def edit(request, process_uuid):
"""Edit existing process metadata"""
api_client = request.user.agave_oauth.api_client
try:
process = Process(api_client=api_client, uuid=process_uuid)
process_type = process.value["process_type"]
except HTTPError as e:
logger.error("Error editing process. {}".format(e.message))
messages.warning(request, "Error editing process.")
return HttpResponseRedirect("/process/{}".format(process_uuid))
except Exception as e:
logger.error("Error editing process. {}".format(e.message))
messages.warning(request, "Process not found.")
return HttpResponseRedirect("/projects/")
process_fields = get_process_fields(process.project, process_type)
#######
# GET #
#######
if request.method == "GET":
context = {
"form_process_edit": ProcessFieldsForm(fields=process_fields, initial=process.value),
"specimen": process.specimen,
"project": process.project,
"process": process,
}
return render(request, "ids_projects/processes/edit.html", context)
########
# POST #
########
elif request.method == "POST":
form = ProcessFieldsForm(process_fields, request.POST)
if form.is_valid():
try:
process.value.update(form.cleaned_data)
process.save()
messages.info(request, "Process successfully edited.")
return HttpResponseRedirect(reverse("ids_projects:process-view", kwargs={"process_uuid": process.uuid}))
except Exception as e:
exception_msg = "Unable to edit process. %s" % e
logger.error(exception_msg)
messages.error(request, exception_msg)
return HttpResponseRedirect(reverse("ids_projects:process-view", kwargs={"process_uuid": process.uuid}))
def view(request, process_uuid):
""" """
if request.user.is_anonymous():
api_client = get_portal_api_client()
else:
api_client = request.user.agave_oauth.api_client
try:
process = Process(api_client=api_client, uuid=process_uuid)
project = process.project
specimen = process.specimen
data = process.data
inputs = process.inputs
outputs = process.outputs
except Exception as e:
exception_msg = "Unable to load process. %s" % e
logger.error(exception_msg)
messages.warning(request, exception_msg)
return HttpResponseRedirect(reverse("ids_projects:project-list-private"))
try:
process_types = get_process_type_keys(project)
process_fields = get_process_fields(project, process.value["process_type"])
process.set_fields(process_fields)
except Exception as e:
exception_msg = "Unable to load config values. %s" % e
logger.warning(exception_msg)
context = {
"process": process,
"project": project,
"specimen": specimen,
"datas": data,
"inputs": inputs,
"outputs": outputs,
"process_types": process_types,
}
return render(request, "ids_projects/processes/detail.html", context)
def create(request):
"""Create a new process related to a specimen"""
# get parent uuid (project or specimen), and process type, if inlcuded in
# the query string
project_uuid = request.GET.get("project_uuid", None)
specimen_uuid = request.GET.get("specimen_uuid", None)
process_type = request.GET.get("process_type", None)
# check to make sure we have at least one parent uuid (project or specimen)
if not specimen_uuid and not project_uuid:
messages.warning(request, "Missing project or specimen UUID, cannot find processes.")
return HttpResponseRedirect(reverse("ids_projects:project-list-private"))
# get the api_client to pass to the model for communication with agave
api_client = request.user.agave_oauth.api_client
# instantiate either a project and a specimen, or just a project (specimen
# objects always have a parent project)
try:
if not specimen_uuid:
specimen = None
project = Project(api_client=api_client, uuid=project_uuid)
else:
specimen = Specimen(api_client=api_client, uuid=specimen_uuid)
project = specimen.project
except Exception as e:
exception_msg = "Unable to load project or specimen, cannot create process. %s" % e
logger.error(exception_msg)
messages.warning(request, exception_msg)
return HttpResponseRedirect(reverse("ids_projects:project-list-private"))
if project is None:
exception_msg = "Missing project, cannot create process."
logger.error(exception_msg)
messages.warning(request, exception_msg)
return HttpResponseRedirect(reverse("ids_projects:project-list-private"))
# add project, specimen to the form context
context = {"project": project, "specimen": specimen}
# get the different types of processes we can create for this project type
try:
process_type_choices = get_process_choices(project)
except Exception as e:
exception_msg = "Missing project type information, cannot create process. %s" % e
logger.error(exception_msg)
messages.warning(request, exception_msg)
return HttpResponseRedirect(reverse("ids_projects:specimen-view", kwargs={"specimen_uuid": specimen.uuid}))
#######
# GET #
#######
if request.method == "GET":
if process_type is None:
context["form_process_type"] = ProcessTypeForm(process_type_choices)
context["form_process_fields"] = None
else:
process_type = request.GET.get("process_type")
process_fields = get_process_fields(project, process_type)
form_process_type = ProcessTypeForm(process_type_choices, initial={"process_type": process_type})
form_process_type.fields["process_type"].widget.attrs["disabled"] = True
form_process_type.fields["process_type"].widget.attrs["readonly"] = True
form_process_fields = ProcessFieldsForm(process_fields)
context["form_process_type"] = form_process_type
context["form_process_fields"] = form_process_fields
context["process_type"] = process_type
context["form_upload_file"] = UploadFileForm()
if request.is_ajax():
return render(request, "ids_projects/processes/get_fields_ajax.html", context)
else:
return render(request, "ids_projects/processes/create.html", context)
########
# POST #
########
elif request.method == "POST":
process_type = request.POST.get("process_type")
process_fields = get_process_fields(project, process_type)
form_process_type = ProcessTypeForm(process_type_choices, request.POST)
form_process_type.fields["process_type"].widget.attrs["disabled"] = True
form_process_type.fields["process_type"].widget.attrs["readonly"] = True
#################################################
# POST includes 'form_process_type' fields only #
#################################################
if not "process_fields" in request.POST:
form_process_fields = ProcessFieldsForm(process_fields)
context["form_process_type"] = form_process_type
context["form_process_fields"] = form_process_fields
context["process_type"] = process_type
################################################################
# POST includes form_process_type & form_process_fields fields #
################################################################
else:
form_process_fields = ProcessFieldsForm(process_fields, request.POST)
if form_process_type.is_valid() and form_process_fields.is_valid():
logger.debug("Process form is valid")
data = {"process_type": process_type}
data.update(form_process_type.cleaned_data.copy())
data.update(form_process_fields.cleaned_data.copy())
# meta data for process
meta = {"value": data}
## Single process registration
if request.FILES["file"] is None:
logger.debug("Single process registration")
if "file" not in request.FILES:
print "single process reg"
try:
process = Process(api_client=api_client, meta=meta)
process.save()
if specimen:
# create two-way relationship to specimen
specimen.add_process(process)
specimen.save()
process.add_specimen(specimen)
process.save()
# create two-way relationship to project
project.add_process(process)
project.save()
process.add_project(project)
process.save()
success_msg = "Successfully created process."
logger.info(success_msg)
messages.success(request, success_msg)
return HttpResponseRedirect(
reverse("ids_projects:process-view", kwargs={"process_uuid": process.uuid})
)
except HTTPError as e:
exception_msg = "Unable to create new process. %s" % e
logger.error(exception_msg)
messages.error(request, exception_msg)
return HttpResponseRedirect(
reverse("ids_projects:specimen-view", kwargs={"specimen_uuid": specimen.uuid})
)
## Bulk ISH process registration
else:
logger.debug("Bulk process registration")
try:
ISH_meta = _validate_ISH(request.FILES["file"], project)
bulk_ISH_registration.apply_async(
args=(ISH_meta, meta, project.uuid, request.user.username), serializer="json"
)
return HttpResponseRedirect(
reverse("ids_projects:project-view", kwargs={"project_uuid": project.uuid})
)
except Exception as e:
traceback.print_exc()
exception_msg = repr(e)
logger.error(exception_msg)
messages.warning(request, exception_msg)
return HttpResponseRedirect(
reverse("ids_projects:project-view"), kwargs={"project_uuid": project_uuid}
)
