Fix Docker runtime issues, add CI checks, and refactor eFP schemas#296

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rmobmina wants to merge 781 commits intoBioAnalyticResource:devfrom

rmobmina:fix/refactor-efp-data-and-schemas

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Commits on Mar 29, 2023

Commits on Mar 30, 2023

Merge pull request #167 from asherpasha/dev
asherpasha
authored
First test of hotspots
Isaiah Hazelwood
committed
Remove volumes for local testing
Isaiah Hazelwood
committed

Commits on Apr 12, 2023

Merge pull request #2 from isaiahah/dev
isaiahah
authored
Cleanup for hotspot tools
Isaiah Hazelwood
committed
Merge pull request #3 from isaiahah/hotspots
isaiahah
authored

Commits on Apr 20, 2023

Formatting fixes
Isaiah Hazelwood
committed
Merge pull request #4 from isaiahah/hotspots
isaiahah
authored

Commits on Apr 21, 2023

flake8 style fixes
Isaiah Hazelwood
committed
Merge pull request #5 from isaiahah/hotspots
isaiahah
authored

Commits on Apr 25, 2023

Commits on Apr 26, 2023

Minor updates.
asherpasha
committed
Merge pull request #172 from asherpasha/dev
asherpasha
authored
Fix static imports
Isaiah Hazelwood
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Add hotspot util tests
Isaiah Hazelwood
committed
Merge pull request #7 from isaiahah/hotspots
isaiahah
authored

Commits on Apr 27, 2023

Merge pull request #173 from isaiahah/dev
asherpasha
authored

Commits on May 31, 2023

Commits on Jun 7, 2023

Commits on Jun 9, 2023

Added strawberry, striga, selaginella.
asherpasha
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Commits on Jun 12, 2023

Added Phelipanche and Triphysaria
asherpasha
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Commits on Jun 14, 2023

Added Brassica rappa and Physcomitrella
asherpasha
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Commits on Jun 15, 2023

Commits on Jun 17, 2023

Merge pull request #178 from asherpasha/dev
asherpasha
authored

Commits on Jul 31, 2023

Commits on Aug 30, 2023

Commits on Sep 19, 2023

Commits on Sep 20, 2023

Commits on Oct 10, 2023

Commits on Oct 17, 2023

Commits on Oct 26, 2023

original docking_utils.py file

Dien Nguyen
authored and
Dien Nguyen
committed
Add constant for hex execution path

Dien Nguyen
authored and
Dien Nguyen
committed

Commits on Nov 1, 2023

Commits on Nov 2, 2023

Commits on Nov 21, 2023

Add classes for refactoring of docking_utils.py file
dien-n-nguyen
committed

Commits on Jan 10, 2024

Commits on Jan 17, 2024

Add methods for each class
dien-n-nguyen
committed

Commits on Jan 18, 2024

Commits on Feb 1, 2024

Commits on Feb 2, 2024

Replace docking_utils.py and remove old version
dien-n-nguyen
committed

Commits on Feb 8, 2024

convert sdf_mapping to OOP and move to docking_utils.py file
dien-n-nguyen
committed

Commits on Feb 16, 2024

Fix bug to prevent creating results folder for invalid protein or ligand
dien-n-nguyen
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Commits on Feb 20, 2024

Add regex check to process bigger receptor
Dien Nguyen
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Add unittests and files for testing
Dien Nguyen
committed

Commits on Feb 27, 2024

Move test_docking_utils.py to tests/utils/ folder
Dien Nguyen
committed

Commits on Mar 4, 2024

Commits on Mar 18, 2024

Commits on Mar 19, 2024

Add regex matching to separate coordinates in docking results pdb
Dien Nguyen
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Merge remote-tracking branch 'upstream/dev' into dev
Dien Nguyen
committed

Commits on Mar 21, 2024

Add timestamp to final energies json
Dien Nguyen
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Fix styling issues
Dien Nguyen
committed

Commits on Mar 22, 2024

Fix styling issues
Dien Nguyen
committed
Fix test for testing docking that already exists
Dien Nguyen
committed

Commits on Mar 28, 2024

Make changes to test file to skip in gitbuh environment
Dien Nguyen
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Add code to skip test in CI
Dien Nguyen
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Fix code to skip test if not running on BAR
Dien Nguyen
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Fix styling
Dien Nguyen
committed

Commits on Apr 4, 2024

Add tests for SDFMapping
Dien Nguyen
committed
Fix tests to skip when not running on the BAR
Dien Nguyen
committed
Add skip tags for tests and remove print statements
Dien Nguyen
committed

Commits on Apr 25, 2024

Commits on Apr 26, 2024

Commits on May 1, 2024

API documentation and refactoring in progess.
asherpasha
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Commits on May 2, 2024

Working on gene information.
asherpasha
committed

Commits on Jun 12, 2024

added publications endpoint in gene_information
TeresasaZ
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Commits on Jun 30, 2024

Merge pull request #216 from asherpasha/dev
asherpasha
authored

Commits on Jul 8, 2024

Commits on Jul 15, 2024

Commits on Jul 22, 2024

Commits on Jul 23, 2024

Merge pull request #229 from TeresasaZ/dev
asherpasha
authored

Commits on Jul 29, 2024

Commits on Jul 30, 2024

Merge pull request #230 from asherpasha/dev
asherpasha
authored

Commits on Aug 7, 2024

llama3 fetch GET endpoint with tests, flake8 tested
VinLau
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Commits on Aug 8, 2024

Commits on Aug 14, 2024

genes by position and query genes endpoints and tests
TeresasaZ
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Commits on Aug 21, 2024

Commits on Sep 12, 2024

query multiple genes into post request; added function query single gene
TeresasaZ
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Commits on Sep 13, 2024

mfinder in interactions, together with input and output files for testing
TeresasaZ
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Commits on Sep 27, 2024

Commits on Oct 2, 2024

Commits on Dec 4, 2024

Commits on Dec 23, 2024

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Commits on Jan 28, 2025

Commits on Mar 3, 2025

mfinder second commit, most functions moved to util file. Modified interactions file, added mfinder utils file, modified test interactions file.
TeresasaZ
committed

Commits on Mar 7, 2025

Merge pull request #259 from TeresasaZ/dev
asherpasha
authored

Commits on Mar 22, 2025

Commits on Mar 28, 2025

Commits on Apr 19, 2025

Commits on Apr 22, 2025

all agent changes, including model, database, cfg, interactions, test code, and testing json files.
TeresasaZ
committed

Commits on Apr 23, 2025

modified mfinder, added github environment skip pytest
TeresasaZ
committed

Commits on May 2, 2025

Merge pull request #266 from TeresasaZ/dev
asherpasha
authored

Commits on May 12, 2025

Commits on May 15, 2025

Merge pull request #267 from TeresasaZ/dev
asherpasha
authored

Commits on Jul 24, 2025

deleted Xiao Feng's SNP additions to RNA-seq data NOT because of code quality but because provided SNP data was inaccurate and could not reach author's to get resolution (BnIR; Yang et al., 2023), …
VinLau
committed

Commits on Nov 18, 2025

edited microarray and added 2 new endpoints and created efp_proxy endpoints
rmobmina
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Commits on Dec 4, 2025

dynamic ORMs
rmobmina
committed

Commits on Jan 22, 2026

fixed comments
rmobmina
committed

Commits on Jan 29, 2026

Commits on Feb 5, 2026

Commits on Feb 12, 2026

removed POST from efp proxy and simplified endpoints to a single one
rmobmina
committed

Commits on Mar 5, 2026

add SQL Alchemy binds
rmobmina
committed

Commits on Mar 12, 2026