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 |
|---|---|---|---|---|---|---|---|---|---|
89,686 | 11.03.2020 15:28:13 | 25,200 | d6f4d5feb3878d329266ce230887e88cea789f8d | bugfix for dealing with import rules | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/qc.py",
"new_path": "ontobio/io/qc.py",
"diff": "@@ -75,16 +75,21 @@ class GoRule(object):\n# Or, if any run_context_tags is in rule_tags_to_match, then run\nreturn len(self.run_context_tags) == 0 or any(self.run_context_tags & rule_tags_to_match)\n... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | bugfix for dealing with import rules |
89,686 | 16.03.2020 13:00:44 | 25,200 | 1bef789cca3bac51ea690794fc31e6f35c1a963c | no longer uses command line option to respect import mode, but looks at metadata | [
{
"change_type": "MODIFY",
"old_path": "bin/validate.py",
"new_path": "bin/validate.py",
"diff": "@@ -194,7 +194,6 @@ Produce validated gaf using the gaf parser/\n@tools.gzips\ndef produce_gaf(dataset, source_gaf, ontology_graph, gpipath=None, paint=False, group=\"unknown\", rule_metadata=None, gore... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | no longer uses command line option to respect import mode, but looks at metadata |
89,686 | 17.03.2020 10:09:50 | 25,200 | 75b4f473e8561a9bbdff323d2027884625b3d66b | command line option bugfix | [
{
"change_type": "MODIFY",
"old_path": "bin/validate.py",
"new_path": "bin/validate.py",
"diff": "@@ -471,7 +471,7 @@ def cli(ctx, verbose):\n@click.option(\"--suppress-rule-reporting-tag\", \"-S\", multiple=True, help=\"Suppress markdown output messages from rules tagged with this tag\")\n@click.op... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | command line option bugfix |
89,686 | 17.03.2020 16:08:32 | 25,200 | bd78614999542bb2a0844bc48eb102907c5bdf7f | setting gorule 30 to be soft/warn | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/qc.py",
"new_path": "ontobio/io/qc.py",
"diff": "@@ -392,7 +392,7 @@ class GoRule29(GoRule):\nclass GoRule30(GoRule):\ndef __init__(self):\n- super().__init__(\"GORULE:0000030\", \"Deprecated GO_REFs are not allowed\", FailMode.HARD)\n+ super().__in... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | setting gorule 30 to be soft/warn |
89,686 | 31.03.2020 19:17:59 | 25,200 | e506a8c29937673d6bc4df5774657bc40c1f69b4 | report warning if qualifiers have spaces and repaired with underscore, filter wrong qualifiers | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/gafparser.py",
"new_path": "ontobio/io/gafparser.py",
"diff": "@@ -397,6 +397,18 @@ def to_association(gaf_line: List[str], report=None, group=\"unknown\", dataset=\"u\nsubject = association.Subject(subject_curie, gaf_line[2], gaf_line[9], gaf_line[... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | report warning if qualifiers have spaces and repaired with underscore, filter wrong qualifiers |
89,686 | 02.04.2020 10:53:09 | 25,200 | 02b73ea3899afa1ec32557a601ddb294bc9ee34d | adding rule 13 test case for IEA, adding IEA to non exp eco ids | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/qc.py",
"new_path": "ontobio/io/qc.py",
"diff": "@@ -214,7 +214,7 @@ class GoRule13(GoRule):\ndef __init__(self):\nsuper().__init__(\"GORULE:0000013\", \"Taxon-appropriate annotation check\", FailMode.HARD)\n- self.non_experimental_evidence = [\"ECO... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | adding rule 13 test case for IEA, adding IEA to non exp eco ids |
89,686 | 03.04.2020 12:08:40 | 25,200 | c909b572c6d5b37916bd30935b83b4b80c5d0b59 | making any noncopliant qualifiers fail with error. | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/gafparser.py",
"new_path": "ontobio/io/gafparser.py",
"diff": "@@ -347,6 +347,7 @@ class GafParser(assocparser.AssocParser):\necomap = EcoMap()\necomap.mappings()\nrelation_tuple = re.compile(r'(.+)\\((.+)\\)')\n+allowed_qualifiers = set([\"contribu... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | making any noncopliant qualifiers fail with error. |
89,686 | 07.04.2020 10:15:15 | 25,200 | 8cc255058e08803b44926f3b798346518d875cd9 | updating gorule 15 implementation | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/qc.py",
"new_path": "ontobio/io/qc.py",
"diff": "@@ -253,8 +253,9 @@ class GoRule15(GoRule):\n# Cache the allowed terms\nif self.allowed_dual_species_terms is None and config.ontology is not None:\ninteraction_terms = config.ontology.descendants(\"G... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | updating gorule 15 implementation |
89,694 | 10.04.2020 16:32:37 | 25,200 | 5c75e7f506974295a944015c7afed6362a9fb49d | first draft at window expansion for IEAs in GAF QC; work on geneontology/go-site#1456 | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/qc.py",
"new_path": "ontobio/io/qc.py",
"diff": "@@ -372,8 +372,9 @@ class GoRule28(RepairRule):\nclass GoRule29(GoRule):\ndef __init__(self):\n- super().__init__(\"GORULE:0000029\", \"All IEAs over a year old are removed\", FailMode.HARD)\n+ super(... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | first draft at window expansion for IEAs in GAF QC; work on geneontology/go-site#1456 |
89,694 | 10.04.2020 16:40:25 | 25,200 | 16299b50aecc60a615679e4762a6df4840a57f27 | whoops; work on geneontology/go-site#1456 | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/qc.py",
"new_path": "ontobio/io/qc.py",
"diff": "@@ -391,9 +391,9 @@ class GoRule29(GoRule):\niea = \"ECO:0000501\"\nif evidence == iea:\n- if time_diff > time_compare_delta_long):\n+ if time_diff > time_compare_delta_long:\nreturn self._result(Fals... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | whoops; work on geneontology/go-site#1456 |
89,686 | 13.04.2020 12:30:51 | 25,200 | daa7769ed4510074db86c370307abddd63eacd1a | date parsing and normalizing moved so associations are more robust | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/assocparser.py",
"new_path": "ontobio/io/assocparser.py",
"diff": "@@ -533,27 +533,6 @@ class AssocParser(object):\nreturn id\n- def _normalize_gaf_date(self, date, line: SplitLine):\n- if date is None or date == \"\":\n- self.report.warning(line.li... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | date parsing and normalizing moved so associations are more robust |
89,686 | 14.04.2020 13:02:33 | 25,200 | b4e640b208e00c44aedf0c4e4f875ff22796e7df | fixing NOT| bug | [
{
"change_type": "MODIFY",
"old_path": "bin/validate.py",
"new_path": "bin/validate.py",
"diff": "@@ -114,14 +114,18 @@ def download_a_dataset_source(group, dataset_metadata, target_dir, source_url, b\nreturn path\n-def download_source_gafs(group_metadata, target_dir, exclusions=[], base_download_ur... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | fixing NOT| bug |
89,686 | 30.04.2020 13:20:15 | 25,200 | b6250a49fc41c0fb7ed7e3d1cf8a2d5a1ebee46a | ontobio now respects gaf 2.2 and parses qualifiers dependent on versions | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/assocparser.py",
"new_path": "ontobio/io/assocparser.py",
"diff": "@@ -308,6 +308,8 @@ class ParseResult:\n# TODO avoid using names that are builtin python: file, id\n+parser_version_regex = re.compile(r\"!([\\w]+)-version:[\\s]*([\\d]+\\.[\\d]+(\\.... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | ontobio now respects gaf 2.2 and parses qualifiers dependent on versions |
89,686 | 04.05.2020 19:07:45 | 25,200 | a93838223d169a223bbb4b7d1087dce234979837 | gaf writer now respects correctness in version numbers | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/assocparser.py",
"new_path": "ontobio/io/assocparser.py",
"diff": "@@ -306,10 +306,12 @@ class ParseResult:\nreport: Optional[Report] = None\nevidence_used: List[str] = None\n+\n# TODO avoid using names that are builtin python: file, id\nparser_vers... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | gaf writer now respects correctness in version numbers |
89,686 | 05.05.2020 14:21:27 | 25,200 | f428d0c7b13d6f7c8ebc0eb66954aca846fd289d | documentation on skipping behavior | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/assocwriter.py",
"new_path": "ontobio/io/assocwriter.py",
"diff": "@@ -176,7 +176,27 @@ class GpadWriter(AssocWriter):\nclass GafWriter(AssocWriter):\n\"\"\"\n- Writes Associations in GAF format. Not yet implemented\n+ Writes Associations in GAF for... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | documentation on skipping behavior |
89,685 | 12.05.2020 14:20:49 | 25,200 | 66058c82cb1dd56610f653d4d85fb7c422371e13 | add require_tld=False to EndpointSchema | [
{
"change_type": "MODIFY",
"old_path": "ontobio/config.py",
"new_path": "ontobio/config.py",
"diff": "@@ -22,7 +22,7 @@ class EndpointSchema(Schema):\n\"\"\"\nConfiguration for a REST or RESTish endpoint\n\"\"\"\n- url = fields.Url()\n+ url = fields.Url(require_tld=False)\ntimeout = fields.Int()\n@p... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | add require_tld=False to EndpointSchema |
89,685 | 12.05.2020 21:09:46 | 25,200 | 37dc8656acee3726ce628c267af82079ef254487 | updates for marshmallow 3+ | [
{
"change_type": "MODIFY",
"old_path": "ontobio/config.py",
"new_path": "ontobio/config.py",
"diff": "@@ -232,10 +232,11 @@ def load_config(path):\nf = open(path,'r')\nobj = yaml.load(f, Loader=yaml.FullLoader)\nschema = ConfigSchema()\n- config = schema.load(obj).data\n- errs = schema.validate(obj)... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | updates for marshmallow 3+ |
89,686 | 05.06.2020 14:10:06 | 25,200 | 28051dac55e04dd1f4a3efc780eb7d1d7ad578b4 | adding option to give ontobio-parse-assocs a gaf inferences file | [
{
"change_type": "MODIFY",
"old_path": "bin/ontobio-parse-assocs.py",
"new_path": "bin/ontobio-parse-assocs.py",
"diff": "@@ -27,6 +27,7 @@ from ontobio.io.gpadparser import GpadParser\nfrom ontobio.io.hpoaparser import HpoaParser\nfrom ontobio.io.assocwriter import GafWriter, GpadWriter\nfrom ontob... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | adding option to give ontobio-parse-assocs a gaf inferences file |
89,686 | 08.06.2020 09:38:33 | 25,200 | 03627a6bfc6edb3d45265ed32b29eadbbdb3068b | removing offending test for the moment | [
{
"change_type": "MODIFY",
"old_path": "Makefile",
"new_path": "Makefile",
"diff": "@@ -25,8 +25,8 @@ foo:\n# only run local tests\ntravis_test:\npytest tests/test_*local*.py tests/test_*parse*.py tests/test*writer*.py tests/test_qc.py \\\n- tests/test_rdfgen.py tests/test_phenosim_engine.py tests/u... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | removing offending test for the moment |
89,686 | 17.06.2020 12:38:10 | 25,200 | 549338571aeb1f5e0a6c17ea10b92d66352232ef | setting PASS variant of example type enum to pass, rather than fail | [
{
"change_type": "MODIFY",
"old_path": "ontobio/validation/rules.py",
"new_path": "ontobio/validation/rules.py",
"diff": "@@ -81,7 +81,7 @@ Relavent schema:\n\"\"\"\nFormatType = enum.Enum(\"FormatType\", [\"RDF\", \"GAF\", \"GPAD\"])\n-ExampleType = enum.Enum(\"ExampleType\", {\"REPAIR\": \"repair\... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | setting PASS variant of example type enum to pass, rather than fail |
89,685 | 17.06.2020 13:22:38 | 25,200 | 04f2bca56dc542090eb31e38bb38617cbe3a4fca | add clinical mod test back | [
{
"change_type": "MODIFY",
"old_path": "Makefile",
"new_path": "Makefile",
"diff": "@@ -26,7 +26,9 @@ foo:\ntravis_test:\npytest tests/test_*local*.py tests/test_*parse*.py tests/test*writer*.py tests/test_qc.py \\\ntests/test_rdfgen.py tests/test_phenosim_engine.py tests/test_ontol.py \\\n- tests/t... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | add clinical mod test back |
89,686 | 26.06.2020 16:20:14 | 25,200 | 30ebeba87e79aa6f7743ce0cda304fdbcbba195e | updating go association model and needed refactoring elsewhere. Tests added for new functionality | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/gaference.py",
"new_path": "ontobio/io/gaference.py",
"diff": "@@ -54,7 +54,7 @@ class RelationTo:\nclass AnnotationKey:\nrelation_to: RelationTo\ntaxon: Uri\n- extension: association.ExtensionConjunctions\n+ extension: association.ConjunctiveSet\n@... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | updating go association model and needed refactoring elsewhere. Tests added for new functionality |
89,686 | 26.06.2020 16:59:35 | 25,200 | e234367a40ef8de0646aa51294836741688ad8d9 | trying instead to update pandas | [
{
"change_type": "MODIFY",
"old_path": "setup.py",
"new_path": "setup.py",
"diff": "@@ -52,9 +52,8 @@ setuptools.setup(\n'sparqlwrapper',\n'prefixcommons',\n'marshmallow==3.0.0b11',\n- 'scipy==1.4.1',\n- 'numpy==1.14.5',\n- 'pandas==0.24.2',\n+ 'scipy',\n+ 'pandas==1.0.5',\n'click==7.0',\n'yamldown'... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | trying instead to update pandas |
89,686 | 30.06.2020 12:25:08 | 25,200 | 063b3435fa97b526df7cb0e5a0611d9166e36159 | updating travis to install the way normally do it locally | [
{
"change_type": "MODIFY",
"old_path": ".travis.yml",
"new_path": ".travis.yml",
"diff": "@@ -6,11 +6,10 @@ python:\n- \"3.6\"\n# command to install dependencies\n+# Install with local setup.py, then install pytest\ninstall:\n- - pip install --upgrade pip setuptools wheel\n- - pip install --only-bin... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | updating travis to install the way normally do it locally |
89,686 | 24.08.2020 20:31:31 | 25,200 | 023b374f48c75437e7631b1ea0b988183a3de328 | geneontology/go-site#1453 biolink/ontobio#450 added test and fix for
pombase bad subject extension not being caught | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/gafparser.py",
"new_path": "ontobio/io/gafparser.py",
"diff": "@@ -345,7 +345,14 @@ def to_association(gaf_line: List[str], report=None, group=\"unknown\", dataset=\"u\nreport.error(source_line, Report.INVALID_SYMBOL, gaf_line[5], first_error.info, ... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | geneontology/go-site#1453 biolink/ontobio#450 added test and fix for
pombase bad subject extension not being caught |
89,686 | 25.08.2020 20:47:27 | 25,200 | b60035c694904ff2adae2135e060103c083f6ca0 | adding gorule55 in qc and a test | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/assocparser.py",
"new_path": "ontobio/io/assocparser.py",
"diff": "@@ -175,6 +175,7 @@ class Report(object):\nEXTENSION_SYNTAX_ERROR = \"Syntax error in annotation extension field\"\nVIOLATES_GO_RULE = \"Violates GO Rule\"\nRULE_PASS = \"Passes GO R... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | adding gorule55 in qc and a test |
89,686 | 03.09.2020 15:35:14 | 25,200 | 310ddec3151e570ffdef9a26d659e4d03fbf83af | hardening errors from escaping parse into data, more testing | [
{
"change_type": "MODIFY",
"old_path": "bin/validate.py",
"new_path": "bin/validate.py",
"diff": "@@ -215,7 +215,7 @@ def produce_gaf(dataset, source_gaf, ontology_graph, gpipath=None, paint=False,\nrule_contexts=rule_contexts\n)\nlogger.info(\"Producing {}\".format(source_gaf))\n- logger.info(\"Ass... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | hardening errors from escaping parse into data, more testing |
89,686 | 14.09.2020 22:34:54 | 25,200 | 967f7c71bc6cbe06c2058d3ac7c4c105032edcf8 | qualifiers from gpad to gaf that are outside the gaf spec just blank out the field | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/assocwriter.py",
"new_path": "ontobio/io/assocwriter.py",
"diff": "@@ -247,8 +247,8 @@ class GafWriter(AssocWriter):\nallowed_qualifiers = {\"contributes_to\", \"colocalizes_with\"}\n# Detect if the qualifier is wrong\nif len(assoc[\"qualifiers\"]) ... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | qualifiers from gpad to gaf that are outside the gaf spec just blank out the field |
89,686 | 15.09.2020 14:18:15 | 25,200 | 5b4a5c1c73b15f89989e306adad2205405263635 | added test for qualifier with gaf 2.2 | [
{
"change_type": "MODIFY",
"old_path": "tests/test_assoc_writer.py",
"new_path": "tests/test_assoc_writer.py",
"diff": "@@ -234,3 +234,28 @@ def test_gpad_qualifier_removed_in_gaf_2_1():\nwriter.write_assoc(assoc)\ngpad_to_gaf_line = [line for line in out.getvalue().split(\"\\n\") if not line.starts... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | added test for qualifier with gaf 2.2 |
89,686 | 17.09.2020 17:34:13 | 25,200 | 1d6e3731245f7e259709ff62ce0ec55333121308 | adding more relations | [
{
"change_type": "MODIFY",
"old_path": "ontobio/rdfgen/relations.py",
"new_path": "ontobio/rdfgen/relations.py",
"diff": "@@ -82,7 +82,9 @@ __relation_label_lookup = bidict({\n\"regulates o results in specification of\": \"http://purl.obolibrary.org/obo/GOREL_0001027\",\n\"results in division of\": ... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | adding more relations |
89,686 | 23.09.2020 17:28:23 | 25,200 | ceb55fcbb501b8cca77d74f41f3834ad1154876d | gpad 2.0 writer for geneontology/go-site#1453 | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/assocwriter.py",
"new_path": "ontobio/io/assocwriter.py",
"diff": "@@ -104,13 +104,18 @@ class AssocWriter():\nfor a in assocs:\nself.write_assoc(a)\n+\n+GPAD_2_0 = \"2.0\"\n+GPAD_1_2 = \"1.2\"\n+\nclass GpadWriter(AssocWriter):\n\"\"\"\nWrites Asso... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | gpad 2.0 writer for geneontology/go-site#1453 |
89,686 | 28.09.2020 15:33:33 | 25,200 | 9324ca28d5470637ca30191825f3a70eea1b974d | correcting the taxon Curie leaking in the report by wrapping in str | [
{
"change_type": "MODIFY",
"old_path": "bin/ontobio-parse-assocs.py",
"new_path": "bin/ontobio-parse-assocs.py",
"diff": "@@ -72,6 +72,8 @@ def main():\nhelp='Increase output verbosity')\nparser.add_argument(\"--allow_paint\", required=False, action=\"store_const\", const=True,\nhelp=\"Allow IBAs in... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | correcting the taxon Curie leaking in the report by wrapping in str |
89,686 | 28.09.2020 18:25:11 | 25,200 | 233102893df6b0c59ae249f54250585d861d0b13 | adding synonymType field to the Synonym class to fix parse bug | [
{
"change_type": "MODIFY",
"old_path": "ontobio/ontol.py",
"new_path": "ontobio/ontol.py",
"diff": "@@ -1109,7 +1109,7 @@ class Synonym(AbstractPropertyValue):\nhasNarrowSynonym='narrow',\nhasRelatedSynonym='related')\n- def __init__(self, class_id, val=None, pred='hasRelatedSynonym', lextype=None, ... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | adding synonymType field to the Synonym class to fix parse bug |
89,686 | 29.09.2020 12:28:09 | 25,200 | b286c934b2dfa0f3c13f87005aa399d9c1cc020a | removing extra experimental parsing code (which will come late) | [
{
"change_type": "MODIFY",
"old_path": "bin/ontobio-parse-assocs.py",
"new_path": "bin/ontobio-parse-assocs.py",
"diff": "@@ -72,8 +72,6 @@ def main():\nhelp='Increase output verbosity')\nparser.add_argument(\"--allow_paint\", required=False, action=\"store_const\", const=True,\nhelp=\"Allow IBAs in... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | removing extra experimental parsing code (which will come late) |
89,686 | 30.09.2020 16:04:06 | 25,200 | 4cf5965f3427d811591db32020bd234f287181a6 | gpad now correctly sets the relation when parsing | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/gpadparser.py",
"new_path": "ontobio/io/gpadparser.py",
"diff": "@@ -263,7 +263,8 @@ def to_association(gpad_line: List[str], report=None, group=\"unknown\", dataset=\"\n[association.Curie.from_str(e) for e in gpad_line[4].split(\"|\") if e],\nassoc... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | gpad now correctly sets the relation when parsing |
89,686 | 15.10.2020 12:04:55 | 25,200 | e4e20dff3e943e5320ca1bdd575ed652f6835c82 | initial collections classes for associations | [
{
"change_type": "MODIFY",
"old_path": "bin/ontobio-parse-assocs.py",
"new_path": "bin/ontobio-parse-assocs.py",
"diff": "@@ -72,6 +72,8 @@ def main():\nhelp='Increase output verbosity')\nparser.add_argument(\"--allow_paint\", required=False, action=\"store_const\", const=True,\nhelp=\"Allow IBAs in... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | initial collections classes for associations |
89,686 | 15.10.2020 12:06:05 | 25,200 | 1ee9e67b33bdd0c7b6b0bf36130b5ab0f6ee85f1 | collections module | [
{
"change_type": "ADD",
"old_path": null,
"new_path": "ontobio/model/collections.py",
"diff": "+import typing\n+import logging\n+from dataclasses import dataclass, field\n+from typing import List, Dict, Callable\n+\n+from ontobio.model import association\n+from ontobio.model.association import GoAss... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | collections module |
89,686 | 15.10.2020 12:18:19 | 25,200 | ad89bf1b6fa12e9d786db2b88173213ee0d9e11b | fixing references to gpad 1.1 to 1.2 | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/assocwriter.py",
"new_path": "ontobio/io/assocwriter.py",
"diff": "@@ -112,7 +112,7 @@ class GpadWriter(AssocWriter):\n\"\"\"\nWrites Associations in GPAD format\n\"\"\"\n- def __init__(self, file=None, version=\"1.1\"):\n+ def __init__(self, file=N... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | fixing references to gpad 1.1 to 1.2 |
89,686 | 15.10.2020 14:10:30 | 25,200 | 8ab08aa05f670d7c7242769e989a6844b8928b94 | Initial logic to parse gpad 2.0 and version switching in the parser | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/gpadparser.py",
"new_path": "ontobio/io/gpadparser.py",
"diff": "@@ -59,7 +59,7 @@ class GpadParser(assocparser.AssocParser):\n}\nprint(\"Loaded {} entities from {}\".format(len(self.gpi.keys()), self.config.gpi_authority_path))\n- def gaf_version(s... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Initial logic to parse gpad 2.0 and version switching in the parser |
89,686 | 20.10.2020 13:34:48 | 25,200 | 8bef33b9b94c36c21e9f4397dc7bcad296f3e37a | gpad parser tests now inspect the expected GoAssociation | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/gpadparser.py",
"new_path": "ontobio/io/gpadparser.py",
"diff": "@@ -239,7 +239,7 @@ def from_1_2(gpad_line: List[str], report=None, group=\"unknown\", dataset=\"unknow\nif len(gpad_line) != 12:\nreport.error(source_line, assocparser.Report.WRONG_NU... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | gpad parser tests now inspect the expected GoAssociation |
89,685 | 23.10.2020 13:48:31 | 14,400 | fb55bf2bc23e538e9eb26fb9e9683f97acc6024e | add support for q param to golr association fx for monarch | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -85,6 +85,7 @@ class GolrFields:\nOBJECT_TAXON_CLOSURE_LABEL_SEARCHABLE = 'object_taxon_closure_label_searchable'\nSUBJECT_GENE_CLOSURE='subject_gene_closure'\nSUBJECT_GENE_LABE... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | add support for q param to golr association fx for monarch |
89,686 | 27.10.2020 17:33:42 | 25,200 | 164780a7c38732bfd5dfed050b359af08143d23c | tests and test fixes for collections | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/gafparser.py",
"new_path": "ontobio/io/gafparser.py",
"diff": "@@ -62,20 +62,9 @@ class GafParser(assocparser.AssocParser):\nself.config = assocparser.AssocParserConfig()\nself.report = assocparser.Report(group=group, dataset=dataset, config=self.co... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | tests and test fixes for collections |
89,686 | 27.10.2020 17:36:35 | 25,200 | 54ef01b0610752275dc2064f9f83ea0b0bec3d1e | undoing Curie validation update in favor of seperate branch from master | [
{
"change_type": "MODIFY",
"old_path": "ontobio/model/association.py",
"new_path": "ontobio/model/association.py",
"diff": "@@ -55,9 +55,6 @@ class Curie:\nif identity == \"\":\nreturn Error(\"Identity of CURIE is empty\")\n- if \" \" in namespace:\n- return Error(\"No spaces allowed in CURIE prefix... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | undoing Curie validation update in favor of seperate branch from master |
89,686 | 27.10.2020 17:50:15 | 25,200 | ad7f4116301b5a65c6c810124eefcd5fc6bb220b | curies should not parse with spaces in them, tests for new validation | [
{
"change_type": "MODIFY",
"old_path": "ontobio/model/association.py",
"new_path": "ontobio/model/association.py",
"diff": "@@ -55,6 +55,9 @@ class Curie:\nif identity == \"\":\nreturn Error(\"Identity of CURIE is empty\")\n+ if \" \" in namespace or \" \" in identity:\n+ return Error(\"No spaces al... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | curies should not parse with spaces in them, tests for new validation |
89,686 | 27.10.2020 17:55:49 | 25,200 | 3bdb040fa43b1de779c62f2a98a762d7475b002b | adding collections tests and cleanup code that is going in another branch | [
{
"change_type": "ADD",
"old_path": null,
"new_path": "tests/test_collections.py",
"diff": "+from ontobio.model import collections\n+from ontobio.model.association import Curie, Subject\n+from ontobio.io import assocparser, gafparser, gpadparser\n+\n+def test_bioentities_get_when_empty():\n+ e = col... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | adding collections tests and cleanup code that is going in another branch |
89,685 | 05.11.2020 20:12:02 | 18,000 | 05e30eb299cad8a0739e46f2c181b4e12563a3d2 | amigo checking | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -971,7 +971,7 @@ class GolrAssociationQuery(GolrAbstractQuery):\nM.OBJECT_CLOSURE\n]\n- if self.sort is None and self.get_config().default_solr_schema != 'amigo':\n+ if self.sor... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | amigo checking |
89,686 | 02.12.2020 22:44:30 | 28,800 | bddab5de45703898138b3c515720815170060799 | gpad parser now takes taxon element out of the list instead of passing on the entire list | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/gpadparser.py",
"new_path": "ontobio/io/gpadparser.py",
"diff": "@@ -302,7 +302,7 @@ def from_1_2(gpad_line: List[str], report=None, group=\"unknown\", dataset=\"unknow\nreport.error(source_line, Report.INVALID_TAXON, taxon_result.original, taxon_re... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | gpad parser now takes taxon element out of the list instead of passing on the entire list |
89,686 | 03.12.2020 10:37:23 | 28,800 | 5f5291605b48411da9d68a3fce3d344454620481 | unlocking some dependencies | [
{
"change_type": "MODIFY",
"old_path": "setup.py",
"new_path": "setup.py",
"diff": "@@ -44,7 +44,7 @@ setuptools.setup(\n# Dependencies\ninstall_requires=[\n- 'networkx==2.2',\n+ 'networkx',\n'jsobject',\n'pyyaml',\n'pysolr',\n@@ -53,7 +53,7 @@ setuptools.setup(\n'prefixcommons',\n'marshmallow==3.0.... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | unlocking some dependencies |
89,686 | 03.12.2020 16:52:23 | 28,800 | 83887480b8b7801dddddb56e504b54087602c244 | adding github action to run tests | [
{
"change_type": "ADD",
"old_path": null,
"new_path": ".github/workflows/make-tests.yaml",
"diff": "+name: refresh-readmes\n+on: [push]\n+jobs:\n+ run-make:\n+ runs-on: ubuntu-latest\n+ steps:\n+ - uses: actions/checkout@v2\n+ with:\n+ ref: ${{ github.head_ref }}\n+ - uses: actions/setup-python@v2\n... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | adding github action to run tests |
89,686 | 10.12.2020 15:23:11 | 28,800 | cc93be1b27b3a942af9b5501703baaa7be6ff707 | adding version option to convert subcommand in ontobio-parse-assocs | [
{
"change_type": "MODIFY",
"old_path": "bin/ontobio-parse-assocs.py",
"new_path": "bin/ontobio-parse-assocs.py",
"diff": "@@ -29,6 +29,7 @@ from ontobio.io.assocwriter import GafWriter, GpadWriter\nfrom ontobio.io import assocparser\nfrom ontobio.io import gaference\nfrom ontobio.slimmer import get_... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | adding version option to convert subcommand in ontobio-parse-assocs |
89,686 | 10.12.2020 15:53:35 | 28,800 | 0894df7f1b951e2aac3b755652065c1142cc17cd | protect against a missing key in dataset yaml | [
{
"change_type": "MODIFY",
"old_path": "bin/validate.py",
"new_path": "bin/validate.py",
"diff": "@@ -135,7 +135,7 @@ def download_source_gafs(group_metadata, target_dir, exclusions=[], base_downloa\n# Local target download path setup - path and then directories\npath = download_a_dataset_source(gro... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | protect against a missing key in dataset yaml |
89,686 | 10.12.2020 16:24:07 | 28,800 | b2922059d4e95272edc6ee9ac0dc082bd6cf25df | protecting against missing field in metadata.py | [
{
"change_type": "MODIFY",
"old_path": "ontobio/validation/metadata.py",
"new_path": "ontobio/validation/metadata.py",
"diff": "@@ -140,7 +140,7 @@ def metayaml_id(rule_path) -> str:\ndef source_path(dataset_metadata, target_dir, group):\nextension = dataset_metadata[\"type\"]\n- if dataset_metadata... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | protecting against missing field in metadata.py |
89,686 | 10.12.2020 18:25:22 | 28,800 | 4ec1d31673fdd057028d01f8bb569d159f81f4ec | switching version option name and properly using default values for version | [
{
"change_type": "MODIFY",
"old_path": "bin/ontobio-parse-assocs.py",
"new_path": "bin/ontobio-parse-assocs.py",
"diff": "@@ -89,7 +89,7 @@ def main():\nparser_n.set_defaults(function=convert_assocs)\nparser_n.add_argument('-t', '--to', type=str, required=True, choices=[\"GAF\", \"GPAD\"],\nhelp='Fo... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | switching version option name and properly using default values for version |
89,686 | 11.12.2020 15:27:00 | 28,800 | 284a2e3d51747b52a75995ef645289e8df4f3021 | bug fixes for writing gaf 2.2 | [
{
"change_type": "MODIFY",
"old_path": "bin/ontobio-parse-assocs.py",
"new_path": "bin/ontobio-parse-assocs.py",
"diff": "@@ -87,9 +87,9 @@ def main():\nparser_n = subparsers.add_parser('convert', help='Convert associations')\nparser_n.set_defaults(function=convert_assocs)\n- parser_n.add_argument('... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | bug fixes for writing gaf 2.2 |
89,686 | 11.12.2020 16:02:29 | 28,800 | 51084cc57d24d7d8cff096a0c5bf280d9b635b74 | adding parse and then write gaf 2.2 test | [
{
"change_type": "MODIFY",
"old_path": "tests/test_assoc_writer.py",
"new_path": "tests/test_assoc_writer.py",
"diff": "@@ -184,6 +184,18 @@ def test_writing_to_gaf_2_2():\ngaf_22_out = assoc.to_gaf_2_2_tsv()\nassert gaf_22_out[3] == \"NOT|involved_in\"\n+def test_full_gaf_2_2_write():\n+ line = \"W... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | adding parse and then write gaf 2.2 test |
89,686 | 07.01.2021 17:46:33 | 28,800 | 67c6cbcc56f773bf6e1847225286a08dd8327919 | updating date parsing locations | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/assocparser.py",
"new_path": "ontobio/io/assocparser.py",
"diff": "@@ -830,26 +830,71 @@ class AssocParser(object):\n-def _normalize_gaf_date(date, report, taxon, line):\n- if date is None or date == \"\":\n- report.warning(line, Report.INVALID_DATE... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | updating date parsing locations |
89,692 | 08.01.2021 17:18:25 | 28,800 | bd9f4b95dd72929304dae5830e1ba19e34376262 | Remove most of the pinned dependencies from requirements.txt | [
{
"change_type": "MODIFY",
"old_path": "requirements.txt",
"new_path": "requirements.txt",
"diff": "@@ -4,19 +4,19 @@ prefixcommons>=0.1.9\nrequests>=0.0\npip>=9.0.1\nwheel>0.25.0\n-pysolr==3.6.0\n-networkx==2.2\n-matplotlib==2.0.0\n-SPARQLWrapper==1.8.0\n+pysolr>=3.6.0\n+networkx>=2.2\n+matplotlib>... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Remove most of the pinned dependencies from requirements.txt |
89,692 | 08.01.2021 17:18:53 | 28,800 | 559f23a287bbb987b087f535a77dce8e9a410c7a | Use requirements from requirements.txt in setup.py | [
{
"change_type": "MODIFY",
"old_path": "setup.py",
"new_path": "setup.py",
"diff": "@@ -17,6 +17,8 @@ with open(init_path) as read_file:\npattern = re.compile(r\"^__version__ = ['\\\"]([^'\\\"]*)['\\\"]\", re.MULTILINE)\nversion = pattern.search(text).group(1)\n+with open(\"requirements.txt\", \"r\"... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Use requirements from requirements.txt in setup.py |
89,686 | 03.02.2021 13:52:22 | 28,800 | 5cd4114ee7560bc9801e265f0a8074a95bcbf3c5 | some parsing errors in gpad 1.2 are now properly caught and handled | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/gpadparser.py",
"new_path": "ontobio/io/gpadparser.py",
"diff": "@@ -139,7 +139,7 @@ class GpadParser(assocparser.AssocParser):\n# At this point, we should have gone through all the header, and a version number should be established\nif self.version... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | some parsing errors in gpad 1.2 are now properly caught and handled |
89,686 | 03.02.2021 14:59:12 | 28,800 | b91c2604fdb88f870e69e359bbb67a26f9ae5d40 | threading gaf output version number through validate and small bugfix in data output | [
{
"change_type": "MODIFY",
"old_path": "bin/validate.py",
"new_path": "bin/validate.py",
"diff": "@@ -197,7 +197,7 @@ 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 | threading gaf output version number through validate and small bugfix in data output |
89,686 | 04.02.2021 14:31:01 | 28,800 | bd9fdfbcd941e0786bb3a60aae7c8330bf35cd53 | setup for making the rule | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/gafparser.py",
"new_path": "ontobio/io/gafparser.py",
"diff": "@@ -2,7 +2,7 @@ import re\nimport logging\nimport json\n-from typing import List, Tuple, Optional\n+from typing import List, Tuple, Set, Dict\nfrom dataclasses import dataclass\nfrom pre... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | setup for making the rule |
89,686 | 05.02.2021 11:34:39 | 28,800 | f5c4da49a5fe985f7c2fdc50a9a328fca327d846 | creating closure and initial qualifier upgrade function | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/gafparser.py",
"new_path": "ontobio/io/gafparser.py",
"diff": "@@ -37,8 +37,10 @@ gaf_line_validators = {\n\"taxon\": assocparser.TaxonValidator()\n}\n-def compute_cell_component_subtree_closures(ontology: Ontology) -> Dict[association.Curie, Set[as... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | creating closure and initial qualifier upgrade function |
89,686 | 08.02.2021 17:43:30 | 28,800 | 299062ba2ef8060362dafb2a5bb680b8a4180929 | tests and corrections for rule 59 qualifiers upgrade | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/gafparser.py",
"new_path": "ontobio/io/gafparser.py",
"diff": "@@ -37,6 +37,7 @@ gaf_line_validators = {\n\"taxon\": assocparser.TaxonValidator()\n}\n+\ndef protein_complex_sublcass_closure(ontology: Ontology) -> Set[str]:\nprotein_containing_comple... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | tests and corrections for rule 59 qualifiers upgrade |
89,686 | 10.02.2021 14:00:30 | 28,800 | c7eea1265b6c5e87050c9c00a3be66c7ede737ba | correcting the output formatter for extensions in gaf 2.2 | [
{
"change_type": "MODIFY",
"old_path": "ontobio/model/association.py",
"new_path": "ontobio/model/association.py",
"diff": "@@ -467,7 +467,8 @@ class GoAssociation:\ntaxon,\nymd_str(self.date, \"\"),\nself.provided_by,\n- ConjunctiveSet.list_to_str(self.object_extensions),\n+ ConjunctiveSet.list_to_... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | correcting the output formatter for extensions in gaf 2.2 |
89,686 | 16.02.2021 13:28:47 | 28,800 | 8b6da0f964906e1a3b8e70634308be4744414c61 | report message calls make sure to wrap taxon objects as strings | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/assocparser.py",
"new_path": "ontobio/io/assocparser.py",
"diff": "@@ -312,13 +312,13 @@ class Report(object):\nself.config = config\nself.header = []\n- def error(self, line, type, obj, msg=\"\", taxon=\"\", rule=None):\n+ def error(self, line, typ... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | report message calls make sure to wrap taxon objects as strings |
89,686 | 16.02.2021 13:31:00 | 28,800 | 75f9ed0eba98d3ac289b997140495a6d1209cc09 | removing .travis.yml since we now have github actions | [
{
"change_type": "DELETE",
"old_path": ".travis.yml",
"new_path": null,
"diff": "-dist: trusty\n-sudo: false\n-\n-language: python\n-python:\n- - \"3.6\"\n-\n-# command to install dependencies\n-# Install with local setup.py, then install pytest\n-install:\n- - pip install .\n- - pip install pytest\... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | removing .travis.yml since we now have github actions |
89,686 | 25.02.2021 17:22:49 | 28,800 | 8d8af838eb3155e6763a8884b99876e5af446c4f | updating gorule 59 upconvert from gaf 2.1 | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/gafparser.py",
"new_path": "ontobio/io/gafparser.py",
"diff": "@@ -281,6 +281,8 @@ class GafParser(assocparser.AssocParser):\nFor GAF 2.1 we will apply an algorithm to find a best fit relation if the qualifier column is empty.\nIf the qualifiers fie... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | updating gorule 59 upconvert from gaf 2.1 |
89,686 | 03.03.2021 20:32:47 | 28,800 | d012f720cda48ccf5efd1d7b79afab6cc31951ca | gorule 61 implementation in ontobio | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/qc.py",
"new_path": "ontobio/io/qc.py",
"diff": "@@ -7,11 +7,12 @@ import logging\nfrom dataclasses import dataclass\n-from typing import List, Dict, Any, Tuple, Union\n+from typing import List, Dict, Any, Optional, Set, Tuple, Union\nfrom prefixcom... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | gorule 61 implementation in ontobio |
89,686 | 08.03.2021 18:13:45 | 28,800 | 6a5de2f3f93c54a21d9f12c6503da30bdeaf7a4c | fixing gorule repair 61 when annotating to CC root | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/qc.py",
"new_path": "ontobio/io/qc.py",
"diff": "@@ -691,14 +691,14 @@ class GoRule61(RepairRule):\ndef test(self, annotation: association.GoAssociation, config: assocparser.AssocParserConfig, group=None) -> TestResult:\n\"\"\"\n- * GO:0005554 \"mol... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | fixing gorule repair 61 when annotating to CC root |
89,686 | 09.03.2021 20:38:52 | 28,800 | 9737521495319938ec7d06d3e321a1985946c611 | updating gorule 61 to repair in bio process | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/qc.py",
"new_path": "ontobio/io/qc.py",
"diff": "@@ -726,8 +726,12 @@ class GoRule61(RepairRule):\nrepair_state = RepairState.REPAIRED\nelif namespace == \"molecular_function\":\nif relation not in self.allowed_mf:\n+ enables = association.Curie(nam... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | updating gorule 61 to repair in bio process |
89,686 | 09.03.2021 21:15:47 | 28,800 | 7e301f3abe5ac5691a29018535e2503708bbfa64 | updating gaf writer to correct new header requirements in gaf 2.2 | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/assocwriter.py",
"new_path": "ontobio/io/assocwriter.py",
"diff": "@@ -171,9 +171,9 @@ class GafWriter(AssocWriter):\nself._write(\"!gaf-version: {}\\n\".format(self.version))\nself._write(\"!\\n\")\n- self._write(\"!Generated by GO Central\\n\")\n+... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | updating gaf writer to correct new header requirements in gaf 2.2 |
89,686 | 10.03.2021 12:56:57 | 28,800 | d1f989a9133670a16f39b4b90632127f75b79a9a | update gorule 61 again | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/qc.py",
"new_path": "ontobio/io/qc.py",
"diff": "@@ -680,6 +680,7 @@ class GoRule61(RepairRule):\nassociation.Curie(\"RO\", \"0004032\"), association.Curie(\"RO\", \"0004033\"), association.Curie(\"RO\", \"0002263\"),\nassociation.Curie(\"RO\", \"00... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | update gorule 61 again |
89,686 | 17.03.2021 14:15:35 | 25,200 | 331c88c1e148ae9078d1ffe5fc58f35f902c006d | updates needed for new pipeline kernel, small bugifxes | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/assocparser.py",
"new_path": "ontobio/io/assocparser.py",
"diff": "@@ -21,7 +21,7 @@ import dateutil.parser\nfrom dataclasses import dataclass\nfrom collections import namedtuple, defaultdict\n-from typing import Optional, List, Dict, Set\n+from typ... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | updates needed for new pipeline kernel, small bugifxes |
89,686 | 07.04.2021 14:16:20 | 25,200 | e041cdd6096ffcf947e17dc299a338b3e92247d2 | a RuleSet is used in the parser config to determine which rules should be run | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/assocparser.py",
"new_path": "ontobio/io/assocparser.py",
"diff": "@@ -21,7 +21,7 @@ import dateutil.parser\nfrom dataclasses import dataclass\nfrom collections import namedtuple, defaultdict\n-from typing import Optional, List, Dict, Set, Union\n+f... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | a RuleSet is used in the parser config to determine which rules should be run |
89,686 | 08.04.2021 16:33:35 | 25,200 | 85ad6ec0b9b2e2fce8a9cbb087242c3c57285423 | adding rule_set to configs in script runners | [
{
"change_type": "MODIFY",
"old_path": "bin/ontobio-parse-assocs.py",
"new_path": "bin/ontobio-parse-assocs.py",
"diff": "@@ -75,6 +75,10 @@ def main():\nhelp=\"Allow IBAs in parser\")\nparser.add_argument(\"-g\", \"--gpi\", type=str, required=False, default=None,\nhelp=\"GPI file\")\n+ parser.add_a... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | adding rule_set to configs in script runners |
89,686 | 08.04.2021 16:44:44 | 25,200 | 5b0ac747a5ae179f8934566d4e973fef3c9e528c | adding new option to ontobio validate for specifying rulesets. Default is all rules | [
{
"change_type": "MODIFY",
"old_path": "bin/validate.py",
"new_path": "bin/validate.py",
"diff": "@@ -197,7 +197,7 @@ 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 new option to ontobio validate for specifying rulesets. Default is all rules |
89,686 | 08.04.2021 17:05:46 | 25,200 | f47d04feeb7eef42fd1921aeaec99ed6e78d9e4c | updating tests config using specific rule_set | [
{
"change_type": "MODIFY",
"old_path": "tests/test_gafparser.py",
"new_path": "tests/test_gafparser.py",
"diff": "@@ -381,7 +381,8 @@ def test_alt_id_repair():\ndef test_gorule_repair():\nconfig = assocparser.AssocParserConfig(\n- ontology=OntologyFactory().create(\"tests/resources/goslim_generic.js... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | updating tests config using specific rule_set |
89,686 | 08.04.2021 17:23:25 | 25,200 | 5c1c6322b92eed3e0685e0fc54fa259a7f4a10cd | updating documentation in the commandline file | [
{
"change_type": "MODIFY",
"old_path": "docs/commandline.rst",
"new_path": "docs/commandline.rst",
"diff": "@@ -273,7 +273,28 @@ convert association files (GAF, GPAD, HPOA etc)\nGO Rules\n^^^^^^^^\n-``ontobio-parse-assocs.py`` will\n+``ontobio-parse-assocs.py`` is capable of running the GO Rules (ht... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | updating documentation in the commandline file |
89,686 | 13.04.2021 22:44:05 | 25,200 | 7df37ddb07449a5fd96d187be9c0b79dcc60dee1 | rule set bugfix where a variable was not being properly set | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/assocparser.py",
"new_path": "ontobio/io/assocparser.py",
"diff": "@@ -7,6 +7,7 @@ All parser objects instantiate a subclass of the abstract `AssocParser` object\n# TODO: Refactor - move some stuff out into generic parser object\n+# from _typeshed i... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | rule set bugfix where a variable was not being properly set |
89,686 | 15.04.2021 12:00:13 | 25,200 | d6a6a0695a6f42ec908ae7e748dc5aacc3141bee | updating requirements to only specify greater-than version dependencies | [
{
"change_type": "MODIFY",
"old_path": "requirements.txt",
"new_path": "requirements.txt",
"diff": "-marshmallow==3.0.0b11\n+marshmallow>=3.0.0b11\njsobject>=0.0\nprefixcommons>=0.1.9\nrequests>=0.0\n@@ -13,7 +13,7 @@ scipy>=1.2.0\ntwine\njsonpickle>=0.0\njsonpath_rw>=0.0\n-PyShEx==0.7.11\n+PyShEx>=... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | updating requirements to only specify greater-than version dependencies |
89,685 | 27.04.2021 19:37:17 | 14,400 | 6cd77fe645f159f29dcd92d4deb53db8e25a94fe | solr search query - add support for filtering based on equivalent curie prefixes, leaf nodes | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -347,6 +347,8 @@ class GolrSearchQuery(GolrAbstractQuery):\ntaxon=None,\nmin_match=None,\nminimal_tokenizer=False,\n+ include_eqs=False,\n+ exclude_groups=False,\nuser_agent=Non... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | solr search query - add support for filtering based on equivalent curie prefixes, leaf nodes |
89,685 | 28.04.2021 12:29:31 | 14,400 | add608c367e73b6a97c9cf8cab6aa00a41e23489 | fix autocomplete test, add new prefix test | [
{
"change_type": "MODIFY",
"old_path": "tests/unit/resources/solr/expected/autocomplete-nocat.json",
"new_path": "tests/unit/resources/solr/expected/autocomplete-nocat.json",
"diff": "],\n\"match\":\"food\",\n\"taxon\":\"\",\n- \"taxon_label\":\"\"\n+ \"taxon_label\":\"\",\n+ \"equivalent_ids\": []\... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | fix autocomplete test, add new prefix test |
89,685 | 28.04.2021 16:25:44 | 14,400 | bc9cc6a9d6c23143356c58120af6777859da22df | add colon to wildcard query | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -502,7 +502,7 @@ class GolrSearchQuery(GolrAbstractQuery):\nif negative_filter:\nif self.include_eqs:\nsingle_filts = [\n- f\"(-prefix:{prefix} OR -equivalent_curie:{prefix}*)\"... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | add colon to wildcard query |
89,685 | 19.05.2021 13:15:55 | 14,400 | 1218e68c53aae73aaff4d8adb62611ee18221f75 | increase owlsim limit to accurately rank non phendodigm metrics | [
{
"change_type": "MODIFY",
"old_path": "ontobio/sim/api/owlsim2.py",
"new_path": "ontobio/sim/api/owlsim2.py",
"diff": "@@ -261,13 +261,26 @@ class OwlSim2Api(SimApi, InformationContentStore, FilteredSearchable):\nOwlsim2 filtered search, resolves taxon and category to a namespace,\ncalls search_by_... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | increase owlsim limit to accurately rank non phendodigm metrics |
89,686 | 19.05.2021 14:24:51 | 25,200 | 11d3e501968084128b604fd228147058653c1aac | documentation for GoRules engine | [
{
"change_type": "MODIFY",
"old_path": "bin/validate.py",
"new_path": "bin/validate.py",
"diff": "@@ -100,6 +100,8 @@ def download_a_dataset_source(group, dataset_metadata, target_dir, source_url, b\n# including scheme and such\nreconstructed_url = urllib.parse.urlunsplit((scheme, urllib.parse.urlpa... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | documentation for GoRules engine |
89,686 | 20.05.2021 12:10:53 | 25,200 | 34d45513b77699967ccc614aa2f769f0136adbce | adding some ontobio-parse-assocs docs | [
{
"change_type": "MODIFY",
"old_path": "docs/commandline.rst",
"new_path": "docs/commandline.rst",
"diff": "@@ -268,7 +268,26 @@ Parsing assoc files\n-------------------\nThe ``ontobio-parse-assocs.py`` command will parse, validate and\n-convert association files (GAF, GPAD, HPOA etc)\n+convert asso... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | adding some ontobio-parse-assocs docs |
89,686 | 20.05.2021 16:17:12 | 25,200 | 6cde39ca5116f4666eba4c8218c12e51b090778f | GoAssociation documentation | [
{
"change_type": "MODIFY",
"old_path": "docs/api.rst",
"new_path": "docs/api.rst",
"diff": "@@ -85,6 +85,18 @@ Association File Parsers\n.. autoclass:: AssocParserConfig\n:members:\n+Go Rules\n+^^^^^^^^\n+\n+.. automodule:: ontobio.io.qc\n+ :members:\n+\n+GoAssociation internal Model\n+^^^^^^^^^^^^^... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | GoAssociation documentation |
89,682 | 25.05.2021 16:13:47 | 25,200 | a32225337b74161d022fe8238ed823dd1cd5559f | adding withfroms back into evidence_with property for binding terms | [
{
"change_type": "MODIFY",
"old_path": "bin/validate.py",
"new_path": "bin/validate.py",
"diff": "@@ -40,6 +40,7 @@ from typing import Dict, Set\nlogger = logging.getLogger(\"ontobio\")\n+\ndef thispath():\nos.path.normpath(os.path.abspath(__file__))\n@@ -115,6 +116,7 @@ def download_a_dataset_sourc... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | adding withfroms back into evidence_with property for binding terms |
89,682 | 26.05.2021 08:27:01 | 25,200 | b9c9087ce009f0dbd613d0824a0a9bcf810700ac | update code to not create duplicate evidence rows | [
{
"change_type": "MODIFY",
"old_path": "ontobio/rdfgen/gocamgen/collapsed_assoc.py",
"new_path": "ontobio/rdfgen/gocamgen/collapsed_assoc.py",
"diff": "@@ -66,10 +66,7 @@ class CollapsedAssociationSet:\nfor wf in separated_with_froms:\nca = self.find_or_create_collapsed_association(a, wf)\nassociati... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | update code to not create duplicate evidence rows |
89,685 | 29.07.2021 16:07:30 | 14,400 | 0bbc6d52b5ce9e01d2dac52555d35655c3368650 | update default owlsim2 to legacy.monarchinitiative | [
{
"change_type": "MODIFY",
"old_path": "ontobio/config.yaml",
"new_path": "ontobio/config.yaml",
"diff": "@@ -23,7 +23,7 @@ scigraph_data:\nurl: \"https://scigraph-data.monarchinitiative.org/scigraph\"\ntimeout: 15\nowlsim2:\n- url: \"https://monarchinitiative.org/owlsim/\"\n+ url: \"https://legacy.... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | update default owlsim2 to legacy.monarchinitiative |
89,689 | 12.09.2021 14:19:53 | -3,600 | 482774c62f21974d8a24803f522028818c227279 | Support more recent versions of marshmallow.
Make sure decorated methods are prepared to receive extra keywords
argument by adding a **kwargs to their declaration, as recommended by
marshmallow developers [1]. Also add a missing import for
ValidationError.
[1] | [
{
"change_type": "MODIFY",
"old_path": "ontobio/config.py",
"new_path": "ontobio/config.py",
"diff": "import logging\nimport yaml\nimport os\n-from marshmallow import Schema, fields, pprint, post_load\n+from marshmallow import Schema, fields, pprint, post_load, ValidationError\nlogger = logging.getL... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Support more recent versions of marshmallow.
Make sure decorated methods are prepared to receive extra keywords
argument by adding a **kwargs to their declaration, as recommended by
marshmallow developers [1]. Also add a missing import for
ValidationError.
[1] https://marshmallow.readthedocs.io/en/stable/upgrading.html#decorated-methods-and-handle-error-receive-many-and-partial |
89,685 | 16.09.2021 15:42:34 | 14,400 | 5d2879a288eb858f3b37f88f0d31150be52dca9a | fix bugs from scigraph util move | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -40,6 +40,7 @@ import json\nimport logging\nimport pysolr\nimport re\n+from dataclasses import asdict\nfrom typing import Dict, List\nimport xml.etree.ElementTree as ET\nfrom co... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | fix bugs from scigraph util move |
89,685 | 21.09.2021 10:18:58 | 14,400 | dd35601369c3267107b4ef4364a5acc8efb4b66c | only get direct phenotypes for input nodes (diseases, genes) | [
{
"change_type": "MODIFY",
"old_path": "ontobio/sim/phenosim_engine.py",
"new_path": "ontobio/sim/phenosim_engine.py",
"diff": "@@ -154,7 +154,7 @@ class PhenoSimEngine():\npheno_list.append(node)\nelse:\nphenotypes = get_objects_for_subject(\n- subject=node, object_category='phenotype', relation='R... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | only get direct phenotypes for input nodes (diseases, genes) |
89,682 | 07.10.2021 09:32:14 | 25,200 | b404cdbe8a66bcf7627db6739603ad44e801c53c | split into its own function for hopeful reuse in gaf parsetr | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/assocparser.py",
"new_path": "ontobio/io/assocparser.py",
"diff": "@@ -671,6 +671,22 @@ class AssocParser(object):\nself.report.error(line.line, Report.INVALID_TAXON, taxon, taxon=taxon)\nreturn False\n+ def _unroll_withfrom_and_replair_obsoletes(se... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | split into its own function for hopeful reuse in gaf parsetr |
89,682 | 07.10.2021 09:46:23 | 25,200 | 9753675577347de8da7708ff2e64294d921815df | add check to gaf and hpoa parsers | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/assocparser.py",
"new_path": "ontobio/io/assocparser.py",
"diff": "@@ -777,7 +777,6 @@ class AssocParser(object):\nvalids.append(i)\nelse:\nreturn None\n-\nreturn sorted(valids)\ndef validate_curie_ids(self, ids: List[association.Curie], line: Split... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | add check to gaf and hpoa parsers |
89,682 | 07.10.2021 10:18:12 | 25,200 | cf778034e357a099918ce05ef92a839814bc838d | adding tests for gaf parser obsolete fix | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/assocparser.py",
"new_path": "ontobio/io/assocparser.py",
"diff": "@@ -588,7 +588,6 @@ class AssocParser(object):\nelse:\nprint(line)\n-\ndef skim(self, file):\n\"\"\"\nLightweight parse of a file into tuples.\n"
},
{
"change_type": "MODIFY"... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | adding tests for gaf parser obsolete fix |
89,682 | 07.10.2021 10:51:16 | 25,200 | ea9fedcdb4645df62d98948510e91414dbe740a2 | add tests for gaf parsing, fix method to respond to gaf or gpad | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/assocparser.py",
"new_path": "ontobio/io/assocparser.py",
"diff": "@@ -670,9 +670,13 @@ class AssocParser(object):\nself.report.error(line.line, Report.INVALID_TAXON, taxon, taxon=taxon)\nreturn False\n- def _unroll_withfrom_and_replair_obsoletes(se... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | add tests for gaf parsing, fix method to respond to gaf or gpad |
89,682 | 07.10.2021 12:15:18 | 25,200 | 46e6e4941654acfa3e4f7fe92d3800a08bb0972a | fix tests for gaf repair | [
{
"change_type": "MODIFY",
"old_path": "tests/test_gafparser.py",
"new_path": "tests/test_gafparser.py",
"diff": "@@ -8,7 +8,7 @@ from ontobio.assoc_factory import AssociationSetFactory\nfrom ontobio.ontol_factory import OntologyFactory\nfrom ontobio.model import association\nfrom ontobio.rdfgen imp... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | fix tests for gaf repair |
89,682 | 07.10.2021 12:28:54 | 25,200 | aed6b49d509e90eac5a4a9b57576b92ce6cf4b18 | reformating to see breaking tests more clearly | [
{
"change_type": "MODIFY",
"old_path": "tests/test_ecomap.py",
"new_path": "tests/test_ecomap.py",
"diff": "from ontobio.ecomap import EcoMap\n+\ndef test_ecomap():\n\"\"\"\ntest mappings between GAF codes and ECO\n"
},
{
"change_type": "MODIFY",
"old_path": "tests/test_hpoaparser.py",
... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | reformating to see breaking tests more clearly |
89,682 | 07.10.2021 12:58:23 | 25,200 | 6d0e8a9962dfa90a653175724af3fd24a900b4ff | fix pombase test | [
{
"change_type": "MODIFY",
"old_path": "ontobio/io/assocparser.py",
"new_path": "ontobio/io/assocparser.py",
"diff": "@@ -679,7 +679,10 @@ class AssocParser(object):\nfor element_set in filter(None, withfrom.split(\"|\")):\ngrouped_fixed_elements = ''\nfor element_individual in filter(None, element_... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | fix pombase test |
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