From a713712bdaa3b6800c1a0e5ad264aef66f0d90f5 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Fri, 12 Jan 2024 14:13:05 -0800 Subject: [PATCH 1/6] remove -aux from golr url --- ontobio/config.yaml | 4 ++-- ontobio/golr/golr_query.py | 2 +- tests/resources/test-config.yaml | 4 ++-- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/ontobio/config.yaml b/ontobio/config.yaml index 2759b6b8..b78a8592 100644 --- a/ontobio/config.yaml +++ b/ontobio/config.yaml @@ -2,7 +2,7 @@ solr_assocs: url: "https://solr.monarchinitiative.org/solr/golr" timeout: 60 amigo_solr_assocs: - url: "http://golr-aux.geneontology.io/solr" + url: "http://golr.geneontology.io/solr" timeout: 15 solr_search: url: "https://solr.monarchinitiative.org/solr/search" @@ -11,7 +11,7 @@ lay_person_search: url: "https://solr.monarchinitiative.org/solr/hpo-pl" timeout: 15 amigo_solr_search: - url: "http://golr-aux.geneontology.io/solr" + url: "http://golr.geneontology.io/solr" timeout: 15 sparql: url: "http://sparql.hegroup.org/sparql" diff --git a/ontobio/golr/golr_query.py b/ontobio/golr/golr_query.py index 85d4fa12..70145016 100644 --- a/ontobio/golr/golr_query.py +++ b/ontobio/golr/golr_query.py @@ -1852,7 +1852,7 @@ def map_id(self,id, prefix, closure_list): ## Should take those URLs from config.yaml class ESOLR(Enum): - GOLR = "http://golr-aux.geneontology.io/solr/" + GOLR = "http://golr.geneontology.io/solr/" MOLR = "https://solr.monarchinitiative.org/solr/search" class ESOLRDoc(Enum): diff --git a/tests/resources/test-config.yaml b/tests/resources/test-config.yaml index f121f626..6cecd11b 100644 --- a/tests/resources/test-config.yaml +++ b/tests/resources/test-config.yaml @@ -2,13 +2,13 @@ solr_assocs: url: "https://example.org" timeout: 999 amigo_solr_assocs: - url: "http://golr-aux.geneontology.io/solr" + url: "http://golr.geneontology.io/solr" timeout: 2 solr_search: url: "https://solr-dev.monarchinitiative.org/solr/search" timeout: 2 amigo_solr_search: - url: "http://golr-aux.geneontology.io/solr" + url: "http://golr.geneontology.io/solr" timeout: 2 sparql: url: "http://sparql.hegroup.org/sparql" From f088ca461f8a50630be83bb3dbe6c05e2fc4076a Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Fri, 12 Jan 2024 14:21:31 -0800 Subject: [PATCH 2/6] remove references to golr.geneontology.io --- ontobio/config.yaml | 4 ++-- ontobio/golr/golr_query.py | 2 +- tests/resources/test-config.yaml | 4 ++-- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/ontobio/config.yaml b/ontobio/config.yaml index b78a8592..80b6280c 100644 --- a/ontobio/config.yaml +++ b/ontobio/config.yaml @@ -2,7 +2,7 @@ solr_assocs: url: "https://solr.monarchinitiative.org/solr/golr" timeout: 60 amigo_solr_assocs: - url: "http://golr.geneontology.io/solr" + url: "http://golr.geneontology.org/solr" timeout: 15 solr_search: url: "https://solr.monarchinitiative.org/solr/search" @@ -11,7 +11,7 @@ lay_person_search: url: "https://solr.monarchinitiative.org/solr/hpo-pl" timeout: 15 amigo_solr_search: - url: "http://golr.geneontology.io/solr" + url: "http://golr.geneontology.org/solr" timeout: 15 sparql: url: "http://sparql.hegroup.org/sparql" diff --git a/ontobio/golr/golr_query.py b/ontobio/golr/golr_query.py index 70145016..d7a8cad9 100644 --- a/ontobio/golr/golr_query.py +++ b/ontobio/golr/golr_query.py @@ -1852,7 +1852,7 @@ def map_id(self,id, prefix, closure_list): ## Should take those URLs from config.yaml class ESOLR(Enum): - GOLR = "http://golr.geneontology.io/solr/" + GOLR = "http://golr.geneontology.org/solr/" MOLR = "https://solr.monarchinitiative.org/solr/search" class ESOLRDoc(Enum): diff --git a/tests/resources/test-config.yaml b/tests/resources/test-config.yaml index 6cecd11b..8bee53c8 100644 --- a/tests/resources/test-config.yaml +++ b/tests/resources/test-config.yaml @@ -2,13 +2,13 @@ solr_assocs: url: "https://example.org" timeout: 999 amigo_solr_assocs: - url: "http://golr.geneontology.io/solr" + url: "http://golr.geneontology.org/solr" timeout: 2 solr_search: url: "https://solr-dev.monarchinitiative.org/solr/search" timeout: 2 amigo_solr_search: - url: "http://golr.geneontology.io/solr" + url: "http://golr.geneontology.org/solr" timeout: 2 sparql: url: "http://sparql.hegroup.org/sparql" From 4fb06d30210879d524c7a1e40c62bd6f4c6e695b Mon Sep 17 00:00:00 2001 From: dustine32 Date: Fri, 12 Jan 2024 14:38:20 -0800 Subject: [PATCH 3/6] Upgrade to v2.8.21 --- ontobio/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ontobio/__init__.py b/ontobio/__init__.py index 5666bdb1..21392059 100644 --- a/ontobio/__init__.py +++ b/ontobio/__init__.py @@ -1,6 +1,6 @@ from __future__ import absolute_import -__version__ = '2.8.20' +__version__ = '2.8.21' from .ontol_factory import OntologyFactory From 06ebfda3a3d35ca467d343c3824641a72095d73d Mon Sep 17 00:00:00 2001 From: dustine32 Date: Wed, 17 Jan 2024 13:08:16 -0800 Subject: [PATCH 4/6] Add underscore to GO_REF:0000033 for geneontology/go-site#2185 --- ontobio/io/qc.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/ontobio/io/qc.py b/ontobio/io/qc.py index 2281071d..808b9039 100644 --- a/ontobio/io/qc.py +++ b/ontobio/io/qc.py @@ -517,7 +517,7 @@ def test(self, annotation: association.GoAssociation, config: assocparser.AssocP class GoRule37(GoRule): def __init__(self): - super().__init__("GORULE:0000037", "IBA annotations should ONLY be assigned_by GO_Central and have GOREF:0000033 as a reference", FailMode.HARD) + super().__init__("GORULE:0000037", "IBA annotations should ONLY be assigned_by GO_Central and have GO_REF:0000033 as a reference", FailMode.HARD) def test(self, annotation: association.GoAssociation, config: assocparser.AssocParserConfig, group=None) -> TestResult: # If the evidence code is IBA, then (1) the assigned_by field must be GO_Central and (2) the reference field must be PMID:21873635 @@ -527,7 +527,7 @@ def test(self, annotation: association.GoAssociation, config: assocparser.AssocP result = self._result(True) # By default we pass if evidence == iba_eco: - result = self._result(assigned_by == "GO_Central" and "GOREF:0000033" in references) + result = self._result(assigned_by == "GO_Central" and "GO_REF:0000033" in references) return result From 8ba79460431ca15edaafff4859c060c5da0cf617 Mon Sep 17 00:00:00 2001 From: dustine32 Date: Wed, 17 Jan 2024 13:17:00 -0800 Subject: [PATCH 5/6] Update GO_REF test for GoRule37 for geneontology/go-site#2185 --- tests/test_qc.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/test_qc.py b/tests/test_qc.py index a5016483..2d0b270f 100644 --- a/tests/test_qc.py +++ b/tests/test_qc.py @@ -462,7 +462,7 @@ def test_gorule30(): assert test_result.result_type == qc.ResultType.PASS def test_gorule37(): - assoc = make_annotation(evidence="IBA", references="GOREF:0000033", assigned_by="GO_Central").associations[0] + assoc = make_annotation(evidence="IBA", references="GO_REF:0000033", assigned_by="GO_Central").associations[0] test_result = qc.GoRule37().test(assoc, all_rules_config()) assert test_result.result_type == qc.ResultType.PASS @@ -476,7 +476,7 @@ def test_gorule37(): test_result = qc.GoRule37().test(assoc, all_rules_config()) assert test_result.result_type == qc.ResultType.ERROR - assoc.evidence.has_supporting_reference = [Curie.from_str("GOREF:0000033")] + assoc.evidence.has_supporting_reference = [Curie.from_str("GO_REF:0000033")] assoc.provided_by = "Pascale" # IBA, but wrong assigned_by test_result = qc.GoRule37().test(assoc, all_rules_config()) assert test_result.result_type == qc.ResultType.ERROR From 7e4ca734e1142d40b38719b37ecdb80f9fca1ac8 Mon Sep 17 00:00:00 2001 From: dustine32 Date: Wed, 17 Jan 2024 13:23:06 -0800 Subject: [PATCH 6/6] Upgrade to v2.8.22 --- ontobio/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ontobio/__init__.py b/ontobio/__init__.py index 21392059..523d6ec0 100644 --- a/ontobio/__init__.py +++ b/ontobio/__init__.py @@ -1,6 +1,6 @@ from __future__ import absolute_import -__version__ = '2.8.21' +__version__ = '2.8.22' from .ontol_factory import OntologyFactory