def test_chemical_structure(model, identifier='benomyl'):
response = json.loads(model.chemical(chemical_identifier=identifier))
assert response is not None
check_obj(response)
assert 'format_name' in response
assert 'chebi_id' in response
assert 'description' in response
def test_reference_structure(model, identifier='17112311'):
response = json.loads(model.reference(reference_identifier=identifier))
assert response is not None
check_reference(response)
assert 'bibentry' in response
assert 'related_references' in response
assert 'abstract' in response
assert 'authors' in response
assert 'reftypes' in response
assert 'counts' in response
assert 'go' in response['counts']
assert 'regulation' in response['counts']
assert 'interaction' in response['counts']
assert 'phenotype' in response['counts']
for url in response['urls']:
check_url(url)
for related_ref in response['related_references']:
#check_reference(related_ref)
#Not embedded as a full reference
assert 'abstract' in related_ref
assert 'reftypes' in related_ref
for author in response['authors']:
check_obj(author)
assert 'format_name' in author
def test_contig_structure(model, identifier='230682'):
response = json.loads(model.contig(contig_identifier=identifier))
assert response is not None
check_obj(response)
assert 'residues' in response
##assert 'length' in response no longer in object
assert 'format_name' in response
def test_go_overview_structure(model, identifier="YFL039C"):
response = json.loads(model.locus(locus_identifier=identifier))
go_overview = response["go_overview"]
assert go_overview is not None
assert "go_slim" in go_overview
assert "date_last_reviewed" in go_overview
for entry in go_overview["go_slim"]:
check_obj(entry)
def check_sequence_evidence(evidence):
check_evidence(evidence)
assert "residues" in evidence
assert "locus" in evidence
##check_obj(evidence['residues'])
check_obj(evidence["locus"])
assert "format_name" in evidence["locus"]
def check_locus(locus):
check_obj(locus)
assert 'sgdid' in locus
assert 'format_name' in locus
assert 'description' in locus
assert 'locus_type' in locus
#assert 'aliases' in locus Seems to be empty
assert 'description' in locus
def test_domain_structure(model, identifier='PTHR11937'):
response = json.loads(model.domain(domain_identifier=identifier))
assert response is not None
check_obj(response)
assert 'interpro_description' in response
assert 'description' in response
assert 'source' in response
assert 'link' in response ## no longer external_link
assert 'interpro_id' in response
def check_reference(reference):
check_obj(reference)
assert 'pubmed_id' in reference
assert 'year' in reference
assert 'journal' in reference
assert 'citation' in reference
assert 'format_name' in reference
assert 'urls' in reference
for url in reference['urls']:
check_url(url)
def test_phenotype_structure(model, identifier='viable'):
response = json.loads(model.phenotype(identifier))
assert response is not None
check_obj(response)
assert 'description' in response
assert 'qualifier' in response
assert 'locus_count' in response
assert 'observable' in response
assert 'format_name' in response
assert 'descendant_locus_count' in response
def test_ec_number_structure(model, identifier='3.4.25.1'):
response = json.loads(model.ec_number(ec_number_identifier=identifier))
assert response is not None
check_obj(response)
#assert 'count' in response NOT there any more
#assert 'child_count' in response NOT there any more
assert 'description' in response
assert 'class_type' in response
assert 'format_name' in response
assert 'display_name' in response
def check_regulation_evidence(evidence):
check_evidence(evidence)
assert 'locus1' in evidence
assert 'locus2' in evidence
#assert 'conditions' in evidence
check_obj(evidence['locus1'])
assert 'format_name' in evidence['locus1']
check_obj(evidence['locus2'])
assert 'format_name' in evidence['locus2']
def check_protein_domain_evidence(evidence):
check_evidence(evidence)
assert 'domain' in evidence
#assert 'protein' in evidence
assert 'status' in evidence
assert 'start' in evidence
assert 'end' in evidence
assert 'date_of_run' in evidence
assert 'evalue' in evidence
check_obj(evidence['domain'])
def test_go_structure(model, identifier="GO:0018706"):
response = json.loads(model.go(go_identifier=identifier))
assert response is not None
check_obj(response)
assert "description" in response
# assert 'aliases' in response Aliases not implemented
assert "locus_count" in response
assert "format_name" in response
assert "go_id" in response
assert "descendant_locus_count" in response
assert "go_aspect" in response
def test_regulation_target_enrichment_structure(model, identifier='ADF1'):
response = json.loads(model.regulation_target_enrichment(locus_identifier=identifier))
assert response is not None
for entry in response:
assert 'go' in entry
assert 'match_count' in entry
assert 'pvalue' in entry
check_obj(entry['go'])
assert 'format_name' in entry['go']
assert 'go_id' in entry['go']
assert 'go_aspect' in entry['go']
def check_phenotype_evidence(evidence):
check_evidence(evidence)
assert 'phenotype' in evidence
assert 'locus' in evidence
#assert 'conditions' in evidence
assert 'category' in evidence['experiment']
assert 'mutant_type' in evidence
check_obj(evidence['phenotype'])
check_obj(evidence['locus'])
assert 'format_name' in evidence['locus']
def test_binding_site_details_structure(model, identifier='GAL4'):
response = json.loads(model.binding_site_details(identifier))
assert response is not None
for entry in response:
check_evidence(entry)
assert 'locus' in entry
assert 'expert_confidence' in entry
assert 'total_score' in entry
assert 'motif_id' in entry
assert 'link' in entry
check_obj(entry['locus'])
assert 'format_name' in entry['locus']
def check_go_evidence(evidence):
##check_evidence(evidence) Not sure this is a valid subclass of Evidence
assert "go" in evidence
assert "locus" in evidence
assert "experiment" in evidence
assert "qualifier" in evidence
assert "go_evidence" in evidence
assert "date_created" in evidence
# assert 'method' in evidence
check_obj(evidence["go"])
assert "go_id" in evidence["go"]
assert "go_aspect" in evidence["go"]
check_obj(evidence["locus"])
assert "format_name" in evidence["locus"]
def check_genomic_sequence_evidence(evidence):
check_sequence_evidence(evidence)
assert "contig" in evidence
assert "tags" in evidence
assert "strand" in evidence
assert "end" in evidence
assert "start" in evidence
check_obj(evidence["contig"])
assert "format_name" in evidence["contig"]
for label in evidence["tags"]:
assert "chromosomal_start" in label
assert "relative_start" in label
assert "relative_end" in label
assert "display_name" in label
assert "chromosomal_end" in label
def check_dataset(dataset):
check_obj(dataset)
assert 'condition_count' in dataset
assert 'reference' in dataset
check_obj(dataset['reference'])
assert 'tags' in dataset
for tag in dataset['tags']:
check_obj(tag)
assert 'pcl_filename' in dataset
assert 'geo_id' in dataset
assert 'short_description' in dataset
def check_interaction_evidence(evidence):
#check_evidence(evidence)
assert 'locus1' in evidence
assert 'locus2' in evidence
assert 'bait_hit' in evidence
assert 'interaction_type' in evidence
assert 'annotation_type' in evidence
check_obj(evidence['locus1'])
assert 'format_name' in evidence['locus1']
check_obj(evidence['locus2'])
assert 'format_name' in evidence['locus2']
if evidence['interaction_type'] == 'Genetic':
assert 'modification' not in evidence
assert 'mutant_type' in evidence
assert 'phenotype' in evidence
if evidence['phenotype'] is not None:
check_obj(evidence['phenotype'])
elif evidence['interaction_type'] == 'Physical':
assert 'phenotype' not in evidence
assert 'modification' in evidence
else:
assert False
def test_author_structure(model, identifier='Bi_E'):
response = json.loads(model.author(author_identifier=identifier))
assert response is not None
check_obj(response)
assert 'format_name' in response
def test_tag_structure(model, identifier='cellular_ion_homeostasis'):
response = json.loads(model.tag(tag_identifier=identifier))
check_obj(response)
assert 'bioitems' in response
def test_bioentity_list_structure(model, bioent_ids=(25, 26, 27, 28, 29)):
response = json.loads(model.bioentity_list(bioent_ids))
assert response is not None
assert len(response) == 5
for entry in response:
check_obj(entry)
