def get_context_data(self, **kwargs):
app_id = int(self.request.GET.get("app"))
visible_containers = Container.filter_by_user(self.request.user)
app_qs = ContainerApp.objects.filter(pk=app_id,
container__in=visible_containers)
app = app_qs.first()
if app is None:
raise Http404("ID {} is not accessible".format(app_id))
context = super(ContainerInputList, self).get_context_data(**kwargs)
context['app'] = app
context['app_url'] = rest_framework.reverse.reverse(
str('containerapp-detail'),
kwargs=dict(pk=app.pk),
request=self.request)
context['batch_form'] = BatchForm()
context['inputs'] = [
dict(name=arg.name,
url=rest_framework.reverse.reverse(
str('containerargument-detail'),
kwargs=dict(pk=arg.pk),
request=self.request)) for arg in app.arguments.filter(
type=ContainerArgument.INPUT).order_by('position')
]
context['priolist'] = [t[0] for t in settings.SLURM_QUEUES]
return context
def get_context_data(self, **kwargs):
app_id = int(self.request.GET.get("app"))
visible_containers = Container.filter_by_user(self.request.user)
app_qs = ContainerApp.objects.filter(pk=app_id,
container__in=visible_containers)
app = app_qs.first()
if app is None:
raise Http404("ID {} is not accessible".format(app_id))
context = super(ContainerInputList, self).get_context_data(**kwargs)
context['app'] = app
context['app_url'] = rest_framework.reverse.reverse(
str('containerapp-detail'),
kwargs=dict(pk=app.pk),
request=self.request)
context['batch_form'] = BatchForm()
context['inputs'] = [
dict(name=arg.name, url=rest_framework.reverse.reverse(
str('containerargument-detail'),
kwargs=dict(pk=arg.pk),
request=self.request))
for arg in app.arguments.filter(
type=ContainerArgument.INPUT).order_by('position')]
context['priolist'] = [t[0] for t in settings.SLURM_QUEUES]
return context
def filter_granted(self, queryset):
""" Args don't have permissions, so filter by parent containers. """
granted_containers = Container.filter_by_user(self.request.user)
return queryset.filter(app__container_id__in=granted_containers)
def method_revise(request, pk):
"""
Add a revision of an existing Method. revision_parent is defined by the
previous version.
"""
t = loader.get_template('method/method.html')
c = {}
creating_user = request.user
# Retrieve the most recent member of this Method's family.
parent_method = Method.check_accessible(pk, creating_user)
family = parent_method.family
# Retrieve the most recent revision of the corresponding CR.
parent_revision = parent_method.driver
if not parent_revision:
this_code_resource = None
all_revisions = []
else:
this_code_resource = parent_revision.coderesource
# Filter the available revisions by user.
all_revisions = CodeResourceRevision.filter_by_user(
creating_user,
queryset=this_code_resource.revisions.all()).order_by(
'-revision_DateTime')
parent_container = parent_method.container
if not parent_container:
this_container_family = None
all_containers = []
else:
this_container_family = parent_container.family
all_containers = Container.filter_by_user(
creating_user, queryset=this_container_family.containers.all())
if request.method == 'POST':
# Because there is no CodeResource specified, the second value is of type MethodReviseForm.
family_form, method_revise_form,\
dep_forms, input_form_tuples,\
output_form_tuples, _ = create_method_forms(request.POST, creating_user, family=family)
if not _method_forms_check_valid(family_form, method_revise_form,
dep_forms, input_form_tuples,
output_form_tuples):
# Bail out now if there are any problems.
c.update({
'coderesource': this_code_resource,
'containerfamily': this_container_family,
'method_revise_form': method_revise_form,
'dep_forms': dep_forms,
'input_forms': input_form_tuples,
'output_forms': output_form_tuples,
'family': family,
'family_form': family_form,
'parent': parent_method,
'docker_default': DockerImage.DEFAULT_IMAGE
})
return HttpResponse(t.render(c, request))
# Next, attempt to build the Method and add it to family.
create_method_from_forms(family_form,
method_revise_form,
dep_forms,
input_form_tuples,
output_form_tuples,
creating_user,
family=family,
parent_method=parent_method)
if _method_forms_check_valid(family_form, method_revise_form,
dep_forms, input_form_tuples,
output_form_tuples):
# Success!
return HttpResponseRedirect('/methods/{}'.format(family.pk))
else:
# Initialize forms with values of parent Method.
family_form = MethodFamilyForm({
"name": family.name,
"description": family.description
})
parent_users_allowed = [
x.username for x in parent_method.users_allowed.all()
]
parent_groups_allowed = [
x.name for x in parent_method.groups_allowed.all()
]
method_revise_form = MethodReviseForm(
initial={
"revision_desc": parent_method.revision_desc,
"driver_revisions": parent_revision and parent_revision.pk,
"docker_image": parent_method.docker_image_id,
"reusable": parent_method.reusable,
"threads": parent_method.threads,
"memory": parent_method.memory,
"permissions": [parent_users_allowed, parent_groups_allowed]
})
dependencies = parent_method.dependencies.all()
dep_forms = []
for i, dependency in enumerate(dependencies):
its_crv = dependency.requirement
its_cr = its_crv.coderesource
dep_form = MethodDependencyForm(user=creating_user,
auto_id='id_%s_' + str(i),
initial={
'coderesource': its_cr.pk,
'revisions': its_crv.pk,
'path': dependency.path,
'filename': dependency.filename
})
dep_forms.append(dep_form)
# If the parent Method has no dependencies, add a blank form.
if len(dep_forms) == 0:
dep_forms.append(
MethodDependencyForm(user=creating_user, auto_id='id_%s_0'))
xput_forms = []
inputs = parent_method.inputs.order_by("dataset_idx")
outputs = parent_method.outputs.order_by("dataset_idx")
for xput_type, xputs in (("in", inputs), ("out", outputs)):
forms = []
for xput in xputs:
tx_form = TransformationXputForm(auto_id='id_%s_{}_{}'.format(
xput_type, len(forms)),
initial={
'dataset_name':
xput.dataset_name,
'dataset_idx':
xput.dataset_idx
})
if xput.has_structure:
structure = xput.structure
xs_form = XputStructureForm(
user=creating_user,
auto_id='id_%s_{}_{}'.format(xput_type, len(forms)),
initial={
'compounddatatype': structure.compounddatatype.id,
'min_row': structure.min_row,
'max_row': structure.max_row
})
else:
xs_form = XputStructureForm(
user=creating_user,
auto_id='id_%s_{}_{}'.format(xput_type, len(forms)),
initial={'compounddatatype': '__raw__'})
forms.append((tx_form, xs_form))
xput_forms.append(forms)
input_form_tuples, output_form_tuples = xput_forms
# if previous Method has no inputs, provide blank forms
if len(input_form_tuples) == 0:
tx_form = TransformationXputForm(auto_id='id_%s_in_0')
xs_form = XputStructureForm(user=creating_user,
auto_id='id_%s_in_0')
input_form_tuples.append((tx_form, xs_form))
method_revise_form.fields['driver_revisions'].widget.choices = [
(str(x.id), '{}: {}'.format(x.revision_number, x.revision_name))
for x in all_revisions
]
method_revise_form.fields['container'].widget.choices = [
(str(x.id), x.tag) for x in all_containers
]
c.update({
'coderesource': this_code_resource,
'containerfamily': this_container_family,
'method_form': method_revise_form,
'dep_forms': dep_forms,
'input_forms': input_form_tuples,
'output_forms': output_form_tuples,
'family': family,
'family_form': family_form,
'parent': parent_method,
'docker_default': DockerImage.DEFAULT_IMAGE
})
return HttpResponse(t.render(c, request))
def filter_granted(self, queryset):
""" Args don't have permissions, so filter by parent containers. """
granted_containers = Container.filter_by_user(self.request.user)
return queryset.filter(app__container_id__in=granted_containers)
def method_revise(request, pk):
"""
Add a revision of an existing Method. revision_parent is defined by the
previous version.
"""
t = loader.get_template('method/method.html')
c = {}
creating_user = request.user
# Retrieve the most recent member of this Method's family.
parent_method = Method.check_accessible(pk, creating_user)
family = parent_method.family
# Retrieve the most recent revision of the corresponding CR.
parent_revision = parent_method.driver
if not parent_revision:
this_code_resource = None
all_revisions = []
else:
this_code_resource = parent_revision.coderesource
# Filter the available revisions by user.
all_revisions = CodeResourceRevision.filter_by_user(
creating_user,
queryset=this_code_resource.revisions.all()).order_by('-revision_DateTime')
parent_container = parent_method.container
if not parent_container:
this_container_family = None
all_containers = []
else:
this_container_family = parent_container.family
all_containers = Container.filter_by_user(
creating_user,
queryset=this_container_family.containers.all())
if request.method == 'POST':
# Because there is no CodeResource specified, the second value is of type MethodReviseForm.
family_form, method_revise_form,\
dep_forms, input_form_tuples,\
output_form_tuples, _ = create_method_forms(request.POST, creating_user, family=family)
if not _method_forms_check_valid(family_form, method_revise_form, dep_forms,
input_form_tuples, output_form_tuples):
# Bail out now if there are any problems.
c.update(
{
'coderesource': this_code_resource,
'containerfamily': this_container_family,
'method_revise_form': method_revise_form,
'dep_forms': dep_forms,
'input_forms': input_form_tuples,
'output_forms': output_form_tuples,
'family': family,
'family_form': family_form,
'parent': parent_method,
'docker_default': DockerImage.DEFAULT_IMAGE
})
return HttpResponse(t.render(c, request))
# Next, attempt to build the Method and add it to family.
create_method_from_forms(
family_form, method_revise_form, dep_forms, input_form_tuples, output_form_tuples, creating_user,
family=family, parent_method=parent_method
)
if _method_forms_check_valid(family_form, method_revise_form, dep_forms,
input_form_tuples, output_form_tuples):
# Success!
return HttpResponseRedirect('/methods/{}'.format(family.pk))
else:
# Initialize forms with values of parent Method.
family_form = MethodFamilyForm({"name": family.name, "description": family.description})
parent_users_allowed = [x.username for x in parent_method.users_allowed.all()]
parent_groups_allowed = [x.name for x in parent_method.groups_allowed.all()]
method_revise_form = MethodReviseForm(
initial={
"revision_desc": parent_method.revision_desc,
"driver_revisions": parent_revision and parent_revision.pk,
"docker_image": parent_method.docker_image_id,
"reusable": parent_method.reusable,
"threads": parent_method.threads,
"memory": parent_method.memory,
"permissions": [parent_users_allowed, parent_groups_allowed]
})
dependencies = parent_method.dependencies.all()
dep_forms = []
for i, dependency in enumerate(dependencies):
its_crv = dependency.requirement
its_cr = its_crv.coderesource
dep_form = MethodDependencyForm(
user=creating_user,
auto_id='id_%s_'+str(i),
initial={
'coderesource': its_cr.pk,
'revisions': its_crv.pk,
'path': dependency.path,
'filename': dependency.filename
}
)
dep_forms.append(dep_form)
# If the parent Method has no dependencies, add a blank form.
if len(dep_forms) == 0:
dep_forms.append(MethodDependencyForm(user=creating_user, auto_id='id_%s_0'))
xput_forms = []
inputs = parent_method.inputs.order_by("dataset_idx")
outputs = parent_method.outputs.order_by("dataset_idx")
for xput_type, xputs in (("in", inputs), ("out", outputs)):
forms = []
for xput in xputs:
tx_form = TransformationXputForm(auto_id='id_%s_{}_{}'.format(xput_type, len(forms)),
initial={'dataset_name': xput.dataset_name,
'dataset_idx': xput.dataset_idx})
if xput.has_structure:
structure = xput.structure
xs_form = XputStructureForm(user=creating_user,
auto_id='id_%s_{}_{}'.format(xput_type, len(forms)),
initial={'compounddatatype': structure.compounddatatype.id,
'min_row': structure.min_row,
'max_row': structure.max_row})
else:
xs_form = XputStructureForm(user=creating_user,
auto_id='id_%s_{}_{}'.format(xput_type, len(forms)),
initial={'compounddatatype': '__raw__'})
forms.append((tx_form, xs_form))
xput_forms.append(forms)
input_form_tuples, output_form_tuples = xput_forms
# if previous Method has no inputs, provide blank forms
if len(input_form_tuples) == 0:
tx_form = TransformationXputForm(auto_id='id_%s_in_0')
xs_form = XputStructureForm(user=creating_user, auto_id='id_%s_in_0')
input_form_tuples.append((tx_form, xs_form))
method_revise_form.fields['driver_revisions'].widget.choices = [
(str(x.id), '{}: {}'.format(x.revision_number, x.revision_name)) for x in all_revisions
]
method_revise_form.fields['container'].widget.choices = [
(str(x.id), x.tag) for x in all_containers]
c.update(
{
'coderesource': this_code_resource,
'containerfamily': this_container_family,
'method_form': method_revise_form,
'dep_forms': dep_forms,
'input_forms': input_form_tuples,
'output_forms': output_form_tuples,
'family': family,
'family_form': family_form,
'parent': parent_method,
'docker_default': DockerImage.DEFAULT_IMAGE
}
)
return HttpResponse(t.render(c, request))