Adding a .env.sample, and remove the shell script for exporting env variables locally.#314
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added 8 commits
May 14, 2025 13:24
Contributor
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As an "outsider", I'd be in favor of this change since it strikes me as being more idiomatic for how environment variables are often used with docker compose setups. One suggested addition, though-- for safety I'd add |
Contributor
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Yea, I want to get this in. ".env" should already be in the gitignore, is it not declared correctly? |
Contributor
Oops, you're right, I was looking at a fork with an older branch. |
- general clean up and improvements for README - renamed env.sample to env.example - removed "source" from the create_env.sh command - removed pythonpath stuff completely, developers should handle that - removed docker platform from .env, it doesn't matter inside the container (I don't think) - moved developer sections of README to CONTRIBUTING
commit 320cbb8 Merge: 59751e9 95c9b42 Author: Evan Morris <evandietzmorris@gmail.com> Date: Thu May 22 14:40:03 2025 -0400 Merge pull request #329 from RobokopU24/ccidb CCIDB commit 59751e9 Merge: cebe4d5 a6782e4 Author: Evan Morris <evandietzmorris@gmail.com> Date: Thu May 22 14:39:23 2025 -0400 Merge pull request #331 from RobokopU24/tmkp removing biolink from tmkp_confidence_score for consistency commit cebe4d5 Merge: 7e2704c 63b4a60 Author: Hong Yi <hongyi@renci.org> Date: Mon May 19 21:39:21 2025 -0400 Merge pull request #291 from RobokopU24/litcoin-pipeline-integration Litcoin pipeline integration including helm chart for k8s deployment commit 63b4a60 Author: Evan Morris <evandietzmorris@gmail.com> Date: Mon May 19 18:51:33 2025 -0400 moving litcoin var to the optional section commit 8ed3ac1 Author: hyi <hongyi@renci.org> Date: Mon May 19 17:38:57 2025 -0400 add LITCOIN prefix to predicate mapping related environment variables and constants to avoid potential confusion commit a6782e4 Author: Evan Morris <evandietzmorris@gmail.com> Date: Mon May 19 15:23:47 2025 -0400 removing biolink from tmkp_confidence_score for consistency commit 95c9b42 Author: Evan Morris <evandietzmorris@gmail.com> Date: Mon May 19 15:22:56 2025 -0400 adding more mappings commit 16feffc Author: Evan Morris <evandietzmorris@gmail.com> Date: Mon May 19 15:22:43 2025 -0400 no more StrEnum - StrEnum isn't available for python 3.9 - apply strip() to all values even from inside lists commit 9f72549 Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri May 16 15:18:28 2025 -0400 removing edge properties with no values more generally commit 508dccf Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri May 16 15:14:26 2025 -0400 adding a comment about the name commit 3c55bfd Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri May 16 14:39:07 2025 -0400 resolving misc modeling issues - made effectors, phenotypes, mode of actions lowercase - clean up usage of disease context qualifier and anatomical context qualifier commit 0dddcd5 Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri May 16 12:52:29 2025 -0400 first pass at CCIDB parser commit 7e2704c Merge: 6206134 58e2f02 Author: Evan Morris <evandietzmorris@gmail.com> Date: Thu May 15 21:29:00 2025 -0400 Merge pull request #326 from Vibhorgupta31/re-import-csv Put `import csv` back in Common/extractor.py commit 58e2f02 Author: Bradford Powell <bpow@drpowell.org> Date: Thu May 15 21:09:48 2025 -0400 A previous commit removed the csv import, which is pretty important commit a1599e2 Author: hyi <hongyi@renci.org> Date: Thu May 15 20:41:49 2025 -0400 updated helm chart for orion worker deployment commit 6206134 Merge: 6fba516 f44a359 Author: Evan Morris <evandietzmorris@gmail.com> Date: Thu May 15 13:43:27 2025 -0400 Merge pull request #323 from RobokopU24/hmdb_directions_review reviewed and modified gene/metabolite edges commit f44a359 Author: Evan Morris <evandietzmorris@gmail.com> Date: Thu May 15 13:42:30 2025 -0400 bumping parser version commit 6fba516 Merge: f2712ae a017712 Author: Evan Morris <evandietzmorris@gmail.com> Date: Thu May 15 13:09:05 2025 -0400 Merge pull request #321 from Vibhorgupta31/extractor_consistency Extractor syntax updates commit 7d6c88f Author: Chris Bizon <bizon@renci.org> Date: Thu May 15 10:53:40 2025 -0400 reviewed and modified gene/metabolite edges commit f2712ae Merge: 55dd740 2caff08 Author: Evan Morris <evandietzmorris@gmail.com> Date: Thu May 15 10:35:26 2025 -0400 Merge pull request #322 from RobokopU24/issue-316 Removing independent run sections from parsers that have them commit 55dd740 Merge: 944a271 b2ddf5a Author: Evan Morris <evandietzmorris@gmail.com> Date: Thu May 15 10:31:24 2025 -0400 Merge pull request #318 from RobokopU24/original Initial attempt to keep original subject/object on edges commit b2ddf5a Author: Evan Morris <evandietzmorris@gmail.com> Date: Thu May 15 10:28:29 2025 -0400 adding original_ ids to edge inversion test commit 2caff08 Author: Hina Shah <hinashah@renci.org> Date: Thu May 15 10:27:01 2025 -0400 Removing independent run sections from parsers that have them commit 944a271 Merge: 0b68f16 e9f44cd Author: Evan Morris <evandietzmorris@gmail.com> Date: Thu May 15 10:16:59 2025 -0400 Merge pull request #320 from ITSskaraden/readme-removal Remove legacy README.md files from parser subdirectories (fixes #315) commit e9f44cd Author: Evan Morris <evandietzmorris@gmail.com> Date: Thu May 15 10:13:42 2025 -0400 adding VP readme back commit 0b68f16 Merge: 98e042b 125e902 Author: Evan Morris <evandietzmorris@gmail.com> Date: Thu May 15 09:54:34 2025 -0400 Merge pull request #317 from RobokopU24/TIGA_edges Update loadPHAROS.py to remove TIGA edges commit 125e902 Author: Evan Morris <evandietzmorris@gmail.com> Date: Thu May 15 09:53:16 2025 -0400 bumping parser version commit 084cdff Author: ITSskaraden <SkaldBjorn@yandex.ru> Date: Thu May 15 01:47:39 2025 +0300 Remove legacy README.md files from parser subdirectories (fixes #315) commit a017712 Author: Bradford Powell <bpow@drpowell.org> Date: Wed Apr 9 14:23:29 2025 -0400 Add some defaults to json_extract This allows easier parsing if someone just so happens to have an array of objects with just the right key=>value pairs. Or if they are using a generator that modifies those items on the way in... This is designed to be fully backwards compatible. commit 3eedc43 Author: Bradford Powell <bpow@drpowell.org> Date: Wed May 14 17:38:34 2025 -0400 Add exclude_unconnected_nodes argument to sql_extract and json_extract This matches the behavior of csv_extract, allowing edges to be ignored by providing an extractor function that returns `None`. A default of `False` is provided to make this completely backwards compatible. This provides consistence with csv_extract, which of the three commit 1b9c987 Author: Chris Bizon <bizon@renci.org> Date: Wed May 14 15:52:53 2025 -0400 Initial attempt to keep original subject/object on edges commit 9b063b3 Author: Kathleen Carter <163005214+eKathleenCarter@users.noreply.github.com> Date: Wed May 14 14:59:36 2025 -0400 Update loadPHAROS.py removed __name__ == '__main__' section removed TIGA edges commit 98e042b Merge: ffacc7e bf90b53 Author: Evan Morris <evandietzmorris@gmail.com> Date: Wed May 14 14:13:41 2025 -0400 Merge pull request #308 from RobokopU24/add-readme Update README commit bf90b53 Author: Hina Shah <hinashah@renci.org> Date: Wed May 14 14:05:40 2025 -0400 ENH: Update the README file with documentation for the two python scripts run through docker commit ffacc7e Merge: fa3979a 3307ff7 Author: Evan Morris <evandietzmorris@gmail.com> Date: Wed May 14 14:01:11 2025 -0400 Merge pull request #309 from RobokopU24/issue-302 Fixing typo for "PREDICATION" commit 3a06922 Author: Evan Morris <evandietzmorris@gmail.com> Date: Wed May 14 13:43:19 2025 -0400 moving the developer section to it's own file commit fe7a9dc Author: Evan Morris <evandietzmorris@gmail.com> Date: Wed May 14 12:08:34 2025 -0400 Removed log in comment and fixed typo commit 3307ff7 Author: Hina Shah <hinashah@renci.org> Date: Wed May 14 11:57:37 2025 -0400 Fixing type predication commit c058727 Author: Hina Shah <hinashah@renci.org> Date: Wed May 14 11:36:28 2025 -0400 Update README commit 1958c86 Author: hyi <hongyi@renci.org> Date: Fri May 9 17:04:35 2025 -0400 get predicate mapping integrated commit ade4945 Author: hyi <hongyi@renci.org> Date: Thu May 8 22:40:22 2025 -0400 first pass to add predicate mapping commit 9a7645c Author: hyi <hongyi@renci.org> Date: Wed Apr 23 19:59:05 2025 -0400 changed logging level from debug to info commit 7ba0a36 Author: hyi <hongyi@renci.org> Date: Wed Apr 23 16:59:18 2025 -0400 fixed celery worker queue name typo issue commit 890e20c Author: hyi <hongyi@renci.org> Date: Tue Apr 22 22:56:48 2025 -0400 update ORION to ingest data generated from the LitCoin pipeline commit 9d88b3b Merge: caf4601 fa3979a Author: hyi <hongyi@renci.org> Date: Wed Apr 9 11:02:26 2025 -0400 Merge branch 'master' into litcoin-pipeline-integration commit caf4601 Author: hyi <hongyi@renci.org> Date: Wed Mar 12 10:35:00 2025 -0400 increase memory to 10GB to address OOM when running example graph ingestion commit c083e73 Author: hyi <hongyi@renci.org> Date: Tue Mar 11 13:35:57 2025 -0400 get orion task run exception propogate to celery without catching it commit a150c14 Author: hyi <hongyi@renci.org> Date: Sun Mar 9 17:27:10 2025 -0400 added ORION worker deployment helm chart
Contributor
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I made some changes, can you review @hina-shah? Thanks |
Contributor
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I tried to resolve the conflicts, I'm not seeing any anymore, but this PR seems to think they exist still, not sure why.. |
…ipts run through docker
This matches the behavior of csv_extract, allowing edges to be ignored by providing an extractor function that returns `None`. A default of `False` is provided to make this completely backwards compatible. This provides consistence with csv_extract, which of the three
This allows easier parsing if someone just so happens to have an array of objects with just the right key=>value pairs. Or if they are using a generator that modifies those items on the way in... This is designed to be fully backwards compatible.
Two major changes: 1) STRING-DB refactor as discussed in issue. Parser version 1.2: Predicate Counts: biolink:coexpressed_with: 9248226 biolink:physically_interacts_with: 1430322 biolink:homologous_to: 232106 biolink:related_to: 58872 Knowledge Level Counts: knowledge_assertion: 10969526 Agent Type Counts: manual_agent: 10969526 Parser version 1.3 biolink:physically_interacts_with: 1007486 biolink:interacts_with: 101568 biolink:coexpressed_with: 11566 biolink:related_to: 676 Knowledge Level Counts: not_provided: 501094 knowledge_assertion: 446380 statistical_association: 91252 prediction: 82570 Agent Type Counts: text_mining_agent: 501094 manual_agent: 443190 data_analysis_pipeline: 148066 computational_model: 28946 2) Added functionality to extractor.py so that you can now give functions that produce lists for the predicate_extractor and the edge_property_extractor.
Added exclude_unconnected_nodes functionality back in Fixed PREDICATION to PREDICTION
small changes to extractor to handle with predicate is None.
Moved the default case to part of the if blocks with a else: removed the check for predicates as strings cleaned up the logic around edge props to make shared mutation less likely
adding full citation Co-authored-by: Kathleen Carter <163005214+eKathleenCarter@users.noreply.github.com>
Co-authored-by: Kathleen Carter <163005214+eKathleenCarter@users.noreply.github.com>
Co-authored-by: Kathleen Carter <163005214+eKathleenCarter@users.noreply.github.com>
Co-authored-by: Kathleen Carter <163005214+eKathleenCarter@users.noreply.github.com>
Co-authored-by: Kathleen Carter <163005214+eKathleenCarter@users.noreply.github.com>
Co-authored-by: Kathleen Carter <163005214+eKathleenCarter@users.noreply.github.com>
Co-authored-by: Kathleen Carter <163005214+eKathleenCarter@users.noreply.github.com>
Co-authored-by: Kathleen Carter <163005214+eKathleenCarter@users.noreply.github.com>
… and constants to avoid potential confusion
Bumps [requests](https://github.com/psf/requests) from 2.32.3 to 2.32.4. - [Release notes](https://github.com/psf/requests/releases) - [Changelog](https://github.com/psf/requests/blob/main/HISTORY.md) - [Commits](psf/requests@v2.32.3...v2.32.4) --- updated-dependencies: - dependency-name: requests dependency-version: 2.32.4 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com>
Author
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Closing this PR, because a new one was created #362 instead of this one. |
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