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chore: clean-up ontology_parser single fetch and bulk fetch methods + account for acceptable non-ontology terms #112

Merged
merged 2 commits into from
Mar 15, 2024
Merged

chore: clean-up ontology_parser single fetch and bulk fetch methods + account for acceptable non-ontology terms #112

merged 2 commits into from
Mar 15, 2024

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nayib-jose-gloria
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@nayib-jose-gloria nayib-jose-gloria commented Mar 14, 2024 •
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Changes

  • support "unknown" and "na" term_ids, which are non-ontology BUT are valid substitutes according to the CxG schema. Note that we may need to version this behavior, should it change in the future (i.e. acceptable non-ontology term added, removed)
  • rename all bulk fetch methods --> "map_"
  • rename all single fetch methods --> "get_"
  • added single fetch methods for high level terms, highest level terms, term descendants
  • added bulk fetch method for ancestors_with_distances and term labels
  • reordered ontology_parser to follow more logical method declarations (but this is causing the diff to look larger than it is, so I can revert if its confusing to review...)

@nayib-jose-gloria nayib-jose-gloria marked this pull request as ready for review March 14, 2024 15:55
@nayib-jose-gloria nayib-jose-gloria merged commit 2ef7435 into main Mar 15, 2024
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@nayib-jose-gloria nayib-jose-gloria deleted the nayib/misc-api-fixes branch March 15, 2024 11:49
This was referenced Mar 15, 2024
Closed
Merged
Bento007 pushed a commit that referenced this pull request Mar 15, 2024
@github-actions
chore(tsmith/api_rc_version): release python-api 0.1.0 (#119)
26ec858 
🤖 I have created a release *beep* *boop*
---


##
[0.1.0](python-api-v0.0.1...python-api-v0.1.0)
(2024-03-15)


### Features

* add data to the python package
([#87](#87))
([0eb6831](0eb6831))
* add is_valid_term_id method to OntologyParser
([#115](#115))
([72c2073](72c2073))
* include license file with python package
([#85](#85))
([2be3d81](2be3d81))
* load GH Release Assets for schema version in memory
([#72](#72))
([58bad0a](58bad0a))
* refactor ancestry mapping to include distance from descendant node +
implement functions to support curated list term mapping
([#96](#96))
([7fc3562](7fc3562))
* refer to ontology source filenames in ontology_info and return that in
get_ontology_download_url
([#106](#106))
([ff9d826](ff9d826))
* split all_ontology into individual files.
([#93](#93))
([ead59e5](ead59e5))
* Support getting download link for ontology from source repo
([#86](#86))
([fd55b76](fd55b76))


### Misc

* clean-up ontology_parser single fetch and bulk fetch methods + account
for acceptable non-ontology terms
([#112](#112))
([2ef7435](2ef7435))
* **deps-dev:** bump semantic-version from 2.8.5 to 2.10.0 in
/api/python
([#98](#98))
([dfe0b39](dfe0b39))


### BugFixes

* imports for api
([4cd3386](4cd3386))
* lint errors
([f5e4583](f5e4583))
* python api releases
([bf0477e](bf0477e))
* update requirements
([#114](#114))
([9888f3d](9888f3d))

---
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>
This was referenced Mar 15, 2024
Closed
Closed
Closed
Merged
Bento007 pushed a commit that referenced this pull request Mar 15, 2024
@github-actions
chore(tsmith/api_rc_version): release python-api 0.1.0 (#125)
24292c4 
🤖 I have created a release *beep* *boop*
---


##
[0.1.0](python-api-v0.0.1...python-api-v0.1.0)
(2024-03-15)


### Features

* add data to the python package
([#87](#87))
([0eb6831](0eb6831))
* add is_valid_term_id method to OntologyParser
([#115](#115))
([72c2073](72c2073))
* include license file with python package
([#85](#85))
([2be3d81](2be3d81))
* load GH Release Assets for schema version in memory
([#72](#72))
([58bad0a](58bad0a))
* refactor ancestry mapping to include distance from descendant node +
implement functions to support curated list term mapping
([#96](#96))
([7fc3562](7fc3562))
* refer to ontology source filenames in ontology_info and return that in
get_ontology_download_url
([#106](#106))
([ff9d826](ff9d826))
* split all_ontology into individual files.
([#93](#93))
([ead59e5](ead59e5))
* Support getting download link for ontology from source repo
([#86](#86))
([fd55b76](fd55b76))


### Misc

* clean-up ontology_parser single fetch and bulk fetch methods + account
for acceptable non-ontology terms
([#112](#112))
([2ef7435](2ef7435))
* **deps-dev:** bump semantic-version from 2.8.5 to 2.10.0 in
/api/python
([#98](#98))
([dfe0b39](dfe0b39))


### BugFixes

* imports for api
([4cd3386](4cd3386))
* lint errors
([f5e4583](f5e4583))
* python api releases
([bf0477e](bf0477e))
* update requirements
([#114](#114))
([9888f3d](9888f3d))

---
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>
This was referenced Mar 15, 2024
Closed
Merged
Bento007 pushed a commit that referenced this pull request Mar 15, 2024
@github-actions
chore(tsmith/api_rc_version): release python-api 0.1.0 (#128)
9e938f0 
🤖 I have created a release *beep* *boop*
---


##
[0.1.0](python-api-v0.0.2...python-api-v0.1.0)
(2024-03-15)


### Features

* add data to the python package
([#87](#87))
([0eb6831](0eb6831))
* add is_valid_term_id method to OntologyParser
([#115](#115))
([72c2073](72c2073))
* include license file with python package
([#85](#85))
([2be3d81](2be3d81))
* refactor ancestry mapping to include distance from descendant node +
implement functions to support curated list term mapping
([#96](#96))
([7fc3562](7fc3562))
* refer to ontology source filenames in ontology_info and return that in
get_ontology_download_url
([#106](#106))
([ff9d826](ff9d826))
* split all_ontology into individual files.
([#93](#93))
([ead59e5](ead59e5))
* Support getting download link for ontology from source repo
([#86](#86))
([fd55b76](fd55b76))


### Misc

* clean-up ontology_parser single fetch and bulk fetch methods + account
for acceptable non-ontology terms
([#112](#112))
([2ef7435](2ef7435))
* **deps-dev:** bump semantic-version from 2.8.5 to 2.10.0 in
/api/python
([#98](#98))
([dfe0b39](dfe0b39))


### BugFixes

* imports for api
([4cd3386](4cd3386))
* update requirements
([#114](#114))
([9888f3d](9888f3d))

---
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>
@github-actions github-actions bot mentioned this pull request Mar 15, 2024
Merged
Bento007 pushed a commit that referenced this pull request Mar 15, 2024
@github-actions
chore: release main (#130)
0b37dc8 
🤖 I have created a release *beep* *boop*
---


<details><summary>python-api: 0.1.0</summary>

##
[0.1.0](python-api-v0.0.2...python-api-v0.1.0)
(2024-03-15)


### Features

* add data to the python package
([#87](#87))
([0eb6831](0eb6831))
* add is_valid_term_id method to OntologyParser
([#115](#115))
([72c2073](72c2073))
* include license file with python package
([#85](#85))
([2be3d81](2be3d81))
* refactor ancestry mapping to include distance from descendant node +
implement functions to support curated list term mapping
([#96](#96))
([7fc3562](7fc3562))
* refer to ontology source filenames in ontology_info and return that in
get_ontology_download_url
([#106](#106))
([ff9d826](ff9d826))
* split all_ontology into individual files.
([#93](#93))
([ead59e5](ead59e5))
* Support getting download link for ontology from source repo
([#86](#86))
([fd55b76](fd55b76))


### Misc

* automate testpypi releases
([#118](#118))
([b5a1a66](b5a1a66))
* clean-up ontology_parser single fetch and bulk fetch methods + account
for acceptable non-ontology terms
([#112](#112))
([2ef7435](2ef7435))
* **deps-dev:** bump semantic-version from 2.8.5 to 2.10.0 in
/api/python
([#98](#98))
([dfe0b39](dfe0b39))


### BugFixes

* imports for api
([4cd3386](4cd3386))
* update requirements
([#114](#114))
([9888f3d](9888f3d))
</details>

<details><summary>ontology-assets: 0.1.0</summary>

##
[0.1.0](ontology-assets-v0.0.1...ontology-assets-v0.1.0)
(2024-03-15)


### Features

* load GH Release Assets for schema version in memory
([#72](#72))
([58bad0a](58bad0a))
* refactor ancestry mapping to include distance from descendant node +
implement functions to support curated list term mapping
([#96](#96))
([7fc3562](7fc3562))
* refer to ontology source filenames in ontology_info and return that in
get_ontology_download_url
([#106](#106))
([ff9d826](ff9d826))
* **release:** generate descendant mapping for tissues and cells
([#100](#100))
([841fddf](841fddf))
* remove all-ontology.json.gz
([83fefd6](83fefd6))
* split all_ontology into individual files.
([#93](#93))
([ead59e5](ead59e5))


### Misc

* update ontology decendant mappings
([#117](#117))
([48451af](48451af))


### BugFixes

* lint errors
([f5e4583](f5e4583))
* Schema format and validation fixes.
([#113](#113))
([0465ee7](0465ee7))
</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>
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@nayib-jose-gloria @Bento007