Neo4j 5 and refactoring #106
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commit 8e0f7ff Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri Jun 28 14:26:56 2024 -0400 adding prod back in and fixing bug for running on all environments commit b0ee58f Author: Evan Morris <evandietzmorris@gmail.com> Date: Thu Jun 6 17:43:22 2024 -0400 cleaning up commit 6790e64 Author: Evan Morris <evandietzmorris@gmail.com> Date: Mon May 13 18:25:41 2024 -0400 added option to run apoc warmup, starting to reorganize and refactor commit df522f9 Author: Evan Morris <evandietzmorris@gmail.com> Date: Mon May 13 18:24:51 2024 -0400 updating with new graphs and deployment environment name commit 49f5f83 Author: Evan Morris <evandietzmorris@gmail.com> Date: Wed May 8 12:53:35 2024 -0400 adding plater version and trapi version to validation checks, updating deployment spec commit 3e1d560 Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri Apr 26 10:24:03 2024 -0400 updating monarch version commit f1497c9 Author: Evan Morris <evandietzmorris@gmail.com> Date: Thu Apr 25 17:06:41 2024 -0400 fixing error message typo commit 4aa6fc7 Author: Evan Morris <evandietzmorris@gmail.com> Date: Thu Apr 25 17:06:32 2024 -0400 updating deployment spec commit 27d52df Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue Apr 23 17:00:51 2024 -0400 updating deployment spec for current configuration commit 45d4fa2 Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue Apr 23 17:00:35 2024 -0400 adding check for edge count as well as nodes commit a7b1831 Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri Apr 19 15:39:39 2024 -0400 making a better deployment spec for multiple environments and updating validate to match commit 5dcc959 Author: Evan Morris <evandietzmorris@gmail.com> Date: Thu Mar 7 14:24:35 2024 -0500 fixing prod url, updating cam-kp commit 6361802 Author: Evan Morris <evandietzmorris@gmail.com> Date: Wed Jan 31 14:03:27 2024 -0500 improving comments commit 3e177ed Author: Evan Morris <evandietzmorris@gmail.com> Date: Wed Jan 31 13:59:33 2024 -0500 changing the output a bit commit cfcfb2f Author: Evan Morris <evandietzmorris@gmail.com> Date: Wed Jan 17 15:05:33 2024 -0500 first pass at a validation script
…o the transpiler - implementation of neo4j bolt driver - removed most attribute handling (sources, qualifiers, biolink checks) because it was moved into the transpiler - attribute type, value type, skip list customization options just get passed to the transpiler now - consolidated setting for neo4j query timeouts
… is not released)
…chnically a jaeger collector, though it doesn't need to be)
…iceUnavailable for failed ping
- made the parameters for these endpoints make more sense (removed unnecessary node type specification when a curie is provided) - added more options for filtering one hops (predicate, node type, offset/limit) - implemented neo4j parameterization for these queries - implemented function caching for biolink leaf type determination - fixed tests
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This includes a lot of changes (too many, sorry)
Related to upgrading to neo4j 5
Refactor of how attributes are handled and customized
Implemented attribute constraints in transpiler instead of post-query in plater, but that broke most of them (should possibly revert this, so I left all the previous code there with a comment)
Using the metaKG to determine which predicates are actually in the graph and not querying for ones that don't exist
Improved error catching and reporting
Switch from JaegerExporter to OTLP
Added actions for auto releasing a neo4j image
First pass at a deployment validation script