author int64 658 755k | date stringlengths 19 19 | timezone int64 -46,800 43.2k | hash stringlengths 40 40 | message stringlengths 5 490 | mods list | language stringclasses 20 values | license stringclasses 3 values | repo stringlengths 5 68 | original_message stringlengths 12 491 |
|---|---|---|---|---|---|---|---|---|---|
89,685 | 24.10.2018 19:10:29 | 25,200 | 849c96fd190072c6423fd801a36ccb68ff15007b | compare functionality | [
{
"change_type": "MODIFY",
"old_path": "ontobio/neo/scigraph_ontology.py",
"new_path": "ontobio/neo/scigraph_ontology.py",
"diff": "@@ -4,7 +4,7 @@ Classes for representing ontologies backed by SciGraph endpoint\nE.g.\nhttps://scigraph-ontology.monarchinitiative.org/scigraph/docs/#!/graph/getNeighbo... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | compare functionality |
89,685 | 25.10.2018 12:35:33 | 25,200 | 71bb1192e37bfd316a1ecd1b97219fc55a8bb055 | compare finished | [
{
"change_type": "MODIFY",
"old_path": "ontobio/model/similarity.py",
"new_path": "ontobio/model/similarity.py",
"diff": "-from typing import List, Optional, Union\n+from typing import List, Optional, Union, Iterable\nclass Node:\n@@ -27,20 +27,36 @@ class ICNode(Node):\nself.IC = IC\n+class TypedNo... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | compare finished |
89,685 | 26.10.2018 17:57:39 | 25,200 | 07df1247ae9bedd2fd9e502a6f1edf146c2971a7 | add functional test for phenosim search, compare | [
{
"change_type": "MODIFY",
"old_path": "Makefile",
"new_path": "Makefile",
"diff": "@@ -21,7 +21,9 @@ foo:\n# only run local tests\ntravis_test:\n- pytest tests/test_*local*.py tests/test_*parser*.py tests/test_qc.py tests/test_rdfgen.py tests/test_parse_ids.py tests/test_parse_taxon.py tests/unit/\... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | add functional test for phenosim search, compare |
89,685 | 26.10.2018 18:50:11 | 25,200 | c45f69e7ad6cdbc76cd116ae527c6c58580407f9 | use fake scigraph output, fewer mocks | [
{
"change_type": "MODIFY",
"old_path": "Makefile",
"new_path": "Makefile",
"diff": "@@ -23,7 +23,7 @@ foo:\ntravis_test:\npytest tests/test_*local*.py tests/test_*parser*.py tests/test_qc.py \\\ntests/test_rdfgen.py tests/test_parse_ids.py tests/test_parse_taxon.py \\\n- tests/unit/\n+ tests/phenosi... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | use fake scigraph output, fewer mocks |
89,685 | 04.12.2018 17:03:22 | 28,800 | cc2503b0859efdb9916abcd444ae09268fb8f6c6 | add limit for owlsim queries, lint fixes | [
{
"change_type": "MODIFY",
"old_path": "ontobio/sim/annotation_scorer.py",
"new_path": "ontobio/sim/annotation_scorer.py",
"diff": "@@ -6,7 +6,7 @@ import numpy as np\nfrom statistics import mean\n-class AnnotationScorer():\n+class AnnotationScorer:\n\"\"\"\nComputes the annotation sufficiency score... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | add limit for owlsim queries, lint fixes |
89,685 | 04.12.2018 17:48:00 | 28,800 | 6682a7f734e6ddb511e5b921e547020ab199aec0 | set all default limits to 100 | [
{
"change_type": "MODIFY",
"old_path": "ontobio/sim/api/owlsim2.py",
"new_path": "ontobio/sim/api/owlsim2.py",
"diff": "@@ -182,7 +182,7 @@ class OwlSim2Api(SimApi, InformationContentStore, FilteredSearchable):\ndef search_by_attribute_set(\nself,\nprofile: List[str],\n- limit: Optional[int] = 20,\n... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | set all default limits to 100 |
89,685 | 14.12.2018 17:24:19 | 28,800 | a6f8ef2124cf51481a770db216a3b9d00dfdf077 | small bug fixes, increase owlsim2 timeout | [
{
"change_type": "MODIFY",
"old_path": "ontobio/config.yaml",
"new_path": "ontobio/config.yaml",
"diff": "@@ -24,7 +24,7 @@ scigraph_data:\ntimeout: 2\nowlsim2:\nurl: \"https://monarchinitiative.org/owlsim/\"\n- timeout: 5\n+ timeout: 10\nowlsim3:\nurl: \"http://owlsim3.monarchinitiative.org/api/\"\... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | small bug fixes, increase owlsim2 timeout |
89,692 | 11.01.2019 15:40:46 | 28,800 | 0f51001eb0a5540e155a6723f067473c2c5c0ff7 | Fix bug where str line was being assumed to be an instance of SplitLine | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/assocparser.py",
"new_path": "ontobio/io/assocparser.py",
"diff": "@@ -292,9 +292,9 @@ class AssocParser(object):\nfor association in associations:\npass\n- def validate_line(self, line: SplitLine):\n+ def validate_line(self, line):\nif line == \"\"... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Fix bug where str line was being assumed to be an instance of SplitLine |
89,692 | 11.01.2019 15:41:10 | 28,800 | b028f4b1e326e3efadf261b7ff4204d9a7e671f4 | Use HGNC for assertion instead of NCBIGene in tests/test_golr_associations.py | [
{
"change_type": "MODIFY",
"old_path": "tests/test_golr_associations.py",
"new_path": "tests/test_golr_associations.py",
"diff": "@@ -4,7 +4,7 @@ Tests for ontobio.golr.golr_associations\nfrom ontobio.golr.golr_associations import search_associations, search_associations_compact, select_distinct_sub... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Use HGNC for assertion instead of NCBIGene in tests/test_golr_associations.py |
89,692 | 11.01.2019 16:37:05 | 28,800 | 1c2cdcb52313ad0dafd673a766b10cd80e31dfe3 | Fix assertion in tests/test_wd_ontol.py to reflect changes made upstream | [
{
"change_type": "MODIFY",
"old_path": "tests/test_wd_ontol.py",
"new_path": "tests/test_wd_ontol.py",
"diff": "@@ -39,7 +39,7 @@ def test_factory():\nlabels = [ont.label(n) for n in nodes]\nprint(labels)\n# Note: it's possible wd may change rendering this false\n- assert 'Fear of frogs' in labels\n... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Fix assertion in tests/test_wd_ontol.py to reflect changes made upstream |
89,685 | 14.01.2019 14:39:00 | 28,800 | 76be55da96bde6ab67afc98266632f0148e3b579 | fix bug when no results are returned | [
{
"change_type": "MODIFY",
"old_path": "ontobio/sim/api/owlsim2.py",
"new_path": "ontobio/sim/api/owlsim2.py",
"diff": "@@ -365,6 +365,7 @@ class OwlSim2Api(SimApi, InformationContentStore, FilteredSearchable):\nsorted_results = sorted(\nresults, reverse=True, key=lambda k: k[OwlSim2Api.method2key[m... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | fix bug when no results are returned |
89,692 | 15.01.2019 10:12:04 | 28,800 | 754b71f6175b9b4ec498c6af2098afde03e4ac02 | Fix bug in scigraph_ontology | [
{
"change_type": "MODIFY",
"old_path": "ontobio/neo/scigraph_ontology.py",
"new_path": "ontobio/neo/scigraph_ontology.py",
"diff": "@@ -157,7 +157,7 @@ class RemoteScigraphOntology(Ontology):\nif reflexive:\nancestors.add(node)\nelse:\n- if node in arr:\n+ if node in ancestors:\nancestors.remove(nod... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Fix bug in scigraph_ontology |
89,692 | 16.01.2019 11:21:04 | 28,800 | 60ab7a87095d70566dfe7c505cb42ce769e32965 | Update requirements from networkx 1.x to 2.x | [
{
"change_type": "MODIFY",
"old_path": "requirements.txt",
"new_path": "requirements.txt",
"diff": "@@ -8,11 +8,11 @@ requests>=0.0\npip>=9.0.1\nwheel>0.25.0\npysolr==3.6.0\n-networkx==1.11\n+networkx==2.2\nmatplotlib==2.0.0\nSPARQLWrapper==1.8.0\npandas>=0.0\n-scipy==0.19.1\n+scipy==1.2.0\ntwine\nj... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Update requirements from networkx 1.x to 2.x |
89,692 | 16.01.2019 12:01:39 | 28,800 | 71d0a8a2393d7df49e9a64dc31126a33a7c4f8ad | networkx 2.0 migration | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/ontol_renderers.py",
"new_path": "ontobio/io/ontol_renderers.py",
"diff": "@@ -219,7 +219,7 @@ class SimpleListGraphRenderer(GraphRenderer):\nfor n in ontol.nodes():\ns += self.render_noderef(ontol, n, **args) + \"\\n\"\n#for n2 in ontol.parents(n):... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | networkx 2.0 migration |
89,692 | 16.01.2019 14:52:25 | 28,800 | a18847cd4c3782bcfd58d80e6d84f41131e90468 | Simplify creation of a list | [
{
"change_type": "MODIFY",
"old_path": "ontobio/ontol.py",
"new_path": "ontobio/ontol.py",
"diff": "@@ -412,7 +412,7 @@ class Ontology():\n\"\"\"\ng = self.get_graph()\nif node in g:\n- parents = [x for x in g.predecessors(node)]\n+ parents = list(g.predecessors(node))\nif relations is None:\nreturn... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Simplify creation of a list |
89,685 | 16.01.2019 16:39:43 | 28,800 | 18603cf3a2629990d59413f4c373d2897b8e0135 | add max ic to sim result object | [
{
"change_type": "MODIFY",
"old_path": "ontobio/model/similarity.py",
"new_path": "ontobio/model/similarity.py",
"diff": "@@ -42,6 +42,14 @@ class TypedNode(Node):\nself.type = type\nself.taxon = taxon\n+class SimMetadata():\n+ \"\"\"\n+ Metadata returned with sim result\n+ \"\"\"\n+\n+ def __init__... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | add max ic to sim result object |
89,685 | 16.01.2019 18:28:26 | 28,800 | 69515f68eac5f194d88e82e156c8e6b8ad4fd9df | adjustments for cachier | [
{
"change_type": "MODIFY",
"old_path": "ontobio/sim/api/owlsim2.py",
"new_path": "ontobio/sim/api/owlsim2.py",
"diff": "@@ -14,6 +14,91 @@ from cachier import cachier\nimport datetime\nimport requests\n+\"\"\"\n+Functions that directly access the owlsim rest API are kept\n+outside the class to utili... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | adjustments for cachier |
89,685 | 16.01.2019 18:39:16 | 28,800 | 669f1b3d08444e899686e863199573617a3bbc84 | missed type annotation | [
{
"change_type": "MODIFY",
"old_path": "ontobio/sim/api/owlsim2.py",
"new_path": "ontobio/sim/api/owlsim2.py",
"diff": "@@ -75,7 +75,7 @@ def compare_attribute_sets(\n@cachier(SHELF_LIFE)\ndef get_attribute_information_profile(\n- url,\n+ url: str,\nprofile: Optional[Tuple[str]]=None,\ncategories: O... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | missed type annotation |
89,692 | 22.01.2019 16:15:09 | 28,800 | e4f928da805d1486a6572b410753517943626f39 | Add support for stats and stats.field to GolrAssociationQuery | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -817,6 +817,8 @@ class GolrAssociationQuery(GolrAbstractQuery):\nfacet_limit=25,\nfacet_mincount=1,\nfacet_pivot_fields=None,\n+ stats=False,\n+ stats_fields=None,\nfacet_on = '... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Add support for stats and stats.field to GolrAssociationQuery |
89,685 | 04.02.2019 20:39:20 | 28,800 | f3734e9aa19704c672b67e427fc1f76f3279b598 | increase solr timeouts | [
{
"change_type": "MODIFY",
"old_path": "ontobio/config.yaml",
"new_path": "ontobio/config.yaml",
"diff": "solr_assocs:\nurl: \"https://solr.monarchinitiative.org/solr/golr\"\n- timeout: 5\n+ timeout: 10\namigo_solr_assocs:\nurl: \"http://golr-aux.geneontology.io/solr\"\ntimeout: 4\nsolr_search:\nurl... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | increase solr timeouts |
89,685 | 19.02.2019 16:34:59 | 28,800 | 928dc8a70ebf2e0b7cc062cb061f68a91add6d6e | move get_owlsim_stats out of owlsim api class | [
{
"change_type": "MODIFY",
"old_path": "ontobio/ontol_factory.py",
"new_path": "ontobio/ontol_factory.py",
"diff": "@@ -75,7 +75,7 @@ class OntologyFactory():\nreturn default_ontology\nreturn create_ontology(handle, **args)\n-#@cachier(stale_after=SHELF_LIFE)\n+@cachier(stale_after=SHELF_LIFE)\ndef ... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | move get_owlsim_stats out of owlsim api class |
89,685 | 19.02.2019 16:44:52 | 28,800 | 12a21698eb84153b0425d639fed0eb139fa6ca11 | re-patch with new function | [
{
"change_type": "MODIFY",
"old_path": "tests/test_phenosim_engine.py",
"new_path": "tests/test_phenosim_engine.py",
"diff": "from ontobio.sim.phenosim_engine import PhenoSimEngine\n-from ontobio.sim.api.owlsim2 import OwlSim2Api, search_by_attribute_set\n+from ontobio.sim.api.owlsim2 import OwlSim2... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | re-patch with new function |
89,692 | 28.02.2019 14:52:13 | 28,800 | fb1efb0e3f2cafb26ce3f6d1671e8f5a1731dc33 | Upgrade pyyaml to v5.1b3 | [
{
"change_type": "MODIFY",
"old_path": "requirements.txt",
"new_path": "requirements.txt",
"diff": "@@ -21,3 +21,4 @@ pytest_logging>=0.0\npydotplus>=0.0\ncachier==1.1.8\nplotly==2.0.7\n+pyyaml==5.1b3\n"
},
{
"change_type": "MODIFY",
"old_path": "setup.py",
"new_path": "setup.py",
... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Upgrade pyyaml to v5.1b3 |
89,692 | 28.02.2019 14:53:10 | 28,800 | f413337d478c10b487fa1f3d60411e9593bad34a | Make use of a proper loader when parsing yaml files via yaml.load | [
{
"change_type": "MODIFY",
"old_path": "bin/ontobio-lexmap.py",
"new_path": "bin/ontobio-lexmap.py",
"diff": "@@ -87,7 +87,7 @@ def main():\nconfig = {}\nif args.config is not None:\nf = open(args.config,'r')\n- config = yaml.load(f)\n+ config = yaml.load(f, Loader=yaml.FullLoader)\nf.close()\n# add... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Make use of a proper loader when parsing yaml files via yaml.load |
89,692 | 11.03.2019 15:44:43 | 25,200 | 8c285306e8214ebc3c633fbe4f3296f2a5e850c2 | Update requirements.txt and setup.py to use the right version of yamldown | [
{
"change_type": "MODIFY",
"old_path": "requirements.txt",
"new_path": "requirements.txt",
"diff": "@@ -22,3 +22,4 @@ pydotplus>=0.0\ncachier==1.1.8\nplotly==2.0.7\npyyaml==5.1b3\n+yamldown>=0.1.7\n"
},
{
"change_type": "MODIFY",
"old_path": "setup.py",
"new_path": "setup.py",
"d... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Update requirements.txt and setup.py to use the right version of yamldown |
89,692 | 11.03.2019 17:10:16 | 25,200 | 9bc0d84fe4cbedb6bef75c8a33f4e8e04091ce3c | Generate SHA256 from file contents | [
{
"change_type": "MODIFY",
"old_path": "ontobio/ontol_factory.py",
"new_path": "ontobio/ontol_factory.py",
"diff": "@@ -162,7 +162,7 @@ def translate_file_to_ontology(handle, **args):\nelse:\nif not (handle.endswith(\".obo\") or handle.endswith(\".owl\")):\nlogging.info(\"Attempting to parse non obo... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Generate SHA256 from file contents |
89,692 | 12.03.2019 17:22:40 | 25,200 | 59ae430926193b78dfff13e62a904791dc83dff4 | Fix usage of _use_amigo_schema method | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -1195,7 +1195,7 @@ class GolrAssociationQuery(GolrAbstractQuery):\nfacet_fields = [ map_field(fn, self.field_mapping) for fn in facet_fields ]\n- if self._use_amigo_schema:\n+ i... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Fix usage of _use_amigo_schema method |
89,692 | 12.03.2019 17:25:26 | 25,200 | e4719b1080f58cdf1261411d32ed0a73adf834e5 | Add 'aspect' field to GOlr query and parse the docs to include 'aspect' as a field for an object in an association | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -111,7 +111,7 @@ class GolrFields:\nEVIDENCE_OBJECT_LABEL='evidence_object_label'\n_VERSION_='_version_'\nSUBJECT_GENE_CLOSURE_LABEL_SEARCHABLE='subject_gene_closure_label_searc... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Add 'aspect' field to GOlr query and parse the docs to include 'aspect' as a field for an object in an association |
89,692 | 12.03.2019 17:38:42 | 25,200 | 8af81b1ef6775fb0f6d616bf4cf7a68647e13b43 | Delete aspect from doc after parsing | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -1450,6 +1450,7 @@ class GolrAssociationQuery(GolrAbstractQuery):\nif 'aspect' in d and id.startswith('GO:'):\nobj['aspect'] = ASPECT_MAP[d['aspect']]\n+ del d['aspect']\ncf = f... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Delete aspect from doc after parsing |
89,692 | 18.03.2019 13:36:15 | 14,400 | c47caae8bae4e2ddbf4d951c8595ea03a3088ba2 | Parse aspect to a BioLink Model type | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -171,9 +171,9 @@ INVERT_FIELDS_MAP = {\n}\nASPECT_MAP = {\n- 'F': 'GO:0003674',\n- 'P': 'GO:0008150',\n- 'C': 'GO:0005575'\n+ 'F': 'molecular_activity',\n+ 'P': 'biological_proc... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Parse aspect to a BioLink Model type |
89,685 | 19.03.2019 17:12:48 | 25,200 | 484769009416a27a56cf881d9b9dfd1f6e81de82 | increase solr timeout | [
{
"change_type": "MODIFY",
"old_path": "ontobio/config.yaml",
"new_path": "ontobio/config.yaml",
"diff": "solr_assocs:\nurl: \"https://solr.monarchinitiative.org/solr/golr\"\n- timeout: 10\n+ timeout: 60\namigo_solr_assocs:\nurl: \"http://golr-aux.geneontology.io/solr\"\ntimeout: 4\nsolr_search:\nur... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | increase solr timeout |
89,692 | 21.03.2019 16:16:41 | 25,200 | 38d8241f52717dd19c05d95616f24b87c82add8f | Rename attribute from 'aspect' to 'category' and use valid BioLink Model types | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -171,9 +171,9 @@ INVERT_FIELDS_MAP = {\n}\nASPECT_MAP = {\n- 'F': 'GO:0003674',\n- 'P': 'GO:0008150',\n- 'C': 'GO:0005575'\n+ 'F': 'molecular_activity',\n+ 'P': 'biological_proc... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Rename attribute from 'aspect' to 'category' and use valid BioLink Model types |
89,692 | 24.04.2019 16:42:57 | 25,200 | 6b4d732ff3fdfbf8dc199cc18af6b16e8448c04f | Include subject category, object category and IRI when fetching associations via golr_query | [
{
"change_type": "MODIFY",
"old_path": "ontobio/config.yaml",
"new_path": "ontobio/config.yaml",
"diff": "@@ -20,7 +20,7 @@ scigraph_ontology:\nurl: \"https://scigraph-ontology.monarchinitiative.org/scigraph/\"\ntimeout: 15\nscigraph_data:\n- url: \"https://scigraph-data.monarchinitiative.org/scigra... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Include subject category, object category and IRI when fetching associations via golr_query |
89,692 | 25.04.2019 10:34:11 | 25,200 | d6caa1aec763346cbc8569afb21de3c3fcc96694 | Fix bug in golr_associations.get_association method | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_associations.py",
"new_path": "ontobio/golr/golr_associations.py",
"diff": "@@ -22,7 +22,8 @@ def get_association(id, **kwargs):\nFetch an association object by ID\n\"\"\"\nresults = search_associations(id=id, **kwargs)\n- return results['ass... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Fix bug in golr_associations.get_association method |
89,692 | 30.04.2019 14:52:51 | 25,200 | 9af7972f91aa638bdcf594b1ebd979f4f7329fb1 | Fix facet parameter in GolrAssociationQuery | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -828,7 +828,7 @@ class GolrAssociationQuery(GolrAbstractQuery):\nfacet_pivot_fields=None,\nstats=False,\nstats_field=None,\n- facet_on = 'on',\n+ facet=True,\npivot_subject_obje... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Fix facet parameter in GolrAssociationQuery |
89,692 | 30.04.2019 15:44:35 | 25,200 | 5574b60b30f7b8019419046f1ff942d52fab463e | Make sure golr query doesn't fail if facet is 'off' | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -903,6 +903,7 @@ class GolrAssociationQuery(GolrAbstractQuery):\nself.non_null_fields = []\nif self.facet_fields is None:\n+ if self.facet:\nself.facet_fields = [\nM.SUBJECT_TAX... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Make sure golr query doesn't fail if facet is 'off' |
89,695 | 08.05.2019 16:15:57 | 14,400 | c9dd9e7d6c5e890dc557dd2626a8785cd1abf043 | updating golr fields and select fields to include frequency and onset in DiseasePhenotype assoc | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -115,6 +115,10 @@ class GolrFields:\nASPECT='aspect'\nRELATION='relation'\nRELATION_LABEL='relation_label'\n+ FREQUENCY='frequency'\n+ FREQUENCY_LABEL='frequency_label'\n+ ONSET... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | updating golr fields and select fields to include frequency and onset in DiseasePhenotype assoc |
89,695 | 13.05.2019 10:51:25 | 14,400 | 7c39de3fe95814a4f0acb0a92bc2d2bd757725e2 | working through adding frequency and onset by pair programming with Kent | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -1554,6 +1554,19 @@ class GolrAssociationQuery(GolrAbstractQuery):\nif M.EVIDENCE_OBJECT in d:\nassoc['evidence'] = d[M.EVIDENCE_OBJECT]\nassoc['types'] = [t for t in d[M.EVIDEN... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | working through adding frequency and onset by pair programming with Kent |
89,695 | 14.05.2019 15:18:50 | 14,400 | e28d4af4712ac13fa8a2c597fecc4dc03f7487ec | adding onset | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_associations.py",
"new_path": "ontobio/golr/golr_associations.py",
"diff": "@@ -29,6 +29,7 @@ def search_associations(**kwargs):\n\"\"\"\nFetch a set of association objects based on a query.\n+ :rtype:\n\"\"\"\nlogging.info(\"CREATING_GOLR_QU... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | adding onset |
89,685 | 17.05.2019 14:37:00 | 25,200 | 202ab57e4334ec752fd5962a8a740f9578504da5 | add test for clinical modifier, adjust GolrAssociationQuery to allow mocking of PySolr | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -912,6 +912,15 @@ class GolrAssociationQuery(GolrAbstractQuery):\nM.OBJECT_CLOSURE\n]\n+ if self.solr is None:\n+ if self.url is None:\n+ endpoint = self.get_config().solr_assoc... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | add test for clinical modifier, adjust GolrAssociationQuery to allow mocking of PySolr |
89,685 | 17.05.2019 15:44:20 | 25,200 | 45623a8451f1a5ca98cf9057f0961849578c89fb | fix amigo solr bug from previous commits refactor | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -973,7 +973,7 @@ class GolrAssociationQuery(GolrAbstractQuery):\n# URL to use for querying solr\nif self._use_amigo_schema(object_category):\n- if self.url is None:\n+ # Overrid... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | fix amigo solr bug from previous commits refactor |
89,685 | 20.05.2019 14:44:14 | 25,200 | 04c9de965a92e5ce62e28d502b0b95d231a44ecd | prioritize primary label when returning best highlight | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -195,12 +195,12 @@ def flip(d, x, y):\nd[y] = dx\n-def solr_quotify(v):\n+def solr_quotify(v, operator=\"OR\"):\nif isinstance(v, list):\nif len(v) == 1:\n- return solr_quotify(... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | prioritize primary label when returning best highlight |
89,692 | 21.05.2019 13:49:15 | 25,200 | f4e0f7aff865fc3553d2d0f906c0ecd8fb38e6cd | Filter for None before calling join | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -425,7 +425,7 @@ class GolrSearchQuery(GolrAbstractQuery):\nparams = {\n'q': '{0} \"{0}\"'.format(self.term),\n\"qt\": \"standard\",\n- 'fl': \",\".join(select_fields),\n+ 'fl':... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Filter for None before calling join |
89,681 | 04.06.2019 01:24:31 | -3,600 | 4a984019b47e9e423fd5d6f003cfb167f787f6b9 | Partial refactor to control caching by config.yaml | [
{
"change_type": "MODIFY",
"old_path": "ontobio/assoc_factory.py",
"new_path": "ontobio/assoc_factory.py",
"diff": "@@ -4,13 +4,12 @@ Factory class for generating association sets based on a variety of handle types\nCurrently only supports golr query\n\"\"\"\n-import networkx as nx\nimport pathlib\n... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Partial refactor to control caching by config.yaml |
89,681 | 04.06.2019 05:06:34 | -3,600 | be144a2321849359e4bd5f98b1761f5e1817edf1 | finished adding ignore_cache directives (to sparql) | [
{
"change_type": "MODIFY",
"old_path": "ontobio/sparql/sparql_ontol_utils.py",
"new_path": "ontobio/sparql/sparql_ontol_utils.py",
"diff": "@@ -69,15 +69,15 @@ def get_digraph(ont, relations=None, writecache=False):\n\"\"\"\nCreates a basic graph object corresponding to a remote ontology\n\"\"\"\n-\... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | finished adding ignore_cache directives (to sparql) |
89,681 | 04.06.2019 06:33:28 | -3,600 | 07b263666e969dcdea17fc6c18f12c6d6f2b9500 | ignore_cache should be a Boolean() parameter | [
{
"change_type": "MODIFY",
"old_path": "ontobio/config.py",
"new_path": "ontobio/config.py",
"diff": "@@ -41,7 +41,7 @@ class ConfigSchema(Schema):\n\"\"\"\nMarshmallow schema for configuration objects.\n\"\"\"\n- ignore_cache = fields.Nested(EndpointSchema)\n+ ignore_cache = fields.Boolean()\nsparq... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | ignore_cache should be a Boolean() parameter |
89,681 | 04.06.2019 22:58:12 | -3,600 | 06f2a5c9cb7fa1362e7f96d0dffa5bb9a404d027 | Need to call RemoteSparqlOntology() superclass in subclasses | [
{
"change_type": "MODIFY",
"old_path": "ontobio/sparql/sparql_ontology.py",
"new_path": "ontobio/sparql/sparql_ontology.py",
"diff": "@@ -229,6 +229,8 @@ class EagerRemoteSparqlOntology(RemoteSparqlOntology):\n\"\"\"\ninitializes based on an ontology name\n\"\"\"\n+ super().__init__()\n+\nself.id = ... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Need to call RemoteSparqlOntology() superclass in subclasses |
89,681 | 05.06.2019 01:50:46 | -3,600 | f2f301fc25b86cd09bed2ba1a01a35950bb0af00 | Update documentation to mention the 'ignore_cache' flag in config.yaml | [
{
"change_type": "MODIFY",
"old_path": "docs/installation.rst",
"new_path": "docs/installation.rst",
"diff": "@@ -23,6 +23,13 @@ The development version can be downloaded from GitHub.\npip install -e .[dev,test]\n+Alternately, pip can be directly used to install the master (or other) branch from git... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Update documentation to mention the 'ignore_cache' flag in config.yaml |
89,686 | 18.06.2019 17:59:43 | 25,200 | e8dbc399dd2990e50366f9c0461bb3329fea459a | turning on rule 6 | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/qc.py",
"new_path": "ontobio/io/qc.py",
"diff": "@@ -285,6 +285,7 @@ class GoRule30(GoRule):\nGoRules = enum.Enum(\"GoRules\", {\n\"GoRule02\": GoRule02(),\n+ \"GoRule06\": GoRule06(),\n\"GoRule08\": GoRule08(),\n\"GoRule11\": GoRule11(),\n\"GoRule1... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | turning on rule 6 |
89,686 | 21.06.2019 10:11:50 | 25,200 | ae44d9de6fe220c5284922a81ba9eef0b2686535 | gorule 37 implementation in ontobio qc | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/qc.py",
"new_path": "ontobio/io/qc.py",
"diff": "@@ -282,6 +282,22 @@ class GoRule30(GoRule):\n# don't accept either of has_goref_33 or has_go_paint\nreturn self._result(not (has_goref_33 or has_go_paint))\n+class GoRule37(GoRule):\n+\n+ def __init_... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | gorule 37 implementation in ontobio qc |
89,686 | 21.06.2019 10:42:43 | 25,200 | efb0a24bded432d436e606d124de3336031550b8 | adding gorule42 impl and tests | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/qc.py",
"new_path": "ontobio/io/qc.py",
"diff": "@@ -299,6 +299,21 @@ class GoRule37(GoRule):\nreturn result\n+class GoRule42(GoRule):\n+\n+ def __init__(self):\n+ super().__init__(\"GORULE:0000042\", \"Qualifier: IKR evidence code requires a NOT qu... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | adding gorule42 impl and tests |
89,686 | 21.06.2019 11:38:16 | 25,200 | d4f7838f6a284563367bd8a29cc3b9dcf07ce71f | implmenting gorule 50 | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/qc.py",
"new_path": "ontobio/io/qc.py",
"diff": "@@ -314,6 +314,23 @@ class GoRule42(GoRule):\nreturn result\n+class GoRule50(GoRule):\n+\n+ def __init__(self):\n+ super().__init__(\"GORULE:0000050\", \"Annotations to ISS, ISA and ISO should not be ... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | implmenting gorule 50 |
89,686 | 31.07.2019 12:29:01 | 25,200 | 8c3245a0fb8f457f6a5e9e38cb37c58a02aa9d55 | updating setup.py with more set versions | [
{
"change_type": "MODIFY",
"old_path": "setup.py",
"new_path": "setup.py",
"diff": "@@ -54,8 +54,8 @@ setuptools.setup(\n'prefixcommons',\n'marshmallow==3.0.0b3',\n'scipy',\n- 'pandas',\n- 'click',\n+ 'pandas==0.24.2',\n+ 'click==7.0',\n'yamldown',\n'dataclasses'\n],\n"
}
] | Python | BSD 3-Clause New or Revised License | biolink/ontobio | updating setup.py with more set versions |
89,692 | 07.08.2019 14:22:59 | 25,200 | 28a40e7540ade8e8d97f8e4d7dd2d1a673679d15 | Remove cachier | [
{
"change_type": "MODIFY",
"old_path": "ontobio/assoc_factory.py",
"new_path": "ontobio/assoc_factory.py",
"diff": "@@ -10,8 +10,6 @@ import logging\nimport os\nimport subprocess\nimport hashlib\n-from cachier import cachier\n-import datetime\nfrom ontobio.golr.golr_associations import bulk_fetch\nf... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Remove cachier |
89,692 | 07.08.2019 15:05:15 | 25,200 | 94f179a59c87feed2911d8ae2856e8a7416b3893 | Remove references to cachier in setup.py and documentation | [
{
"change_type": "MODIFY",
"old_path": "docs/inputs.rst",
"new_path": "docs/inputs.rst",
"diff": "@@ -203,11 +203,6 @@ access. Currently an *eager* strategy is used, in which large blocks\nare fetched in advance, though in future *lazy* strategies are\noptionally employed.\n-.. warning ::\n-\n- We u... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Remove references to cachier in setup.py and documentation |
89,686 | 15.08.2019 17:53:27 | 25,200 | 4fb422e61488b479cfa4fd664b4f311a7fdafd92 | gorule 15, interacting taxon check | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/qc.py",
"new_path": "ontobio/io/qc.py",
"diff": "@@ -124,7 +124,7 @@ class GoRule07(GoRule):\ncatalytic_activity = \"GO:0003824\"\nif config.ontology is not None and self.children_of_catalytic_activity is None:\n# We'll define children_of_catalytic_... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | gorule 15, interacting taxon check |
89,685 | 26.08.2019 13:27:48 | 25,200 | 35077a39688c503483e1c1a12fedf6a48ba497dc | revert configs back to prod services | [
{
"change_type": "MODIFY",
"old_path": "ontobio/config.yaml",
"new_path": "ontobio/config.yaml",
"diff": "solr_assocs:\n- url: \"https://solr-dev.monarchinitiative.org/solr/golr\"\n+ url: \"https://solr.monarchinitiative.org/solr/golr\"\ntimeout: 60\namigo_solr_assocs:\nurl: \"http://golr-aux.geneon... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | revert configs back to prod services |
89,685 | 26.08.2019 13:59:45 | 25,200 | 33fd0f3f8b8af11d0c644a3a8affb09bfb29d64c | fix clinical mod test | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -1586,6 +1586,7 @@ class GolrAssociationQuery(GolrAbstractQuery):\n}\nif M.FREQUENCY_LABEL in d:\nassoc[M.FREQUENCY]['label'] = d[M.FREQUENCY_LABEL]\n+\nif M.ONSET in d:\nassoc[... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | fix clinical mod test |
89,685 | 28.08.2019 13:17:51 | 25,200 | 189fc4f1edb528aed15331c3af0692695e167b20 | fix call to get_config | [
{
"change_type": "MODIFY",
"old_path": "ontobio/util/scigraph_util.py",
"new_path": "ontobio/util/scigraph_util.py",
"diff": "@@ -177,7 +177,7 @@ def get_curie_map(url=None):\n\"\"\"\ncurie_map = {}\nif url is None:\n- url = '{}/cypher/curies'.format(get_config().scigraph_data)\n+ url = '{}/cypher/c... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | fix call to get_config |
89,685 | 29.08.2019 11:57:25 | 25,200 | 47a4650fce778e282f8e98d6109f04f916095bf1 | check if we're querying go solr when proc evidence | [
{
"change_type": "MODIFY",
"old_path": "bin/clear-cache.py",
"new_path": "bin/clear-cache.py",
"diff": "@@ -6,4 +6,4 @@ from diskcache import Cache\nimport tempfile\ncache = Cache(tempfile.gettempdir())\n-cache.clear() # Clear on start up\n+cache.clear()\n"
},
{
"change_type": "MODIFY",
... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | check if we're querying go solr when proc evidence |
89,685 | 26.09.2019 14:32:10 | 25,200 | 7b8cb668b5a1d8d4b27ae0976a78b201627439a9 | updates to golr search queries | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -39,7 +39,7 @@ TODO\nimport json\nimport logging\nimport pysolr\n-import requests\n+import re\nfrom typing import Dict, List\nimport xml.etree.ElementTree as ET\nfrom collection... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | updates to golr search queries |
89,685 | 26.09.2019 15:26:44 | 25,200 | 91a2e78671a414869231b05caf40de4e6837dc51 | adjust weights slightly for search | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -401,7 +401,7 @@ class GolrSearchQuery(GolrAbstractQuery):\nself._set_solr(**solr_config)\nself._set_user_agent(self.user_agent)\n- def solr_params(self):\n+ def solr_params(sel... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | adjust weights slightly for search |
89,685 | 18.10.2019 13:24:38 | 25,200 | b2275d9f13a3f4a7b7998b6056ee7775bd7840b1 | use curies in ev table, default publications list | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -875,6 +875,7 @@ class GolrAssociationQuery(GolrAbstractQuery):\nhomology_type=None,\nnon_null_fields=None,\nuser_agent=None,\n+ association_type=None,\n**kwargs):\n\"\"\"Fetch ... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | use curies in ev table, default publications list |
89,685 | 18.10.2019 13:55:07 | 25,200 | b6698bf0d48af67faa2f9433e02cdcff021c9f11 | fix test, add sort | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -876,6 +876,7 @@ class GolrAssociationQuery(GolrAbstractQuery):\nnon_null_fields=None,\nuser_agent=None,\nassociation_type=None,\n+ sort=None,\n**kwargs):\n\"\"\"Fetch a set of ... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | fix test, add sort |
89,685 | 18.10.2019 18:38:30 | 25,200 | cb1e62c9c141fa5dff6d790718d640bb4152642c | use get_curie() for contract_uri | [
{
"change_type": "MODIFY",
"old_path": "ontobio/obograph_util.py",
"new_path": "ontobio/obograph_util.py",
"diff": "@@ -4,8 +4,7 @@ Mapping between obograph-JSON format and networkx\nfrom ontobio.ontol import LogicalDefinition, PropertyChainAxiom\nfrom ontobio.vocabulary.relations import map_legacy_... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | use get_curie() for contract_uri |
89,685 | 21.10.2019 09:40:14 | 25,200 | 060be688918fe5b062089365177f0a406efd1649 | cache evidence table | [
{
"change_type": "MODIFY",
"old_path": "ontobio/obograph_util.py",
"new_path": "ontobio/obograph_util.py",
"diff": "@@ -4,13 +4,18 @@ Mapping between obograph-JSON format and networkx\nfrom ontobio.ontol import LogicalDefinition, PropertyChainAxiom\nfrom ontobio.vocabulary.relations import map_legac... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | cache evidence table |
89,685 | 25.10.2019 14:06:08 | 25,200 | 778f81bd17591fc3b57fa993181042162ac676d3 | add is_publication param to evidence table | [
{
"change_type": "MODIFY",
"old_path": "ontobio/obograph_util.py",
"new_path": "ontobio/obograph_util.py",
"diff": "@@ -276,7 +276,7 @@ def _triple_to_association(digraph, subject, predicate, obj):\nreturn association\n-def obograph_to_assoc_results(digraph):\n+def obograph_to_assoc_results(digraph,... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | add is_publication param to evidence table |
89,685 | 02.11.2019 09:47:05 | 25,200 | 8adc0026ac54924bcc339b4ddcc5f61cf1c662d0 | filter out has_affected_feature for gene_disease ev graphs | [
{
"change_type": "MODIFY",
"old_path": "ontobio/obograph_util.py",
"new_path": "ontobio/obograph_util.py",
"diff": "@@ -276,7 +276,7 @@ def _triple_to_association(digraph, subject, predicate, obj):\nreturn association\n-def obograph_to_assoc_results(digraph, is_publication=False):\n+def obograph_to_... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | filter out has_affected_feature for gene_disease ev graphs |
89,685 | 02.11.2019 10:02:14 | 25,200 | d7caa9e9f59d6184cc4a7259f518cd07857db99e | add association_type to return object | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -62,6 +62,7 @@ class GolrFields:\n\"\"\"\nID='id'\n+ ASSOCIATION_TYPE='association_type'\nSOURCE='source'\nOBJECT_CLOSURE='object_closure'\nSOURCE_CLOSURE_MAP='source_closure_ma... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | add association_type to return object |
89,685 | 02.11.2019 13:07:50 | 25,200 | 6bc55ef08208b0a3e9129cd5bd8c407a1c7978ad | use association type instead of boolean param | [
{
"change_type": "MODIFY",
"old_path": "ontobio/obograph_util.py",
"new_path": "ontobio/obograph_util.py",
"diff": "@@ -294,7 +294,7 @@ def obograph_to_assoc_results(digraph, assoc_type, is_publication=False):\n'OBAN:association_has_predicate',\n'RO:0002558' # ECO codes, etc\n]\n- if not is_publicat... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | use association type instead of boolean param |
89,685 | 02.11.2019 23:39:16 | 25,200 | 3d21f3f2af44120846c92da698661cde2f76f8ce | should be not | [
{
"change_type": "MODIFY",
"old_path": "ontobio/obograph_util.py",
"new_path": "ontobio/obograph_util.py",
"diff": "@@ -294,7 +294,7 @@ def obograph_to_assoc_results(digraph, assoc_type, is_publication=False):\n'OBAN:association_has_predicate',\n'RO:0002558' # ECO codes, etc\n]\n- if assoc_type.star... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | should be not |
89,685 | 02.11.2019 23:54:41 | 25,200 | 700fdd74f66eb11b89320bd0ee22b949510028ae | javascript startsWith is not python startswith | [
{
"change_type": "MODIFY",
"old_path": "ontobio/obograph_util.py",
"new_path": "ontobio/obograph_util.py",
"diff": "@@ -294,7 +294,7 @@ def obograph_to_assoc_results(digraph, assoc_type, is_publication=False):\n'OBAN:association_has_predicate',\n'RO:0002558' # ECO codes, etc\n]\n- if not assoc_type.... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | javascript startsWith is not python startswith |
89,685 | 19.11.2019 16:36:31 | 28,800 | 764de8330f102e651efd485c563c705013086199 | add object direct | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -840,6 +840,7 @@ class GolrAssociationQuery(GolrAbstractQuery):\nobject=None,\nobjects=None,\nsubject_direct=False,\n+ object_direct=False,\nsubject_taxon=None,\nobject_taxon=No... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | add object direct |
89,685 | 22.11.2019 15:30:34 | 28,800 | b8fac05c84742f68d6c022daaa8a7a2a1b791fdc | add taxon_direct params | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -842,7 +842,9 @@ class GolrAssociationQuery(GolrAbstractQuery):\nsubject_direct=False,\nobject_direct=False,\nsubject_taxon=None,\n+ subject_taxon_direct=False,\nobject_taxon=No... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | add taxon_direct params |
89,685 | 26.11.2019 08:26:05 | 28,800 | 1ff187b1c40638a388a7a38010f8145d868095a4 | switch scigraph and owlsim to post requests for sim search | [
{
"change_type": "MODIFY",
"old_path": "ontobio/sim/api/owlsim2.py",
"new_path": "ontobio/sim/api/owlsim2.py",
"diff": "@@ -47,7 +47,7 @@ def search_by_attribute_set(\n'limit': limit,\n'target': namespace_filter\n}\n- return requests.get(owlsim_url, params=params, timeout=TIMEOUT).json()\n+ return r... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | switch scigraph and owlsim to post requests for sim search |
89,686 | 06.02.2020 16:59:38 | 28,800 | dd37f71107d838407039e5405855f8f4b7dca9cc | adding exception for ecycyc and iea filtering | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/qc.py",
"new_path": "ontobio/io/qc.py",
"diff": "@@ -344,8 +344,12 @@ class GoRule29(GoRule):\nnow = datetime.datetime.today()\n+ time_compare_delta = self.one_year\n+ if annotation.provided_by in [\"EcoCyc\" or \"EcoliWiki\"]:\n+ time_compare_delta... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | adding exception for ecycyc and iea filtering |
89,686 | 10.02.2020 11:54:39 | 28,800 | 7f762ffdcbe1f9a12aa2392080b5e75591230fda | passing along group and testing if group is ecocyc | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/gafparser.py",
"new_path": "ontobio/io/gafparser.py",
"diff": "@@ -33,6 +33,7 @@ class GafParser(assocparser.AssocParser):\nconfig : a AssocParserConfig object\n\"\"\"\nself.config = config\n+ self.group = group\nif config is None:\nself.config = as... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | passing along group and testing if group is ecocyc |
89,686 | 02.12.2019 16:25:43 | 28,800 | 399a3246b6cc3bc106fd77955a4b1c81a3a5a9b7 | fixing rule example runner to look at gaf spec failures | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/gafparser.py",
"new_path": "ontobio/io/gafparser.py",
"diff": "@@ -141,7 +141,6 @@ class GafParser(assocparser.AssocParser):\nself.report.error(line, Report.INVALID_ID, \"EMPTY\", \"reference column 6 is empty\", taxon=vals[TAXON_INDEX], rule=1)\nre... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | fixing rule example runner to look at gaf spec failures |
89,686 | 04.12.2019 13:29:31 | 28,800 | de9a982388d1cfb0b34c47785871d1fc23932c65 | adding some tests for gaference and taxon checks | [
{
"change_type": "MODIFY",
"old_path": "tests/resources/test.inferences.json",
"new_path": "tests/resources/test.inferences.json",
"diff": "],\n\"satisfiable\" : true,\n\"taxonProblem\" : false\n+ },\n+ {\n+ \"annotation\" : {\n+ \"annotation\" : {\n+ \"relation\" : \"http://purl.obolibrary.org/obo/... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | adding some tests for gaference and taxon checks |
89,686 | 11.12.2019 14:22:29 | 28,800 | 26377845f3e1a3b1a2998d72323f55557d186104 | skipping gorule-0000015 if not ontology provided | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/qc.py",
"new_path": "ontobio/io/qc.py",
"diff": "@@ -206,12 +206,13 @@ class GoRule15(GoRule):\nself.allowed_dual_species_terms = None\ndef test(self, annotation: List, config: assocparser.AssocParserConfig) -> TestResult:\n-\n# Cache the allowed te... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | skipping gorule-0000015 if not ontology provided |
89,686 | 12.12.2019 14:15:15 | 28,800 | c8128a606c3d3b39cbebcb65e24320c0c7887786 | removing prints that were used in tests | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/gaference.py",
"new_path": "ontobio/io/gaference.py",
"diff": "@@ -106,7 +106,6 @@ def build_annotation_inferences(gaferencer_out: List[Dict]) -> Dict[AnnotationKe\ndef produce_inferences(gaf: association.GoAssociation, inference_table: Dict[Annotat... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | removing prints that were used in tests |
89,686 | 12.12.2019 14:19:24 | 28,800 | b3b371af888b893829e129e7ba9b6fbdb6c78174 | some leftover print statements | [
{
"change_type": "MODIFY",
"old_path": "tests/test_qc.py",
"new_path": "tests/test_qc.py",
"diff": "@@ -156,7 +156,6 @@ def test_go_rules_13():\na = [\"PomBase\", \"SPBC11B10.09\", \"cdc2\", \"\", \"GO:0007275\", \"PMID:21873635\", \"IBA\", \"PANTHER:PTN000623979|TAIR:locus:2099478\", \"P\", \"Cycli... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | some leftover print statements |
89,686 | 17.12.2019 16:09:06 | 28,800 | 4ad5bc936ae2363114fa5e187f6abbb1a2f75b13 | wip for adding GoAssociation and rules to gpads | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/assocparser.py",
"new_path": "ontobio/io/assocparser.py",
"diff": "@@ -18,6 +18,8 @@ import gzip\nimport datetime\nimport dateutil.parser\n+from dataclasses import dataclass\n+\nfrom collections import namedtuple, defaultdict\nfrom typing import Opt... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | wip for adding GoAssociation and rules to gpads |
89,686 | 19.12.2019 15:22:46 | 28,800 | cbf8105433c5cde36015a3f3bbdbe0fa4c3cbef4 | checking for fields existing | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/entityparser.py",
"new_path": "ontobio/io/entityparser.py",
"diff": "from ontobio.io import assocparser\n+from ontobio.model import association\n+\n+from typing import Dict, List\n+\nimport logging\nimport json\n@@ -177,6 +181,9 @@ class GpiParser(E... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | checking for fields existing |
89,686 | 06.01.2020 14:32:20 | 28,800 | 94ed18b2f20968fdb330133649dec665bda4fc9f | adding gorules running to gpad parser | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/entityparser.py",
"new_path": "ontobio/io/entityparser.py",
"diff": "@@ -181,7 +181,7 @@ class GpiParser(EntityParser):\n}\nreturn line, [obj]\n- def as_entities(self) -> Dict[association.Curie, association.GeneEntity]:\n+ def as_entities(self):\npa... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | adding gorules running to gpad parser |
89,686 | 07.01.2020 17:24:01 | 28,800 | 4810935bfcc5cacfc0185583c875a2bb0f0f2c08 | fixing curie relation issue from | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/assocparser.py",
"new_path": "ontobio/io/assocparser.py",
"diff": "@@ -129,6 +129,7 @@ class Report(object):\nINVALID_ID_DBXREF = \"ID or symbol not present in DB xrefs file\"\nUNKNOWN_ID = \"Unknown identifier\"\nINVALID_IDSPACE = \"Invalid identif... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | fixing curie relation issue from #416 |
89,686 | 07.01.2020 18:09:41 | 28,800 | 17dcd6be709485c2cc5827717ce07cd725ef99ac | moving comment and changing error message | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/gafparser.py",
"new_path": "ontobio/io/gafparser.py",
"diff": "@@ -420,7 +420,7 @@ def to_association(gaf_line: List[str], report=None, group=\"unknown\", dataset=\"u\nobject_extensions = association.ExtensionExpression(conjunctions)\nlooked_up_rel ... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | moving comment and changing error message |
89,686 | 15.01.2020 10:24:24 | 28,800 | 0bbca211d906135ff018e5250c3ea7bb7d4c8a13 | passing in group metadata to ontobio parser config | [
{
"change_type": "MODIFY",
"old_path": "bin/validate.py",
"new_path": "bin/validate.py",
"diff": "@@ -185,7 +185,7 @@ def create_parser(config, group, dataset, format=\"gaf\"):\nProduce validated gaf using the gaf parser/\n\"\"\"\n@tools.gzips\n-def produce_gaf(dataset, source_gaf, ontology_graph, g... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | passing in group metadata to ontobio parser config |
89,686 | 15.01.2020 11:47:33 | 28,800 | 6030316570952e68bff37f8cc19b1f0486dc699f | fixing a bug in to_association for gpad | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/gpadparser.py",
"new_path": "ontobio/io/gpadparser.py",
"diff": "@@ -311,8 +311,8 @@ def to_association(gpad_line: List[str], report=None, group=\"unknown\", dataset=\"\nqualifiers = [curie_util.contract_uri(q)[0] for q in looked_up_qualifiers]\ncon... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | fixing a bug in to_association for gpad |
89,686 | 06.02.2020 16:04:01 | 28,800 | b33cd2dae18ed586026229ad5ca96b671af998aa | continuation of new gocamgen rules | [
{
"change_type": "MODIFY",
"old_path": "bin/validate.py",
"new_path": "bin/validate.py",
"diff": "@@ -185,9 +185,22 @@ def create_parser(config, group, dataset, format=\"gaf\"):\nProduce validated gaf using the gaf parser/\n\"\"\"\n@tools.gzips\n-def produce_gaf(dataset, source_gaf, ontology_graph, ... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | continuation of new gocamgen rules |
89,686 | 26.02.2020 10:23:48 | 28,800 | 58ead949b77822716f409645f2ff7a9ce7c024b8 | final gorule 58 implementation and tests | [
{
"change_type": "MODIFY",
"old_path": "bin/validate.py",
"new_path": "bin/validate.py",
"diff": "@@ -195,19 +195,6 @@ Produce validated gaf using the gaf parser/\ndef produce_gaf(dataset, source_gaf, ontology_graph, gpipath=None, paint=False, group=\"unknown\", rule_metadata=None, goref_metadata=No... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | final gorule 58 implementation and tests |
89,686 | 27.02.2020 15:43:49 | 28,800 | 90b5715096fd6619ff9139592bddac93e0f03c8e | extending rules for gorule 13 | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/qc.py",
"new_path": "ontobio/io/qc.py",
"diff": "@@ -190,13 +190,18 @@ class GoRule11(GoRule):\nclass GoRule13(GoRule):\ndef __init__(self):\n- super().__init__(\"GORULE:0000013\", \"Taxon-appropriate annotation check\", FailMode.SOFT)\n+ super().__... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | extending rules for gorule 13 |
89,686 | 02.03.2020 13:47:23 | 28,800 | d12563409c1a734cdc0910258e005eec404f34c3 | spelling name of metadata file correctly | [
{
"change_type": "MODIFY",
"old_path": "ontobio/validation/metadata.py",
"new_path": "ontobio/validation/metadata.py",
"diff": "@@ -105,7 +105,7 @@ def dataset_metadata_file(metadata, group, empty_ok=False) -> Dict:\nreturn None\ndef extensions_constraints_file(metadata):\n- constraints_path = os.pa... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | spelling name of metadata file correctly |
89,686 | 03.03.2020 11:09:36 | 28,800 | f67bc3d6eee4eb5466e604b7c62bc2bf12420431 | adding ruleset tag semantics in ontobio | [
{
"change_type": "MODIFY",
"old_path": "bin/validate.py",
"new_path": "bin/validate.py",
"diff": "@@ -192,7 +192,7 @@ def create_parser(config, group, dataset, format=\"gaf\"):\nProduce validated gaf using the gaf parser/\n\"\"\"\n@tools.gzips\n-def produce_gaf(dataset, source_gaf, ontology_graph, g... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | adding ruleset tag semantics in ontobio |
89,686 | 03.03.2020 13:02:34 | 28,800 | ba98c14bd070de0f743c61c645bda489b7c2ffba | all validations now produce reports like before v1.15.6 | [
{
"change_type": "MODIFY",
"old_path": "bin/validate.py",
"new_path": "bin/validate.py",
"diff": "@@ -192,7 +192,7 @@ def create_parser(config, group, dataset, format=\"gaf\"):\nProduce validated gaf using the gaf parser/\n\"\"\"\n@tools.gzips\n-def produce_gaf(dataset, source_gaf, ontology_graph, g... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | all validations now produce reports like before v1.15.6 |
89,686 | 04.03.2020 18:59:06 | 28,800 | fdeb85c4f22a407d2d6c86cb55cd64f18200ce77 | capability to add run contexts to go rule implementations | [
{
"change_type": "MODIFY",
"old_path": "bin/validate.py",
"new_path": "bin/validate.py",
"diff": "@@ -425,7 +425,7 @@ def merge_all_mixin_gaf_into_mod_gaf(valid_gaf_path, mixin_gaf_paths):\nreturn merged_path\n-def mixin_a_dataset(valid_gaf, mixin_metadata_list, group_id, dataset, target, ontology, ... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | capability to add run contexts to go rule implementations |
89,686 | 05.03.2020 17:11:35 | 28,800 | 8167430a2ded6874d0dff6821eaaa640d7149a53 | adding extennsions-constraints.yaml test resource | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/qc.py",
"new_path": "ontobio/io/qc.py",
"diff": "@@ -524,7 +524,7 @@ class GoRule50(GoRule):\nclass GoRule57(GoRule):\ndef __init__(self):\n- super().__init__(\"GORULE:0000057\", \"Group specific filter rules should be applied to annotations\", Fail... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | adding extennsions-constraints.yaml test resource |
89,686 | 05.03.2020 17:14:18 | 28,800 | 96781d94d9cba0dcf5df3e61b36a7e5647237692 | cleaning up minor typos | [
{
"change_type": "MODIFY",
"old_path": "bin/validate.py",
"new_path": "bin/validate.py",
"diff": "@@ -525,9 +525,8 @@ def produce(ctx, group, metadata_dir, gpad, ttl, target, ontology, exclude, base\ngroup_idspace=group_ids,\nsuppress_rule_reporting_tags=suppress_rule_reporting_tag,\nannotation_infe... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | cleaning up minor typos |
89,685 | 07.03.2020 17:40:32 | 28,800 | 9de2ae3e36067c8b057c56f0cdd824aa606b9bdf | add fq pass through param to solr search | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -332,6 +332,7 @@ class GolrSearchQuery(GolrAbstractQuery):\nsolr=None,\nconfig=None,\nfq=None,\n+ fq_string=None,\nhl=True,\nfacet_fields=None,\nfacet=True,\n@@ -360,6 +361,10 @... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | add fq pass through param to solr search |
89,686 | 09.03.2020 15:31:50 | 25,200 | 30f31689b0b7f606b9aaf7d7e59a3285f9ddace3 | using a comparison of number of items in container rather than comparing type of container | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/qc.py",
"new_path": "ontobio/io/qc.py",
"diff": "@@ -3,6 +3,7 @@ import enum\nimport collections\nimport datetime\nimport copy\n+import logging\nfrom dataclasses import dataclass\n@@ -14,6 +15,8 @@ from ontobio.io import gaference\nfrom ontobio.mode... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | using a comparison of number of items in container rather than comparing type of container |
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