def view(request, specimen_uuid):
""" """
if request.user.is_anonymous():
api_client = get_portal_api_client()
else:
api_client = request.user.agave_oauth.api_client
try:
specimen = Specimen(api_client=api_client, uuid=specimen_uuid)
project = specimen.project
processes = specimen.processes
except Exception as e:
exception_msg = 'Unable to load specimen. %s' % e
logger.error(exception_msg)
messages.warning(request, exception_msg)
return HttpResponseRedirect('/projects')
try:
process_types = get_process_type_keys(project)
specimen_fields = get_specimen_fields(project)
specimen.set_fields(specimen_fields)
context = {'project': project,
'specimen': specimen,
'processes': processes,
'process_types': process_types}
return render(request, 'ids_projects/specimens/detail.html', context)
except Exception as e:
exception_msg = 'Unable to load config values. %s' % e
logger.warning(exception_msg)
messages.warning(request, exception_msg)
return HttpResponseRedirect(reverse('ids_projects:project-list-private'))
def edit(request, specimen_uuid):
"""Edit a specimen, given the uuid"""
api_client = request.user.agave_oauth.api_client
try:
specimen = Specimen(api_client=api_client, uuid=specimen_uuid)
project = specimen.project
except Exception as e:
exception_msg = 'Unable to edit specimen. %s' % e
logger.exception(exception_msg)
messages.warning(request, exception_msg)
return HttpResponseRedirect('/projects/')
try:
specimen_fields = get_specimen_fields(project)
except Exception as e:
exception_msg = 'Missing project type information, cannot edit specimen. %s' % e
logger.error(exception_msg)
messages.warning(request, exception_msg)
return HttpResponseRedirect(
reverse('ids_projects:project-view',
kwargs={'project_uuid': project.uuid}))
#######
# GET #
#######
if request.method == 'GET':
context = {'form_specimen_edit': SpecimenForm(fields=specimen_fields, initial=specimen.value),
'specimen': specimen,
'project': specimen.project}
return render(request, 'ids_projects/specimens/create.html', context)
########
# POST #
########
elif request.method == 'POST':
form = SpecimenForm(specimen_fields, request.POST)
if form.is_valid():
try:
specimen.value.update(form.cleaned_data)
specimen.save()
messages.info(request, 'Specimen successfully edited.')
return HttpResponseRedirect(
reverse('ids_projects:specimen-view',
kwargs={'specimen_uuid': specimen.uuid}))
except Exception as e:
exception_msg = 'Unable to edit specimen. %s' % e
logger.error(exception_msg)
messages.error(request, exception_msg)
return HttpResponseRedirect(
reverse('ids_projects:specimen-view',
kwargs={'specimen_uuid': specimen.uuid}))
def _validate_specimens(f, project):
""" process uploaded csv file to register specimens """
# NEED TO ADD VALIDATION
header = True
specimen_fields = get_specimen_fields(project)
logger.debug("Specimen fields: {}".format(specimen_fields))
reader = csv.reader(f)
row_num = 0
specimens_meta = []
if header:
row = next(reader, None)
for index in range(len(row)):
if row[index].lower() != specimen_fields[index]['id']:
raise Exception("Fields does not match!")
else:
logger.debug("Field match OK: %s" % row[index])
# reading metadata
for row in reader:
meta = {}
col_num = 0
for field in specimen_fields[:-1]:
meta[field['id']] = row[col_num]
col_num = col_num + 1
specimens_meta.append(meta)
row_num = row_num + 1
logger.debug("Specimens meta: {}".format(specimens_meta))
return specimens_meta
def create(request):
"""Create a new specimen related to a project"""
project_uuid = request.GET.get('project_uuid', False)
if not project_uuid:
messages.warning(request, 'Missing project UUID, cannot create specimen.')
return HttpResponseRedirect(reverse('ids_projects:project-list-private'))
api_client = request.user.agave_oauth.api_client
try:
project = Project(api_client=api_client, uuid=project_uuid)
except Exception as e:
exception_msg = 'Unable to load project. %s' % e
logger.exception(exception_msg)
messages.warning(request, exception_msg)
return HttpResponseRedirect('/projects/')
try:
specimen_fields = get_specimen_fields(project)
except Exception as e:
exception_msg = 'Missing project type information, cannot create specimen. %s' % e
logger.error(exception_msg)
messages.warning(request, exception_msg)
return HttpResponseRedirect(
reverse('ids_projects:project-view',
kwargs={'project_uuid': project.uuid}))
#######
# GET #
#######
if request.method == 'GET':
context = {'form_specimen_create': SpecimenForm(specimen_fields),
'project': project,
'specimen': None}
return render(request, 'ids_projects/specimens/create.html', context)
########
# POST #
########
elif request.method == 'POST':
form = SpecimenForm(specimen_fields, request.POST)
if form.is_valid():
meta = {'value': form.cleaned_data}
try:
specimen = Specimen(api_client=api_client, meta=meta)
specimen.save()
# create two-way relationship to project
# add_part: specimen
project.add_specimen(specimen)
project.save()
# add_container: project
specimen.add_project(project)
specimen.save()
success_msg = 'Successfully created specimen.'
logger.info(success_msg)
messages.success(request, success_msg)
return HttpResponseRedirect(
reverse('ids_projects:specimen-view',
kwargs={'specimen_uuid': specimen.uuid}))
except Exception as e:
exception_msg = 'Unable to create new specimen. %s' % e
logger.error(exception_msg)
messages.error(request, exception_msg)
return HttpResponseRedirect(
reverse('ids_projects:project-view',
kwargs={'project_uuid': project_uuid}))