From 06d08b31d661459569ed6788c01f98761f7a5253 Mon Sep 17 00:00:00 2001 From: Patrick Kalita Date: Thu, 14 Apr 2022 16:16:47 -0700 Subject: [PATCH 1/3] Convert test files into unittest.TestCase classes --- src/mapping_walker/pipeline/pipeline.py | 8 ++-- tests/test_boomer.py | 22 +++++----- tests/test_mapping_walker.py | 29 +++++++------ tests/test_oxo_endpoint.py | 19 +++++---- tests/test_oxo_walker.py | 54 +++++++++++++------------ tests/test_schema.py | 17 ++++---- 6 files changed, 81 insertions(+), 68 deletions(-) diff --git a/src/mapping_walker/pipeline/pipeline.py b/src/mapping_walker/pipeline/pipeline.py index cfe13a2..cde94a6 100644 --- a/src/mapping_walker/pipeline/pipeline.py +++ b/src/mapping_walker/pipeline/pipeline.py @@ -137,7 +137,7 @@ def load_mappings_and_write_ptable(self): def write_ptable(self, doc: MappingSetDocument, output: Union[Path, str, TextIO] = sys.stdout): - if not isinstance(output, TextIO): + if isinstance(output, Path) or isinstance(output, str): output = open(str(output), 'w', encoding='utf-8') for mapping in doc.mapping_set.mappings: if not mapping.confidence: @@ -172,11 +172,11 @@ def add_label(curie: str, label: str): g.serialize(destination=output) def write_prefixmap(self, doc: MappingSetDocument, output: Union[str, Path, TextIO] = sys.stdout): - if isinstance(output, TextIO): - yaml.dump(doc.prefix_map, stream=output) - else: + if isinstance(output, Path) or isinstance(output, str): with open(output, 'w', encoding='utf-8') as stream: yaml.dump(doc.prefix_map, stream=stream) + else: + yaml.dump(doc.prefix_map, stream=output) @click.command() @click.option("-v", "--verbose", count=True) diff --git a/tests/test_boomer.py b/tests/test_boomer.py index 92d615b..6ab4197 100644 --- a/tests/test_boomer.py +++ b/tests/test_boomer.py @@ -1,5 +1,6 @@ import json from pathlib import Path +import unittest from linkml_runtime.loaders import json_loader, yaml_loader from mapping_walker.pipeline.pipeline import Pipeline @@ -8,16 +9,17 @@ from tests import INPUT_DIR, OUTPUT_DIR +class TestBoomer(unittest.TestCase): -def test_outputs(): - infile = str(Path(INPUT_DIR) / 'oxo-walk.yaml') - mapping_set = yaml_loader.load(infile, target_class=MappingSet) - doc = MappingSetDocument(mapping_set=mapping_set, prefix_map={}) - boomer = Pipeline() - with open(str(Path(OUTPUT_DIR) / 'oxo-walk.ptable.tsv'), 'w', encoding='utf-8') as stream: - boomer.write_ptable(doc, output=stream) - boomer.write_ontology(doc, str(Path(OUTPUT_DIR) / 'oxo-walk.ontology.ttl')) - with open(str(Path(OUTPUT_DIR) / 'oxo-walk.prefixes.yaml'), 'w', encoding='utf-8') as stream: - boomer.write_prefixmap(doc, output=stream) + def test_outputs(self): + infile = str(Path(INPUT_DIR) / 'oxo-walk.yaml') + mapping_set = yaml_loader.load(infile, target_class=MappingSet) + doc = MappingSetDocument(mapping_set=mapping_set, prefix_map={}) + boomer = Pipeline() + with open(str(Path(OUTPUT_DIR) / 'oxo-walk.ptable.tsv'), 'w', encoding='utf-8') as stream: + boomer.write_ptable(doc, output=stream) + boomer.write_ontology(doc, str(Path(OUTPUT_DIR) / 'oxo-walk.ontology.ttl')) + with open(str(Path(OUTPUT_DIR) / 'oxo-walk.prefixes.yaml'), 'w', encoding='utf-8') as stream: + boomer.write_prefixmap(doc, output=stream) diff --git a/tests/test_mapping_walker.py b/tests/test_mapping_walker.py index a851def..eb9f469 100644 --- a/tests/test_mapping_walker.py +++ b/tests/test_mapping_walker.py @@ -1,4 +1,5 @@ from pathlib import Path +import unittest from mapping_walker import __version__ from mapping_walker.pipeline.pipeline import Pipeline @@ -9,17 +10,19 @@ WD = Path(OUTPUT_DIR) / 'tmp' CURIE = 'UBERON:0013141' -def test_pipeline(): - """ - test end to end pipeline, using OxO endpoint - :return: - """ - ec = EndpointConfiguration(type=EndpointEnum.OxO) - conf = PipelineConfiguration(working_directory=str(WD), - stylesheet=str(Path(INPUT_DIR) / 'style.json'), - endpoint_configurations=[ec]) - pipeline = Pipeline(configuration=conf) - result = pipeline.run(CURIE) - print(f'PNGS={result.pngs}') - assert len(result.pngs) == 2 +class TestMappingWalker(unittest.TestCase): + + def test_pipeline(self): + """ + test end to end pipeline, using OxO endpoint + :return: + """ + ec = EndpointConfiguration(type=EndpointEnum.OxO) + conf = PipelineConfiguration(working_directory=str(WD), + stylesheet=str(Path(INPUT_DIR) / 'style.json'), + endpoint_configurations=[ec]) + pipeline = Pipeline(configuration=conf) + result = pipeline.run(CURIE) + print(f'PNGS={result.pngs}') + assert len(result.pngs) == 2 diff --git a/tests/test_oxo_endpoint.py b/tests/test_oxo_endpoint.py index 629e34e..b8efd64 100644 --- a/tests/test_oxo_endpoint.py +++ b/tests/test_oxo_endpoint.py @@ -1,5 +1,6 @@ import json from pathlib import Path +import unittest from mapping_walker.utils.sssom_utils import save_mapping_set_doc, get_iri_from_curie @@ -16,12 +17,14 @@ OUT_FILE = Path(OUTPUT_DIR) / 'uberon-oxo-result.yaml' -def test_oxo_endpoint(): - endpoint = OxoEndpoint() - msdoc = endpoint.get_direct_mappings('UBERON:0013141') - #print(yaml_dumper.dumps(msdoc.mapping_set)) - save_mapping_set_doc(msdoc, OUT_FILE) - for m in msdoc.mapping_set.mappings: - uri = get_iri_from_curie(m.object_id, msdoc) - print(f'{m.object_id} = {uri}') +class TestOxOEndpoint(unittest.TestCase): + + def test_oxo_endpoint(self): + endpoint = OxoEndpoint() + msdoc = endpoint.get_direct_mappings('UBERON:0013141') + #print(yaml_dumper.dumps(msdoc.mapping_set)) + save_mapping_set_doc(msdoc, OUT_FILE) + for m in msdoc.mapping_set.mappings: + uri = get_iri_from_curie(m.object_id, msdoc) + print(f'{m.object_id} = {uri}') diff --git a/tests/test_oxo_walker.py b/tests/test_oxo_walker.py index c966268..4a7afdd 100644 --- a/tests/test_oxo_walker.py +++ b/tests/test_oxo_walker.py @@ -1,5 +1,6 @@ import json from pathlib import Path +import unittest from mapping_walker.pipeline.pipeline_config import PipelineConfiguration from mapping_walker.utils.sssom_utils import load_mapping_set_doc, save_mapping_set_doc @@ -19,29 +20,30 @@ CURIE = 'UBERON:0013141' -def test_oxo_walker(): - """ - Tests iterative walking over OxO endpoint - """ - endpoint = OxoEndpoint() - walker = MappingWalker(endpoints=[endpoint]) - config = PipelineConfiguration(max_clique_size=100, max_hops=3) - msdoc = walker.walk(CURIE, config=config) - assert len(msdoc.mapping_set.mappings) > 4 - with open(str(Path(OUTPUT_DIR) / 'oxo-walk.yaml'), 'w', encoding='utf-8') as stream: - stream.write(yaml_dumper.dumps(msdoc.mapping_set)) - -def test_oxo_fill_gaps(): - """ - uses a predefined mapping file to test gap-filling using OLS - :return: - """ - msdoc = load_mapping_set_doc(str(Path(INPUT_DIR) / 'neoplasm.sssom.yaml')) - endpoint = OxoEndpoint() - n = endpoint.fill_gaps(msdoc) - print(n) - save_mapping_set_doc(msdoc, str(Path(OUTPUT_DIR) / 'neoplasm-gap-filled.sssom.yaml')) - for m in msdoc.mapping_set.mappings: - if m.predicate_id == 'rdfs:subClassOf': - print(yaml_dumper.dumps(m)) - assert n > 0 +class TestOxOWalker(unittest.TestCase): + def test_oxo_walker(self): + """ + Tests iterative walking over OxO endpoint + """ + endpoint = OxoEndpoint() + walker = MappingWalker(endpoints=[endpoint]) + config = PipelineConfiguration(max_clique_size=100, max_hops=3) + msdoc = walker.walk(CURIE, config=config) + assert len(msdoc.mapping_set.mappings) > 4 + with open(str(Path(OUTPUT_DIR) / 'oxo-walk.yaml'), 'w', encoding='utf-8') as stream: + stream.write(yaml_dumper.dumps(msdoc.mapping_set)) + + def test_oxo_fill_gaps(self): + """ + uses a predefined mapping file to test gap-filling using OLS + :return: + """ + msdoc = load_mapping_set_doc(str(Path(INPUT_DIR) / 'neoplasm.sssom.yaml')) + endpoint = OxoEndpoint() + n = endpoint.fill_gaps(msdoc) + print(n) + save_mapping_set_doc(msdoc, str(Path(OUTPUT_DIR) / 'neoplasm-gap-filled.sssom.yaml')) + for m in msdoc.mapping_set.mappings: + if m.predicate_id == 'rdfs:subClassOf': + print(yaml_dumper.dumps(m)) + assert n > 0 diff --git a/tests/test_schema.py b/tests/test_schema.py index c65630d..e14b287 100644 --- a/tests/test_schema.py +++ b/tests/test_schema.py @@ -1,5 +1,6 @@ import json from pathlib import Path +import unittest from linkml_runtime.loaders import json_loader from mapping_walker.utils.oxo_utils import load_oxo_payload @@ -9,11 +10,13 @@ from mapping_walker.ext_schemas.oxo import Container -def test_schema(): - infile = str(Path(INPUT_DIR) / 'oxo-example-uberon.json') - with open(infile, encoding='utf-8') as stream: - obj = json.load(stream) - print(obj) - container = load_oxo_payload(obj) - print(container) +class TestSchema(unittest.TestCase): + + def test_schema(self): + infile = str(Path(INPUT_DIR) / 'oxo-example-uberon.json') + with open(infile, encoding='utf-8') as stream: + obj = json.load(stream) + print(obj) + container = load_oxo_payload(obj) + print(container) From 96b297fe39de9721fc06df64518df3fe0cfc986f Mon Sep 17 00:00:00 2001 From: Patrick Kalita Date: Thu, 14 Apr 2022 16:17:28 -0700 Subject: [PATCH 2/3] Add oaklib as a dependency --- poetry.lock | 523 ++++++++++++++++++++++++++++++++++++++++++++++++- pyproject.toml | 1 + 2 files changed, 519 insertions(+), 5 deletions(-) diff --git a/poetry.lock b/poetry.lock index f91ba83..6eacf37 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,3 +1,34 @@ +[[package]] +name = "aiohttp" +version = "3.8.1" +description = "Async http client/server framework (asyncio)" +category = "main" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +aiosignal = ">=1.1.2" +async-timeout = ">=4.0.0a3,<5.0" +attrs = ">=17.3.0" +charset-normalizer = ">=2.0,<3.0" +frozenlist = ">=1.1.1" +multidict = ">=4.5,<7.0" +yarl = ">=1.0,<2.0" + +[package.extras] +speedups = ["aiodns", "brotli", "cchardet"] + +[[package]] +name = "aiosignal" +version = "1.2.0" +description = "aiosignal: a list of registered asynchronous callbacks" +category = "main" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +frozenlist = ">=1.1.0" + [[package]] name = "alabaster" version = "0.7.12" @@ -6,6 +37,22 @@ category = "main" optional = false python-versions = "*" +[[package]] +name = "appdirs" +version = "1.4.4" +description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." +category = "main" +optional = false +python-versions = "*" + +[[package]] +name = "async-timeout" +version = "4.0.2" +description = "Timeout context manager for asyncio programs" +category = "main" +optional = false +python-versions = ">=3.6" + [[package]] name = "atomicwrites" version = "1.4.0" @@ -73,6 +120,14 @@ category = "main" optional = false python-versions = "*" +[[package]] +name = "chardet" +version = "4.0.0" +description = "Universal encoding detector for Python 2 and 3" +category = "main" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" + [[package]] name = "charset-normalizer" version = "2.0.12" @@ -144,6 +199,57 @@ category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +[[package]] +name = "fastobo" +version = "0.11.1" +description = "Faultless AST for Open Biomedical Ontologies in Python." +category = "main" +optional = false +python-versions = ">=3.6" + +[[package]] +name = "frozenlist" +version = "1.3.0" +description = "A list-like structure which implements collections.abc.MutableSequence" +category = "main" +optional = false +python-versions = ">=3.7" + +[[package]] +name = "fsspec" +version = "2022.3.0" +description = "File-system specification" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +aiohttp = {version = "*", optional = true, markers = "extra == \"http\""} +requests = {version = "*", optional = true, markers = "extra == \"http\""} + +[package.extras] +abfs = ["adlfs"] +adl = ["adlfs"] +arrow = ["pyarrow (>=1)"] +dask = ["dask", "distributed"] +dropbox = ["dropboxdrivefs", "requests", "dropbox"] +entrypoints = ["importlib-metadata"] +fuse = ["fusepy"] +gcs = ["gcsfs"] +git = ["pygit2"] +github = ["requests"] +gs = ["gcsfs"] +gui = ["panel"] +hdfs = ["pyarrow (>=1)"] +http = ["requests", "aiohttp"] +libarchive = ["libarchive-c"] +oci = ["ocifs"] +s3 = ["s3fs"] +sftp = ["paramiko"] +smb = ["smbprotocol"] +ssh = ["paramiko"] +tqdm = ["tqdm"] + [[package]] name = "greenlet" version = "1.1.2" @@ -253,7 +359,7 @@ format_nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339- [[package]] name = "linkml-runtime" -version = "1.2.2" +version = "1.2.6" description = "Runtime environment for LinkML, the Linked open data modeling language" category = "main" optional = false @@ -267,7 +373,7 @@ json-flattener = ">=0.1.9" jsonasobj2 = ">=1.0.4,<2.0.0" jsonschema = ">=3.2.0" prefixcommons = "*" -pyyaml = ">=5.1.0" +pyyaml = "*" rdflib = ">=6.0.0" requests = "*" @@ -298,6 +404,14 @@ category = "dev" optional = false python-versions = ">=3.5" +[[package]] +name = "multidict" +version = "6.0.2" +description = "multidict implementation" +category = "main" +optional = false +python-versions = ">=3.7" + [[package]] name = "networkx" version = "2.7.1" @@ -321,6 +435,42 @@ category = "main" optional = false python-versions = ">=3.8" +[[package]] +name = "nxontology" +version = "0.4.1" +description = "NetworkX for ontologies" +category = "main" +optional = false +python-versions = ">=3.8" + +[package.dependencies] +fsspec = {version = "*", extras = ["http"]} +networkx = ">=2" +pronto = ">=2.4.0" + +[package.extras] +dev = ["fire", "pandas", "pre-commit", "pytest"] +viz = ["pygraphviz"] + +[[package]] +name = "oaklib" +version = "0.1.6" +description = "Ontology Access Kit: Python library for common ontology operations over a variety of backends" +category = "main" +optional = false +python-versions = ">=3.9,<4.0" + +[package.dependencies] +appdirs = ">=1.4.4,<2.0.0" +linkml-runtime = ">=1.2.3,<2.0.0" +networkx = ">=2.7.1,<3.0.0" +nxontology = ">=0.4.0,<0.5.0" 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From: Patrick Kalita Date: Fri, 15 Apr 2022 13:39:45 -0700 Subject: [PATCH 3/3] Replace OxoEndpoint method implementations with calls to oak methods --- src/mapping_walker/walkers/endpoints.py | 70 ++++++------------------- tests/test_oxo_endpoint.py | 3 ++ 2 files changed, 19 insertions(+), 54 deletions(-) diff --git a/src/mapping_walker/walkers/endpoints.py b/src/mapping_walker/walkers/endpoints.py index 2a30618..1468294 100644 --- a/src/mapping_walker/walkers/endpoints.py +++ b/src/mapping_walker/walkers/endpoints.py @@ -1,23 +1,16 @@ import logging from dataclasses import dataclass, field -from typing import Union, Dict, List +from typing import Dict, List, Union -import requests -import urllib -from mapping_walker.ext_schemas.oxo import Container, OntologyIdentifier, ScopeEnum -from mapping_walker.utils.oxo_utils import load_oxo_payload -from mapping_walker.utils.sssom_utils import all_curies_in_doc, get_iri_from_curie, curie_to_uri_map -from sssom.sssom_datamodel import MappingSet, Mapping, MatchTypeEnum - -from mapping_walker.pipeline.pipeline_config import PipelineConfiguration, EndpointConfiguration +from oaklib.datamodels.vocabulary import IS_A +from oaklib.implementations.ols.ols_implementation import OlsImplementation +from sssom.sssom_datamodel import Mapping, MappingSet, MatchTypeEnum from sssom.sssom_document import MappingSetDocument -oxo_pred_mappings = { - ScopeEnum.EXACT.text: 'skos:exactMatch', - ScopeEnum.BROADER.text: 'skos:broadMatch', - ScopeEnum.NARROWER.text: 'skos:narrowMatch', - ScopeEnum.RELATED.text: 'skos:closeMatch', -} +from mapping_walker.ext_schemas.oxo import OntologyIdentifier, ScopeEnum +from mapping_walker.pipeline.pipeline_config import EndpointConfiguration +from mapping_walker.utils.sssom_utils import curie_to_uri_map + @dataclass class Endpoint: @@ -47,52 +40,21 @@ def add_prefix(self, curie: str, uri: str): @dataclass class OxoEndpoint(Endpoint): - base_url = "https://www.ebi.ac.uk/spot/oxo/api/mappings" - ols_base_url = "https://www.ebi.ac.uk/ols/api/ontologies/" + def __post_init__(self): + self.ols = OlsImplementation() + def get_direct_mappings(self, curie: Union[str, OntologyIdentifier]) -> MappingSetDocument: - result = requests.get(self.base_url, params=dict(fromId=curie)) - obj = result.json() - container = load_oxo_payload(obj) - return self.convert_payload(container) - - def convert_payload(self, container: Container) -> MappingSetDocument: - oxo_mappings = container._embedded.mappings - mappings: Mapping = [] - for oxo_mapping in oxo_mappings: - oxo_s = oxo_mapping.fromTerm - oxo_o = oxo_mapping.toTerm - mapping = Mapping(subject_id=oxo_s.curie, - subject_label=oxo_s.label, - subject_source=oxo_s.datasource.prefix if oxo_s.datasource else None, - predicate_id=oxo_pred_mappings[str(oxo_mapping.scope)], - match_type=MatchTypeEnum.Unspecified, - object_id=oxo_o.curie, - object_label=oxo_o.label, - object_source=oxo_o.datasource.prefix if oxo_o.datasource else None, - mapping_provider=oxo_mapping.datasource.prefix) - self.add_prefix(oxo_s.curie, oxo_s.uri) - self.add_prefix(oxo_o.curie, oxo_o.uri) - mappings.append(mapping) - ms = MappingSet(mapping_set_id=container._links.link_to_self.href, + mappings = list(self.ols.get_sssom_mappings_by_curie(curie)) + ms = MappingSet(mapping_set_id=OlsImplementation.base_url, license='http://example.org/mixed', mappings=mappings) return MappingSetDocument(mapping_set=ms, - prefix_map=self.prefix_map) + prefix_map=self.ols.get_prefix_map()) def get_ancestors(self, term_id: str, ontology: str = None) -> List[str]: - # must be double encoded https://www.ebi.ac.uk/ols/docs/api - term_id_quoted = urllib.parse.quote(term_id, safe='') - term_id_quoted = urllib.parse.quote(term_id_quoted, safe='') - url = f'{self.ols_base_url}{ontology}/terms/{term_id_quoted}/ancestors' - logging.debug(f'URL={url}') - result = requests.get(url) - obj = result.json() - if result.status_code == 200 and '_embedded' in obj: - ancs = [x['obo_id'] for x in obj['_embedded']['terms']] - else: - logging.debug(f'No ancestors for {url} (maybe ontology not indexed in OLS?)') - ancs = [] + self.ols.focus_ontology = ontology + ancs = self.ols.ancestors(term_id, predicates=[IS_A]) return ancs def fill_gaps(self, msdoc: MappingSetDocument, confidence: float = 1.0) -> int: diff --git a/tests/test_oxo_endpoint.py b/tests/test_oxo_endpoint.py index b8efd64..3f225b6 100644 --- a/tests/test_oxo_endpoint.py +++ b/tests/test_oxo_endpoint.py @@ -27,4 +27,7 @@ def test_oxo_endpoint(self): for m in msdoc.mapping_set.mappings: uri = get_iri_from_curie(m.object_id, msdoc) print(f'{m.object_id} = {uri}') + + assert any(mapping for mapping in msdoc.mapping_set.mappings if mapping.object_id == 'FMA:45632') + assert msdoc.prefix_map['FMA']