diff --git a/isatools/convert/experimental/nih_dcc_flux.py b/isatools/convert/experimental/nih_dcc_flux.py index 08a88305..08a405b6 100644 --- a/isatools/convert/experimental/nih_dcc_flux.py +++ b/isatools/convert/experimental/nih_dcc_flux.py @@ -281,7 +281,7 @@ def nihdcc2isa_convert(json_path, output_path): material_out.characteristics.append(material_type) study.assays[0].samples.append(material_in) - study.assays[0].materials["other_material"].append(material_in) + study.assays[0].other_material.append(material_in) try: material_separation_process except NameError: @@ -300,7 +300,7 @@ def nihdcc2isa_convert(json_path, output_path): value=OntologyAnnotation(term=sample_json["type"], term_source=obi), ) material_in.characteristics.append(material_type) - study.assays[0].materials["other_material"].append(material_in) + study.assays[0].other_material.append(material_in) data_acq_process = Process(executes_protocol=study.get_prot(sample_json["protocol.id"])) data_acq_process.name = sample_json["id"] diff --git a/isatools/database/models/ontology_annotation.py b/isatools/database/models/ontology_annotation.py index 0211cf60..facc560d 100644 --- a/isatools/database/models/ontology_annotation.py +++ b/isatools/database/models/ontology_annotation.py @@ -82,12 +82,14 @@ def to_sql(self, session): if oa: return oa term_source_id = self.term_source.to_sql(session) if self.term_source else None + comments_objs = [c.to_sql(session) for c in self.comments] + oa = OntologyAnnotation( ontology_annotation_id=self.id, annotation_value=self.term, term_accession=self.term_accession, term_source_id=term_source_id.ontology_source_id if term_source_id else None, - comments=[comment.to_sql() for comment in self.comments], + comments=comments_objs, ) session.add(oa) return oa diff --git a/isatools/net/ols.py b/isatools/net/ols.py index 4f3afa3e..12cd5c49 100644 --- a/isatools/net/ols.py +++ b/isatools/net/ols.py @@ -23,7 +23,7 @@ def get_ols_ontologies(): """Returns a list of OntologySource objects according to what's in OLS""" - ontologiesUri = OLS_API_BASE_URI + "/ontologies?size=" + str(OLS_PAGINATION_SIZE) + ontologiesUri = OLS_API_BASE_URI + "/ontologies?" + str(OLS_PAGINATION_SIZE) log.debug(ontologiesUri) J = json.loads(urlopen(ontologiesUri).read().decode("utf-8")) ontology_sources = [] @@ -43,28 +43,24 @@ def get_ols_ontologies(): return ontology_sources -def get_ols_ontology(ontology_name): +def get_ols_ontology(ontology_name, page: int): """Returns a single OntologySource objects according to what's in OLS""" - ontologiesUri = OLS_API_BASE_URI + "/ontologies?size=" + str(OLS_PAGINATION_SIZE) + ontologiesUri = OLS_API_BASE_URI + "/ontologies?page=" + str(page) + "&size=" + str(OLS_PAGINATION_SIZE) log.debug(ontologiesUri) J = json.loads(urlopen(ontologiesUri).read().decode("utf-8")) - print("EMBEDDED: ", J["_embedded"]["ontologies"]) ontology_sources = [] for ontology_source_json in J["_embedded"]["ontologies"]: - ontology_sources.append( - OntologySource( - name=ontology_source_json["ontologyId"], - version=ontology_source_json["config"]["version"] if ontology_source_json["config"]["version"] else "", - description=ontology_source_json["config"]["title"] if ontology_source_json["config"]["title"] else "", - file=ontology_source_json["_links"]["self"]["href"], + if ontology_source_json["ontologyId"] == ontology_name: + ontology_sources.append( + OntologySource( + name=ontology_source_json["ontologyId"], + version=ontology_source_json["config"]["version"] if ontology_source_json["config"]["version"] else "", + description=ontology_source_json["config"]["title"] if ontology_source_json["config"]["title"] else "", + file=ontology_source_json["_links"]["self"]["href"], + ) ) - ) - print("NAME: ", ontology_name) - print("SOURCES: ", [o.name for o in ontology_sources]) - hits = [o for o in ontology_sources if o.name == ontology_name] - print("HITS: ", hits) - if len(hits) == 1: - return hits[0] + if len(ontology_sources) == 1: + return ontology_sources[0] return None @@ -80,6 +76,8 @@ def search_ols(term, ontology_source): query = "{0}&queryFields=label&ontology={1}&exact=True".format(term, os_search) url += "?q={}".format(query) + + #print("OLS_URL", url) log.debug(url) import requests diff --git a/isatools/sampletab.py b/isatools/sampletab.py index 3e3c3993..405c7834 100644 --- a/isatools/sampletab.py +++ b/isatools/sampletab.py @@ -8,6 +8,11 @@ import io import logging + +# Suggestion to hide these warnings as not being useful: +# https://stackoverflow.com/a/76306267 +# https://stackoverflow.com/a/79416245 +import warnings from io import StringIO from math import isnan @@ -515,248 +520,249 @@ def dumps(investigation): """ # build MSI section + with warnings.catch_warnings(): + warnings.simplefilter("ignore", category=pd.errors.PerformanceWarning) + metadata_DF = pd.DataFrame( + columns=( + "Submission Title", + "Submission Identifier", + "Submission Description", + "Submission Version", + "Submission Reference Layer", + "Submission Release Date", + "Submission Update Date", + ) + ) + iversion_hits = [x for x in investigation.comments if x.name == "Submission Version"] + if len(iversion_hits) == 1: + investigation_version = iversion_hits[0].value + else: + investigation_version = "" + ireference_layer_hits = [x for x in investigation.comments if x.name == "Submission Reference Layer"] + if len(ireference_layer_hits) == 1: + investigation_reference_layer = ireference_layer_hits[0].value + else: + investigation_reference_layer = "" + iversion_update_date = [x for x in investigation.comments if x.name == "Submission Update Date"] + if len(iversion_update_date) == 1: + investigation_update_date = iversion_update_date[0].value + else: + investigation_update_date = "" + metadata_DF.loc[0] = [ + investigation.title, + investigation.identifier, + investigation.description, + investigation_version, + investigation_reference_layer, + investigation.submission_date, + investigation_update_date, + ] - metadata_DF = pd.DataFrame( - columns=( - "Submission Title", - "Submission Identifier", - "Submission Description", - "Submission Version", - "Submission Reference Layer", - "Submission Release Date", - "Submission Update Date", + org_DF = pd.DataFrame( + columns=( + "Organization Name", + "Organization Address", + "Organization URI", + "Organization Email", + "Organization Role", + ) ) - ) - iversion_hits = [x for x in investigation.comments if x.name == "Submission Version"] - if len(iversion_hits) == 1: - investigation_version = iversion_hits[0].value - else: - investigation_version = "" - ireference_layer_hits = [x for x in investigation.comments if x.name == "Submission Reference Layer"] - if len(ireference_layer_hits) == 1: - investigation_reference_layer = ireference_layer_hits[0].value - else: - investigation_reference_layer = "" - iversion_update_date = [x for x in investigation.comments if x.name == "Submission Update Date"] - if len(iversion_update_date) == 1: - investigation_update_date = iversion_update_date[0].value - else: - investigation_update_date = "" - metadata_DF.loc[0] = [ - investigation.title, - investigation.identifier, - investigation.description, - investigation_version, - investigation_reference_layer, - investigation.submission_date, - investigation_update_date, - ] + org_name_hits = [x for x in investigation.comments if x.name.startswith("Organization Name")] + org_address_hits = [x for x in investigation.comments if x.name.startswith("Organization Address")] + org_uri_hits = [x for x in investigation.comments if x.name.startswith("Organization URI")] + org_email_hits = [x for x in investigation.comments if x.name.startswith("Organization Email")] + org_role_hits = [x for x in investigation.comments if x.name.startswith("Organization Role")] + for i, org_name in enumerate(org_name_hits): + try: + org_name = org_name_hits[i].value + except IndexError: + org_name = "" + try: + org_address = org_address_hits[i].value + except IndexError: + org_address = "" + try: + org_uri = org_uri_hits[i].value + except IndexError: + org_uri = "" + try: + org_email = org_email_hits[i].value + except IndexError: + org_email = "" + try: + org_role = org_role_hits[i].value + except IndexError: + org_role = "" + org_DF.loc[i] = [org_name, org_address, org_uri, org_email, org_role] - org_DF = pd.DataFrame( - columns=( - "Organization Name", - "Organization Address", - "Organization URI", - "Organization Email", - "Organization Role", + people_DF = pd.DataFrame( + columns=("Person Last Name", "Person Initials", "Person First Name", "Person Email", "Person Role") ) - ) - org_name_hits = [x for x in investigation.comments if x.name.startswith("Organization Name")] - org_address_hits = [x for x in investigation.comments if x.name.startswith("Organization Address")] - org_uri_hits = [x for x in investigation.comments if x.name.startswith("Organization URI")] - org_email_hits = [x for x in investigation.comments if x.name.startswith("Organization Email")] - org_role_hits = [x for x in investigation.comments if x.name.startswith("Organization Role")] - for i, org_name in enumerate(org_name_hits): - try: - org_name = org_name_hits[i].value - except IndexError: - org_name = "" - try: - org_address = org_address_hits[i].value - except IndexError: - org_address = "" - try: - org_uri = org_uri_hits[i].value - except IndexError: - org_uri = "" - try: - org_email = org_email_hits[i].value - except IndexError: - org_email = "" - try: - org_role = org_role_hits[i].value - except IndexError: - org_role = "" - org_DF.loc[i] = [org_name, org_address, org_uri, org_email, org_role] - - people_DF = pd.DataFrame( - columns=("Person Last Name", "Person Initials", "Person First Name", "Person Email", "Person Role") - ) - for i, contact in enumerate(investigation.contacts): - if len(contact.roles) == 1: - role = contact.roles[0].term - else: - role = "" - people_DF.loc[i] = [contact.last_name, contact.mid_initials, contact.first_name, contact.email, role] - - term_sources_DF = pd.DataFrame(columns=("Term Source Name", "Term Source URI", "Term Source Version")) - for i, term_source in enumerate(investigation.ontology_source_references): - term_sources_DF.loc[i] = [term_source.name, term_source.file, term_source.version] - msi_DF = pd.concat([metadata_DF, org_DF, people_DF, term_sources_DF], axis=1) - msi_DF = msi_DF.set_index("Submission Title").T - msi_DF = msi_DF.map(lambda x: np.nan if x == "" else x) - msi_memf = StringIO() - msi_DF.to_csv(path_or_buf=msi_memf, index=True, sep="\t", encoding="utf-8", index_label="Submission Title") - msi_memf.seek(0) - - scd_DF = pd.DataFrame( - columns=( - "Sample Name", - "Sample Accession", - "Sample Description", - "Derived From", - "Group Name", - "Group Accession", + for i, contact in enumerate(investigation.contacts): + if len(contact.roles) == 1: + role = contact.roles[0].term + else: + role = "" + people_DF.loc[i] = [contact.last_name, contact.mid_initials, contact.first_name, contact.email, role] + + term_sources_DF = pd.DataFrame(columns=("Term Source Name", "Term Source URI", "Term Source Version")) + for i, term_source in enumerate(investigation.ontology_source_references): + term_sources_DF.loc[i] = [term_source.name, term_source.file, term_source.version] + msi_DF = pd.concat([metadata_DF, org_DF, people_DF, term_sources_DF], axis=1) + msi_DF = msi_DF.set_index("Submission Title").T + msi_DF = msi_DF.map(lambda x: np.nan if x == "" else x) + msi_memf = StringIO() + msi_DF.to_csv(path_or_buf=msi_memf, index=True, sep="\t", encoding="utf-8", index_label="Submission Title") + msi_memf.seek(0) + + scd_DF = pd.DataFrame( + columns=( + "Sample Name", + "Sample Accession", + "Sample Description", + "Derived From", + "Group Name", + "Group Accession", + ) ) - ) - - all_samples = [] - for study in investigation.studies: - all_samples += study.sources - all_samples += study.samples - - all_samples = list(set(all_samples)) - if isa_logging.show_pbars: - pbar = ProgressBar( - min_value=0, - max_value=len(all_samples), - widgets=[ - "Writing {} samples: ".format(len(all_samples)), - SimpleProgress(), - Bar(left=" |", right="| "), - ETA(), - ], - ).start() - else: - def pbar(x): - return x - - for i, s in pbar(enumerate(all_samples)): - derived_from = "" - if isinstance(s, Sample) and s.derives_from is not None: - if len(s.derives_from) == 1: - derived_from_obj = s.derives_from[0] - derives_from_accession_hits = [ - x for x in derived_from_obj.characteristics if x.category.term == "Sample Accession" - ] - if len(derives_from_accession_hits) == 1: - derived_from = derives_from_accession_hits[0].value - else: - log.warning( - "WARNING! No Sample Accession available so " - "referencing Derived From relation using " - 'Sample Name "{}" instead'.format(derived_from_obj.name) - ) - derived_from = derived_from_obj.name - sample_accession_hits = [x for x in s.characteristics if x.category.term == "Sample Accession"] - if len(sample_accession_hits) == 1: - sample_accession = sample_accession_hits[0].value - else: - sample_accession = "" - sample_description_hits = [x for x in s.characteristics if x.category.term == "Sample Description"] - if len(sample_description_hits) == 1: - sample_description = sample_description_hits[0].value + all_samples = [] + for study in investigation.studies: + all_samples += study.sources + all_samples += study.samples + + all_samples = list(set(all_samples)) + if isa_logging.show_pbars: + pbar = ProgressBar( + min_value=0, + max_value=len(all_samples), + widgets=[ + "Writing {} samples: ".format(len(all_samples)), + SimpleProgress(), + Bar(left=" |", right="| "), + ETA(), + ], + ).start() else: - sample_description = "" - if isinstance(s, Sample): - group_name_hits = [x for x in s.factor_values if x.factor_name.name == "Group Name"] - if len(group_name_hits) == 1: - group_name = group_name_hits[0].value - else: - group_name = "" - group_accession_hits = [x for x in s.factor_values if x.factor_name.name == "Group Accession"] - if len(group_accession_hits) == 1: - group_accession = group_accession_hits[0].value + def pbar(x): + return x + + for i, s in pbar(enumerate(all_samples)): + derived_from = "" + if isinstance(s, Sample) and s.derives_from is not None: + if len(s.derives_from) == 1: + derived_from_obj = s.derives_from[0] + derives_from_accession_hits = [ + x for x in derived_from_obj.characteristics if x.category.term == "Sample Accession" + ] + if len(derives_from_accession_hits) == 1: + derived_from = derives_from_accession_hits[0].value + else: + log.warning( + "WARNING! No Sample Accession available so " + "referencing Derived From relation using " + 'Sample Name "{}" instead'.format(derived_from_obj.name) + ) + derived_from = derived_from_obj.name + sample_accession_hits = [x for x in s.characteristics if x.category.term == "Sample Accession"] + if len(sample_accession_hits) == 1: + sample_accession = sample_accession_hits[0].value else: - group_accession = "" - else: - group_name_hits = [x for x in s.characteristics if x.category.term == "Group Name"] - if len(group_name_hits) == 1: - group_name = group_name_hits[0].value + sample_accession = "" + sample_description_hits = [x for x in s.characteristics if x.category.term == "Sample Description"] + if len(sample_description_hits) == 1: + sample_description = sample_description_hits[0].value else: - group_name = "" - group_accession_hits = [x for x in s.characteristics if x.category.term == "Group Accession"] - if len(group_accession_hits) == 1: - group_accession = group_accession_hits[0].value + sample_description = "" + + if isinstance(s, Sample): + group_name_hits = [x for x in s.factor_values if x.factor_name.name == "Group Name"] + if len(group_name_hits) == 1: + group_name = group_name_hits[0].value + else: + group_name = "" + group_accession_hits = [x for x in s.factor_values if x.factor_name.name == "Group Accession"] + if len(group_accession_hits) == 1: + group_accession = group_accession_hits[0].value + else: + group_accession = "" else: - group_accession = "" - - scd_DF.loc[i, "Sample Name"] = s.name - scd_DF.loc[i, "Sample Accession"] = sample_accession - scd_DF.loc[i, "Sample Description"] = sample_description - scd_DF.loc[i, "Derived From"] = derived_from - scd_DF.loc[i, "Group Name"] = group_name - scd_DF.loc[i, "Group Accession"] = group_accession - - characteristics = [ - x - for x in s.characteristics - if x.category.term not in ["Sample Description", "Derived From", "Sample Accession"] - ] - for characteristic in characteristics: - characteristic_label = "Characteristic[{}]".format(characteristic.category.term) - if characteristic_label not in scd_DF.columns: - scd_DF[characteristic_label] = "" - for val_col in get_value_columns(characteristic_label, characteristic): - scd_DF[val_col] = "" - if isinstance(characteristic.value, (int, float)) and characteristic.unit: - if isinstance(characteristic.unit, OntologyAnnotation): - scd_DF.loc[i, characteristic_label] = characteristic.value - scd_DF.loc[i, characteristic_label + ".Unit"] = characteristic.unit.term - scd_DF.loc[i, characteristic_label + ".Unit.Term Source REF"] = ( - characteristic.unit.term_source.name if characteristic.unit.term_source else "" - ) - scd_DF.loc[i, characteristic_label + ".Unit.Term Accession Number"] = ( - characteristic.unit.term_accession + group_name_hits = [x for x in s.characteristics if x.category.term == "Group Name"] + if len(group_name_hits) == 1: + group_name = group_name_hits[0].value + else: + group_name = "" + group_accession_hits = [x for x in s.characteristics if x.category.term == "Group Accession"] + if len(group_accession_hits) == 1: + group_accession = group_accession_hits[0].value + else: + group_accession = "" + + scd_DF.loc[i, "Sample Name"] = s.name + scd_DF.loc[i, "Sample Accession"] = sample_accession + scd_DF.loc[i, "Sample Description"] = sample_description + scd_DF.loc[i, "Derived From"] = derived_from + scd_DF.loc[i, "Group Name"] = group_name + scd_DF.loc[i, "Group Accession"] = group_accession + + characteristics = [ + x + for x in s.characteristics + if x.category.term not in ["Sample Description", "Derived From", "Sample Accession"] + ] + for characteristic in characteristics: + characteristic_label = "Characteristic[{}]".format(characteristic.category.term) + if characteristic_label not in scd_DF.columns: + scd_DF[characteristic_label] = "" + for val_col in get_value_columns(characteristic_label, characteristic): + scd_DF[val_col] = "" + if isinstance(characteristic.value, (int, float)) and characteristic.unit: + if isinstance(characteristic.unit, OntologyAnnotation): + scd_DF.loc[i, characteristic_label] = characteristic.value + scd_DF.loc[i, characteristic_label + ".Unit"] = characteristic.unit.term + scd_DF.loc[i, characteristic_label + ".Unit.Term Source REF"] = ( + characteristic.unit.term_source.name if characteristic.unit.term_source else "" + ) + scd_DF.loc[i, characteristic_label + ".Unit.Term Accession Number"] = ( + characteristic.unit.term_accession + ) + else: + scd_DF.loc[i, characteristic_label] = characteristic.value + scd_DF.loc[i, characteristic_label + ".Unit"] = characteristic.unit + elif isinstance(characteristic.value, OntologyAnnotation): + scd_DF.loc[i, characteristic_label] = characteristic.value.term + scd_DF.loc[i, characteristic_label + ".Term Source REF"] = ( + characteristic.value.term_source.name if characteristic.value.term_source else "" ) + scd_DF.loc[i, characteristic_label + ".Term Accession Number"] = characteristic.value.term_accession else: scd_DF.loc[i, characteristic_label] = characteristic.value - scd_DF.loc[i, characteristic_label + ".Unit"] = characteristic.unit - elif isinstance(characteristic.value, OntologyAnnotation): - scd_DF.loc[i, characteristic_label] = characteristic.value.term - scd_DF.loc[i, characteristic_label + ".Term Source REF"] = ( - characteristic.value.term_source.name if characteristic.value.term_source else "" - ) - scd_DF.loc[i, characteristic_label + ".Term Accession Number"] = characteristic.value.term_accession - else: - scd_DF.loc[i, characteristic_label] = characteristic.value - - scd_DF = scd_DF.map(lambda x: np.nan if x == "" else x) - columns = list(scd_DF.columns) - for i, col in enumerate(columns): - if col.endswith("Term Source REF"): - columns[i] = "Term Source REF" - elif col.endswith("Term Accession Number"): - columns[i] = "Term Source ID" - elif col.endswith("Unit"): - columns[i] = "Unit" - scd_DF.columns = columns - scd_memf = StringIO() - scd_DF.to_csv(path_or_buf=scd_memf, index=False, sep="\t", encoding="utf-8") - scd_memf.seek(0) - - sampletab_memf = StringIO() - sampletab_memf.write("[MSI]\n") - for line in msi_memf: - sampletab_memf.write(line.rstrip() + "\n") - sampletab_memf.write("[SCD]\n") - for line in scd_memf: - sampletab_memf.write(line.rstrip() + "\n") - sampletab_memf.seek(0) - - return sampletab_memf.read() + + scd_DF = scd_DF.map(lambda x: np.nan if x == "" else x) + columns = list(scd_DF.columns) + for i, col in enumerate(columns): + if col.endswith("Term Source REF"): + columns[i] = "Term Source REF" + elif col.endswith("Term Accession Number"): + columns[i] = "Term Source ID" + elif col.endswith("Unit"): + columns[i] = "Unit" + scd_DF.columns = columns + scd_memf = StringIO() + scd_DF.to_csv(path_or_buf=scd_memf, index=False, sep="\t", encoding="utf-8") + scd_memf.seek(0) + + sampletab_memf = StringIO() + sampletab_memf.write("[MSI]\n") + for line in msi_memf: + sampletab_memf.write(line.rstrip() + "\n") + sampletab_memf.write("[SCD]\n") + for line in scd_memf: + sampletab_memf.write(line.rstrip() + "\n") + sampletab_memf.seek(0) + + return sampletab_memf.read() def dump(investigation, out_fp): diff --git a/tests/convert/test_isatab2sra.py b/tests/convert/test_isatab2sra.py index 7758408f..0546fcba 100644 --- a/tests/convert/test_isatab2sra.py +++ b/tests/convert/test_isatab2sra.py @@ -114,7 +114,6 @@ def test_isatab2sra_dump_submission_xml_biis7(self): actual_submission_xml_biis7 = etree.fromstring(submission_xml) self.assertTrue(utils.assert_xml_equal(self._expected_submission_xml_biis7, actual_submission_xml_biis7)) - @unittest.skip("Not working yet") def test_isatab2sra_dump_project_set_xml_biis7(self): isatab2sra.convert(self._biis7_dir, self._tmp_dir, validate_first=False) with open(os.path.join(self._tmp_dir, "project_set.xml"), "rb") as ps_fp: diff --git a/tests/convert/test_sampletab2isatab.py b/tests/convert/test_sampletab2isatab.py index 31fd371f..daf5aeba 100644 --- a/tests/convert/test_sampletab2isatab.py +++ b/tests/convert/test_sampletab2isatab.py @@ -6,8 +6,6 @@ from isatools.convert import sampletab2isatab from isatools.tests import utils -SLOW_TESTS = int(os.getenv("SLOW_TESTS", "0")) - def setUpModule(): if not os.path.exists(utils.DATA_DIR): @@ -35,17 +33,16 @@ def test_sampletab2isatab_test_2(self): with open(os.path.join(self._sampletab_dir, "test2.txt")) as sampletab_fp: sampletab2isatab.convert(source_sampletab_fp=sampletab_fp, target_dir=self._tmp_dir) - @unittest.skipIf(not SLOW_TESTS, "slow") + @unittest.skip("deprecated method pending deletion") def test_sampletab2isatab_GSB_3(self): with open(os.path.join(self._sampletab_dir, "GSB-3.txt")) as sampletab_fp: sampletab2isatab.convert(source_sampletab_fp=sampletab_fp, target_dir=self._tmp_dir) - @unittest.skipIf(not SLOW_TESTS, "slow") + @unittest.skip("deprecated method pending deletion") def test_sampletab2isatab_GSB_537(self): with open(os.path.join(self._sampletab_dir, "GSB-537.txt")) as sampletab_fp: sampletab2isatab.convert(source_sampletab_fp=sampletab_fp, target_dir=self._tmp_dir) - @unittest.skip("slow") def test_sampletab2isatab_GSB_718(self): with open(os.path.join(self._sampletab_dir, "GSB-718.txt")) as sampletab_fp: sampletab2isatab.convert(source_sampletab_fp=sampletab_fp, target_dir=self._tmp_dir) diff --git a/tests/isatab/test_isatab.py b/tests/isatab/test_isatab.py index 646f4a38..af3ccfca 100644 --- a/tests/isatab/test_isatab.py +++ b/tests/isatab/test_isatab.py @@ -2005,9 +2005,7 @@ def test_isatab_protocol_chain_parsing(self): for proc in nucleotide_sequencing_assay.process_sequence if proc.executes_protocol.name == "genomic DNA extraction - standard procedure 4" ) - extract = next( - mat for mat in nucleotide_sequencing_assay.materials["other_material"] if mat.name == "GSM255770.e1" - ) + extract = next(mat for mat in nucleotide_sequencing_assay.other_material if mat.name == "GSM255770.e1") self.assertTrue(nucl_ac_extraction_process.next_process is gen_dna_extraction_process) self.assertEqual(len(gen_dna_extraction_process.outputs), 1) self.assertFalse(nucl_ac_extraction_process.outputs) diff --git a/tests/test_clients/fixtures/ST00010.json b/tests/test_clients/fixtures/ST00010.json new file mode 100644 index 00000000..c332f561 --- /dev/null +++ b/tests/test_clients/fixtures/ST00010.json @@ -0,0 +1 @@ +{"1":{"study_id":"ST000100","analysis_id":"AN000165","analysis_summary":"HESI positive ion mode","analysis_type":"MS","chromatography system":"Thermo Dionex Ultimate 3000 RS","column_name":"Waters Acquity HSS T3 (100 x 2.1mm,1.8um)","chromatography_type":"Reversed phase","ms_instrument_name":"Thermo Q Exactive Orbitrap","ms_instrument_type":"Orbitrap","ms_type":"ESI","ion_mode":"POSITIVE","nmr_instrument_type":"","nmr_experiment_type":"","spectrometer_frequency":"","nmr_solvent":"","units":""},"2":{"study_id":"ST000100","analysis_id":"AN000166","analysis_summary":"HESI 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ICS-5000+","column_name":"Unspecified","chromatography_type":"Ion Chromatography","ms_instrument_name":"Thermo Fusion Tribrid Orbitrap","ms_instrument_type":"FT-ICR-MS","ms_type":"ESI","ion_mode":"NEGATIVE","nmr_instrument_type":"","nmr_experiment_type":"","spectrometer_frequency":"","nmr_solvent":"","units":"normalized corrected peak area"},"2":{"study_id":"ST000367","analysis_id":"AN000601","analysis_summary":"Retsch homogenization (IC-FTMS2)","analysis_type":"MS","chromatography system":"Thermo Dionex ICS-5000+","column_name":"Unspecified","chromatography_type":"Ion Chromatography","ms_instrument_name":"Thermo Fusion Tribrid Orbitrap","ms_instrument_type":"FT-ICR-MS","ms_type":"ESI","ion_mode":"NEGATIVE","nmr_instrument_type":"","nmr_experiment_type":"","spectrometer_frequency":"","nmr_solvent":"","units":"normalized corrected peak area"}} \ No newline at end of file diff --git a/tests/test_clients/fixtures/TOTO.json b/tests/test_clients/fixtures/TOTO.json new file mode 100644 index 00000000..0637a088 --- /dev/null +++ b/tests/test_clients/fixtures/TOTO.json @@ -0,0 +1 @@ +[] \ No newline at end of file diff --git a/tests/test_clients/test_mw2isa.py b/tests/test_clients/test_mw2isa.py index c34b1e0b..0267e7ff 100644 --- a/tests/test_clients/test_mw2isa.py +++ b/tests/test_clients/test_mw2isa.py @@ -1,8 +1,11 @@ +import json import logging import os import shutil import tempfile import unittest +from pathlib import Path +from unittest.mock import Mock, patch from isatools import isatab from isatools.net.mw2isa import mw2isa_convert @@ -19,7 +22,31 @@ def setUp(self): def tearDown(self): shutil.rmtree(self._tmp_dir) - def test_conversion_ms(self): + def _load_fixture(self, name): + data_path = Path(__file__).parent / "fixtures" / name + return data_path.read_bytes() + + def _make_requests_response(self, body_bytes, status=200, headers=None): + m = Mock() + m.status_code = status + m.content = body_bytes + m.text = body_bytes.decode("utf-8") + + # Provide .json() for convenience if used by code + def _json(): + return json.loads(m.text) + + m.json = _json + m.headers = headers or {} + return m + + @patch("isatools.net.mw2isa.mw2isa_convert") + def test_conversion_ms(self, mock_get): + def _side_effect(): + return self._make_requests_response(self._load_fixture("ST000367.json")) + + mock_get.side_effect = _side_effect + success, study_id, validate = mw2isa_convert( studyid="ST000367", outputdir=self._tmp_dir, dl_option="no", validate_option=True ) @@ -37,8 +64,13 @@ def test_conversion_ms(self): else: self.fail("conversion failed, validation was not invoked") - def test_conversion_nmr(self): - report = {} + @patch("isatools.net.mw2isa.mw2isa_convert") + def test_conversion_nmr(self, mock_get): + def _side_effect(): + return self._make_requests_response(self._load_fixture("ST000102.json")) + + mock_get.side_effect = _side_effect + success, study_id, validate = mw2isa_convert( studyid="ST000102", outputdir=self._tmp_dir, dl_option="no", validate_option=True ) @@ -50,13 +82,25 @@ def test_conversion_nmr(self): else: self.assertFalse(success) - def test_conversion_invalid_id(self): + @patch("isatools.net.mw2isa.mw2isa_convert") + def test_conversion_invalid_id(self, mock_get): + def _side_effect(): + return self._make_requests_response(self._load_fixture("TOTO.json")) + + mock_get.side_effect = _side_effect + success, study_id, validate = mw2isa_convert( studyid="TOTO", outputdir=self._tmp_dir, dl_option="no", validate_option=True ) self.assertFalse(success) - def test_conversion_invalid_dloption(self): + @patch("isatools.net.mw2isa.mw2isa_convert") + def test_conversion_invalid_dloption(self, mock_get): + def _side_effect(): + return self._make_requests_response(self._load_fixture("ST000102.json")) + + mock_get.side_effect = _side_effect + with self.assertRaises(Exception) as context: success, study_id, validate = mw2isa_convert( studyid="ST000102", outputdir=self._tmp_dir, dl_option="TOTO", validate_option=False diff 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horse blood sr0050. mix well and pour into sterile petri dishes.", + "25°c directions suspend 64 grams in 1 litre of distilled water and soak for 15 minutes, with occasional stirring. distribute into 18mm diameter tubes to a depth of 50mm so that the bottom of the tube is filled with liver particles. agitate frequently during distribution to keep the liver tissue in suspension. sterilise by autoclaving for 20 minutes at 115° c. inoculate when cool and then aseptically seal with a layer of sterile 2% oxoid agar no.3 (lp0013) solution. description a liver infusion medium, containing liver particles, for the examination of foods for saccharolytic or putrefactive mesophilic and thermophilic anaerobes. also recommended for the maintenance of aerobes and anaerobes in pure culture. technique gillespie in communication with scarr1 recommended liver broth for the examination of canners’ sugar for hydrogen swells caused by thermophilic anaerobes (clostridium thermosaccharolyticum). a 20% w/v 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def test_get_ontologies(self): + @patch("isatools.net.ols") + def test_get_ontologies(self, mock_get): + def _side_effect(): + return self._make_requests_response(self._load_fixture("ontologies.json")) + + mock_get.side_effect = _side_effect + ontology_sources = ols.get_ols_ontologies() self.assertGreater(len(ontology_sources), 0) self.assertIsInstance(ontology_sources, list) self.assertIsInstance(ontology_sources[0], OntologySource) - @unittest.skip("efo is not available from https://www.ebi.ac.uk/ols4/api/ontologies") - def test_get_ontology(self): - ontology_source = ols.get_ols_ontology("efo") + # @unittest.skip("efo is not available from https://www.ebi.ac.uk/ols4/api/ontologies") + @patch("isatools.net.ols") + def test_get_ontology0(self, mock_get): + def _side_effect(): + return self._make_requests_response(self._load_fixture("ontologies.json")) + + mock_get.side_effect = _side_effect + ontology_source = ols.get_ols_ontology("ado", 0) + self.assertIsInstance(ontology_source, OntologySource) + self.assertEqual(ontology_source.name, "ado") + self.assertIn("://www.ebi.ac.uk/ols", ontology_source.file) + self.assertIn("/api/ontologies/ado?lang=en", ontology_source.file) + self.assertIsInstance(ontology_source.version, str) + self.assertEqual(ontology_source.description, "Alzheimer's Disease Ontology (ADO)") + + @patch("isatools.net.ols") + def test_get_ontology1(self, mock_get): + def _side_effect(): + return self._make_requests_response(self._load_fixture("ontologies.json")) + + mock_get.side_effect = _side_effect + ontology_source = ols.get_ols_ontology("stato", 0) + self.assertIsInstance(ontology_source, OntologySource) + self.assertEqual(ontology_source.name, "stato") + self.assertIn("://www.ebi.ac.uk/ols", ontology_source.file) + self.assertIn("/api/ontologies/stato?lang=en", ontology_source.file) + self.assertIsInstance(ontology_source.version, str) + self.assertEqual(ontology_source.description, "STATO: the statistical methods ontology") + + @patch("isatools.net.ols") + def test_get_ontology2(self, mock_get): + def _side_effect(): + return self._make_requests_response(self._load_fixture("ontologies.json")) + + mock_get.side_effect = _side_effect + ontology_source = ols.get_ols_ontology("efo", 0) self.assertIsInstance(ontology_source, OntologySource) self.assertEqual(ontology_source.name, "efo") self.assertIn("://www.ebi.ac.uk/ols", ontology_source.file) @@ -149,16 +207,37 @@ def test_get_ontology(self): self.assertIsInstance(ontology_source.version, str) self.assertEqual(ontology_source.description, "Experimental Factor Ontology") - @unittest.skip("efo is not available from https://www.ebi.ac.uk/ols4/api/ontologies") - def test_search_for_term(self): - ontology_source = ols.get_ols_ontology("efo") - ontology_annotations = ols.search_ols("cell type", ontology_source) + # @unittest.skip("efo is not available from https://www.ebi.ac.uk/ols4/api/ontologies") + @patch("isatools.net.ols") + def test_search_for_term_p0(self, mock_get): + def _side_effect(): + return self._make_requests_response(self._load_fixture("ontologies.json")) + + mock_get.side_effect = _side_effect + ontology_source = ols.get_ols_ontology("chmo", 0) + ontology_annotations = ols.search_ols("mobile phase", ontology_source) + self.assertIsInstance(ontology_annotations, list) + self.assertGreater(len(ontology_annotations), 0) + ontology_annotations = [oa for oa in ontology_annotations if oa.term == "mobile phase"] + self.assertIsInstance(ontology_annotations[-1], OntologyAnnotation) + self.assertEqual(ontology_annotations[-1].term, "mobile phase") + self.assertIn("http://purl.obolibrary.org/obo/CHMO_0000995", [oa.term_accession for oa in ontology_annotations]) + self.assertEqual(ontology_annotations[-1].term_source, ontology_source) + + @patch("isatools.net.ols") + def test_search_for_term_p1(self, mock_get): + def _side_effect(): + return self._make_requests_response(self._load_fixture("ontologies.json")) + + mock_get.side_effect = _side_effect + ontology_source = ols.get_ols_ontology("efo", 0) + ontology_annotations = ols.search_ols("time", ontology_source) self.assertIsInstance(ontology_annotations, list) self.assertGreater(len(ontology_annotations), 0) - ontology_annotations = [oa for oa in ontology_annotations if oa.term == "cell type"] + ontology_annotations = [oa for oa in ontology_annotations if oa.term == "time"] self.assertIsInstance(ontology_annotations[-1], OntologyAnnotation) - self.assertEqual(ontology_annotations[-1].term, "cell type") - self.assertIn("http://www.ebi.ac.uk/efo/EFO_0000324", [oa.term_accession for oa in ontology_annotations]) + self.assertEqual(ontology_annotations[-1].term, "time") + self.assertIn("http://www.ebi.ac.uk/efo/EFO_0000721", [oa.term_accession for oa in ontology_annotations]) self.assertEqual(ontology_annotations[-1].term_source, ontology_source) diff --git a/tests/validators/test_validate_test_data.py b/tests/validators/test_validate_test_data.py index 4033afe3..c5e77561 100644 --- a/tests/validators/test_validate_test_data.py +++ b/tests/validators/test_validate_test_data.py @@ -404,7 +404,7 @@ def test_validate_testdata_treatment_sequence_json(self): with open(os.path.join(utils.JSON_DATA_DIR, "create", "treatment_sequence_test.json")) as test_case_fp: with open(os.path.join(self.v2_create_schemas_path, "treatment_sequence_schema.json")) as fp: treatment_sequence_schema = json.load(fp) - 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