def analysis_results(request, pk):
analysis = Analysis.objects.filter(is_active=True, pk=pk).first()
if not analysis:
return api.json(404, detail='Analysis not found')
if not analysis.success:
return api.json(404, detail='Analysis failed or not finished yet')
return HttpResponse(frame_dumps(analysis.results_df()),
content_type='application/json')
def upload_to_zenodo(request, snap_id):
snap = get_object_or_404(Snapshot, pk=snap_id)
# Minimum length for title and description on zenodo is 3
if len(snap.title) < 3:
return api.json(400, detail='Need title of length 3 or more')
description = snap.description if len(
snap.description) >= 3 else 'no description'
# Create deposition
meta = {
'title':
snap.title,
'description':
description,
'upload_type':
'dataset',
'creators': [{
'name':
'%s, %s' % (request.user.last_name, request.user.first_name)
}],
}
res = request.zenodo.post('https://zenodo.org/api/deposit/depositions',
json={'metadata': meta})
res.raise_for_status()
snap.zenodo = deposit = res.json()
snap.save()
# Upload files
for file in snap.files:
name = re.sub(r'\W+', '-', snap.title).strip('-').lower() or 'file'
filename = '%s.%s' % (name, file['format'])
data = {'filename': filename}
files = {'file': file.open()}
res = request.zenodo.post(deposit['links']['files'],
data=data,
files=files)
res.raise_for_status()
# Rename file, see Zenodo bug https://github.com/zenodo/zenodo/issues/940
file_desc = res.json()
if file_desc['filename'] != filename:
res = request.zenodo.put(file_desc['links']['self'],
json={'filename': filename})
res.raise_for_status()
# Publish
res = request.zenodo.post(deposit['links']['publish'])
res.raise_for_status()
# Update info
res = request.zenodo.get(deposit['links']['self'])
res.raise_for_status()
snap.zenodo = deposit = res.json()
snap.save()
return api.json(deposit)
def platform_probes(request, gpl_name):
if not Platform.objects.filter(gpl_name=gpl_name).exists():
return api.json(404, detail='Platform not found')
qs = PlatformProbe.objects.filter(platform__gpl_name=gpl_name)
probes_df = qs.to_dataframe(
fieldnames=['probe', 'mygene_sym', 'mygene_entrez'])
return HttpResponse(frame_dumps(probes_df),
content_type='application/json')
def series_samples(request, gse_name):
series = Series.objects.get(gse_name=gse_name)
samples = api.queryset(series.samples.exclude(deleted='T')).values(
'gsm_name',
'attrs',
gse_name='series__gse_name',
gpl_name='platform__gpl_name')
# Filter by platform
if request.GET.get('gpl_name'):
samples = samples.filter(
platform__gpl_name=request.GET.get('gpl_name'))
return api.json(samples)
def annotate(request, data):
canonical = SeriesAnnotation.objects.filter(
series=data['series'], tag=data['tag'],
platform=data['platform']).first()
data['tag_id'] = data.pop('tag').id
data['series_id'] = data.pop('series').id
data['user_id'] = request.user.id
data['from_api'] = True
try:
if canonical:
save_validation(canonical.id, data)
else:
save_annotation(data)
except AnnotationError as e:
return api.json(409, detail=str(e))
return HttpResponse(status=204)
def platform_detail(request, gpl_name):
return api.json(api.get_or_404(platforms_qs, gpl_name=gpl_name))
def platforms(request):
return api.json(api.paginate(request, platforms_qs, per_page=PER_PAGE))
def series_detail(request, gse_name):
return api.json(api.get_or_404(series_qs, gse_name=gse_name))
def series(request):
return api.json(api.paginate(request, series_qs, per_page=PER_PAGE))
def tag_detail(request, pk):
return api.json(api.get_or_404(tags_qs, pk=pk))
def analysis_detail(request, pk):
return api.json(api.get_or_404(analysis_qs, pk=pk))
def annotation_samples(request, pk):
if not annotations_qs.filter(pk=pk).exists():
return api.json(404, detail='Annotation not found')
samples = api.queryset(SampleAnnotation).filter(series_annotation=pk) \
.values_list('sample__gsm_name', 'annotation')
return api.json(dict(samples))
def annotation_detail(request, pk):
return api.json(api.get_or_404(annotations_qs, pk=pk))
def annotations(request):
return api.json(api.paginate(request, annotations_qs, per_page=PER_PAGE))
def analysis_create(request, analysis):
analysis.created_by_id = analysis.modified_by_id = request.user.id
analysis.save()
analysis_task.delay(analysis.pk)
return api.json(201, created=analysis.pk)
def analysis_list(request):
return api.json(api.paginate(request, analysis_qs, per_page=PER_PAGE))
def tags(request):
return api.json(tags_qs)