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Neo4j 5 #252
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Neo4j 5 #252
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…etadata to be a metadata object not just dict
…ether on-disk merge is needed
…tform an env var instead of hard coded
commit 1f01b43 Merge: ec6b7d8 734cc6e Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri Jul 19 14:38:15 2024 -0400 Merge pull request #232 from RobokopU24/binding-predicate-update Modified predicates affected by biolink:binds commit 734cc6e Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri Jul 19 14:32:02 2024 -0400 bumping parsing versions for binds refactor parsers commit ec6b7d8 Merge: e44cae6 00c6627 Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri Jul 19 14:28:50 2024 -0400 Merge pull request #233 from RobokopU24/pharos_KL/AT Improving the KL/AT in Pharos commit 00c6627 Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri Jul 19 14:26:48 2024 -0400 bumping parsing version commit 766c5b7 Author: eKathleenCarter <163005214+eKathleenCarter@users.noreply.github.com> Date: Tue Jul 16 12:42:45 2024 -0400 Update predicates.py forgot to revert changes for interacts_with. Will keep it unmodified until further clarification. commit 4cb0188 Author: eKathleenCarter <163005214+eKathleenCarter@users.noreply.github.com> Date: Tue Jul 16 12:41:36 2024 -0400 Update predicates.py after comments Made changes to reflect comments by Chris: 1. Do not modify "ed50": f"RO:0002434" until we know where this predicate comes from. "But I guess the main point is that it makes no sense to have an ed50 between a chemical and a gene/protein. Is it possible to see whether we actually have any of these?" 2. "gi50": f"RO:0002434" -> {DGIDB}:Inhibitor 3. Do not modify "interacts_with" until we know where this predicate comes from. I" guess it would be easier to be sure if we know the context in which "interacts-with" was found in our ingestss. (but I'd be tempted to put 2436 for this one)" Main take away: where do these predicates come from? Can we track down how this was generated? commit 711ac5a Author: Kathleen <ekcarter@renci.org> Date: Wed Jul 10 15:10:28 2024 -0400 Improving the KL/AT in Phaors commit a687f30 Author: Kathleen <ekcarter@renci.org> Date: Wed Jul 10 12:32:26 2024 -0400 Modified predicates affected by biolink:binds commit e44cae6 Merge: 7ba9538 fa8ebf0 Author: Evan Morris <evandietzmorris@gmail.com> Date: Wed Jun 26 16:38:02 2024 -0400 Merge pull request #231 from RobokopU24/requirements.txt-patch Update requirements.txt commit fa8ebf0 Author: beasleyjonm <85600465+beasleyjonm@users.noreply.github.com> Date: Wed Jun 26 16:37:03 2024 -0400 Update requirements.txt Updated requests 2.32.0 -> 2.32.3
…est version, changed so that downloaded data files wont have version in their name
…g requests sessions for retries and performance, cleaned up comments
commit 8d8b643 Merge: 1f01b43 b0cf278 Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue Jul 23 15:01:08 2024 -0400 Merge pull request #230 from RobokopU24/drugcentral_treats_refactor Refactored treats edges for DrugCentral to differentiate between indi… commit b0cf278 Author: eKathleenCarter <163005214+eKathleenCarter@users.noreply.github.com> Date: Tue Jul 23 12:04:39 2024 -0400 Update loaddrugcentral.py kathleen modifications changed the mapping of symptomatic treatment to RO:0002606 (instead of RO:0003307) changed the mapping of diagnosis to DrugCentral:5271 commit 1f01b43 Merge: ec6b7d8 734cc6e Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri Jul 19 14:38:15 2024 -0400 Merge pull request #232 from RobokopU24/binding-predicate-update Modified predicates affected by biolink:binds commit 734cc6e Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri Jul 19 14:32:02 2024 -0400 bumping parsing versions for binds refactor parsers commit ec6b7d8 Merge: e44cae6 00c6627 Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri Jul 19 14:28:50 2024 -0400 Merge pull request #233 from RobokopU24/pharos_KL/AT Improving the KL/AT in Pharos commit 00c6627 Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri Jul 19 14:26:48 2024 -0400 bumping parsing version commit 766c5b7 Author: eKathleenCarter <163005214+eKathleenCarter@users.noreply.github.com> Date: Tue Jul 16 12:42:45 2024 -0400 Update predicates.py forgot to revert changes for interacts_with. Will keep it unmodified until further clarification. commit 4cb0188 Author: eKathleenCarter <163005214+eKathleenCarter@users.noreply.github.com> Date: Tue Jul 16 12:41:36 2024 -0400 Update predicates.py after comments Made changes to reflect comments by Chris: 1. Do not modify "ed50": f"RO:0002434" until we know where this predicate comes from. "But I guess the main point is that it makes no sense to have an ed50 between a chemical and a gene/protein. Is it possible to see whether we actually have any of these?" 2. "gi50": f"RO:0002434" -> {DGIDB}:Inhibitor 3. Do not modify "interacts_with" until we know where this predicate comes from. I" guess it would be easier to be sure if we know the context in which "interacts-with" was found in our ingestss. (but I'd be tempted to put 2436 for this one)" Main take away: where do these predicates come from? Can we track down how this was generated? commit 711ac5a Author: Kathleen <ekcarter@renci.org> Date: Wed Jul 10 15:10:28 2024 -0400 Improving the KL/AT in Phaors commit a687f30 Author: Kathleen <ekcarter@renci.org> Date: Wed Jul 10 12:32:26 2024 -0400 Modified predicates affected by biolink:binds commit e44cae6 Merge: 7ba9538 fa8ebf0 Author: Evan Morris <evandietzmorris@gmail.com> Date: Wed Jun 26 16:38:02 2024 -0400 Merge pull request #231 from RobokopU24/requirements.txt-patch Update requirements.txt commit fa8ebf0 Author: beasleyjonm <85600465+beasleyjonm@users.noreply.github.com> Date: Wed Jun 26 16:37:03 2024 -0400 Update requirements.txt Updated requests 2.32.0 -> 2.32.3 commit ef231fc Author: beasleyjonm <beasleyjonm@gmail.com> Date: Fri May 24 14:01:06 2024 -0400 Refactored treats edges for DrugCentral to differentiate between indications, off-label use, prevention, and treatment of symptoms.
…rties to merge where only one is a list
…ersion in file name), also reverting some changes see description I had made a change that would store the downloaded files with consistent names so that get_latest_version would be called fewer times, but it's not really worth it because it's slow to recompress the archive and it doesn't prevent all calls to latest version.. there are better ways to do this
EvanDietzMorris
requested review from
eKathleenCarter,
DnlRKorn and
beasleyjonm
August 13, 2024 14:47
beasleyjonm
approved these changes
Aug 13, 2024
EvanDietzMorris
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that referenced
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Aug 23, 2024
commit b124dfb Merge: 74ea571 0a22609 Author: beasleyjonm <85600465+beasleyjonm@users.noreply.github.com> Date: Tue Aug 13 11:24:52 2024 -0400 Merge pull request #252 from RobokopU24/neo4j_5 Neo4j 5 commit 74ea571 Merge: 6836058 eeacd0b Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue Aug 13 10:58:48 2024 -0400 Merge pull request #245 from RobokopU24/DnlRKorn-patch-7 Set filenames to be based on object settings in all functions loadHistoneMap.py commit 6836058 Merge: 0f389ab 2f0d2e7 Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue Aug 13 10:57:17 2024 -0400 Merge pull request #239 from RobokopU24/DnlRKorn-patch-1 Update loadFDB.py commit 0f389ab Merge: 9f75017 f83234c Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue Aug 13 10:54:42 2024 -0400 Merge pull request #241 from RobokopU24/DnlRKorn-patch-3 Added TODO to loadGTEx.py commit 9f75017 Merge: 0cf45a0 a45698f Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue Aug 13 10:50:59 2024 -0400 Merge pull request #243 from RobokopU24/DnlRKorn-patch-5 Update loadIA.py commit 0cf45a0 Merge: 8db9527 827751d Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue Aug 13 10:50:14 2024 -0400 Merge pull request #244 from RobokopU24/DnlRKorn-patch-6 Added TODO to loadPanther.py commit 8db9527 Merge: e94d556 40cad6f Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue Aug 13 10:49:25 2024 -0400 Merge pull request #246 from RobokopU24/DnlRKorn-patch-8 Added TODO to loadUniRef.py commit 0a22609 Merge: 77c92b3 e94d556 Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue Aug 13 10:47:12 2024 -0400 Merge branch 'master' into neo4j_5 commit 77c92b3 Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue Aug 13 10:45:36 2024 -0400 changed bd_file_name in accordance with changes in BINDING (no more version in file name), also reverting some changes see description I had made a change that would store the downloaded files with consistent names so that get_latest_version would be called fewer times, but it's not really worth it because it's slow to recompress the archive and it doesn't prevent all calls to latest version.. there are better ways to do this commit 5acb052 Author: Evan Morris <evandietzmorris@gmail.com> Date: Mon Aug 12 19:05:43 2024 -0400 removing import, not in use (yet) commit 17ff6ae Author: Evan Morris <evandietzmorris@gmail.com> Date: Mon Aug 12 18:48:39 2024 -0400 making quote usage consistent commit 487863b Author: Evan Morris <evandietzmorris@gmail.com> Date: Mon Aug 12 18:14:03 2024 -0400 upgrading Reactome to neo4j 5, adding 4 to 5 migration step commit 6af1635 Author: Evan Morris <evandietzmorris@gmail.com> Date: Mon Aug 12 17:18:22 2024 -0400 commenting these out so they are truly optional by default commit 7540dde Author: Evan Morris <evandietzmorris@gmail.com> Date: Mon Aug 12 17:17:35 2024 -0400 adding edge id commit daa90bc Author: Evan Morris <evandietzmorris@gmail.com> Date: Thu Aug 8 16:29:08 2024 -0400 fixing literal comparison commit 7268385 Author: Evan Morris <evandietzmorris@gmail.com> Date: Thu Aug 8 14:45:17 2024 -0400 oops, fixing source id commit 222db0c Author: Evan Morris <evandietzmorris@gmail.com> Date: Thu Aug 8 14:22:49 2024 -0400 adding a spec for ctkp and changing source id to ClinicalTrialsKP in the mappings commit e94d556 Merge: 8d8b643 f369559 Author: Evan Morris <evandietzmorris@gmail.com> Date: Thu Aug 8 14:13:16 2024 -0400 Merge pull request #250 from RobokopU24/docs-fix fixing remnants of data_services commit f369559 Author: Evan Morris <evandietzmorris@gmail.com> Date: Thu Aug 8 14:06:17 2024 -0400 fixing remnants of data_services commit db4c548 Author: Evan Morris <evandietzmorris@gmail.com> Date: Thu Aug 8 13:51:37 2024 -0400 adding CTKP commit 5bf7bda Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue Aug 6 16:10:06 2024 -0400 merging of properties more robust, avoid failure when there are properties to merge where only one is a list commit 265e4e8 Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri Aug 2 02:08:54 2024 -0400 bumping bl versions commit 40cad6f Author: DnlRKorn <6885702+DnlRKorn@users.noreply.github.com> Date: Tue Jul 30 16:52:44 2024 -0400 Added TODO to loadUniRef.py commit eeacd0b Author: DnlRKorn <6885702+DnlRKorn@users.noreply.github.com> Date: Fri Jul 26 16:41:36 2024 -0400 Set filenames to be based on object settings in all functions loadHistoneMap.py commit 827751d Author: DnlRKorn <6885702+DnlRKorn@users.noreply.github.com> Date: Fri Jul 26 10:19:57 2024 -0400 Added TODO to loadPanther.py commit a45698f Author: DnlRKorn <6885702+DnlRKorn@users.noreply.github.com> Date: Fri Jul 26 10:11:53 2024 -0400 Update loadIA.py Changed hardcoded URLs to class variables. commit f83234c Author: DnlRKorn <6885702+DnlRKorn@users.noreply.github.com> Date: Thu Jul 25 12:08:30 2024 -0400 Added TODO to loadGTEx.py commit 2f0d2e7 Author: DnlRKorn <6885702+DnlRKorn@users.noreply.github.com> Date: Thu Jul 25 11:21:21 2024 -0400 Update loadFDB.py Added small safety check in get_data. commit 8d8b643 Merge: 1f01b43 b0cf278 Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue Jul 23 15:01:08 2024 -0400 Merge pull request #230 from RobokopU24/drugcentral_treats_refactor Refactored treats edges for DrugCentral to differentiate between indi… commit b0cf278 Author: eKathleenCarter <163005214+eKathleenCarter@users.noreply.github.com> Date: Tue Jul 23 12:04:39 2024 -0400 Update loaddrugcentral.py kathleen modifications changed the mapping of symptomatic treatment to RO:0002606 (instead of RO:0003307) changed the mapping of diagnosis to DrugCentral:5271 commit 1f01b43 Merge: ec6b7d8 734cc6e Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri Jul 19 14:38:15 2024 -0400 Merge pull request #232 from RobokopU24/binding-predicate-update Modified predicates affected by biolink:binds commit 734cc6e Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri Jul 19 14:32:02 2024 -0400 bumping parsing versions for binds refactor parsers commit ec6b7d8 Merge: e44cae6 00c6627 Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri Jul 19 14:28:50 2024 -0400 Merge pull request #233 from RobokopU24/pharos_KL/AT Improving the KL/AT in Pharos commit 00c6627 Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri Jul 19 14:26:48 2024 -0400 bumping parsing version commit 766c5b7 Author: eKathleenCarter <163005214+eKathleenCarter@users.noreply.github.com> Date: Tue Jul 16 12:42:45 2024 -0400 Update predicates.py forgot to revert changes for interacts_with. Will keep it unmodified until further clarification. commit 4cb0188 Author: eKathleenCarter <163005214+eKathleenCarter@users.noreply.github.com> Date: Tue Jul 16 12:41:36 2024 -0400 Update predicates.py after comments Made changes to reflect comments by Chris: 1. Do not modify "ed50": f"RO:0002434" until we know where this predicate comes from. "But I guess the main point is that it makes no sense to have an ed50 between a chemical and a gene/protein. Is it possible to see whether we actually have any of these?" 2. "gi50": f"RO:0002434" -> {DGIDB}:Inhibitor 3. Do not modify "interacts_with" until we know where this predicate comes from. I" guess it would be easier to be sure if we know the context in which "interacts-with" was found in our ingestss. (but I'd be tempted to put 2436 for this one)" Main take away: where do these predicates come from? Can we track down how this was generated? commit 711ac5a Author: Kathleen <ekcarter@renci.org> Date: Wed Jul 10 15:10:28 2024 -0400 Improving the KL/AT in Phaors commit a687f30 Author: Kathleen <ekcarter@renci.org> Date: Wed Jul 10 12:32:26 2024 -0400 Modified predicates affected by biolink:binds commit e44cae6 Merge: 7ba9538 fa8ebf0 Author: Evan Morris <evandietzmorris@gmail.com> Date: Wed Jun 26 16:38:02 2024 -0400 Merge pull request #231 from RobokopU24/requirements.txt-patch Update requirements.txt commit fa8ebf0 Author: beasleyjonm <85600465+beasleyjonm@users.noreply.github.com> Date: Wed Jun 26 16:37:03 2024 -0400 Update requirements.txt Updated requests 2.32.0 -> 2.32.3 commit ef231fc Author: beasleyjonm <beasleyjonm@gmail.com> Date: Fri May 24 14:01:06 2024 -0400 Refactored treats edges for DrugCentral to differentiate between indications, off-label use, prevention, and treatment of symptoms.
EvanDietzMorris
added a commit
that referenced
this pull request
Sep 11, 2024
commit 83a8863 Merge: b124dfb f4e4003 Author: beasleyjonm <85600465+beasleyjonm@users.noreply.github.com> Date: Wed Sep 11 12:27:06 2024 -0400 Merge pull request #256 from RobokopU24/PHAROS_target_for_edges Add "target_for" edges from loadPHAROS.py commit f4e4003 Author: beasleyjonm <85600465+beasleyjonm@users.noreply.github.com> Date: Fri Aug 23 13:47:54 2024 -0400 Add "target_for" edges from loadPHAROS.py commit b124dfb Merge: 74ea571 0a22609 Author: beasleyjonm <85600465+beasleyjonm@users.noreply.github.com> Date: Tue Aug 13 11:24:52 2024 -0400 Merge pull request #252 from RobokopU24/neo4j_5 Neo4j 5 commit 74ea571 Merge: 6836058 eeacd0b Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue Aug 13 10:58:48 2024 -0400 Merge pull request #245 from RobokopU24/DnlRKorn-patch-7 Set filenames to be based on object settings in all functions loadHistoneMap.py commit 6836058 Merge: 0f389ab 2f0d2e7 Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue Aug 13 10:57:17 2024 -0400 Merge pull request #239 from RobokopU24/DnlRKorn-patch-1 Update loadFDB.py commit 0f389ab Merge: 9f75017 f83234c Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue Aug 13 10:54:42 2024 -0400 Merge pull request #241 from RobokopU24/DnlRKorn-patch-3 Added TODO to loadGTEx.py commit 9f75017 Merge: 0cf45a0 a45698f Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue Aug 13 10:50:59 2024 -0400 Merge pull request #243 from RobokopU24/DnlRKorn-patch-5 Update loadIA.py commit 0cf45a0 Merge: 8db9527 827751d Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue Aug 13 10:50:14 2024 -0400 Merge pull request #244 from RobokopU24/DnlRKorn-patch-6 Added TODO to loadPanther.py commit 8db9527 Merge: e94d556 40cad6f Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue Aug 13 10:49:25 2024 -0400 Merge pull request #246 from RobokopU24/DnlRKorn-patch-8 Added TODO to loadUniRef.py commit 0a22609 Merge: 77c92b3 e94d556 Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue Aug 13 10:47:12 2024 -0400 Merge branch 'master' into neo4j_5 commit 77c92b3 Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue Aug 13 10:45:36 2024 -0400 changed bd_file_name in accordance with changes in BINDING (no more version in file name), also reverting some changes see description I had made a change that would store the downloaded files with consistent names so that get_latest_version would be called fewer times, but it's not really worth it because it's slow to recompress the archive and it doesn't prevent all calls to latest version.. there are better ways to do this commit 5acb052 Author: Evan Morris <evandietzmorris@gmail.com> Date: Mon Aug 12 19:05:43 2024 -0400 removing import, not in use (yet) commit 17ff6ae Author: Evan Morris <evandietzmorris@gmail.com> Date: Mon Aug 12 18:48:39 2024 -0400 making quote usage consistent commit 487863b Author: Evan Morris <evandietzmorris@gmail.com> Date: Mon Aug 12 18:14:03 2024 -0400 upgrading Reactome to neo4j 5, adding 4 to 5 migration step commit 6af1635 Author: Evan Morris <evandietzmorris@gmail.com> Date: Mon Aug 12 17:18:22 2024 -0400 commenting these out so they are truly optional by default commit 7540dde Author: Evan Morris <evandietzmorris@gmail.com> Date: Mon Aug 12 17:17:35 2024 -0400 adding edge id commit daa90bc Author: Evan Morris <evandietzmorris@gmail.com> Date: Thu Aug 8 16:29:08 2024 -0400 fixing literal comparison commit 7268385 Author: Evan Morris <evandietzmorris@gmail.com> Date: Thu Aug 8 14:45:17 2024 -0400 oops, fixing source id commit 222db0c Author: Evan Morris <evandietzmorris@gmail.com> Date: Thu Aug 8 14:22:49 2024 -0400 adding a spec for ctkp and changing source id to ClinicalTrialsKP in the mappings commit e94d556 Merge: 8d8b643 f369559 Author: Evan Morris <evandietzmorris@gmail.com> Date: Thu Aug 8 14:13:16 2024 -0400 Merge pull request #250 from RobokopU24/docs-fix fixing remnants of data_services commit f369559 Author: Evan Morris <evandietzmorris@gmail.com> Date: Thu Aug 8 14:06:17 2024 -0400 fixing remnants of data_services commit db4c548 Author: Evan Morris <evandietzmorris@gmail.com> Date: Thu Aug 8 13:51:37 2024 -0400 adding CTKP commit 5bf7bda Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue Aug 6 16:10:06 2024 -0400 merging of properties more robust, avoid failure when there are properties to merge where only one is a list commit 265e4e8 Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri Aug 2 02:08:54 2024 -0400 bumping bl versions commit 8422572 Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri Aug 2 01:36:37 2024 -0400 allowing nodes with no names, with the condition they get their id set as the name commit 669de09 Author: Evan Morris <evandietzmorris@gmail.com> Date: Wed Jul 31 12:29:23 2024 -0400 fixing load argument from-path for neo4j 5 commit 40cad6f Author: DnlRKorn <6885702+DnlRKorn@users.noreply.github.com> Date: Tue Jul 30 16:52:44 2024 -0400 Added TODO to loadUniRef.py commit eeacd0b Author: DnlRKorn <6885702+DnlRKorn@users.noreply.github.com> Date: Fri Jul 26 16:41:36 2024 -0400 Set filenames to be based on object settings in all functions loadHistoneMap.py commit 827751d Author: DnlRKorn <6885702+DnlRKorn@users.noreply.github.com> Date: Fri Jul 26 10:19:57 2024 -0400 Added TODO to loadPanther.py commit a45698f Author: DnlRKorn <6885702+DnlRKorn@users.noreply.github.com> Date: Fri Jul 26 10:11:53 2024 -0400 Update loadIA.py Changed hardcoded URLs to class variables. commit 350f7b6 Author: Evan Morris <evandietzmorris@gmail.com> Date: Thu Jul 25 14:50:44 2024 -0400 reverting to sequential node norm calls commit f83234c Author: DnlRKorn <6885702+DnlRKorn@users.noreply.github.com> Date: Thu Jul 25 12:08:30 2024 -0400 Added TODO to loadGTEx.py commit 2f0d2e7 Author: DnlRKorn <6885702+DnlRKorn@users.noreply.github.com> Date: Thu Jul 25 11:21:21 2024 -0400 Update loadFDB.py Added small safety check in get_data. commit 1613f62 Author: Evan Morris <evandietzmorris@gmail.com> Date: Wed Jul 24 15:04:45 2024 -0400 fixing pool size and making backoff factor slower for node norm commit 3302b5a Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue Jul 23 15:28:25 2024 -0400 Squashed commit of the following: commit 8d8b643 Merge: 1f01b43 b0cf278 Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue Jul 23 15:01:08 2024 -0400 Merge pull request #230 from RobokopU24/drugcentral_treats_refactor Refactored treats edges for DrugCentral to differentiate between indi… commit b0cf278 Author: eKathleenCarter <163005214+eKathleenCarter@users.noreply.github.com> Date: Tue Jul 23 12:04:39 2024 -0400 Update loaddrugcentral.py kathleen modifications changed the mapping of symptomatic treatment to RO:0002606 (instead of RO:0003307) changed the mapping of diagnosis to DrugCentral:5271 commit 1f01b43 Merge: ec6b7d8 734cc6e Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri Jul 19 14:38:15 2024 -0400 Merge pull request #232 from RobokopU24/binding-predicate-update Modified predicates affected by biolink:binds commit 734cc6e Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri Jul 19 14:32:02 2024 -0400 bumping parsing versions for binds refactor parsers commit ec6b7d8 Merge: e44cae6 00c6627 Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri Jul 19 14:28:50 2024 -0400 Merge pull request #233 from RobokopU24/pharos_KL/AT Improving the KL/AT in Pharos commit 00c6627 Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri Jul 19 14:26:48 2024 -0400 bumping parsing version commit 766c5b7 Author: eKathleenCarter <163005214+eKathleenCarter@users.noreply.github.com> Date: Tue Jul 16 12:42:45 2024 -0400 Update predicates.py forgot to revert changes for interacts_with. Will keep it unmodified until further clarification. commit 4cb0188 Author: eKathleenCarter <163005214+eKathleenCarter@users.noreply.github.com> Date: Tue Jul 16 12:41:36 2024 -0400 Update predicates.py after comments Made changes to reflect comments by Chris: 1. Do not modify "ed50": f"RO:0002434" until we know where this predicate comes from. "But I guess the main point is that it makes no sense to have an ed50 between a chemical and a gene/protein. Is it possible to see whether we actually have any of these?" 2. "gi50": f"RO:0002434" -> {DGIDB}:Inhibitor 3. Do not modify "interacts_with" until we know where this predicate comes from. I" guess it would be easier to be sure if we know the context in which "interacts-with" was found in our ingestss. (but I'd be tempted to put 2436 for this one)" Main take away: where do these predicates come from? Can we track down how this was generated? commit 711ac5a Author: Kathleen <ekcarter@renci.org> Date: Wed Jul 10 15:10:28 2024 -0400 Improving the KL/AT in Phaors commit a687f30 Author: Kathleen <ekcarter@renci.org> Date: Wed Jul 10 12:32:26 2024 -0400 Modified predicates affected by biolink:binds commit e44cae6 Merge: 7ba9538 fa8ebf0 Author: Evan Morris <evandietzmorris@gmail.com> Date: Wed Jun 26 16:38:02 2024 -0400 Merge pull request #231 from RobokopU24/requirements.txt-patch Update requirements.txt commit fa8ebf0 Author: beasleyjonm <85600465+beasleyjonm@users.noreply.github.com> Date: Wed Jun 26 16:37:03 2024 -0400 Update requirements.txt Updated requests 2.32.0 -> 2.32.3 commit ef231fc Author: beasleyjonm <beasleyjonm@gmail.com> Date: Fri May 24 14:01:06 2024 -0400 Refactored treats edges for DrugCentral to differentiate between indications, off-label use, prevention, and treatment of symptoms. commit ccd0e57 Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue Jul 23 15:27:07 2024 -0400 increasing connection pool size and retry attempts for node norm commit 8d8b643 Merge: 1f01b43 b0cf278 Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue Jul 23 15:01:08 2024 -0400 Merge pull request #230 from RobokopU24/drugcentral_treats_refactor Refactored treats edges for DrugCentral to differentiate between indi… commit b0cf278 Author: eKathleenCarter <163005214+eKathleenCarter@users.noreply.github.com> Date: Tue Jul 23 12:04:39 2024 -0400 Update loaddrugcentral.py kathleen modifications changed the mapping of symptomatic treatment to RO:0002606 (instead of RO:0003307) changed the mapping of diagnosis to DrugCentral:5271 commit 9f19660 Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue Jul 23 11:36:10 2024 -0400 improving error catching and logging for node normalization commit 7731c4a Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue Jul 23 01:48:49 2024 -0400 implemented concurrent calls to node normalizer for performance, using requests sessions for retries and performance, cleaned up comments commit 4bdeb7d Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue Jul 23 01:37:56 2024 -0400 implemented better timeouts, retries, and failure for determining latest version, changed so that downloaded data files wont have version in their name commit 6bc0270 Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri Jul 19 16:44:32 2024 -0400 Squashed commit of the following: commit 1f01b43 Merge: ec6b7d8 734cc6e Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri Jul 19 14:38:15 2024 -0400 Merge pull request #232 from RobokopU24/binding-predicate-update Modified predicates affected by biolink:binds commit 734cc6e Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri Jul 19 14:32:02 2024 -0400 bumping parsing versions for binds refactor parsers commit ec6b7d8 Merge: e44cae6 00c6627 Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri Jul 19 14:28:50 2024 -0400 Merge pull request #233 from RobokopU24/pharos_KL/AT Improving the KL/AT in Pharos commit 00c6627 Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri Jul 19 14:26:48 2024 -0400 bumping parsing version commit 766c5b7 Author: eKathleenCarter <163005214+eKathleenCarter@users.noreply.github.com> Date: Tue Jul 16 12:42:45 2024 -0400 Update predicates.py forgot to revert changes for interacts_with. Will keep it unmodified until further clarification. commit 4cb0188 Author: eKathleenCarter <163005214+eKathleenCarter@users.noreply.github.com> Date: Tue Jul 16 12:41:36 2024 -0400 Update predicates.py after comments Made changes to reflect comments by Chris: 1. Do not modify "ed50": f"RO:0002434" until we know where this predicate comes from. "But I guess the main point is that it makes no sense to have an ed50 between a chemical and a gene/protein. Is it possible to see whether we actually have any of these?" 2. "gi50": f"RO:0002434" -> {DGIDB}:Inhibitor 3. Do not modify "interacts_with" until we know where this predicate comes from. I" guess it would be easier to be sure if we know the context in which "interacts-with" was found in our ingestss. (but I'd be tempted to put 2436 for this one)" Main take away: where do these predicates come from? Can we track down how this was generated? commit 711ac5a Author: Kathleen <ekcarter@renci.org> Date: Wed Jul 10 15:10:28 2024 -0400 Improving the KL/AT in Phaors commit a687f30 Author: Kathleen <ekcarter@renci.org> Date: Wed Jul 10 12:32:26 2024 -0400 Modified predicates affected by biolink:binds commit e44cae6 Merge: 7ba9538 fa8ebf0 Author: Evan Morris <evandietzmorris@gmail.com> Date: Wed Jun 26 16:38:02 2024 -0400 Merge pull request #231 from RobokopU24/requirements.txt-patch Update requirements.txt commit fa8ebf0 Author: beasleyjonm <85600465+beasleyjonm@users.noreply.github.com> Date: Wed Jun 26 16:37:03 2024 -0400 Update requirements.txt Updated requests 2.32.0 -> 2.32.3 commit 1f01b43 Merge: ec6b7d8 734cc6e Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri Jul 19 14:38:15 2024 -0400 Merge pull request #232 from RobokopU24/binding-predicate-update Modified predicates affected by biolink:binds commit 734cc6e Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri Jul 19 14:32:02 2024 -0400 bumping parsing versions for binds refactor parsers commit ec6b7d8 Merge: e44cae6 00c6627 Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri Jul 19 14:28:50 2024 -0400 Merge pull request #233 from RobokopU24/pharos_KL/AT Improving the KL/AT in Pharos commit 00c6627 Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri Jul 19 14:26:48 2024 -0400 bumping parsing version commit 766c5b7 Author: eKathleenCarter <163005214+eKathleenCarter@users.noreply.github.com> Date: Tue Jul 16 12:42:45 2024 -0400 Update predicates.py forgot to revert changes for interacts_with. Will keep it unmodified until further clarification. commit 4cb0188 Author: eKathleenCarter <163005214+eKathleenCarter@users.noreply.github.com> Date: Tue Jul 16 12:41:36 2024 -0400 Update predicates.py after comments Made changes to reflect comments by Chris: 1. Do not modify "ed50": f"RO:0002434" until we know where this predicate comes from. "But I guess the main point is that it makes no sense to have an ed50 between a chemical and a gene/protein. Is it possible to see whether we actually have any of these?" 2. "gi50": f"RO:0002434" -> {DGIDB}:Inhibitor 3. Do not modify "interacts_with" until we know where this predicate comes from. I" guess it would be easier to be sure if we know the context in which "interacts-with" was found in our ingestss. (but I'd be tempted to put 2436 for this one)" Main take away: where do these predicates come from? Can we track down how this was generated? commit 711ac5a Author: Kathleen <ekcarter@renci.org> Date: Wed Jul 10 15:10:28 2024 -0400 Improving the KL/AT in Phaors commit a687f30 Author: Kathleen <ekcarter@renci.org> Date: Wed Jul 10 12:32:26 2024 -0400 Modified predicates affected by biolink:binds commit e44cae6 Merge: 7ba9538 fa8ebf0 Author: Evan Morris <evandietzmorris@gmail.com> Date: Wed Jun 26 16:38:02 2024 -0400 Merge pull request #231 from RobokopU24/requirements.txt-patch Update requirements.txt commit fa8ebf0 Author: beasleyjonm <85600465+beasleyjonm@users.noreply.github.com> Date: Wed Jun 26 16:37:03 2024 -0400 Update requirements.txt Updated requests 2.32.0 -> 2.32.3 commit 8ea9ecb Author: Evan Morris <evandietzmorris@gmail.com> Date: Wed Jun 5 15:01:41 2024 -0400 switching to pypi version of robokop-genetics commit 86cf66a Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue Jun 4 12:46:18 2024 -0400 updating bl version commit 0d72f7c Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue May 28 12:02:05 2024 -0400 updating release actions to new versions commit 5678229 Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue May 28 12:00:17 2024 -0400 updating dockerfile and docker compose for neo4j 5, making docker platform an env var instead of hard coded commit 905d6f7 Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue May 28 11:09:30 2024 -0400 updating neo4j tools for neo4j 5 commit 2bad6d3 Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue May 28 11:08:47 2024 -0400 making it so that specific subgraph sources matter for determining whether on-disk merge is needed commit 1a2a5fb Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue May 28 11:06:03 2024 -0400 moved NormalizationScheme into normalization file, altered subgraph metadata to be a metadata object not just dict commit ef231fc Author: beasleyjonm <beasleyjonm@gmail.com> Date: Fri May 24 14:01:06 2024 -0400 Refactored treats edges for DrugCentral to differentiate between indications, off-label use, prevention, and treatment of symptoms. commit cc81717 Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue May 21 15:29:50 2024 -0400 bumping versions of all dependencies commit 7ba9538 Merge: 69a9d5c 4a0236e Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue May 21 14:46:17 2024 -0400 Merge pull request #229 from RobokopU24/dependabot/pip/requests-2.32.0 Bump requests from 2.31.0 to 2.32.0 commit 4a0236e Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue May 21 08:27:19 2024 +0000 --- updated-dependencies: - dependency-name: requests dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> commit 69a9d5c Merge: 67a5dbf 3cfa692 Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri May 17 10:11:55 2024 -0400 Merge pull request #228 from RobokopU24/deployment-updates Deployment updates commit 3cfa692 Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue May 14 13:11:21 2024 -0400 adding error checking for output_format==None commit 3af2ee2 Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue May 14 12:48:01 2024 -0400 improving output_format parsing commit 2bf5721 Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue May 14 12:46:29 2024 -0400 removing jsonl which does nothing commit bc3779b Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue May 14 12:45:22 2024 -0400 fixing ubergraph source id commit 55b48c3 Author: Evan Morris <evandietzmorris@gmail.com> Date: Mon May 13 17:34:48 2024 -0400 adding redundant jsonl output commit d0cf880 Author: Evan Morris <evandietzmorris@gmail.com> 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 <evandietzmorris@gmail.com> Date: Mon May 13 17:23:55 2024 -0400 moving redundant kg generation into Common commit 132221a Author: Evan Morris <evandietzmorris@gmail.com> 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 <evandietzmorris@gmail.com> Date: Fri May 10 16:54:59 2024 -0400 adding rule mining kg commit a26349f Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri May 10 16:51:13 2024 -0400 pinning pharos version in the parser instead of graph specs commit fac5c00 Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri May 10 16:37:49 2024 -0400 adding dug graph spec commit d1a3612 Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri May 10 16:37:41 2024 -0400 adding a slim resources values option commit 26aabc3 Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri May 10 16:36:59 2024 -0400 updating image and biolink versions commit 67a5dbf Merge: 63f33bd adf4b0f Author: Evan Morris <evandietzmorris@gmail.com> 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 <evandietzmorris@gmail.com> 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 <evandietzmorris@gmail.com> Date: Fri May 10 15:49:01 2024 -0400 adding drugmechdb to baseline in yobokop commit 0de4d26 Author: beasleyjonm <beasleyjonm@gmail.com> Date: Thu May 9 13:29:23 2024 -0400 Fixed broken link for SGD Gene2GOTerm download file. commit adf4b0f Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri May 3 15:53:24 2024 -0400 added knowledge level and agent type to pharos commit 5f3e996 Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri May 3 14:32:12 2024 -0400 added test for edge merging with qualifiers commit 20220ec Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri May 3 13:33:50 2024 -0400 implementation for having edge merging include qualifiers in matching key commit c54edc8 Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri May 3 13:28:18 2024 -0400 implementing removal of subclass_of loop edges commit 45d6ced Author: Evan Morris <evandietzmorris@gmail.com> 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 <evandietzmorris@gmail.com> 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 <evandietzmorris@gmail.com> 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 <evandietzmorris@gmail.com> Date: Wed May 1 16:14:39 2024 -0400 fixed missing prefix bug commit df44bc6 Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri Apr 12 15:15:03 2024 -0400 bumping parsing version commit 5968f3e Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri Apr 12 15:14:38 2024 -0400 fixing agent type typo commit 55b99b5 Author: Evan Morris <evandietzmorris@gmail.com> 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 <evandietzmorris@gmail.com> Date: Fri Apr 12 00:23:52 2024 -0400 adding some new env vars to the docker-compose commit 335b91c Author: Evan Morris <evandietzmorris@gmail.com> 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 <evandietzmorris@gmail.com> Date: Thu Apr 11 11:25:45 2024 -0400 bumping vp parsing version commit 81d790f Author: Evan Morris <evandietzmorris@gmail.com> 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 <evandietzmorris@gmail.com> Date: Thu Apr 11 10:08:14 2024 -0400 fixing leftover staticmethod declaration commit d3d5739 Author: Evan Morris <evandietzmorris@gmail.com> Date: Thu Apr 11 04:11:20 2024 -0400 added publication nodes and edges commit 4eca7be Author: Evan Morris <evandietzmorris@gmail.com> 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 <evandietzmorris@gmail.com> 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 <evandietzmorris@gmail.com> 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 <evandietzmorris@gmail.com> Date: Thu Apr 11 04:08:46 2024 -0400 adding knowledge level and agent type, using some more constants commit 214b104 Author: Evan Morris <evandietzmorris@gmail.com> Date: Thu Apr 11 04:08:20 2024 -0400 adding knowledge level and agent type commit 00503f9 Author: Evan Morris <evandietzmorris@gmail.com> Date: Thu Apr 11 04:06:29 2024 -0400 added evidence code to knowledge level and agent type mapping commit 2359a69 Author: Evan Morris <evandietzmorris@gmail.com> 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 <evandietzmorris@gmail.com> 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 <evandietzmorris@gmail.com> Date: Thu Apr 11 04:04:05 2024 -0400 adding knowledge level and agent type, general clean up commit b9b07a8 Author: Evan Morris <evandietzmorris@gmail.com> Date: Thu Apr 11 04:03:04 2024 -0400 adding knowledge level and agent type commit 7785179 Author: Evan Morris <evandietzmorris@gmail.com> 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 <evandietzmorris@gmail.com> 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 <evandietzmorris@gmail.com> 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 <evandietzmorris@gmail.com> Date: Thu Apr 11 01:35:51 2024 -0400 Merge remote-tracking branch 'origin/DrugMechDBfulldataparser' into molepro commit fc1786e Author: beasleyjonm <85600465+beasleyjonm@users.noreply.github.com> Date: Wed Apr 10 15:08:49 2024 -0400 Update loadDrugMechDB.py Changed "qualifier_predicate" to "qualified_predicate" commit a9be99f Author: beasleyjonm <85600465+beasleyjonm@users.noreply.github.com> 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 <evandietzmorris@gmail.com> 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 <evandietzmorris@gmail.com> Date: Mon Apr 8 11:08:54 2024 -0400 fixed data_services env var commit 63aac81 Author: beasleyjonm <beasleyjonm@gmail.com> 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 <beasleyjonm@gmail.com> 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 <evandietzmorris@gmail.com> Date: Fri Apr 5 17:35:49 2024 -0400 adding knowledge level and agent type commit 51881ad Author: Evan Morris <evandietzmorris@gmail.com> 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 <evandietzmorris@gmail.com> 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 <evandietzmorris@gmail.com> Date: Tue Mar 26 15:06:54 2024 -0400 adding error checking and fallback for ssl issues commit f3b1d37 Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue Mar 26 14:19:09 2024 -0400 switching to http due to ssl errors with the https commit a83c7a8 Author: Evan Morris <evandietzmorris@gmail.com> Date: Tue Mar 26 11:50:32 2024 -0400 bumping parsing versions commit 5923994 Author: Evan Morris <evandietzmorris@gmail.com> 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 <evandietzmorris@gmail.com> Date: Mon Mar 25 23:19:46 2024 -0400 updating latest image commit 88bf8fd Author: Evan Morris <evandietzmorris@gmail.com> Date: Mon Mar 25 23:18:59 2024 -0400 removing extra entity extractor graph commit 0c245f9 Author: Evan Morris <evandietzmorris@gmail.com> 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 <evandietzmorris@gmail.com> 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 <evandietzmorris@gmail.com> 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 <evandietzmorris@gmail.com> 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 <evandietzmorris@gmail.com> Date: Thu Mar 21 16:07:58 2024 -0400 updating version for monarch kg commit 27d338b Author: Evan Morris <evandietzmorris@gmail.com> Date: Thu Mar 21 16:06:25 2024 -0400 adding aggregator knowledge source for cam kp commit 54b8cc2 Author: Evan Morris <evandietzmorris@gmail.com> Date: Wed Mar 20 15:11:16 2024 -0400 forcing just one primary knowledge source instead of splitting commit 837c339 Author: Evan Morris <evandietzmorris@gmail.com> Date: Wed Mar 20 11:56:22 2024 -0400 updating with better defaults for sterling commit 0aa6a2e Author: Evan Morris <evandietzmorris@gmail.com> Date: Wed Mar 20 11:55:25 2024 -0400 bumping requirements for bmt and jsonlines commit e2c462a Author: Evan Morris <evandietzmorris@gmail.com> 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 <evandietzmorris@gmail.com> Date: Wed Mar 20 11:53:33 2024 -0400 improving neo4j dump generation options and logging from cli entrypoint commit be5ba67 Author: Evan Morris <evandietzmorris@gmail.com> 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 <evandietzmorris@gmail.com> 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 <evandietzmorris@gmail.com> 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 <evandietzmorris@gmail.com> Date: Wed Mar 20 05:58:09 2024 -0400 removing extra empty properties, handling multiple primary knowledge sources commit cf541c2 Author: Evan Morris <evandietzmorris@gmail.com> 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 <evandietzmorris@gmail.com> Date: Wed Mar 20 03:27:08 2024 -0400 Squashed commit of the following: commit 28fe0f5 Author: james0032 <jchung@renci.org> Date: Fri Mar 8 21:44:56 2024 +0000 predicate format corrected commit b0ba22d Merge: 9bf375c 421a9a1 Author: James Chung <jchung@renci.org> Date: Wed Nov 22 10:55:22 2023 -0500 merge for snakify curie commit 9bf375c Author: James Chung <jchung@renci.org> Date: Wed Nov 22 10:43:25 2023 -0500 QUALIFIED_PREDICATE commit 421a9a1 Author: Evan Morris <evandietzmorris@gmail.com> Date: Fri Nov 17 14:15:27 2023 -0500 converting predicates from bmt get_ancestors to snakified biolink curies commit e92b623 Author: James Chung <jchung@renci.org> Date: Fri Aug 25 14:56:27 2023 -0400 First version of redundant graph generator commit 1ae25c9 Author: Evan Morris <evandietzmorris@gmail.com> 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 <evandietzmorris@gmail.com> Date: Wed Mar 20 03:13:05 2024 -0400 adding the other form of synonym property commit 373af9c Author: Evan Morris <evandietzmorris@gmail.com> Date: Wed Mar 20 03:12:38 2024 -0400 adding a way to write just one normalized node commit 6a16c0e Author: Evan Morris <evandietzmorris@gmail.com> Date: Wed Mar 20 03:12:07 2024 -0400 adding more groupings commit a0dffb3 Author: Evan Morris <evandietzmorris@gmail.com> 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 <evandietzmorris@gmail.com> Date: Wed Mar 20 01:14:02 2024 -0400 cleaning up unnecessary defaults for nodes, this is functionally equivalent commit fda2bf2 Author: Evan Morris <evandietzmorris@gmail.com> Date: Wed Mar 20 01:13:22 2024 -0400 updating binding to use appropriate edge property constants commit 1f0e6f4 Author: Evan Morris <evandietzmorris@gmail.com> Date: Wed Mar 20 01:12:25 2024 -0400 removing obsolete imports commit 5d0e150 Author: Evan Morris <evandietzmorris@gmail.com> 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
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Upgraded all instances of neo4j commands and cypher syntax from neo4j 4 to neo4j 5
Upgraded Dockerfile base image to neo4j:5.19.0-community-bullseye
Changed NodeNormalizer api calls so that they use a requests.adapters HTTPAdapter and Retry instead of implementing retries in ORION. Implemented a way to call NodeNormalizer many times concurrently but commented it out for now because the service can't or won't handle that many calls that fast from one place.
Changed merging.py entity_merging_function to handle cases where lists should be merged but one instance of the property is not already a list. This is kind of nasty, it should probably be handled upstream. AFAIK LitCoin is the only case where this happens, but in theory we should be able to handle those cases if we don't enforce attribute types upstream.
Small changes in build_manager and kgxmodel/SubGraphSource so that subgraph sources can be considered when determining whether a graph has resource hogs or not.
Changed kgx_file_converter so that nodes without names can still be processed, in those cases the id is assigned as the name.
Updated many dependencies in requirements.txt
Moved NormalizationScheme and NormalizationFailedError to normalization.py
Completely removed NormalizationBrokenError
Removed is_gzip functionality from utils pull_via_http
Added option to save a file with a different name from the source file in utils pull_via_http
Added Clinical Trials KP as a data source
Added some new biolink constants for CTKP
Fixed Reactome for neo4j 5 and added the needed migrate db function for neo4j 4 to 5 migrations
Implemented retries for BINDING DB version call and updated file name to new format
Updated docker-compose removing some obsolete lines and removing platform: linux/amd64 as the default (suggestion that platform can optionally be set as an env var was added to the set_up script).
Updated versions of actions in the release github workflow
This branch also includes commits that were already merged from #232 and #233