df](77916df)) * move over all_ontology.json generator script + gha to repo from single-cell-curation ([f90fb05](f90fb05)) * move over all_ontology.json generator script + gha to repo from single-cell-curation ([#27](#27)) ([49237a7](49237a7)) * moving the generated artifacts ([c03c8e3](c03c8e3)) * refactor all_ontology_generator for cleanliness and modularity ([b96c552](b96c552)) * refactor all_ontology_generator for cleanliness and modularity ([b96c552](b96c552)) * refactor all_ontology_generator for cleanliness and modularity ([4384459](4384459)) * release 0.0.2 ([4972aa2](4972aa2)) * release 0.0.2 ([#42](#42)) ([19079d4](19079d4)) * remove unused release.yml configs ([ce00bef](ce00bef)) * test-release ([5f20d18](5f20d18)) ### BugFixes * .release-please-manifest.json is valid json ([c09f2cc](c09f2cc)) * add dependabot.yml ([575f371](575f371)) * add ontology-assets ([8d51dea](8d51dea)) * add ontology-assets ([01f504d](01f504d)) * README.md ([d19efeb](d19efeb)) * README.md ([1eae21d](1eae21d)) * release pr format ([20d9d1d](20d9d1d)) * remove root from release-please-config.json ([8265b3e](8265b3e)) * test branch ([f68622a](f68622a)) * test branch ([fac02bb](fac02bb)) * test release ([aab95e8](aab95e8)) * trigger all-ontology generation if schema changes ([#46](#46)) ([3121833](3121833)) </details> --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please).

🤖 I have created a release *beep* *boop* --- <details><summary>python-api: 0.0.1</summary> ## 0.0.1 (2024-02-26) ### Features * Add API ontology querying module ([68f3168](68f3168)) * Add API ontology querying module ([#39](#39)) ([239ef2b](239ef2b)) * **API:** setup python library ([211a099](211a099)) * **API:** setup python library ([f60f897](f60f897)) * **API:** Setup the library for development ([1f7ce03](1f7ce03)) * implement stubbed query functions ([334deb5](334deb5)) * set version regex for pyton api ([3720dab](3720dab)) ### Misc * release tsmith/release-assets ([63b782d](63b782d)) * release tsmith/release-assets ([#57](#57)) ([6a6b02a](6a6b02a)) ### BugFixes * README.md ([1eae21d](1eae21d)) </details> <details><summary>ontology-assets: 0.0.1</summary> ## 0.0.1 (2024-02-26) ### Misc * move curated lists to ontology-assets ([#48](#48)) ([77916df](77916df)) * moving the generated artifacts ([c03c8e3](c03c8e3)) * release tsmith/release-assets ([63b782d](63b782d)) * release tsmith/release-assets ([#57](#57)) ([6a6b02a](6a6b02a)) </details> <details><summary>0.0.1</summary> ## 0.0.1 (2024-02-26) ### Features * Add API ontology querying module ([68f3168](68f3168)) * Add API ontology querying module ([#39](#39)) ([239ef2b](239ef2b)) * **API:** setup python library ([211a099](211a099)) * **API:** setup python library ([f60f897](f60f897)) * **API:** Setup the library for development ([1f7ce03](1f7ce03)) * **data release:** add hand curated_lists.py and orphans with comments and a generator s… ([#33](#33)) ([413dc23](413dc23)) * Define JSON Schemas for ontology data release artifacts ([#32](#32)) ([b23894a](b23894a)) * fix changelog ([0285ef7](0285ef7)) * implement stubbed query functions ([334deb5](334deb5)) * regenerate all_ontology if the schema changes ([5f74bfb](5f74bfb)) * set version regex for pyton api ([3720dab](3720dab)) * setup Lintes for repo ([4a70384](4a70384)) * Store branch ancestors ("part_of" relationships) in all_ontology.json ([80e1f0d](80e1f0d)) * Store branch ancestors ("part_of" relationships) in all_ontology.json ([#38](#38)) ([64c2653](64c2653)) * **testing:** add testing for ontology-builder ([e087eca](e087eca)) * **testing:** add testing for ontology-builder ([e087eca](e087eca)) * upload assets on release ([81725db](81725db)) ### Misc * add ontology-assets to release ([b09c814](b09c814)) * add ontology-assets to release ([04835c0](04835c0)) * bootstrap release-please ([f32db86](f32db86)) * bootstrap release-please ([7d0554f](7d0554f)) * change bootstrap-sha ([f2571e8](f2571e8)) * check that pr titles follow conventional commit format ([#41](#41)) ([bd6d842](bd6d842)) * clean-up extract ontology term metadata parsing ([b9d2959](b9d2959)) * configure release-please ([#40](#40)) ([879ead2](879ead2)) * **deps:** bump owlready2 from 0.38 to 0.45 in /tools/ontology-builder ([5466a08](5466a08)) * **deps:** bump owlready2 from 0.38 to 0.45 in /tools/ontology-builder ([#37](#37)) ([db3e5c8](db3e5c8)) * **deps:** bump pyyaml from 6.0 to 6.0.1 in /tools/ontology-builder ([98dfba2](98dfba2)) * **deps:** bump pyyaml from 6.0 to 6.0.1 in /tools/ontology-builder ([#36](#36)) ([72e7e40](72e7e40)) * enable release-please for API and Assets ([#55](#55)) ([9ecda79](9ecda79)) * move curated lists to ontology-assets ([#48](#48)) ([77916df](77916df)) * move over all_ontology.json generator script + gha to repo from single-cell-curation ([f90fb05](f90fb05)) * move over all_ontology.json generator script + gha to repo from single-cell-curation ([#27](#27)) ([49237a7](49237a7)) * moving the generated artifacts ([c03c8e3](c03c8e3)) * refactor all_ontology_generator for cleanliness and modularity ([b96c552](b96c552)) * refactor all_ontology_generator for cleanliness and modularity ([b96c552](b96c552)) * refactor all_ontology_generator for cleanliness and modularity ([4384459](4384459)) * release 0.0.2 ([4972aa2](4972aa2)) * release 0.0.2 ([#42](#42)) ([19079d4](19079d4)) * release tsmith/release-assets ([63b782d](63b782d)) * release tsmith/release-assets ([#57](#57)) ([6a6b02a](6a6b02a)) * remove unused release.yml configs ([ce00bef](ce00bef)) * test-release ([5f20d18](5f20d18)) ### BugFixes * .release-please-manifest.json is valid json ([c09f2cc](c09f2cc)) * add dependabot.yml ([575f371](575f371)) * add ontology-assets ([8d51dea](8d51dea)) * add ontology-assets ([01f504d](01f504d)) * README.md ([d19efeb](d19efeb)) * README.md ([1eae21d](1eae21d)) * release pr format ([20d9d1d](20d9d1d)) * remove root from release-please-config.json ([8265b3e](8265b3e)) * test branch ([f68622a](f68622a)) * test branch ([fac02bb](fac02bb)) * test release ([aab95e8](aab95e8)) * trigger all-ontology generation if schema changes ([#46](#46)) ([3121833](3121833)) </details> --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please).

🤖 I have created a release *beep* *boop* --- <details><summary>python-api: 0.1.0</summary> ## [0.1.0](python-api-v0.0.1...python-api-v0.1.0) (2024-02-26) ### Features * Add API ontology querying module ([68f3168](68f3168)) * Add API ontology querying module ([#39](#39)) ([239ef2b](239ef2b)) * **API:** setup python library ([211a099](211a099)) * **API:** setup python library ([f60f897](f60f897)) * **API:** Setup the library for development ([1f7ce03](1f7ce03)) * implement stubbed query functions ([334deb5](334deb5)) * set version regex for pyton api ([3720dab](3720dab)) ### Misc * release test-release ([77e72fe](77e72fe)) * release test-release ([#66](#66)) ([e968ef3](e968ef3)) * release tsmith/release-assets ([63b782d](63b782d)) * release tsmith/release-assets ([#57](#57)) ([6a6b02a](6a6b02a)) ### BugFixes * README.md ([1eae21d](1eae21d)) </details> <details><summary>ontology-assets: 0.0.2</summary> ## [0.0.2](ontology-assets-v0.0.1...ontology-assets-v0.0.2) (2024-02-26) ### Misc * move curated lists to ontology-assets ([#48](#48)) ([77916df](77916df)) * moving the generated artifacts ([c03c8e3](c03c8e3)) * release test-release ([77e72fe](77e72fe)) * release test-release ([#66](#66)) ([e968ef3](e968ef3)) * release tsmith/release-assets ([63b782d](63b782d)) * release tsmith/release-assets ([#57](#57)) ([6a6b02a](6a6b02a)) </details> <details><summary>0.1.0</summary> ## [0.1.0](v0.0.1...v0.1.0) (2024-02-26) ### Features * Add API ontology querying module ([68f3168](68f3168)) * Add API ontology querying module ([#39](#39)) ([239ef2b](239ef2b)) * **API:** setup python library ([211a099](211a099)) * **API:** setup python library ([f60f897](f60f897)) * **API:** Setup the library for development ([1f7ce03](1f7ce03)) * **data release:** add hand curated_lists.py and orphans with comments and a generator s… ([#33](#33)) ([413dc23](413dc23)) * Define JSON Schemas for ontology data release artifacts ([#32](#32)) ([b23894a](b23894a)) * fix changelog ([0285ef7](0285ef7)) * implement stubbed query functions ([334deb5](334deb5)) * regenerate all_ontology if the schema changes ([5f74bfb](5f74bfb)) * set version regex for pyton api ([3720dab](3720dab)) * setup Lintes for repo ([4a70384](4a70384)) * Store branch ancestors ("part_of" relationships) in all_ontology.json ([80e1f0d](80e1f0d)) * Store branch ancestors ("part_of" relationships) in all_ontology.json ([#38](#38)) ([64c2653](64c2653)) * **testing:** add testing for ontology-builder ([e087eca](e087eca)) * **testing:** add testing for ontology-builder ([e087eca](e087eca)) * upload assets on release ([81725db](81725db)) ### Misc * add ontology-assets to release ([b09c814](b09c814)) * add ontology-assets to release ([04835c0](04835c0)) * bootstrap release-please ([f32db86](f32db86)) * bootstrap release-please ([7d0554f](7d0554f)) * change bootstrap-sha ([f2571e8](f2571e8)) * check that pr titles follow conventional commit format ([#41](#41)) ([bd6d842](bd6d842)) * clean-up extract ontology term metadata parsing ([b9d2959](b9d2959)) * configure release-please ([#40](#40)) ([879ead2](879ead2)) * **deps:** bump owlready2 from 0.38 to 0.45 in /tools/ontology-builder ([5466a08](5466a08)) * **deps:** bump owlready2 from 0.38 to 0.45 in /tools/ontology-builder ([#37](#37)) ([db3e5c8](db3e5c8)) * **deps:** bump pyyaml from 6.0 to 6.0.1 in /tools/ontology-builder ([98dfba2](98dfba2)) * **deps:** bump pyyaml from 6.0 to 6.0.1 in /tools/ontology-builder ([#36](#36)) ([72e7e40](72e7e40)) * enable release-please for API and Assets ([#55](#55)) ([9ecda79](9ecda79)) * move curated lists to ontology-assets ([#48](#48)) ([77916df](77916df)) * move over all_ontology.json generator script + gha to repo from single-cell-curation ([f90fb05](f90fb05)) * move over all_ontology.json generator script + gha to repo from single-cell-curation ([#27](#27)) ([49237a7](49237a7)) * moving the generated artifacts ([c03c8e3](c03c8e3)) * refactor all_ontology_generator for cleanliness and modularity ([b96c552](b96c552)) * refactor all_ontology_generator for cleanliness and modularity ([b96c552](b96c552)) * refactor all_ontology_generator for cleanliness and modularity ([4384459](4384459)) * release 0.0.2 ([4972aa2](4972aa2)) * release 0.0.2 ([#42](#42)) ([19079d4](19079d4)) * release test-release ([77e72fe](77e72fe)) * release test-release ([#66](#66)) ([e968ef3](e968ef3)) * release tsmith/release-assets ([63b782d](63b782d)) * release tsmith/release-assets ([#57](#57)) ([6a6b02a](6a6b02a)) * remove unused release.yml configs ([ce00bef](ce00bef)) * test-release ([5f20d18](5f20d18)) ### BugFixes * .release-please-manifest.json is valid json ([c09f2cc](c09f2cc)) * add dependabot.yml ([575f371](575f371)) * add ontology-assets ([8d51dea](8d51dea)) * add ontology-assets ([01f504d](01f504d)) * README.md ([d19efeb](d19efeb)) * README.md ([1eae21d](1eae21d)) * release pr format ([20d9d1d](20d9d1d)) * remove root from release-please-config.json ([8265b3e](8265b3e)) * test branch ([f68622a](f68622a)) * test branch ([fac02bb](fac02bb)) * test release ([aab95e8](aab95e8)) * trigger all-ontology generation if schema changes ([#46](#46)) ([3121833](3121833)) </details> --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please).

🤖 I have created a release *beep* *boop* --- <details><summary>python-api: 0.2.0</summary> ## [0.2.0](python-api-v0.1.0...python-api-v0.2.0) (2024-02-26) ### Features * Add API ontology querying module ([68f3168](68f3168)) * Add API ontology querying module ([#39](#39)) ([239ef2b](239ef2b)) * **API:** setup python library ([211a099](211a099)) * **API:** setup python library ([f60f897](f60f897)) * **API:** Setup the library for development ([1f7ce03](1f7ce03)) * implement stubbed query functions ([334deb5](334deb5)) * set version regex for pyton api ([3720dab](3720dab)) ### Misc * release test-release ([48815dc](48815dc)) * release test-release ([77e72fe](77e72fe)) * release test-release ([#66](#66)) ([e968ef3](e968ef3)) * release test-release ([#67](#67)) ([d1057a8](d1057a8)) * release tsmith/release-assets ([63b782d](63b782d)) * release tsmith/release-assets ([#57](#57)) ([6a6b02a](6a6b02a)) ### BugFixes * README.md ([1eae21d](1eae21d)) </details> <details><summary>ontology-assets: 0.0.3</summary> ## [0.0.3](ontology-assets-v0.0.2...ontology-assets-v0.0.3) (2024-02-26) ### Misc * move curated lists to ontology-assets ([#48](#48)) ([77916df](77916df)) * moving the generated artifacts ([c03c8e3](c03c8e3)) * release test-release ([48815dc](48815dc)) * release test-release ([77e72fe](77e72fe)) * release test-release ([#66](#66)) ([e968ef3](e968ef3)) * release test-release ([#67](#67)) ([d1057a8](d1057a8)) * release tsmith/release-assets ([63b782d](63b782d)) * release tsmith/release-assets ([#57](#57)) ([6a6b02a](6a6b02a)) </details> <details><summary>0.2.0</summary> ## [0.2.0](v0.1.0...v0.2.0) (2024-02-26) ### Features * Add API ontology querying module ([68f3168](68f3168)) * Add API ontology querying module ([#39](#39)) ([239ef2b](239ef2b)) * **API:** setup python library ([211a099](211a099)) * **API:** setup python library ([f60f897](f60f897)) * **API:** Setup the library for development ([1f7ce03](1f7ce03)) * **data release:** add hand curated_lists.py and orphans with comments and a generator s… ([#33](#33)) ([413dc23](413dc23)) * Define JSON Schemas for ontology data release artifacts ([#32](#32)) ([b23894a](b23894a)) * fix changelog ([0285ef7](0285ef7)) * implement stubbed query functions ([334deb5](334deb5)) * regenerate all_ontology if the schema changes ([5f74bfb](5f74bfb)) * set version regex for pyton api ([3720dab](3720dab)) * setup Lintes for repo ([4a70384](4a70384)) * Store branch ancestors ("part_of" relationships) in all_ontology.json ([80e1f0d](80e1f0d)) * Store branch ancestors ("part_of" relationships) in all_ontology.json ([#38](#38)) ([64c2653](64c2653)) * **testing:** add testing for ontology-builder ([e087eca](e087eca)) * **testing:** add testing for ontology-builder ([e087eca](e087eca)) * upload assets on release ([81725db](81725db)) ### Misc * add ontology-assets to release ([b09c814](b09c814)) * add ontology-assets to release ([04835c0](04835c0)) * bootstrap release-please ([f32db86](f32db86)) * bootstrap release-please ([7d0554f](7d0554f)) * change bootstrap-sha ([f2571e8](f2571e8)) * check that pr titles follow conventional commit format ([#41](#41)) ([bd6d842](bd6d842)) * clean-up extract ontology term metadata parsing ([b9d2959](b9d2959)) * configure release-please ([#40](#40)) ([879ead2](879ead2)) * **deps:** bump owlready2 from 0.38 to 0.45 in /tools/ontology-builder ([5466a08](5466a08)) * **deps:** bump owlready2 from 0.38 to 0.45 in /tools/ontology-builder ([#37](#37)) ([db3e5c8](db3e5c8)) * **deps:** bump pyyaml from 6.0 to 6.0.1 in /tools/ontology-builder ([98dfba2](98dfba2)) * **deps:** bump pyyaml from 6.0 to 6.0.1 in /tools/ontology-builder ([#36](#36)) ([72e7e40](72e7e40)) * enable release-please for API and Assets ([#55](#55)) ([9ecda79](9ecda79)) * move curated lists to ontology-assets ([#48](#48)) ([77916df](77916df)) * move over all_ontology.json generator script + gha to repo from single-cell-curation ([f90fb05](f90fb05)) * move over all_ontology.json generator script + gha to repo from single-cell-curation ([#27](#27)) ([49237a7](49237a7)) * moving the generated artifacts ([c03c8e3](c03c8e3)) * refactor all_ontology_generator for cleanliness and modularity ([b96c552](b96c552)) * refactor all_ontology_generator for cleanliness and modularity ([b96c552](b96c552)) * refactor all_ontology_generator for cleanliness and modularity ([4384459](4384459)) * release 0.0.2 ([4972aa2](4972aa2)) * release 0.0.2 ([#42](#42)) ([19079d4](19079d4)) * release test-release ([48815dc](48815dc)) * release test-release ([77e72fe](77e72fe)) * release test-release ([#66](#66)) ([e968ef3](e968ef3)) * release test-release ([#67](#67)) ([d1057a8](d1057a8)) * release tsmith/release-assets ([63b782d](63b782d)) * release tsmith/release-assets ([#57](#57)) ([6a6b02a](6a6b02a)) * remove unused release.yml configs ([ce00bef](ce00bef)) * test-release ([5f20d18](5f20d18)) ### BugFixes * .release-please-manifest.json is valid json ([c09f2cc](c09f2cc)) * add dependabot.yml ([575f371](575f371)) * add ontology-assets ([8d51dea](8d51dea)) * add ontology-assets ([01f504d](01f504d)) * README.md ([d19efeb](d19efeb)) * README.md ([1eae21d](1eae21d)) * release pr format ([20d9d1d](20d9d1d)) * remove root from release-please-config.json ([8265b3e](8265b3e)) * test branch ([f68622a](f68622a)) * test branch ([fac02bb](fac02bb)) * test release ([aab95e8](aab95e8)) * trigger all-ontology generation if schema changes ([#46](#46)) ([3121833](3121833)) </details> --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please).

🤖 I have created a release *beep* *boop* --- <details><summary>python-api: 0.0.1</summary> ## 0.0.1 (2024-02-26) ### Features * Add API ontology querying module ([68f3168](68f3168)) * Add API ontology querying module ([#39](#39)) ([239ef2b](239ef2b)) * **API:** setup python library ([211a099](211a099)) * **API:** setup python library ([f60f897](f60f897)) * **API:** Setup the library for development ([1f7ce03](1f7ce03)) * implement stubbed query functions ([334deb5](334deb5)) * set version regex for pyton api ([3720dab](3720dab)) ### Misc * release tsmith/release-assets ([63b782d](63b782d)) * release tsmith/release-assets ([#57](#57)) ([6a6b02a](6a6b02a)) ### BugFixes * README.md ([1eae21d](1eae21d)) </details> <details><summary>ontology-assets: 0.0.1</summary> ## 0.0.1 (2024-02-26) ### Misc * move curated lists to ontology-assets ([#48](#48)) ([77916df](77916df)) * moving the generated artifacts ([c03c8e3](c03c8e3)) * release tsmith/release-assets ([63b782d](63b782d)) * release tsmith/release-assets ([#57](#57)) ([6a6b02a](6a6b02a)) </details> <details><summary>0.0.1</summary> ## 0.0.1 (2024-02-26) ### Features * Add API ontology querying module ([68f3168](68f3168)) * Add API ontology querying module ([#39](#39)) ([239ef2b](239ef2b)) * **API:** setup python library ([211a099](211a099)) * **API:** setup python library ([f60f897](f60f897)) * **API:** Setup the library for development ([1f7ce03](1f7ce03)) * **data release:** add hand curated_lists.py and orphans with comments and a generator s… ([#33](#33)) ([413dc23](413dc23)) * Define JSON Schemas for ontology data release artifacts ([#32](#32)) ([b23894a](b23894a)) * fix changelog ([0285ef7](0285ef7)) * implement stubbed query functions ([334deb5](334deb5)) * regenerate all_ontology if the schema changes ([5f74bfb](5f74bfb)) * set version regex for pyton api ([3720dab](3720dab)) * setup Lintes for repo ([4a70384](4a70384)) * Store branch ancestors ("part_of" relationships) in all_ontology.json ([80e1f0d](80e1f0d)) * Store branch ancestors ("part_of" relationships) in all_ontology.json ([#38](#38)) ([64c2653](64c2653)) * **testing:** add testing for ontology-builder ([e087eca](e087eca)) * **testing:** add testing for ontology-builder ([e087eca](e087eca)) * upload assets on release ([81725db](81725db)) ### Misc * add ontology-assets to release ([b09c814](b09c814)) * add ontology-assets to release ([04835c0](04835c0)) * bootstrap release-please ([f32db86](f32db86)) * bootstrap release-please ([7d0554f](7d0554f)) * change bootstrap-sha ([f2571e8](f2571e8)) * check that pr titles follow conventional commit format ([#41](#41)) ([bd6d842](bd6d842)) * clean-up extract ontology term metadata parsing ([b9d2959](b9d2959)) * configure release-please ([#40](#40)) ([879ead2](879ead2)) * **deps:** bump owlready2 from 0.38 to 0.45 in /tools/ontology-builder ([5466a08](5466a08)) * **deps:** bump owlready2 from 0.38 to 0.45 in /tools/ontology-builder ([#37](#37)) ([db3e5c8](db3e5c8)) * **deps:** bump pyyaml from 6.0 to 6.0.1 in /tools/ontology-builder ([98dfba2](98dfba2)) * **deps:** bump pyyaml from 6.0 to 6.0.1 in /tools/ontology-builder ([#36](#36)) ([72e7e40](72e7e40)) * enable release-please for API and Assets ([#55](#55)) ([9ecda79](9ecda79)) * move curated lists to ontology-assets ([#48](#48)) ([77916df](77916df)) * move over all_ontology.json generator script + gha to repo from single-cell-curation ([f90fb05](f90fb05)) * move over all_ontology.json generator script + gha to repo from single-cell-curation ([#27](#27)) ([49237a7](49237a7)) * moving the generated artifacts ([c03c8e3](c03c8e3)) * refactor all_ontology_generator for cleanliness and modularity ([b96c552](b96c552)) * refactor all_ontology_generator for cleanliness and modularity ([b96c552](b96c552)) * refactor all_ontology_generator for cleanliness and modularity ([4384459](4384459)) * release 0.0.2 ([4972aa2](4972aa2)) * release 0.0.2 ([#42](#42)) ([19079d4](19079d4)) * release tsmith/release-assets ([63b782d](63b782d)) * release tsmith/release-assets ([#57](#57)) ([6a6b02a](6a6b02a)) * remove unused release.yml configs ([ce00bef](ce00bef)) * test-release ([5f20d18](5f20d18)) ### BugFixes * .release-please-manifest.json is valid json ([c09f2cc](c09f2cc)) * add dependabot.yml ([575f371](575f371)) * add ontology-assets ([8d51dea](8d51dea)) * add ontology-assets ([01f504d](01f504d)) * README.md ([d19efeb](d19efeb)) * README.md ([1eae21d](1eae21d)) * release pr format ([20d9d1d](20d9d1d)) * remove root from release-please-config.json ([8265b3e](8265b3e)) * test branch ([f68622a](f68622a)) * test branch ([fac02bb](fac02bb)) * test release ([aab95e8](aab95e8)) * trigger all-ontology generation if schema changes ([#46](#46)) ([3121833](3121833)) * use matrix ([b4d5298](b4d5298)) </details> --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please).

🤖 I have created a release *beep* *boop* --- <details><summary>python-api: 0.0.1</summary> ## 0.0.1 (2024-02-26) ### Features * Add API ontology querying module ([68f3168](68f3168)) * Add API ontology querying module ([#39](#39)) ([239ef2b](239ef2b)) * **API:** setup python library ([211a099](211a099)) * **API:** setup python library ([f60f897](f60f897)) * **API:** Setup the library for development ([1f7ce03](1f7ce03)) * implement stubbed query functions ([334deb5](334deb5)) * set version regex for pyton api ([3720dab](3720dab)) ### Misc * release tsmith/release-assets ([63b782d](63b782d)) * release tsmith/release-assets ([#57](#57)) ([6a6b02a](6a6b02a)) ### BugFixes * README.md ([1eae21d](1eae21d)) </details> <details><summary>ontology-assets: 0.0.1</summary> ## 0.0.1 (2024-02-26) ### Features * upload assets on release ([#56](#56)) ([84a1c5d](84a1c5d)) ### Misc * move curated lists to ontology-assets ([#48](#48)) ([77916df](77916df)) * moving the generated artifacts ([c03c8e3](c03c8e3)) * release tsmith/release-assets ([63b782d](63b782d)) * release tsmith/release-assets ([#57](#57)) ([6a6b02a](6a6b02a)) </details> <details><summary>0.0.1</summary> ## 0.0.1 (2024-02-26) ### Features * Add API ontology querying module ([68f3168](68f3168)) * Add API ontology querying module ([#39](#39)) ([239ef2b](239ef2b)) * **API:** setup python library ([211a099](211a099)) * **API:** setup python library ([f60f897](f60f897)) * **API:** Setup the library for development ([1f7ce03](1f7ce03)) * **data release:** add hand curated_lists.py and orphans with comments and a generator s… ([#33](#33)) ([413dc23](413dc23)) * Define JSON Schemas for ontology data release artifacts ([#32](#32)) ([b23894a](b23894a)) * fix changelog ([0285ef7](0285ef7)) * implement stubbed query functions ([334deb5](334deb5)) * regenerate all_ontology if the schema changes ([5f74bfb](5f74bfb)) * set version regex for pyton api ([3720dab](3720dab)) * setup Lintes for repo ([4a70384](4a70384)) * Store branch ancestors ("part_of" relationships) in all_ontology.json ([80e1f0d](80e1f0d)) * Store branch ancestors ("part_of" relationships) in all_ontology.json ([#38](#38)) ([64c2653](64c2653)) * **testing:** add testing for ontology-builder ([e087eca](e087eca)) * **testing:** add testing for ontology-builder ([e087eca](e087eca)) * upload assets on release ([81725db](81725db)) * upload assets on release ([#56](#56)) ([84a1c5d](84a1c5d)) ### Misc * add ontology-assets to release ([b09c814](b09c814)) * add ontology-assets to release ([04835c0](04835c0)) * bootstrap release-please ([f32db86](f32db86)) * bootstrap release-please ([7d0554f](7d0554f)) * change bootstrap-sha ([f2571e8](f2571e8)) * check that pr titles follow conventional commit format ([#41](#41)) ([bd6d842](bd6d842)) * clean-up extract ontology term metadata parsing ([b9d2959](b9d2959)) * configure release-please ([#40](#40)) ([879ead2](879ead2)) * **deps:** bump owlready2 from 0.38 to 0.45 in /tools/ontology-builder ([5466a08](5466a08)) * **deps:** bump owlready2 from 0.38 to 0.45 in /tools/ontology-builder ([#37](#37)) ([db3e5c8](db3e5c8)) * **deps:** bump pyyaml from 6.0 to 6.0.1 in /tools/ontology-builder ([98dfba2](98dfba2)) * **deps:** bump pyyaml from 6.0 to 6.0.1 in /tools/ontology-builder ([#36](#36)) ([72e7e40](72e7e40)) * enable release-please for API and Assets ([#55](#55)) ([9ecda79](9ecda79)) * move curated lists to ontology-assets ([#48](#48)) ([77916df](77916df)) * move over all_ontology.json generator script + gha to repo from single-cell-curation ([f90fb05](f90fb05)) * move over all_ontology.json generator script + gha to repo from single-cell-curation ([#27](#27)) ([49237a7](49237a7)) * moving the generated artifacts ([c03c8e3](c03c8e3)) * refactor all_ontology_generator for cleanliness and modularity ([b96c552](b96c552)) * refactor all_ontology_generator for cleanliness and modularity ([b96c552](b96c552)) * refactor all_ontology_generator for cleanliness and modularity ([4384459](4384459)) * release 0.0.2 ([4972aa2](4972aa2)) * release 0.0.2 ([#42](#42)) ([19079d4](19079d4)) * release tsmith/release-assets ([63b782d](63b782d)) * release tsmith/release-assets ([#57](#57)) ([6a6b02a](6a6b02a)) * remove unused release.yml configs ([ce00bef](ce00bef)) * test-release ([5f20d18](5f20d18)) ### BugFixes * .release-please-manifest.json is valid json ([c09f2cc](c09f2cc)) * add dependabot.yml ([575f371](575f371)) * add ontology-assets ([8d51dea](8d51dea)) * add ontology-assets ([01f504d](01f504d)) * README.md ([d19efeb](d19efeb)) * README.md ([1eae21d](1eae21d)) * release pr format ([20d9d1d](20d9d1d)) * remove root from release-please-config.json ([8265b3e](8265b3e)) * test branch ([f68622a](f68622a)) * test branch ([fac02bb](fac02bb)) * test release ([aab95e8](aab95e8)) * trigger all-ontology generation if schema changes ([#46](#46)) ([3121833](3121833)) * use matrix ([b4d5298](b4d5298)) </details> --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

nayib-jose-gloria added 8 commits February 20, 2024 14:32

feat: Store branch ancestors ("part_of" relationships) in all_ontolog…

80e1f0d

…y.json

Merge branch 'main' into nayib/get-branch-ancestors

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# Conflicts: # tools/ontology-builder/src/ontology-references/all_ontology.json.gz

lint

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feat: Add API ontology querying module

68f3168

feat: implement stubbed query functions

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add unit test todo to track

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Merge branch 'main' into nayib/ontology-query-api

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# Conflicts: # tools/ontology-builder/src/env.py

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query.py --> OntologyParser object, init by schema_version

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add docstring for OntologyParser class + __init__

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feat: Add API ontology querying module #39

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