def change_project_name(request, project_pk):
"""
Called (via ajax) to change the name of the project
"""
project = helpers.check_ownership(project_pk, request.user)
if project is not None:
project.name = request.POST.get('new_name')
project.save()
return HttpResponse("")
else:
return HttpResponseBadRequest('')
def show_in_progress(request, project_pk):
project = helpers.check_ownership(project_pk, request.user)
if project:
start_date = project.start_time.strftime('%b %d, %Y')
start_time = project.start_time.strftime('%H:%M')
time_str = 'Started on %s at %s' % (start_date, start_time)
return render(request, 'analysis_portal/in_progress.html', {
'project_name': project.name,
'time_str': time_str
})
else:
return HttpResponseBadRequest('')
def create_sample(request, project_pk):
"""
Called (via ajax) when creating a new sample in the UI
"""
project = helpers.check_ownership(project_pk, request.user)
if project is not None:
name = request.POST.get('name')
metadata = request.POST.get('metadata')
s = Sample(name=name, metadata=metadata, project=project)
s.save()
return HttpResponse('');
else:
return HttpResponseBadRequest('')
def map_files_to_samples(request, project_pk):
project = helpers.check_ownership(project_pk, request.user)
if project is not None:
j = json.loads(request.POST.get('mapping'))
for sample, files in j.items():
sample_obj = project.sample_set.get(name=sample)
for f in files:
f = os.path.join(settings.UPLOAD_PREFIX,f)
ds = DataSource.objects.get(filepath=f, project=project)
ds.sample = sample_obj
ds.save()
return HttpResponse('')
else:
return HttpResponseBadRequest('')
def summary(request, project_pk):
"""
Summarizes the project prior to performing the analysis
"""
project = helpers.check_ownership(project_pk, request.user)
if project is not None:
full_mapping = {}
all_samples = project.sample_set.all()
for s in all_samples:
data_sources = s.datasource_set.all()
full_mapping[s] = ', '.join([os.path.basename(x.filepath) for x in data_sources])
return render(request, 'analysis_portal/summary.html', {'mapping':full_mapping, 'project_pk':project.pk})
else:
return HttpResponseBadRequest('')
def problem(request, project_pk):
project = helpers.check_ownership(project_pk, request.user)
if project is not None:
all_samples = project.sample_set.all()
allowed_samples = project.max_sample_number
return render(
request, 'analysis_portal/problem.html', {
'project_pk': project.pk,
'project_name': project.name,
'allowed_samples': allowed_samples,
'total_samples': len(all_samples)
})
else:
return HttpResponseBadRequest('')
def add_new_file(request, project_pk):
project = helpers.check_ownership(project_pk, request.user)
if project is not None:
newfile = request.POST.get('filename')
newfile = os.path.join(settings.UPLOAD_PREFIX, newfile)
# see if it already exists:
if DataSource.objects.filter(project=project, filepath=newfile).exists():
# file was updated in google storage, but nothing to do here. Return 204 so the front-end doesn't make more 'icons' for this updated file
return HttpResponse(status=204)
else:
new_ds = DataSource(project=project, source_type = 'fastq', filepath=newfile)
new_ds.save()
return HttpResponse('')
else:
return HttpResponseBadRequest('')
def delete_file(request, project_pk):
"""
Called (via ajax) when removing a file. Note that this does not remove the file from google storage bucket.
It only removes the record of it from our database.
TODO: change that-- remove from google storage as well.
"""
project = helpers.check_ownership(project_pk, request.user)
if project is not None:
file_to_rm = request.POST.get('filename')
file_to_rm = os.path.join(settings.UPLOAD_PREFIX, file_to_rm)
instance = DataSource.objects.get(filepath=file_to_rm, project=project)
instance.delete()
return HttpResponse('')
else:
return HttpResponseBadRequest('')
def kickoff(request, project_pk):
"""
Starts the analysis
TODO: abstract this for ease
"""
project = helpers.check_ownership(project_pk, request.user)
if project is not None:
project_samples = project.sample_set.all()
if len(project_samples) <= project.max_sample_number:
pk = project.pk
if project.service.name == 'rnaseq':
rnaseq_process.start_analysis(pk)
project.in_progress = True
project.start_time = datetime.datetime.now()
project.status_message = 'Performing alignments'
project.next_action_text = 'Processing...'
project.next_action_url = reverse('in_progress_view',
kwargs={'project_pk': pk})
project.save()
elif project.service.name == 'variant_calling_from_bam':
variant_process_submission_from_bam.start_analysis(pk)
elif project.service.name == 'variant_calling_from_fastq':
variant_process_submission_from_fastq.start_analysis(pk)
elif project.service.name == 'pooled_crispr':
pooled_crispr_process.start_analysis(pk)
project.in_progress = True
project.start_time = datetime.datetime.now()
project.status_message = 'Performing quantification'
project.next_action_text = 'Processing...'
project.next_action_url = ''
project.save()
elif project.service.name == 'circ_rna':
circ_rna_process.start_analysis(pk)
project.in_progress = True
project.start_time = datetime.datetime.now()
project.status_message = 'Performing quantification'
project.next_action_text = 'Processing...'
project.next_action_url = ''
project.save()
else:
print 'Could not figure out project type'
return redirect('analysis_home_view')
else:
# had too many samples
return redirect('problem_view', project_pk=project_pk)
else:
return HttpResponseBadRequest('')
def kickoff(request, project_pk):
"""
Starts the analysis
TODO: abstract this for ease
"""
project = helpers.check_ownership(project_pk, request.user)
if project is not None:
if project.service.name == 'RNA-Seq':
pk = project.pk
rnaseq_process.start_analysis(pk)
project.in_progress = True
project.start_time = datetime.datetime.now()
project.save()
else:
print 'Could not figure out project type'
return HttpResponseRedirect('/')
def set_genome(request, project_pk):
"""
Called (by ajax) when setting the selecting/setting the reference genome
"""
project = helpers.check_ownership(project_pk, request.user)
print 'back in set_genome, project=%s' % project
if project is not None:
service = project.service
selected_genome = request.POST.get('selected_genome')
org = Organism.objects.get(reference_genome=selected_genome,
service=service)
project.reference_organism = org
project.save()
return HttpResponse('')
else:
return HttpResponseBadRequest('')
def annotate_files_and_samples(request, project_pk):
"""
Populates the annotation page
TODO: infer samples from filenames
"""
project = helpers.check_ownership(project_pk, request.user)
if project is not None:
zero_uploaded_files = True
# gets all files associated with project. Some may be sample-specific, some not
uploaded_files = project.datasource_set.all()
# filter down to sample-specific files
sample_datasource_objs = []
for f in uploaded_files:
try:
ds = f.sampledatasource
sample_datasource_objs.append(f)
except ObjectDoesNotExist as ex:
print 'object was a regular DataSource, NOT a SampleDataSource. Skip'
if len(sample_datasource_objs) > 0:
zero_uploaded_files = False
existing_samples = project.sample_set.all(
) # any samples that were already defined
unassigned_files = []
assigned_files = {x.name: [] for x in existing_samples}
for f in sample_datasource_objs:
fds = f.sampledatasource
fdisplay = FileDisplay('', f.pk, f.filepath)
if fds.sample in existing_samples:
assigned_files[fds.sample.name].append(fdisplay)
else:
unassigned_files.append(fdisplay)
previous_url, next_url = helpers.get_bearings(project)
context = {'project_name': project.name, \
'unassigned_files':unassigned_files, \
'assigned_files': assigned_files, \
'project_pk': project_pk, \
'no_uploaded_files':zero_uploaded_files,
'previous_page_url':previous_url, \
'next_page_url':next_url}
return render(request, 'analysis_portal/annotate.html', context)
else:
return HttpResponseBadRequest('')
def show_complete(request, project_pk):
project = helpers.check_ownership(project_pk, request.user)
if project:
start_date = project.start_time.strftime('%b %d, %Y')
start_time = project.start_time.strftime('%H:%M')
start_time_str = 'Started on %s at %s' % (start_date, start_time)
finish_date = project.finish_time.strftime('%b %d, %Y')
finish_time = project.finish_time.strftime('%H:%M')
finish_time_str = 'Finished on %s at %s' % (finish_date, finish_time)
return render(
request, 'analysis_portal/complete.html', {
'project_name': project.name,
'start_time_str': start_time_str,
'finish_time_str': finish_time_str
})
else:
return HttpResponseBadRequest('')
def add_new_file(request, project_pk):
project = helpers.check_ownership(project_pk, request.user)
if project is not None:
print request.POST
newfile = request.POST.get('filename')
is_sample_source_upload = request.POST.get('sample_source_upload')
if is_sample_source_upload.lower() == 'true':
is_sample_source_upload = True
else:
is_sample_source_upload = False
print 'is_sample_source_upload: %s' % is_sample_source_upload
newfile = os.path.join(settings.UPLOAD_PREFIX, newfile)
try:
return helpers.add_datasource_to_database(project, newfile,
is_sample_source_upload)
except helpers.UndeterminedFiletypeException as ex:
return HttpResponseBadRequest(ex.message)
else:
return HttpResponseBadRequest('')
def summary(request, project_pk):
"""
Summarizes the project prior to performing the analysis
"""
project = helpers.check_ownership(project_pk, request.user)
if project is not None:
full_mapping = {}
all_samples = project.sample_set.all()
for s in all_samples:
data_sources = s.sampledatasource_set.all()
full_mapping[s] = ', '.join(
[os.path.basename(x.filepath) for x in data_sources])
previous_url, next_url = helpers.get_bearings(project)
context = {'mapping':full_mapping, \
'project_pk':project.pk, \
'project_name':project.name,\
'previous_page_url':previous_url, \
'next_page_url':next_url}
return render(request, 'analysis_portal/summary.html', context)
else:
return HttpResponseBadRequest('')
def rm_sample(request, project_pk):
"""
Removes a sample.
As part of this, resets the 'sample' attribute of the DataSource.
So, keeps the datasource, but just removes that file's association with the deleted sample
"""
project = helpers.check_ownership(project_pk, request.user)
if project is not None:
name = request.POST.get('samplename')
s = Sample.objects.get(name=name, project=project)
# get all the data sources assigned to this sample and set their sample attribute to be None
ds_set = s.datasource_set.all()
for ds in ds_set:
ds.sample = None
ds.save()
# finally, delete the Sample object
s.delete()
return HttpResponse('')
else:
return HttpResponseBadRequest('')
def genome_selection_page(request, project_pk):
"""
Sets up the page where users select their reference genome
"""
project = helpers.check_ownership(project_pk, request.user)
if project is not None:
# get the service type which informs which genomes to present
service = project.service
d = {}
orgs = service.organism_set.all(
) # the references associated with the service
for org in orgs:
d[org.reference_genome] = org.description
previous_url, next_url = helpers.get_bearings(project)
context = {'project_pk': project.pk, \
'references':d, \
'project_name':project.name, \
'previous_page_url':previous_url, \
'next_page_url':next_url}
return render(request, 'analysis_portal/choose_genome.html', context)
else:
return HttpResponseBadRequest('')
def annotate_files_and_samples(request, project_pk):
"""
Populates the annotation page
TODO: infer samples from filenames
"""
project = helpers.check_ownership(project_pk, request.user)
if project is not None:
zero_uploaded_files = True
uploaded_files = project.datasource_set.all() # gets the files with this as their project
if len(uploaded_files) > 0:
zero_uploaded_files = False
existing_samples = project.sample_set.all() # any samples that were already defined
unassigned_files = []
assigned_files = {x.name:[] for x in existing_samples}
for f in uploaded_files:
fdisplay = FileDisplay('', f.pk, f.filepath)
if f.sample in existing_samples:
assigned_files[f.sample.name].append(fdisplay)
else:
unassigned_files.append(fdisplay)
return render(request, 'analysis_portal/annotate.html', {'project_name': project.name, 'unassigned_files':unassigned_files, 'assigned_files': assigned_files, 'project_pk': project_pk, 'no_uploaded_files':zero_uploaded_files})
else:
return HttpResponseBadRequest('')
def upload_page(request, project_pk):
"""
This fills out the upload page
"""
project = helpers.check_ownership(project_pk, request.user)
if project is not None:
service = project.service
view_name = request.resolver_match.url_name
current_workflow_step = service.workflow_set.get(step_url=view_name)
extra = {}
try:
extra = json.loads(current_workflow_step.extra)
except ValueError as ex:
print 'was no extra info for this workflow step'
# if no extra information was specified for this step, catch this exception and ignore it
pass
sample_source_upload = False
if 'sample_source_upload' in extra:
sample_source_upload = True
existing_files = []
if sample_source_upload:
uploaded_files = project.datasource_set.all(
) # gets the files with this as their project
sample_datasource_objs = []
for f in uploaded_files:
try:
ds = f.sampledatasource
if ds.sample:
samplename = ds.sample.name
else:
samplename = None
existing_files.append(
FileDisplay(samplename, f.pk, f.filepath))
except ObjectDoesNotExist as ex:
print 'object was a regular DataSource, NOT a SampleDataSource. Skip'
pass
else:
uploaded_files = project.datasource_set.all(
) # gets the files with this as their project
for f in uploaded_files:
try:
# if the uploaded file was NOT associated with a sample, it will throw an exception
ds = f.sampledatasource
except ObjectDoesNotExist as ex:
# catch the exception, which means we have a sample-agnostic file
existing_files.append(FileDisplay(None, f.pk, f.filepath))
instructions = current_workflow_step.instructions
previous_url, next_url = helpers.get_bearings(project)
context = {'project_name': project.name, \
'existing_files':existing_files, \
'project_pk': project_pk, \
'instructions':instructions, \
'previous_page_url':previous_url, \
'next_page_url':next_url, \
'sample_source_upload':sample_source_upload, \
'title_text': current_workflow_step.title_text \
}
return render(request, 'analysis_portal/upload_page.html', context)
else:
return HttpResponseBadRequest('')
class FileDisplay(object):
"""
A simple container class used to display file details in the UI
"""
def __init__(self, samplename, pk, filepath):
self.samplename = samplename
self.pk = pk
self.file_string = os.path.basename(filepath)
@login_required
def set_genome(request, project_pk):
"""
Called (by ajax) when setting the selecting/setting the reference genome
"""
project = helpers.check_ownership(project_pk, request.user)
if project is not None:
selected_genome = request.POST.get('selected_genome')
org = Organism.objects.get(reference_genome = selected_genome)
project.reference_organism = org
project.save()
return HttpResponse('')
else:
return HttpResponseBadRequest('')
@login_required
def genome_selection_page(request, project_pk):
"""
Sets up the page where users select their reference genome
"""
