def phenotype_detail(request, q, format=None):
"""
Detailed information about the phenotype
---
parameters:
- name: q
description: the id or doi of the phenotype
required: true
type: string
paramType: path
serializer: PhenotypeListSerializer
omit_serializer: false
produces:
- text/csv
- application/json
"""
doi = _is_doi(DOI_PATTERN_PHENOTYPE, q)
try:
id = doi if doi else int(q)
phenotype = Phenotype.objects.published().get(pk=id)
except:
return HttpResponse(status=404)
if request.method == "GET":
serializer = PhenotypeListSerializer(phenotype, many=False)
return Response(serializer.data)
def study_all_pheno(request, q=None, format=None):
"""
List all phenotypes for a study
---
serializer: PhenotypeListSerializer
omit_serializer: false
produces:
- text/csv
- application/json
"""
doi = _is_doi(DOI_PATTERN_STUDY, q)
try:
id = doi if doi else int(q)
study = Study.objects.published().get(pk=id)
except:
return HttpResponse(status=404)
if request.method == "GET":
serializer = PhenotypeListSerializer(
study.phenotype_set.all().annotate(
num_values=Count('phenotypevalue')),
many=True)
return Response(serializer.data)
def _create_phenotypes_files(studies, folder):
renderer = PhenotypeListRenderer()
for study in studies:
serializer = PhenotypeListSerializer(study.phenotype_set.all(),
many=True)
content = renderer.render(serializer.data)
study_filename = os.path.join(folder, str(study.id),
'study_%s_phenotypes.csv' % study.id)
with open(study_filename, 'w') as f:
f.write(content)
pass
def phenotype_list(request, format=None):
"""
List all available phenotypes
---
serializer: PhenotypeListSerializer
omit_serializer: false
produces:
- text/csv
- application/json
"""
phenotypes = Phenotype.objects.published().all()
if request.method == "GET":
serializer = PhenotypeListSerializer(phenotypes, many=True)
return Response(serializer.data)
def search(request, query_term=None, format=None):
"""
Search for a phenotype or study
---
parameters:
- name: query_term
description: the search term
required: true
type: string
paramType: path
serializer: PhenotypeListSerializer
omit_serializer: false
produces:
- text/csv
- application/json
"""
if request.method == "GET":
if query_term == None:
studies = Study.objects.published().all()
phenotypes = Phenotype.objects.published().all()
accessions = Accession.objects.all()
ontologies = OntologyTerm.objects.all()
else:
studies = Study.objects.published().filter(
name__icontains=query_term)
phenotypes = Phenotype.objects.published().filter(
Q(name__icontains=query_term)
| Q(to_term__id__icontains=query_term)
| Q(to_term__name__icontains=query_term))
accessions = Accession.objects.filter(
Q(id__icontains=query_term) | Q(name__icontains=query_term))
ontologies = OntologyTerm.objects.filter(
name__icontains=query_term)
study_serializer = StudyListSerializer(studies, many=True)
phenotype_serializer = PhenotypeListSerializer(phenotypes, many=True)
accession_serializer = AccessionListSerializer(accessions, many=True)
ontology_serializer = OntologyTermListSerializer(ontologies, many=True)
return Response({
'phenotype_search_results': phenotype_serializer.data,
'study_search_results': study_serializer.data,
'accession_search_results': accession_serializer.data,
'ontology_search_results': ontology_serializer.data
})
def accession_phenotypes(request, pk, format=None):
"""
List all phenotypes for an accession
---
serializer: PhenotypeListSerializer
omit_serializer: false
produces:
- text/csv
- application/json
"""
phenotypes = Phenotype.objects.published().filter(
phenotypevalue__obs_unit__accession_id=pk)
if request.method == "GET":
serializer = PhenotypeListSerializer(phenotypes, many=True)
return Response(serializer.data)
def phenotype_similar_list(request, q, format=None):
"""
List all available phenotypes matching phenotype q's trait ontology
---
serializer: PhenotypeListSerializer
omit_serializer: false
produces:
- text/csv
- application/json
"""
doi = _is_doi(DOI_PATTERN_PHENOTYPE, q)
try:
id = doi if doi else int(q)
phenotype = Phenotype.objects.published().get(pk=id)
except:
return HttpResponse(status=404)
to_term = phenotype.to_term.id
phenotypes = Phenotype.objects.published().filter(to_term__id=to_term)
if request.method == "GET":
serializer = PhenotypeListSerializer(phenotypes, many=True)
return Response(serializer.data)