Adding options of custom edge merging attributes and edge id attribute for LitCoin #299
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- this primarily reworks the connected_edge_subset merge strategy and makes it actually merge nodes and edges - incorporates dont_merge better - implements ability to merge one node or edge at a time - implements node/edge buffer for on disk merging to avoid processing small chunks separately - abstracts and caches biolink is_qualifier
commit 2f05969 Merge: fc56630 29e9323 Author: Jason Reilly <[email protected]> Date: Thu Feb 20 14:13:50 2025 -0500 Merge pull request #284 from RobokopU24/include-cfde-filtered-nodes Include cfde filtered nodes commit 29e9323 Author: Jason Reilly <[email protected]> Date: Thu Feb 20 14:09:27 2025 -0500 adding GWASCatalog & GTex commit 24dbdd4 Author: Jason Reilly <[email protected]> Date: Thu Feb 20 14:07:06 2025 -0500 removing strict normalization from default commit 03f8e41 Author: Jason Reilly <[email protected]> Date: Thu Feb 20 14:06:36 2025 -0500 adding parsers from Robokop commit 003f30a Author: Jason Reilly <[email protected]> Date: Wed Feb 19 17:53:16 2025 -0500 fixing predicate mapping commit a303fc8 Author: Jason Reilly <[email protected]> Date: Wed Feb 19 17:51:55 2025 -0500 setting strict_normalization to False commit 0145e9a Author: Jason Reilly <[email protected]> Date: Wed Feb 19 17:51:24 2025 -0500 neo4j as output_format, setting strict_normalization to False commit fc56630 Author: Evan Morris <[email protected]> Date: Tue Feb 18 15:32:18 2025 -0500 bumping image commit 630cb40 Author: Evan Morris <[email protected]> Date: Wed Feb 5 12:49:23 2025 -0500 changing defaults commit e5a8c8b Merge: 9fb1f5d fcb6f28 Author: Evan Morris <[email protected]> Date: Tue Feb 4 12:52:33 2025 -0500 Merge pull request #283 from RobokopU24/signor_refactor refactoring signor commit fcb6f28 Author: Evan Morris <[email protected]> Date: Tue Feb 4 12:11:56 2025 -0500 fixing logic of edge creation commit bd82ce1 Merge: 97e48ff 9fb1f5d Author: Jason Reilly <[email protected]> Date: Tue Feb 4 10:30:49 2025 -0500 Merge branch 'master' of github.com:RobokopU24/ORION commit 97e48ff Author: Jason Reilly <[email protected]> Date: Tue Feb 4 10:30:46 2025 -0500 adding .env and .idea commit 9fb1f5d Author: Evan Morris <[email protected]> Date: Tue Feb 4 00:27:47 2025 -0500 output build results for any requested graphs that are stable not just new ones commit 9b5eaa2 Author: Evan Morris <[email protected]> Date: Tue Feb 4 00:25:43 2025 -0500 updating/fixing SNPEFF switch to downloading snpeff from renci server, changing provenance infores to robokop-snpeff, adding original snpeff effect property commit 0cc5f8c Author: Evan Morris <[email protected]> Date: Mon Feb 3 17:15:39 2025 -0500 accumulating qualifiers bug commit de55e84 Author: Evan Morris <[email protected]> Date: Mon Feb 3 17:08:13 2025 -0500 refactoring signor commit 9b65b10 Author: Evan Morris <[email protected]> Date: Tue Jan 28 13:06:51 2025 -0500 catching ConnectionError as well for binding-db, fixing genomealliance commit a867b84 Author: Evan Morris <[email protected]> Date: Mon Jan 27 23:42:40 2025 -0500 hotfix for binding db version issue commit 0fb1399 Author: Evan Morris <[email protected]> Date: Mon Jan 27 23:26:32 2025 -0500 bumping image commit 529e9a5 Author: Evan Morris <[email protected]> Date: Mon Jan 27 23:26:12 2025 -0500 Adding sources to robokopkg commit 24b3b6a Author: Evan Morris <[email protected]> Date: Mon Jan 27 23:22:15 2025 -0500 only write nodes that actually have MONDO properties commit 58e5744 Author: Evan Morris <[email protected]> Date: Mon Jan 27 23:10:49 2025 -0500 bumping some parsing versions
…n disk graph merger
it's possible that the graph kgx files were already built but neo4j dumps or other outputs still need to be done, this return statement prevented that from working properly
EvanDietzMorris
approved these changes
Apr 9, 2025
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@EvanDietzMorris This PR adds options of custom edge merging attributes and edge id addition flag under graph (rather than under sources) in the graph spec as we discussed and determined for LitCoin. I added tests to cover the new functionalities in edge merging tests and they all passed, so hopefully things are just working as expected. It'd be great if you could test out the litcoin graph spec ingestion locally to make sure it works in case I missed anything. I am currently using the bagel cache file you generated previously to test things locally.