class MethodForm(SaveFormInitMixin, forms.ModelForm):
phase = ModelChoiceField(
queryset=None,
help_text="Which phase is this evaluation container for?",
)
chunked_upload = UploadedAjaxFileList(
widget=uploader.AjaxUploadWidget(multifile=False, auto_commit=False),
label="Evaluation Method Container",
validators=[
ExtensionValidator(allowed_extensions=(".tar", ".tar.gz"))
],
help_text=(
".tar.gz archive of the container image produced from the command "
"'docker save IMAGE | gzip -c > IMAGE.tar.gz'. See "
"https://docs.docker.com/engine/reference/commandline/save/"),
)
def __init__(self, *args, user, challenge, **kwargs):
super().__init__(*args, **kwargs)
self.fields["chunked_upload"].widget.user = user
self.fields["phase"].queryset = challenge.phase_set.all()
class Meta:
model = Method
fields = ["phase", "chunked_upload"]
class AlgorithmForm(forms.ModelForm):
ipython_notebook = forms.FileField(
validators=[MimeTypeValidator(allowed_types=("text/plain", ))],
required=False,
help_text=(
"Please upload an iPython notebook that describes your algorithm"),
)
chunked_upload = UploadedAjaxFileList(
widget=algorithm_upload_widget,
label="Algorithm Image",
validators=[
ExtensionValidator(allowed_extensions=(".tar", ".tar.gz"))
],
help_text=(
".tar.gz archive of the container image produced from the command "
"'docker save IMAGE > IMAGE.tar | gzip'. See "
"https://docs.docker.com/engine/reference/commandline/save/"),
)
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.helper = FormHelper(self)
class Meta:
model = Algorithm
fields = (
"title",
"requires_gpu",
"ipython_notebook",
"chunked_upload",
)
class AlgorithmImageForm(ModelForm):
chunked_upload = UploadedAjaxFileList(
widget=uploader.AjaxUploadWidget(multifile=False),
label="Algorithm Image",
validators=[
ExtensionValidator(allowed_extensions=(".tar", ".tar.gz"))
],
help_text=(
".tar.gz archive of the container image produced from the command "
"'docker save IMAGE | gzip -c > IMAGE.tar.gz'. See "
"https://docs.docker.com/engine/reference/commandline/save/"),
)
requires_memory_gb = IntegerField(
min_value=1,
max_value=24,
initial=4,
help_text=
"The maximum system memory required by the algorithm in gigabytes.",
)
def __init__(self, *args, user, **kwargs):
super().__init__(*args, **kwargs)
self.helper = FormHelper(self)
self.fields["chunked_upload"].widget.user = user
class Meta:
model = AlgorithmImage
fields = ("requires_gpu", "requires_memory_gb", "chunked_upload")
class AlgorithmForm(forms.ModelForm):
ipython_notebook = forms.FileField(
validators=[
MimeTypeValidator(allowed_types=('text/plain',))
],
required=False,
help_text=(
"Please upload an iPython notebook that describes your algorithm"
),
)
chunked_upload = UploadedAjaxFileList(
widget=algorithm_upload_widget,
label='Algorithm Image',
validators=[
ExtensionValidator(allowed_extensions=('.tar',))
],
help_text=(
'Tar archive of the container image produced from the command '
'`docker save IMAGE > IMAGE.tar`. See '
'https://docs.docker.com/engine/reference/commandline/save/'
),
)
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.helper = FormHelper(self)
class Meta:
model = Algorithm
fields = ('ipython_notebook', 'chunked_upload',)
class AlgorithmImageForm(forms.ModelForm):
chunked_upload = UploadedAjaxFileList(
widget=algorithm_image_upload_widget,
label="Algorithm Image",
validators=[
ExtensionValidator(allowed_extensions=(".tar", ".tar.gz"))
],
help_text=(
".tar.gz archive of the container image produced from the command "
"'docker save IMAGE | gzip -c > IMAGE.tar.gz'. See "
"https://docs.docker.com/engine/reference/commandline/save/"
),
)
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.helper = FormHelper(self)
class Meta:
model = AlgorithmImage
fields = (
"title",
"requires_gpu",
"description",
"logo",
"chunked_upload",
)
class ImportForm(SaveFormInitMixin, forms.Form):
products_file = forms.FileField()
companies_file = forms.FileField()
images_zip = UploadedAjaxFileList(widget=uploader.AjaxUploadWidget(
multifile=False, auto_commit=False), )
def __init__(self, *args, user, **kwargs):
super().__init__(*args, **kwargs)
self.helper = FormHelper()
self.helper.add_input(Submit("save", "Submit"))
self.fields["images_zip"].widget.user = user
def test_form_field_to_python():
form_field = UploadedAjaxFileList()
uuid_string = "4dec34db-930f-48be-bb65-d7f8319ff654," + "5d901b2c-7cd1-416e-9952-d30b6a0edcba," + "4a3c5731-0050-4489-8364-282278f7190f"
staged_files = form_field.to_python(uuid_string)
assert ",".join(str(sf.uuid) for sf in staged_files) == uuid_string
with pytest.raises(ValidationError):
form_field.to_python("asdfasdfsdafasdf")
other_string = uuid_string[10:]
with pytest.raises(ValidationError):
form_field.to_python(other_string)
class SubmissionForm(forms.ModelForm):
chunked_upload = UploadedAjaxFileList(
widget=uploader.AjaxUploadWidget(multifile=False),
label="Predictions File",
validators=[ExtensionValidator(allowed_extensions=(".zip", ".csv"))],
)
def __init__(
self,
*args,
user,
display_comment_field=False,
supplementary_file_choice=Config.OFF,
supplementary_file_label="",
supplementary_file_help_text="",
publication_url_choice=Config.OFF,
**kwargs,
):
"""
Conditionally render the comment field based on the
display_comment_field kwarg
"""
super().__init__(*args, **kwargs)
if not display_comment_field:
del self.fields["comment"]
if supplementary_file_label:
self.fields["supplementary_file"].label = supplementary_file_label
if supplementary_file_help_text:
self.fields[
"supplementary_file"].help_text = supplementary_file_help_text
if supplementary_file_choice == Config.REQUIRED:
self.fields["supplementary_file"].required = True
elif supplementary_file_choice == Config.OFF:
del self.fields["supplementary_file"]
if publication_url_choice == Config.REQUIRED:
self.fields["publication_url"].required = True
elif publication_url_choice == Config.OFF:
del self.fields["publication_url"]
self.helper = FormHelper(self)
self.fields["chunked_upload"].widget.user = user
class Meta:
model = Submission
fields = submission_fields
class SubmissionForm(forms.ModelForm):
chunked_upload = UploadedAjaxFileList(
widget=submission_upload_widget,
label='Predictions File',
validators=[ExtensionValidator(allowed_extensions=('.zip', '.csv'))],
)
def __init__(self, *args, **kwargs):
"""
Conditionally render the comment field based on the
display_comment_field kwarg
"""
display_comment_field = kwargs.pop('display_comment_field', False)
allow_supplementary_file = kwargs.pop(
'allow_supplementary_file', False
)
require_supplementary_file = kwargs.pop(
'require_supplementary_file', False
)
supplementary_file_label = kwargs.pop('supplementary_file_label', '')
supplementary_file_help_text = kwargs.pop(
'supplementary_file_help_text', ''
)
super(SubmissionForm, self).__init__(*args, **kwargs)
if not display_comment_field:
del self.fields['comment']
if supplementary_file_label:
self.fields['supplementary_file'].label = supplementary_file_label
if supplementary_file_help_text:
self.fields[
'supplementary_file'
].help_text = supplementary_file_help_text
if require_supplementary_file:
self.fields['supplementary_file'].required = True
elif not allow_supplementary_file:
del self.fields['supplementary_file']
self.helper = FormHelper(self)
class Meta:
model = Submission
fields = ('comment', 'supplementary_file', 'chunked_upload')
class UploadRawImagesForm(forms.ModelForm):
files = UploadedAjaxFileList(
widget=uploader.AjaxUploadWidget(multifile=True, auto_commit=False),
label="Image files",
help_text=IMAGE_UPLOAD_HELP_TEXT,
)
def __init__(self, *args, user, linked_task=None, **kwargs):
super().__init__(*args, **kwargs)
self.helper = FormHelper()
self.helper.add_input(Submit("save", "Submit"))
self.fields["files"].widget.user = user
self._linked_task = linked_task
def clean_files(self):
files = self.cleaned_data["files"]
if len({f.name for f in files}) != len(files):
raise ValidationError("Filenames must be unique.")
if sum([f.size for f in files]) > settings.UPLOAD_SESSION_MAX_BYTES:
raise ValidationError(
"Total size of all files exceeds the upload limit.")
return files
def save(self, commit=True):
instance = super().save(commit=False) # type: RawImageUploadSession
# Create links between the created session and all uploaded files
uploaded_files = self.cleaned_data[
"files"] # type: List[StagedAjaxFile]
raw_files = [
RawImageFile(
upload_session=instance,
filename=uploaded_file.name,
staged_file_id=uploaded_file.uuid,
) for uploaded_file in uploaded_files
]
if commit:
instance.save()
RawImageFile.objects.bulk_create(raw_files)
instance.process_images(linked_task=self._linked_task)
return instance
class Meta:
model = RawImageUploadSession
fields = ["files"]
class AnnotationSetUpdateLabelsForm(forms.ModelForm):
chunked_upload = UploadedAjaxFileList(
widget=labels_upload_widget,
label="Labels File",
validators=[ExtensionValidator(allowed_extensions=(".csv", ))],
)
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.helper = FormHelper(self)
class Meta:
model = AnnotationSet
fields = ("chunked_upload", )
class AnnotationSetUpdateLabelsForm(forms.ModelForm):
chunked_upload = UploadedAjaxFileList(
widget=uploader.AjaxUploadWidget(multifile=False),
label="Labels File",
validators=[ExtensionValidator(allowed_extensions=(".csv",))],
)
def __init__(self, *args, user, **kwargs):
super().__init__(*args, **kwargs)
self.helper = FormHelper(self)
self.fields["chunked_upload"].widget.user = user
class Meta:
model = AnnotationSet
fields = ("chunked_upload",)
class SubmissionForm(forms.ModelForm):
chunked_upload = UploadedAjaxFileList(
widget=submission_upload_widget,
label="Predictions File",
validators=[ExtensionValidator(allowed_extensions=(".zip", ".csv"))],
)
def __init__(self, *args, **kwargs):
"""
Conditionally render the comment field based on the
display_comment_field kwarg
"""
display_comment_field = kwargs.pop("display_comment_field", False)
allow_supplementary_file = kwargs.pop("allow_supplementary_file",
False)
require_supplementary_file = kwargs.pop("require_supplementary_file",
False)
supplementary_file_label = kwargs.pop("supplementary_file_label", "")
supplementary_file_help_text = kwargs.pop(
"supplementary_file_help_text", "")
super().__init__(*args, **kwargs)
if not display_comment_field:
del self.fields["comment"]
if supplementary_file_label:
self.fields["supplementary_file"].label = supplementary_file_label
if supplementary_file_help_text:
self.fields[
"supplementary_file"].help_text = supplementary_file_help_text
if require_supplementary_file:
self.fields["supplementary_file"].required = True
elif not allow_supplementary_file:
del self.fields["supplementary_file"]
self.helper = FormHelper(self)
class Meta:
model = Submission
fields = ("comment", "supplementary_file", "chunked_upload")
class MethodForm(forms.ModelForm):
chunked_upload = UploadedAjaxFileList(
widget=method_upload_widget,
label="Evaluation Method Container",
validators=[ExtensionValidator(allowed_extensions=(".tar", ))],
help_text=(
"Tar archive of the container image produced from the command "
"`docker save IMAGE > IMAGE.tar`. See "
"https://docs.docker.com/engine/reference/commandline/save/"),
)
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.helper = FormHelper(self)
class Meta:
model = Method
fields = ["chunked_upload"]
class MethodForm(forms.ModelForm):
chunked_upload = UploadedAjaxFileList(
widget=uploader.AjaxUploadWidget(multifile=False),
label="Evaluation Method Container",
validators=[
ExtensionValidator(allowed_extensions=(".tar", ".tar.gz"))
],
help_text=(
".tar.gz archive of the container image produced from the command "
"'docker save IMAGE | gzip -c > IMAGE.tar.gz'. See "
"https://docs.docker.com/engine/reference/commandline/save/"),
)
def __init__(self, *args, user, **kwargs):
super().__init__(*args, **kwargs)
self.helper = FormHelper(self)
self.fields["chunked_upload"].widget.user = user
class Meta:
model = Method
fields = ["chunked_upload"]
def test_form_field_to_python():
form_field = UploadedAjaxFileList()
uuid_string = ",".join(
(
"4dec34db-930f-48be-bb65-d7f8319ff654",
"5d901b2c-7cd1-416e-9952-d30b6a0edcba",
"4a3c5731-0050-4489-8364-282278f7190f",
)
)
staged_files = form_field.to_python(uuid_string)
assert ",".join(str(sf.uuid) for sf in staged_files) == uuid_string
with pytest.raises(ValidationError):
form_field.to_python("asdfasdfsdafasdf")
other_string = uuid_string[10:]
with pytest.raises(ValidationError):
form_field.to_python(other_string)
class UploadRawImagesForm(forms.ModelForm):
files = UploadedAjaxFileList(
widget=upload_raw_files_widget,
label="Image files",
help_text=(
'Upload images for creating a new archive'
),
)
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.helper = FormHelper()
self.helper.add_input(Submit("save", "Submit"))
def save(self, commit=True):
instance = super().save(commit=False)
# Create links between the created session and all uploaded files
uploaded_files = self.cleaned_data[
"files"] # type: List[StagedAjaxFile]
raw_files = [
RawImageFile(
upload_session=instance,
filename=uploaded_file.name,
staged_file_id=uploaded_file.uuid,
) for uploaded_file in uploaded_files
]
if commit:
with transaction.atomic():
instance.save()
RawImageFile.objects.bulk_create(raw_files)
return instance
class Meta:
model = RawImageUploadSession
fields = ['files']
class UploadForm(forms.Form):
title = forms.CharField(label="Blah")
something = forms.CharField(label="Blabl")
upload_form = UploadedAjaxFileList(widget=test_upload_widget)
upload_form2 = UploadedAjaxFileList(widget=test_upload_widget2)
class SubmissionForm(forms.ModelForm):
chunked_upload = UploadedAjaxFileList(
widget=uploader.AjaxUploadWidget(multifile=False, auto_commit=False),
label="Predictions File",
validators=[ExtensionValidator(allowed_extensions=(".zip", ".csv"))],
)
algorithm = ModelChoiceField(
queryset=None,
help_text=format_lazy(
"Select one of your algorithms to submit as a solution to this "
"challenge. If you have not created your algorithm yet you can "
"do so <a href={}>on this page</a>.",
reverse_lazy("algorithms:create"),
),
)
def __init__(
self,
*args,
user,
algorithm_submission=False,
display_comment_field=False,
supplementary_file_choice=Config.OFF,
supplementary_file_label="",
supplementary_file_help_text="",
publication_url_choice=Config.OFF,
**kwargs,
):
"""
Conditionally render the comment field based on the
display_comment_field kwarg
"""
super().__init__(*args, **kwargs)
if not display_comment_field:
del self.fields["comment"]
if supplementary_file_label:
self.fields["supplementary_file"].label = supplementary_file_label
if supplementary_file_help_text:
self.fields[
"supplementary_file"].help_text = supplementary_file_help_text
if supplementary_file_choice == Config.REQUIRED:
self.fields["supplementary_file"].required = True
elif supplementary_file_choice == Config.OFF:
del self.fields["supplementary_file"]
if publication_url_choice == Config.REQUIRED:
self.fields["publication_url"].required = True
elif publication_url_choice == Config.OFF:
del self.fields["publication_url"]
if algorithm_submission:
del self.fields["chunked_upload"]
self.fields["algorithm"].queryset = get_objects_for_user(
user,
f"{Algorithm._meta.app_label}.change_{Algorithm._meta.model_name}",
Algorithm,
).order_by("title")
else:
del self.fields["algorithm"]
self.fields["chunked_upload"].widget.user = user
self.helper = FormHelper(self)
self.helper.layout.append(Submit("save", "Save"))
def clean_algorithm(self):
algorithm = self.cleaned_data["algorithm"]
if algorithm.latest_ready_image is None:
raise ValidationError(
"This algorithm does not have a usable container image. "
"Please add one and try again.")
return algorithm
class Meta:
model = Submission
fields = submission_fields
class UploadRawImagesForm(forms.ModelForm):
files = UploadedAjaxFileList(
widget=uploader.AjaxUploadWidget(multifile=True, auto_commit=False),
label="Image files",
help_text=(
"The total size of all files uploaded in a single session "
"cannot exceed 10 GB.<br>"
"The following file formats are supported: "
".mha, .mhd, .raw, .zraw, .dcm, .nii, .nii.gz, "
".tiff, .png, .jpeg and .jpg.<br>"
"The following file formats can be uploaded and will be converted to "
"tif: Aperio(.svs), Hamamatsu(.vms, .vmu, .ndpi), Leica(.scn), MIRAX"
"(.mrxs) and Ventana(.bif)."
),
)
def __init__(self, *args, user, linked_task=None, **kwargs):
super().__init__(*args, **kwargs)
self.helper = FormHelper()
self.helper.add_input(Submit("save", "Submit"))
self.fields["files"].widget.user = user
self._linked_task = linked_task
def clean_files(self):
files = self.cleaned_data["files"]
if len({f.name for f in files}) != len(files):
raise ValidationError("Filenames must be unique.")
if sum([f.size for f in files]) > settings.UPLOAD_SESSION_MAX_BYTES:
raise ValidationError(
"Total size of all files exceeds the upload limit."
)
return files
def save(self, commit=True):
instance = super().save(commit=False) # type: RawImageUploadSession
# Create links between the created session and all uploaded files
uploaded_files = self.cleaned_data[
"files"
] # type: List[StagedAjaxFile]
raw_files = [
RawImageFile(
upload_session=instance,
filename=uploaded_file.name,
staged_file_id=uploaded_file.uuid,
)
for uploaded_file in uploaded_files
]
if commit:
instance.save()
RawImageFile.objects.bulk_create(raw_files)
instance.process_images(linked_task=self._linked_task)
return instance
class Meta:
model = RawImageUploadSession
fields = ["files"]
def test_form_field_prepare_value_not_implemented():
form_field = UploadedAjaxFileList()
assert form_field.prepare_value("") is None
def test_form_field_prepare_value_not_implemented():
form_field = UploadedAjaxFileList()
assert form_field.prepare_value("") is None
class SubmissionForm(forms.ModelForm):
chunked_upload = UploadedAjaxFileList(
widget=uploader.AjaxUploadWidget(multifile=False, auto_commit=False),
label="Predictions File",
validators=[ExtensionValidator(allowed_extensions=(".zip", ".csv"))],
)
algorithm = ModelChoiceField(
queryset=None,
help_text=format_lazy(
"Select one of your algorithms to submit as a solution to this "
"challenge. If you have not created your algorithm yet you can "
"do so <a href={}>on this page</a>.",
reverse_lazy("algorithms:create"),
),
)
def __init__(
self,
*args,
user,
creator_must_be_verified=False,
algorithm_submission=False,
display_comment_field=False,
supplementary_file_choice=Phase.OFF,
supplementary_file_label="",
supplementary_file_help_text="",
publication_url_choice=Phase.OFF,
**kwargs,
):
"""
Conditionally render the comment field based on the
display_comment_field kwarg
"""
super().__init__(*args, **kwargs)
self.creator_must_be_verified = creator_must_be_verified
if not display_comment_field:
del self.fields["comment"]
if supplementary_file_label:
self.fields["supplementary_file"].label = supplementary_file_label
if supplementary_file_help_text:
self.fields[
"supplementary_file"].help_text = supplementary_file_help_text
if supplementary_file_choice == Phase.REQUIRED:
self.fields["supplementary_file"].required = True
elif supplementary_file_choice == Phase.OFF:
del self.fields["supplementary_file"]
if publication_url_choice == Phase.REQUIRED:
self.fields["publication_url"].required = True
elif publication_url_choice == Phase.OFF:
del self.fields["publication_url"]
if algorithm_submission:
del self.fields["chunked_upload"]
self.fields["algorithm"].queryset = get_objects_for_user(
user,
f"{Algorithm._meta.app_label}.change_{Algorithm._meta.model_name}",
Algorithm,
).order_by("title")
else:
del self.fields["algorithm"]
self.fields["chunked_upload"].widget.user = user
self.fields["creator"].queryset = get_user_model().objects.filter(
pk=user.pk)
self.fields["creator"].initial = user
self.helper = FormHelper(self)
self.helper.layout.append(Submit("save", "Save"))
def clean_algorithm(self):
algorithm = self.cleaned_data["algorithm"]
if algorithm.latest_ready_image is None:
raise ValidationError(
"This algorithm does not have a usable container image. "
"Please add one and try again.")
return algorithm
def clean_creator(self):
creator = self.cleaned_data["creator"]
try:
user_is_verified = creator.verification.is_verified
except ObjectDoesNotExist:
user_is_verified = False
if self.creator_must_be_verified and not user_is_verified:
error_message = format_html(
"You must verify your account before you can make a "
"submission to this phase. Please "
'<a href="{}"> request verification here</a>.',
reverse("verifications:create"),
)
# Add this to the non-field errors as we use a HiddenInput
self.add_error(None, error_message)
raise ValidationError(error_message)
return creator
class Meta:
model = Submission
fields = submission_fields
widgets = {"creator": forms.HiddenInput}