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Treats refactor #204

Merged
merged 4 commits into from
Mar 5, 2024
Merged

Treats refactor #204

merged 4 commits into from
Mar 5, 2024

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EvanDietzMorris
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updating treats predicate for CTD,
updating some normalization tests according to changes in the clingen allele registry

@EvanDietzMorris EvanDietzMorris requested a review from cbizon March 5, 2024 20:39
@EvanDietzMorris EvanDietzMorris merged commit d0ca276 into master Mar 5, 2024
3 checks passed
EvanDietzMorris added a commit that referenced this pull request May 16, 2024
@EvanDietzMorris
Squashed commit of the following:
59fa121 
commit 3cfa692
Author: Evan Morris <[email protected]>
Date:   Tue May 14 13:11:21 2024 -0400

    adding error checking for output_format==None

commit 3af2ee2
Author: Evan Morris <[email protected]>
Date:   Tue May 14 12:48:01 2024 -0400

    improving output_format parsing

commit 2bf5721
Author: Evan Morris <[email protected]>
Date:   Tue May 14 12:46:29 2024 -0400

    removing jsonl which does nothing

commit bc3779b
Author: Evan Morris <[email protected]>
Date:   Tue May 14 12:45:22 2024 -0400

    fixing ubergraph source id

commit 55b48c3
Author: Evan Morris <[email protected]>
Date:   Mon May 13 17:34:48 2024 -0400

    adding redundant jsonl output

commit d0cf880
Author: Evan Morris <[email protected]>
Date:   Mon May 13 17:31:49 2024 -0400

    adding option for redundant edge kg file output to the graph spec

commit aa8125b
Author: Evan Morris <[email protected]>
Date:   Mon May 13 17:23:55 2024 -0400

    moving redundant kg generation into Common

commit 132221a
Author: Evan Morris <[email protected]>
Date:   Mon May 13 17:13:45 2024 -0400

    bail before generating dumps on QC failures, but don't fail based on infores identifiers

commit 0458291
Author: Evan Morris <[email protected]>
Date:   Fri May 10 16:54:59 2024 -0400

    adding rule mining kg

commit a26349f
Author: Evan Morris <[email protected]>
Date:   Fri May 10 16:51:13 2024 -0400

    pinning pharos version in the parser instead of graph specs

commit fac5c00
Author: Evan Morris <[email protected]>
Date:   Fri May 10 16:37:49 2024 -0400

    adding dug graph spec

commit d1a3612
Author: Evan Morris <[email protected]>
Date:   Fri May 10 16:37:41 2024 -0400

    adding a slim resources values option

commit 26aabc3
Author: Evan Morris <[email protected]>
Date:   Fri May 10 16:36:59 2024 -0400

    updating image and biolink versions

commit 67a5dbf
Merge: 63f33bd adf4b0f
Author: Evan Morris <[email protected]>
Date:   Fri May 10 15:59:41 2024 -0400

    Merge pull request #225 from RobokopU24/subclass_loops

    Subclass loops and qualifier merging

commit 63f33bd
Merge: 16b24ca 78eb0e0
Author: Evan Morris <[email protected]>
Date:   Fri May 10 15:59:19 2024 -0400

    Merge pull request #224 from RobokopU24/yobokop_go2gene_fix

    Fixed broken link for SGD Gene2GOTerm download file.

commit 78eb0e0
Author: Evan Morris <[email protected]>
Date:   Fri May 10 15:49:01 2024 -0400

    adding drugmechdb to baseline in yobokop

commit 0de4d26
Author: beasleyjonm <[email protected]>
Date:   Thu May 9 13:29:23 2024 -0400

    Fixed broken link for SGD Gene2GOTerm download file.

commit adf4b0f
Author: Evan Morris <[email protected]>
Date:   Fri May 3 15:53:24 2024 -0400

    added knowledge level and agent type to pharos

commit 5f3e996
Author: Evan Morris <[email protected]>
Date:   Fri May 3 14:32:12 2024 -0400

    added test for edge merging with qualifiers

commit 20220ec
Author: Evan Morris <[email protected]>
Date:   Fri May 3 13:33:50 2024 -0400

    implementation for having edge merging include qualifiers in matching key

commit c54edc8
Author: Evan Morris <[email protected]>
Date:   Fri May 3 13:28:18 2024 -0400

    implementing removal of subclass_of loop edges

commit 45d6ced
Author: Evan Morris <[email protected]>
Date:   Fri May 3 12:55:01 2024 -0400

    making public instance of drugcentral the default in the helm chart

commit 16b24ca
Merge: 6149183 1aec57c
Author: Evan Morris <[email protected]>
Date:   Fri May 3 12:34:32 2024 -0400

    Merge pull request #221 from RobokopU24/molepro

    A PR with way too many things in it

commit 1aec57c
Author: Evan Morris <[email protected]>
Date:   Thu May 2 14:20:38 2024 -0400

    removing specific version from logging error which conflicted with the actual default

commit 8168864
Author: Evan Morris <[email protected]>
Date:   Wed May 1 16:14:39 2024 -0400

    fixed missing prefix bug

commit df44bc6
Author: Evan Morris <[email protected]>
Date:   Fri Apr 12 15:15:03 2024 -0400

    bumping parsing version

commit 5968f3e
Author: Evan Morris <[email protected]>
Date:   Fri Apr 12 15:14:38 2024 -0400

    fixing agent type typo

commit 55b99b5
Author: Evan Morris <[email protected]>
Date:   Fri Apr 12 00:44:36 2024 -0400

    removing biolink prefix from edge and node properties, removing properties with no values from headers, improved comments

commit 759c513
Author: Evan Morris <[email protected]>
Date:   Fri Apr 12 00:23:52 2024 -0400

    adding some new env vars to the docker-compose

commit 335b91c
Author: Evan Morris <[email protected]>
Date:   Fri Apr 12 00:13:42 2024 -0400

    changing args for neo4j_dump so that the output directory and sources can be in different places

commit 26c4aa6
Author: Evan Morris <[email protected]>
Date:   Thu Apr 11 11:25:45 2024 -0400

    bumping vp parsing version

commit 81d790f
Author: Evan Morris <[email protected]>
Date:   Thu Apr 11 11:22:28 2024 -0400

    moving get_goa_edge_properties back outside of the class (to fix viral proteome)

commit fd9033a
Author: Evan Morris <[email protected]>
Date:   Thu Apr 11 10:08:14 2024 -0400

    fixing leftover staticmethod declaration

commit d3d5739
Author: Evan Morris <[email protected]>
Date:   Thu Apr 11 04:11:20 2024 -0400

    added publication nodes and edges

commit 4eca7be
Author: Evan Morris <[email protected]>
Date:   Thu Apr 11 04:10:30 2024 -0400

    added knowledge level and agent type, commented out extra gene groups file download

commit 24cebab
Author: Evan Morris <[email protected]>
Date:   Thu Apr 11 04:09:57 2024 -0400

    fixed bug with backwards increases_transport_of edges, added knowledge level and agent type

commit 555fb00
Author: Evan Morris <[email protected]>
Date:   Thu Apr 11 04:09:27 2024 -0400

    fixed missing publications and qualified_predicate bug, added knowledge level and agent type

commit b62a969
Author: Evan Morris <[email protected]>
Date:   Thu Apr 11 04:08:46 2024 -0400

    adding knowledge level and agent type, using some more constants

commit 214b104
Author: Evan Morris <[email protected]>
Date:   Thu Apr 11 04:08:20 2024 -0400

    adding knowledge level and agent type

commit 00503f9
Author: Evan Morris <[email protected]>
Date:   Thu Apr 11 04:06:29 2024 -0400

    added evidence code to knowledge level and agent type mapping

commit 2359a69
Author: Evan Morris <[email protected]>
Date:   Thu Apr 11 04:06:03 2024 -0400

    adding knowledge level and agent type, switching to use some constants

commit 08faa26
Author: Evan Morris <[email protected]>
Date:   Thu Apr 11 04:05:34 2024 -0400

    adding ability to fetch data from public DB, bumping source data version, adding knowledge level and agent type, adding drugbank knowledge source mapping and logging unmapped ks

commit 3e12154
Author: Evan Morris <[email protected]>
Date:   Thu Apr 11 04:04:05 2024 -0400

    adding knowledge level and agent type, general clean up

commit b9b07a8
Author: Evan Morris <[email protected]>
Date:   Thu Apr 11 04:03:04 2024 -0400

    adding knowledge level and agent type

commit 7785179
Author: Evan Morris <[email protected]>
Date:   Thu Apr 11 04:00:49 2024 -0400

    adding knowledge level and agent type, a bit of general clean up

commit b679768
Author: Evan Morris <[email protected]>
Date:   Thu Apr 11 03:59:19 2024 -0400

    fixing extra quote and commenting out drugmechdb until we decide to put it on automat

commit e16628d
Author: Evan Morris <[email protected]>
Date:   Thu Apr 11 03:56:25 2024 -0400

    adding predicate counts organized by knowledge source to metadata

commit 8df1571
Merge: cb3c2d2 fc1786e
Author: Evan Morris <[email protected]>
Date:   Thu Apr 11 01:35:51 2024 -0400

    Merge remote-tracking branch 'origin/DrugMechDBfulldataparser' into molepro

commit fc1786e
Author: beasleyjonm <[email protected]>
Date:   Wed Apr 10 15:08:49 2024 -0400

    Update loadDrugMechDB.py

    Changed "qualifier_predicate" to "qualified_predicate"

commit a9be99f
Author: beasleyjonm <[email protected]>
Date:   Wed Apr 10 15:08:04 2024 -0400

    Update drugmechdb_predicate_map.json

    Changed "qualifier_predicate" to "qualified_predicate"

commit cb3c2d2
Author: Evan Morris <[email protected]>
Date:   Mon Apr 8 15:53:47 2024 -0400

    moving biolink prefix mapping to bl_utils, removing some obsolete workarounds for biolink prefix / IRI mappings

commit 2f295b3
Author: Evan Morris <[email protected]>
Date:   Mon Apr 8 11:08:54 2024 -0400

    fixed data_services env var

commit 63aac81
Author: beasleyjonm <[email protected]>
Date:   Mon Apr 8 00:56:02 2024 -0400

    Updated parser to consolidate all relevant drugmechdb path ids into list on unique edges.

commit c16aa70
Author: beasleyjonm <[email protected]>
Date:   Sun Apr 7 01:04:17 2024 -0400

    Updated parser to parse every edge in the original db. Manually mapped un-normalized ids.

commit 632db5c
Author: Evan Morris <[email protected]>
Date:   Fri Apr 5 17:35:49 2024 -0400

    adding knowledge level and agent type

commit 51881ad
Author: Evan Morris <[email protected]>
Date:   Tue Mar 26 15:08:57 2024 -0400

    updating some requirement versions and changing everything to specific pinned versions

commit 2a00d29
Author: Evan Morris <[email protected]>
Date:   Tue Mar 26 15:08:27 2024 -0400

    adding bl_version to helm charts and removing unnecessary neo4j password

commit 9c0ea2b
Author: Evan Morris <[email protected]>
Date:   Tue Mar 26 15:06:54 2024 -0400

    adding error checking and fallback for ssl issues

commit f3b1d37
Author: Evan Morris <[email protected]>
Date:   Tue Mar 26 14:19:09 2024 -0400

    switching to http due to ssl errors with the https

commit a83c7a8
Author: Evan Morris <[email protected]>
Date:   Tue Mar 26 11:50:32 2024 -0400

    bumping parsing versions

commit 5923994
Author: Evan Morris <[email protected]>
Date:   Tue Mar 26 11:49:30 2024 -0400

    adding error checking for fields coming from llm that aren't strings

commit 2730218
Author: Evan Morris <[email protected]>
Date:   Mon Mar 25 23:19:46 2024 -0400

    updating latest image

commit 88bf8fd
Author: Evan Morris <[email protected]>
Date:   Mon Mar 25 23:18:59 2024 -0400

    removing extra entity extractor graph

commit 0c245f9
Author: Evan Morris <[email protected]>
Date:   Mon Mar 25 23:18:08 2024 -0400

    updated for new data, added abstract id to entity extractor and changed over to csv format output

commit 3ee028a
Author: Evan Morris <[email protected]>
Date:   Mon Mar 25 22:34:49 2024 -0400

    making a couple env vars optional, adding name res endpoint as an env var

commit cde0bce
Author: Evan Morris <[email protected]>
Date:   Mon Mar 25 22:28:57 2024 -0400

    fixing bug where fetch retry didn't try to fetch for the same version as it tried

commit 996e8e4
Author: Evan Morris <[email protected]>
Date:   Mon Mar 25 22:28:00 2024 -0400

    adding litcoin from litcoin branches - merge was messy so new commits

commit fcaa439
Author: Evan Morris <[email protected]>
Date:   Thu Mar 21 16:07:58 2024 -0400

    updating version for monarch kg

commit 27d338b
Author: Evan Morris <[email protected]>
Date:   Thu Mar 21 16:06:25 2024 -0400

    adding aggregator knowledge source for cam kp

commit 54b8cc2
Author: Evan Morris <[email protected]>
Date:   Wed Mar 20 15:11:16 2024 -0400

    forcing just one primary knowledge source instead of splitting

commit 837c339
Author: Evan Morris <[email protected]>
Date:   Wed Mar 20 11:56:22 2024 -0400

    updating with better defaults for sterling

commit 0aa6a2e
Author: Evan Morris <[email protected]>
Date:   Wed Mar 20 11:55:25 2024 -0400

    bumping requirements for bmt and jsonlines

commit e2c462a
Author: Evan Morris <[email protected]>
Date:   Wed Mar 20 11:54:42 2024 -0400

    making neo4j logs write to same scratch directory (hoping to solve permissions issues)

commit 19423b2
Author: Evan Morris <[email protected]>
Date:   Wed Mar 20 11:53:33 2024 -0400

    improving neo4j dump generation options and logging from cli entrypoint

commit be5ba67
Author: Evan Morris <[email protected]>
Date:   Wed Mar 20 11:27:35 2024 -0400

    cleaning up qualifier value ancestors and making sure the edge with no qualifiers gets written

commit 859a9eb
Author: Evan Morris <[email protected]>
Date:   Wed Mar 20 06:10:38 2024 -0400

    making BL_VERSION configurable with an env var and enforced with bmt

commit 49e55d1
Author: Evan Morris <[email protected]>
Date:   Wed Mar 20 06:02:09 2024 -0400

    refactoring for performance and cleanup, now handles cases with direction but no aspect, using constants for qualifiers, make tqdm optional

commit 5574f28
Author: Evan Morris <[email protected]>
Date:   Wed Mar 20 05:58:09 2024 -0400

    removing extra empty properties, handling multiple primary knowledge sources

commit cf541c2
Author: Evan Morris <[email protected]>
Date:   Wed Mar 20 05:55:13 2024 -0400

    making it so that invalid infores ids don't crash normalization again

commit 74f0b02
Author: Evan Morris <[email protected]>
Date:   Wed Mar 20 03:27:08 2024 -0400

    Squashed commit of the following:

    commit 28fe0f5
    Author: james0032 <[email protected]>
    Date:   Fri Mar 8 21:44:56 2024 +0000

        predicate format corrected

    commit b0ba22d
    Merge: 9bf375c 421a9a1
    Author: James Chung <[email protected]>
    Date:   Wed Nov 22 10:55:22 2023 -0500

        merge for snakify curie

    commit 9bf375c
    Author: James Chung <[email protected]>
    Date:   Wed Nov 22 10:43:25 2023 -0500

        QUALIFIED_PREDICATE

    commit 421a9a1
    Author: Evan Morris <[email protected]>
    Date:   Fri Nov 17 14:15:27 2023 -0500

        converting predicates from bmt get_ancestors to snakified biolink curies

    commit e92b623
    Author: James Chung <[email protected]>
    Date:   Fri Aug 25 14:56:27 2023 -0400

        First version of redundant graph generator

commit 1ae25c9
Author: Evan Morris <[email protected]>
Date:   Wed Mar 20 03:14:32 2024 -0400

    first pass at molepro parser, really the first implementation of a generic parser

commit 36b8463
Author: Evan Morris <[email protected]>
Date:   Wed Mar 20 03:13:05 2024 -0400

    adding the other form of synonym property

commit 373af9c
Author: Evan Morris <[email protected]>
Date:   Wed Mar 20 03:12:38 2024 -0400

    adding a way to write just one normalized node

commit 6a16c0e
Author: Evan Morris <[email protected]>
Date:   Wed Mar 20 03:12:07 2024 -0400

    adding more groupings

commit a0dffb3
Author: Evan Morris <[email protected]>
Date:   Wed Mar 20 01:41:59 2024 -0400

    adding more node constants and rearranging some, removing biolink from knowledge source attributes

commit 53b3375
Author: Evan Morris <[email protected]>
Date:   Wed Mar 20 01:14:02 2024 -0400

    cleaning up unnecessary defaults for nodes, this is functionally equivalent

commit fda2bf2
Author: Evan Morris <[email protected]>
Date:   Wed Mar 20 01:13:22 2024 -0400

    updating binding to use appropriate edge property constants

commit 1f0e6f4
Author: Evan Morris <[email protected]>
Date:   Wed Mar 20 01:12:25 2024 -0400

    removing obsolete imports

commit 5d0e150
Author: Evan Morris <[email protected]>
Date:   Wed Mar 20 01:11:50 2024 -0400

    reorganized constants: moved node_types.py into biolink_constants.py, added lots of edge properties, changed from using ROOT_ENTITY to just NAMED_THING

commit 6149183
Merge: f341395 190b7d7
Author: beasleyjonm <[email protected]>
Date:   Wed Mar 13 15:12:37 2024 -0400

    Merge pull request #210 from RobokopU24/graph_spec_tweak

    adding option for specifying normalization_code_version in graph spec

commit f341395
Merge: d0ca276 24c4fb0
Author: Evan Morris <[email protected]>
Date:   Wed Mar 13 14:56:12 2024 -0400

    Merge pull request #208 from RobokopU24/update-infores-catalog-link

    Update infores catalog link

commit 24c4fb0
Author: beasleyjonm <[email protected]>
Date:   Mon Mar 11 14:16:15 2024 -0400

    Updating the infores catalog link to the new repo for infores.

commit f682479
Author: beasleyjonm <[email protected]>
Date:   Fri Mar 8 14:13:09 2024 -0500

    Added parser for the KinAce database of kinase-substrate phosphorylation reactions.

commit 190b7d7
Author: Evan Morris <[email protected]>
Date:   Wed Mar 6 13:00:48 2024 -0500

    adding option for specifying normalization_code_version in graph spec

commit d0ca276
Merge: 0daa63f dda70ae
Author: Evan Morris <[email protected]>
Date:   Tue Mar 5 16:16:42 2024 -0500

    Merge pull request #204 from RobokopU24/treats_refactor

    Treats refactor

commit dda70ae
Merge: bdff1c5 0daa63f
Author: Evan Morris <[email protected]>
Date:   Tue Mar 5 15:37:41 2024 -0500

    Merge branch 'master' into treats_refactor

commit 0daa63f
Merge: bfdc5c4 0482595
Author: Evan Morris <[email protected]>
Date:   Tue Mar 5 15:37:04 2024 -0500

    Merge pull request #202 from RobokopU24/dependabot/pip/orjson-3.9.15

    Bump orjson from 3.8.10 to 3.9.15

commit bdff1c5
Author: Evan Morris <[email protected]>
Date:   Tue Mar 5 15:30:21 2024 -0500

    removing obsolete comment

commit a79e7de
Author: Evan Morris <[email protected]>
Date:   Tue Mar 5 15:28:34 2024 -0500

    use treats_or_applied_or_studied_to_treat instead of ameloriates

commit 034c1ab
Author: Evan Morris <[email protected]>
Date:   Tue Mar 5 14:42:24 2024 -0500

    updating variant normalization tests in accordance with changes in the clingen allele registry

commit 0482595
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Feb 26 21:39:25 2024 +0000

    Bump orjson from 3.8.10 to 3.9.15

    Bumps [orjson](https://github.com/ijl/orjson) from 3.8.10 to 3.9.15.
    - [Release notes](https://github.com/ijl/orjson/releases)
    - [Changelog](https://github.com/ijl/orjson/blob/master/CHANGELOG.md)
    - [Commits](ijl/orjson@3.8.10...3.9.15)

    ---
    updated-dependencies:
    - dependency-name: orjson
      dependency-type: direct:production
    ...

    Signed-off-by: dependabot[bot] <[email protected]>

commit bfdc5c4
Merge: 7e5c208 71a6936
Author: beasleyjonm <[email protected]>
Date:   Mon Feb 19 16:05:43 2024 -0500

    Merge pull request #201 from RobokopU24/logging_cleanup

    Logging cleanup

commit 71a6936
Author: Evan Morris <[email protected]>
Date:   Mon Feb 19 15:16:50 2024 -0500

    create the graphs directory like the others by default

commit 18b3d01
Author: Evan Morris <[email protected]>
Date:   Mon Feb 19 15:16:25 2024 -0500

    removing remnants of old logging initialization - this happens in the parent class now

commit 6013c12
Author: Evan Morris <[email protected]>
Date:   Mon Feb 19 15:15:24 2024 -0500

    removing obsolete function

commit 7e5c208
Merge: 2c777a2 2507270
Author: Evan Morris <[email protected]>
Date:   Wed Feb 14 14:29:14 2024 -0500

    Merge pull request #195 from bpow/branding-orion

    Branding changes for the ORION name

commit 2507270
Merge: 2269f42 2c777a2
Author: Evan Morris <[email protected]>
Date:   Wed Feb 14 14:11:01 2024 -0500

    Merge branch 'master' into branding-orion

commit 2c777a2
Merge: 39c2780 ed43a35
Author: beasleyjonm <[email protected]>
Date:   Mon Feb 12 15:44:52 2024 -0500

    Merge pull request #200 from RobokopU24/sgd_fixes

    fixing publications issues

commit ed43a35
Author: Evan Morris <[email protected]>
Date:   Mon Feb 12 12:23:15 2024 -0500

    fixing publications issues - don't include ? entries, make sure the ids are strings not floats

commit 39c2780
Merge: 4dea03a 805648b
Author: beasleyjonm <[email protected]>
Date:   Fri Feb 9 13:58:45 2024 -0500

    Merge pull request #199 from RobokopU24/data_modeling_fixes

    Data modeling fixes & normalization conflation

commit 805648b
Author: Evan Morris <[email protected]>
Date:   Fri Feb 9 13:57:02 2024 -0500

    fixing qualifier key

commit b33332c
Author: Evan Morris <[email protected]>
Date:   Fri Feb 9 13:54:20 2024 -0500

    changing reactome regulator edges to use affects increased/decreased expression model instead of regulates

commit 28780d3
Author: Evan Morris <[email protected]>
Date:   Fri Feb 9 13:28:48 2024 -0500

    adding qualified predicate and object aspect to regulates edges, minor syntax cleanup

commit 4dea03a
Merge: 5ade525 a7b53d9
Author: beasleyjonm <[email protected]>
Date:   Mon Feb 5 11:11:12 2024 -0500

    Merge pull request #198 from RobokopU24/yeast_stuff

    Yeast stuff

commit 1dd32df
Merge: 3c39ead a7b53d9
Author: Evan Morris <[email protected]>
Date:   Mon Feb 5 11:03:42 2024 -0500

    Merge branch 'yeast_stuff' into data_modeling_fixes

commit a7b53d9
Author: Evan Morris <[email protected]>
Date:   Mon Feb 5 11:03:06 2024 -0500

    updating histone modification go term (the old one was obsoleted)

commit 8caa33b
Author: Evan Morris <[email protected]>
Date:   Mon Feb 5 11:02:41 2024 -0500

    removing whitespace from sgd versions

commit 3c39ead
Merge: 329f091 501e797
Author: Evan Morris <[email protected]>
Date:   Fri Feb 2 14:27:04 2024 -0500

    Merge branch 'yeast_stuff' into data_modeling_fixes

commit 501e797
Author: Evan Morris <[email protected]>
Date:   Fri Feb 2 13:37:58 2024 -0500

    bumping source versions for yeast parsers without good versioning to start fresh

commit e9fa2a1
Author: Evan Morris <[email protected]>
Date:   Fri Feb 2 13:35:13 2024 -0500

    implemented version retrieval, consolidated duplicate extractors reading from the same files, switched to constants for some hard coded indexes, clean up to match changes to the retrieval (added cpx prefixes and removed some unneeded string manipulations)

commit ecde913
Author: Evan Morris <[email protected]>
Date:   Fri Feb 2 13:20:44 2024 -0500

    fixing newline bug in gene2complex properties, moving complex link creation to parser, removing CPX prefix from complex2goterm and cleaning up

commit 8d82ba9
Author: Evan Morris <[email protected]>
Date:   Fri Feb 2 11:38:29 2024 -0500

    cleaning up comment and print

commit edaac97
Author: Evan Morris <[email protected]>
Date:   Wed Jan 31 15:51:21 2024 -0500

    implemented real source versioning

commit 329f091
Author: Evan Morris <[email protected]>
Date:   Tue Jan 30 13:39:59 2024 -0500

    changing HGNC modify date to exclude days to prevent excessive updates

commit 49c59ea
Author: Evan Morris <[email protected]>
Date:   Tue Jan 30 13:39:17 2024 -0500

    adding exclude_day option for get_ftp_file_date

commit 8f03972
Author: Evan Morris <[email protected]>
Date:   Tue Jan 30 13:07:14 2024 -0500

    adding retries for node norm 5xx errors, turning on drug chemical conflate, bumping normalization code version, general clean up

commit 71ab0be
Author: Evan Morris <[email protected]>
Date:   Mon Jan 29 10:59:29 2024 -0500

    fixing encoding for compounds file - default/utf cannot read all characters, cleaning up metadata

commit deae0c7
Author: Evan Morris <[email protected]>
Date:   Fri Jan 26 14:49:45 2024 -0500

    bumping parsing version

commit 544440e
Author: Evan Morris <[email protected]>
Date:   Fri Jan 26 14:48:27 2024 -0500

    updating baseline description

commit 5ac6121
Author: Evan Morris <[email protected]>
Date:   Fri Jan 26 12:03:30 2024 -0500

    cleaning up hmdb some and fixing direction of affects abundance edges

commit b9e4051
Author: Evan Morris <[email protected]>
Date:   Fri Jan 26 12:01:20 2024 -0500

    fixing mismatch between regulates predicate and qualifiers

commit 2269f42
Author: Bradford Powell <[email protected]>
Date:   Fri Jan 5 15:40:32 2024 -0500

    replace obsolete repository name

commit 9e5a172
Author: Bradford Powell <[email protected]>
Date:   Fri Jan 5 15:39:36 2024 -0500

    branding changes for helm chart

commit 6d80579
Author: Bradford Powell <[email protected]>
Date:   Fri Jan 5 15:29:06 2024 -0500

    branding: the project is now ORION

    s/DATA_SERVICES/ORION/g, and
    s/Data_services/ORION/g

commit 27f3566
Author: Bradford Powell <[email protected]>
Date:   Fri Jan 5 15:23:19 2024 -0500

    update repository URL

commit 5ade525
Merge: 79a8241 379bee4
Author: Evan Morris <[email protected]>
Date:   Tue Jan 2 10:58:29 2024 -0500

    Merge pull request #194 from RobokopU24/monarch-kg-and-ubergraph

    Parser updates

commit 379bee4
Author: Evan Morris <[email protected]>
Date:   Tue Dec 12 12:01:39 2023 -0500

    fixing biolink url that changed

commit eeb342b
Author: Evan Morris <[email protected]>
Date:   Mon Dec 11 21:34:13 2023 -0500

    removing extra graph spec

commit 3070153
Author: Evan Morris <[email protected]>
Date:   Mon Dec 11 21:33:45 2023 -0500

    updating graph specs to reflect changes biolink->monarchkg and ubergraph->ubergraphnonredundant,
    unpinning mondoprops version

commit 470402b
Author: Evan Morris <[email protected]>
Date:   Mon Dec 11 21:19:31 2023 -0500

    updating ubergraph infores to ubergraph,
    removing default node descriptions from ubergraph,
    making redundant vs nonredundant more explicit in source ids and constants

commit 897b122
Author: Evan Morris <[email protected]>
Date:   Mon Dec 11 19:14:29 2023 -0500

    adding source version to release metadata

commit ce29861
Merge: 2908a5d 17bf1aa
Author: Evan Morris <[email protected]>
Date:   Mon Dec 11 18:56:36 2023 -0500

    Merge branch 'FixingBindingDBPublications' into monarch-kg-and-ubergraph

commit 17bf1aa
Author: Evan Morris <[email protected]>
Date:   Mon Dec 11 18:56:18 2023 -0500

    bumped parsing version, unpinned binding db version and fixed for new file name format, bit of clean up

commit 2908a5d
Author: Evan Morris <[email protected]>
Date:   Mon Dec 11 15:50:59 2023 -0500

    updating actions versions

commit 40e71e6
Author: Evan Morris <[email protected]>
Date:   Mon Dec 11 15:44:23 2023 -0500

    changing so that all invalid infores ids are output in the logs, not just the first one encountered

commit bb1468c
Author: Evan Morris <[email protected]>
Date:   Mon Dec 11 15:42:55 2023 -0500

    replacing biolink parser with new format of monarch kg

commit 571deb7
Author: Evan Morris <[email protected]>
Date:   Mon Dec 11 15:40:57 2023 -0500

    updating text and fixing typo for cam kp automat

commit 58a0b29
Author: Evan Morris <[email protected]>
Date:   Mon Dec 11 15:40:10 2023 -0500

    adding gzip option to jsonl file iterator

commit 63ef381
Author: Evan Morris <[email protected]>
Date:   Mon Dec 11 15:39:45 2023 -0500

    adding better error message for node norm 422 respones,
    decreasing # of curies sent to bl lookup

commit 4864232
Author: beasleyjonm <[email protected]>
Date:   Thu Dec 7 13:02:14 2023 -0500

    Fixed a previous change that was causing publications to not be added properly. Also adding back in Pubchem assay ids and patent ids.

commit 79a8241
Merge: 6167ba6 2cd4ed7
Author: beasleyjonm <[email protected]>
Date:   Fri Oct 27 10:38:17 2023 -0400

    Merge pull request #188 from RobokopU24/parser_and_normalization_updates

    Parser and normalization updates

commit 2cd4ed7
Author: Evan Morris <[email protected]>
Date:   Wed Oct 11 15:45:05 2023 -0400

    reverting drug chemical conflation flag for now (waiting on node norm bug fix)

commit 2f79860
Author: Evan Morris <[email protected]>
Date:   Wed Oct 11 15:43:31 2023 -0400

    pulling in changes from JM - adding a few edge types

commit 0ddc8cc
Author: Evan Morris <[email protected]>
Date:   Fri Oct 6 10:29:10 2023 -0400

    fixing broken keyword argument

commit 900d511
Author: Evan Morris <[email protected]>
Date:   Fri Oct 6 01:22:39 2023 -0400

    removing cam kp from resource hog list, it's not really that big right now

commit abb07b8
Merge: 894d6e0 c597606
Author: Evan Morris <[email protected]>
Date:   Fri Oct 6 01:20:17 2023 -0400

    Merge branch 'reactome_complex_handling' into parser_and_normalization_updates

commit c597606
Author: Evan Morris <[email protected]>
Date:   Fri Oct 6 01:19:40 2023 -0400

    cleaning up DRY code a bit

commit d43789e
Author: Evan Morris <[email protected]>
Date:   Fri Oct 6 00:55:25 2023 -0400

    removing duplicate entry

commit f06e324
Author: Evan Morris <[email protected]>
Date:   Fri Oct 6 00:54:23 2023 -0400

    removing duplicate entry

commit 3fd2347
Merge: 7d15da1 6167ba6
Author: beasleyjonm <[email protected]>
Date:   Wed Oct 4 02:01:40 2023 -0400

    Merge branch 'master' into reactome_complex_handling

commit 7d15da1
Author: beasleyjonm <[email protected]>
Date:   Tue Oct 3 16:30:58 2023 -0400

    Edges from complexes are now represented as edges from the individual components of the complex, with a 'comple_context' edge property to record the complex name the edge was derived from.

commit 894d6e0
Author: Evan Morris <[email protected]>
Date:   Tue Oct 3 15:38:52 2023 -0400

    fixing broken source id

commit 45b40b2
Author: Evan Morris <[email protected]>
Date:   Tue Oct 3 15:23:38 2023 -0400

    un-pinning GWASCatalog version woohoo

commit 646b8b4
Author: Evan Morris <[email protected]>
Date:   Tue Oct 3 15:21:47 2023 -0400

    updating output url and image tag

commit 243fb67
Author: Evan Morris <[email protected]>
Date:   Tue Oct 3 15:20:43 2023 -0400

    using description constant

commit f0b932a
Author: Evan Morris <[email protected]>
Date:   Tue Oct 3 15:19:58 2023 -0400

    added p prefix to affinity parameter, discarding empty affinity or affinity parameter

commit eb24239
Author: Evan Morris <[email protected]>
Date:   Tue Oct 3 15:14:14 2023 -0400

    added support for qualifiers

commit cdd812f
Author: Evan Morris <[email protected]>
Date:   Tue Oct 3 14:20:41 2023 -0400

    bumping BINDING parser version after previous changes

commit 515978a
Author: Evan Morris <[email protected]>
Date:   Tue Oct 3 14:20:12 2023 -0400

    improved error handling for bad node types

commit 23578ad
Author: Evan Morris <[email protected]>
Date:   Mon Oct 2 11:03:17 2023 -0400

    adding descriptions and drug_chemical_conflate to node normalization

commit fff7b86
Author: Evan Morris <[email protected]>
Date:   Mon Oct 2 10:59:36 2023 -0400

    adding a nested try block for more accurate error messaging

commit 6167ba6
Merge: 89183d8 e2eee0c
Author: beasleyjonm <[email protected]>
Date:   Mon Sep 18 13:12:51 2023 -0400

    Merge pull request #181 from RobokopU24/realign_bindingdb

    aligned bindingdb

commit e2eee0c
Author: cbizon <[email protected]>
Date:   Mon Sep 18 09:00:43 2023 -0400

    Removed on/off, set Ki back to binds

commit 385c98a
Author: cbizon <[email protected]>
Date:   Fri Sep 15 15:39:17 2023 -0400

    aligned bindingdb

commit 08aa891
Author: beasleyjonm <[email protected]>
Date:   Wed Sep 6 14:25:31 2023 -0400

    Fixed issues with downloading file and getting latest source version.

commit f979316
Author: beasleyjonm <[email protected]>
Date:   Wed Sep 6 13:41:17 2023 -0400

    Parser for DrugMechDB Protein/Gene-[biolink:target_for]->DiseaseOrPhenotypicFeature edges.

commit 89183d8
Merge: 39135f8 e423ff4
Author: Evan Morris <[email protected]>
Date:   Tue Aug 22 22:34:43 2023 -0400

    Merge pull request #176 from RobokopU24/BindingDB-Updates

    Binding db updates

commit e423ff4
Author: Evan Morris <[email protected]>
Date:   Tue Aug 22 16:37:56 2023 -0400

    replacing deduplication technique with a more simple/efficient way of doing it,
    using constant for publications and affinity,
    bumping parsing version

commit 975ceff
Author: Evan Morris <[email protected]>
Date:   Tue Aug 22 16:31:11 2023 -0400

    making default node name an empty string instead of null (unrelated to binding)

commit 39135f8
Merge: 696468d 7ca750e
Author: Evan Morris <[email protected]>
Date:   Tue Aug 22 14:37:36 2023 -0400

    Merge pull request #179 from RobokopU24/beasleyjonm-patch-1

    Update loadReactome.py

commit 7ca750e
Author: Evan Morris <[email protected]>
Date:   Tue Aug 22 14:34:56 2023 -0400

    switching to use the categories init parameter of kgxnode and a constant instead of hardcoding node category

commit 81ac2ec
Author: beasleyjonm <[email protected]>
Date:   Tue Aug 22 14:16:52 2023 -0400

    Update loadReactome.py

    Just changed 'categories' to 'category' on node property keys.

commit b6f6aa8
Author: beasleyjonm <[email protected]>
Date:   Wed Aug 16 14:06:32 2023 -0400

    Greatly improved speed of BindingDB parser.

commit 784a446
Author: beasleyjonm <[email protected]>
Date:   Fri Aug 11 10:36:57 2023 -0400

    Updated BindingDB parser to correctly add all references to a 'publications' edge property.

commit 696468d
Merge: e9cc03c 4d01f74
Author: Evan Morris <[email protected]>
Date:   Thu Aug 10 23:30:00 2023 -0400

    Merge pull request #175 from RobokopU24/loadingReactome

    Adding 'MacromolecularComplex' category to Complex nodes, making a few other fixes.

commit 4d01f74
Author: beasleyjonm <[email protected]>
Date:   Thu Aug 10 06:12:50 2023 -0400

    Adding 'MacromolecularComplex' category to Complex nodes.

commit e9cc03c
Merge: 9180707 75386b1
Author: beasleyjonm <[email protected]>
Date:   Wed Aug 9 13:21:26 2023 -0400

    Merge pull request #174 from RobokopU24/neo_cli_patch

    fixing neo4j cli and adding option to specify node and edge filenames

commit 75386b1
Author: Evan Morris <[email protected]>
Date:   Wed Aug 9 13:18:25 2023 -0400

    fixing neo4j cli and adding option to specify node and edge filenames

commit 9180707
Merge: aaa5b53 e3bb245
Author: Evan Morris <[email protected]>
Date:   Wed Aug 9 13:05:35 2023 -0400

    Merge pull request #173 from RobokopU24/loadingReactome

    Loading reactome

commit e3bb245
Author: beasleyjonm <[email protected]>
Date:   Mon Aug 7 16:40:12 2023 -0400

    Updated Reactome parser to include Complex nodes and gene expression regulation edges.

commit 161f32a
Author: beasleyjonm <[email protected]>
Date:   Fri Aug 4 16:12:45 2023 -0400

    Updated to create cross-mapping dictionary in one step.

commit aaa5b53
Merge: 75d021c 7d80ce4
Author: beasleyjonm <[email protected]>
Date:   Fri Aug 4 12:28:49 2023 -0400

    Merge pull request #171 from RobokopU24/string-db-patch

    fixing string db download url that changed

commit 75d021c
Merge: 73c6622 682cbeb
Author: Evan Morris <[email protected]>
Date:   Fri Aug 4 12:18:03 2023 -0400

    Merge pull request #172 from RobokopU24/loadingReactome

    Loading reactome

commit 682cbeb
Merge: 3087273 88ac79f
Author: beasleyjonm <[email protected]>
Date:   Wed Aug 2 11:56:03 2023 -0400

    Working version of Reactome with new node ID mapping strategy.

commit 3087273
Author: beasleyjonm <[email protected]>
Date:   Wed Aug 2 11:53:28 2023 -0400

    Working version of Reactome with current triples. New node ID mapping strategy.

commit 7d80ce4
Author: Evan Morris <[email protected]>
Date:   Wed Aug 2 11:16:54 2023 -0400

    fixing string db download url that changed
@EvanDietzMorris EvanDietzMorris deleted the treats_refactor branch May 21, 2024 18:55
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@EvanDietzMorris @cbizon