First draft at #346

src/edrnsite.content/src/edrnsite/content/_biomarker_submission_form.py

@@ -0,0 +1,187 @@
+# encoding: utf-8
+
+'''😌 EDRN Site Content: metadata collection form.'''
+
+from .base_forms import (
+    AbstractEDRNForm, pi_site_choices, discipline_choices, data_category_choices, ALL_USERS_DN,
+    protocol_choices, organ_choices
+)
+from .base_models import AbstractFormPage
+from captcha.fields import ReCaptchaField
+from django import forms
+from .tasks import send_email
+from django.conf import settings
+from eke.knowledge.models import Person, Protocol, BodySystem, Site
+from io import StringIO
+from urllib.parse import urlparse
+from wagtail.admin.panels import FieldPanel, FieldRowPanel, MultiFieldPanel
+from wagtail.contrib.forms.models import EmailFormMixin
+from django.core.exceptions import ValidationError
+
+
+class BiomarkerSubmissionForm(AbstractEDRNForm):
+    '''Form to make biomarkers submit.'''
+
+    @staticmethod
+    def get_encoding_type() -> str:
+        return 'multipart/form-data'
+
+    template_name = 'edrnsite.content/biomarker-submission-form.html'
+    _file_help_text = "A file describing new biomarker(s); PDF preferred but Word is acceptable. If you use this option, there's no need to enter any text in the next box." 
+    _text_help_text = "Describe the biomarker(s) being submitted. If you use this option, there's no need to upload a file."
+
+    submitter_name = forms.CharField(
+        label='Submitter Name', help_text='The name of the person submitting a biomarker.', max_length=100
+    )
+    submitter_email = forms.EmailField(label='Submitter Email', help_text="Submitter's email address.")
+
+    biomarker_file = forms.FileField(
+        label='Biomarker(s) File', help_text=_file_help_text, allow_empty_file=False, required=False
+    )
+    biomarker_text = forms.CharField(
+        label='Biomarker(s) Researched', help_text=_text_help_text, required=False, max_length=5000,
+        widget=forms.Textarea
+    )
+    pi_site = forms.ChoiceField(label='Lead PI and Institution', help_text='Select a primary investigator and the institution to which they belong.', choices=pi_site_choices)
+
+    protocol = forms.ChoiceField(
+        label='Protocol', help_text='Select the protocol that generated the data.', choices=protocol_choices
+    )
+    organs = forms.MultipleChoiceField(
+        label='Organs', help_text='Select the body systems. You can select more than one.', choices=organ_choices
+    )
+    biomarker_types = forms.MultipleChoiceField(
+        widget=forms.CheckboxSelectMultiple,
+        required=True,
+        label='Biomarker Type',
+        help_text='Select the kinds of biomarker(s). You can select more than one, but check at least one.',
+        choices=(
+            ('molecular', 'Molecular'),
+            ('histologic', 'Histologic'),
+            ('radiographic', 'Radiographic'),
+            ('physiological', 'Physiological')
+        )
+    )
+    molecular_subtype = forms.ChoiceField(
+        widget=forms.RadioSelect,
+        required=False,
+        label='Molecular Subtype',
+        help_text='If you selected "Molecular" as a type, please indicate the subtype by checking a box here.',
+        choices=(
+            ('chemical', 'Chemical'),
+            ('protein', 'Protein'),
+            ('dna', 'DNA (Genetics)'),
+            ('karyotypic', 'Karyotypic'),
+        )
+    )
+
+    if not settings.DEBUG:
+        captcha = ReCaptchaField()
+
+    def clean(self):
+        cleaned_data = super().clean()
+
+        f, t = cleaned_data.get('biomarker_file'), cleaned_data.get('biomarker_text')
+        if not f and not t:
+            raise ValidationError('You must either provide a file or fill in the text box describing biomarkers.')
+        elif f and t:
+            raise ValidationError('Please provide only a file or fill in the text box describing biomarkers—not both.')
+
+        t, st = cleaned_data.get('biomarker_types'), cleaned_data.get('molecular_subtype')
+        if t and 'molecular' in t and not st:
+            raise ValidationError('If you select "molecular" as a type, you must also select a subtype.')
+
+        return cleaned_data
+
+
+class BiomarkerSubmissionFormPage(AbstractFormPage, EmailFormMixin):
+    '''Page containing a form for making biomarkers submit.'''
+    page_description = 'Page containing a form for biomarker submission'
+
+    content_panels = AbstractFormPage.content_panels + [
+        MultiFieldPanel([
+            FieldRowPanel([
+                FieldPanel('from_address', classname='col6', help_text='From whom this email will originate'),
+                FieldPanel('to_address', classname='col6', help_text='Who should receive this email; commas in between multiple addresses')
+            ]),
+            FieldPanel('subject')
+        ], 'Email')
+    ]
+
+    def get_form(self) -> type:
+        return BiomarkerSubmissionForm
+
+    def get_initial_values(self, request) -> dict:
+        initial = super().get_initial_values(request)
+        if request.user.is_authenticated:
+            try:
+                name = request.user.ldap_user.attrs['cn'][0]
+            except (AttributeError, KeyError, IndexError, TypeError):
+                name = f'{request.user.first_name} {request.user.last_name}'.strip()
+            initial['submitter_name'] = name
+            try:
+                email = request.user.ldap_user.attrs['mail'][0]
+            except (AttributeError, KeyError, IndexError, TypeError):
+                email = request.user.email
+            initial['submitter_email'] = email
+        return initial
+
+    def get_landing_page(self) -> str:
+        return 'edrnsite.content/biomarker-submission-landing.html'
+
+    def _code(self, identifier: str) -> str:
+        return urlparse(identifier).path.split('/')[-1]
+
+    def process_submission(self, form: forms.Form) -> dict:
+        # The ``EmailFormMixin`` nicely provides both the from/to/subject fields and also this handy function:
+        #     self.send_mail(form)
+        # which we can't use since it doesn't handle attachments.
+        if not settings.DEBUG:
+            del form.cleaned_data['captcha']
+        data = form.cleaned_data
+        rendered = f'Submitter Name: {data["submitter_name"]}\nSubmitter Email: {data["submitter_email"]}'
+
+        site_id, pi_id = data['pi_site'].split('-')
+        pi = Person.objects.filter(personID=pi_id).first()
+        if pi:
+            rendered += f'\nPI ID: {pi_id}'
+            rendered += f'\nPI Name: {pi.title}'
+        site = Site.objects.filter(dmccSiteID=site_id).first()
+        if site:
+            rendered += f'\nInstitution ID: {site_id}'
+            rendered += f'\nInstitution Name: {site.title}'
+
+        protocol = Protocol.objects.filter(identifier=data['protocol']).first()
+        if protocol:
+            rendered += f'\nProtocol ID: {self._code(data["protocol"])}'
+            rendered += f'\nProtocol Name: {protocol.title}'
+
+        organ_identifiers = data.get('organs')
+        if organ_identifiers:
+            names = [i for i in BodySystem.objects.filter(
+                identifier__in=organ_identifiers
+            ).order_by('title').values_list('title', flat=True)]
+            rendered += f'\nOrgans: {", ".join(names)}'
+
+        types = data.get('biomarker_types')
+        if types:
+            rendered += f'\nBiomarker Types: {", ".join(types)}'
+
+        subtype = data.get('molecular_subtype')
+        if subtype:
+            rendered += f'\nMolecular Subtype: {subtype}'
+
+        biomarker_file = form.cleaned_data['biomarker_file']
+        if biomarker_file:
+            rendered += '\nA biomarker file was uploaded; it is attached'
+            attachment_data = biomarker_file.read()
+            send_email(
+                self.from_address, self.to_address.split(','), self.subject, rendered,
+                {'name': biomarker_file.name, 'data': attachment_data, 'content_type': biomarker_file.content_type}, 10
+            )
+        else:
+            rendered += f'\nBiomarker(s) Researched:\n{data["biomarker_text"]}'
+            send_email(self.from_address, self.to_address.split(','), self.subject, rendered, None, 10)
+
+        # And we're done
+        return {'name': form.cleaned_data['submitter_name'], 'email': form.cleaned_data['submitter_email']}

src/edrnsite.content/src/edrnsite/content/_metadata_collection_form.py

@@ -3,7 +3,8 @@
 '''😌 EDRN Site Content: metadata collection form.'''
 
 from .base_forms import (
-    AbstractEDRNForm, pi_site_choices, discipline_choices, data_category_choices, ALL_USERS_DN
+    AbstractEDRNForm, pi_site_choices, discipline_choices, data_category_choices, ALL_USERS_DN,
+    protocol_choices, organ_choices
 )
 from .base_models import AbstractFormPage
 from captcha.fields import ReCaptchaField
@@ -17,14 +18,6 @@
 from wagtail.contrib.forms.models import EmailFormMixin
 
 
-def _protocols():
-    return [(i.identifier, f'{i.title} ({i.protocolID})') for i in Protocol.objects.all().order_by('title')]
-
-
-def _organs():
-    return [(i.identifier, i.title) for i in BodySystem.objects.all().order_by('title')]
-
-
 def _species():
     species = (
         'Homo sapiens',
@@ -47,7 +40,7 @@ class MetadataCollectionForm(AbstractEDRNForm):
     custodian = forms.CharField(label='Data Custodian', help_text='Genrally, this is your name.')
     custodian_email = forms.EmailField(label='Data Custodian Email', help_text='Email address for the data custodian.')
     pi_site = forms.ChoiceField(label='Lead PI and Institution', help_text='Select a primary investigator and the institution to which they belong.', choices=pi_site_choices)
-    protocol = forms.ChoiceField(label='Protocol', help_text='Select the protocol that generated the data.', choices=_protocols)
+    protocol = forms.ChoiceField(label='Protocol', help_text='Select the protocol that generated the data.', choices=protocol_choices)
     biomarkers_researched = forms.CharField(
         required=False, label='Biomarkers Researched', widget=forms.Textarea, max_length=5000,
         help_text='Describe the cancer biomarkers being researched by this data.'
@@ -68,7 +61,7 @@ class MetadataCollectionForm(AbstractEDRNForm):
         label='Other Data Category', help_text='If you selected Other above ↑, enter the category here.',
         max_length=100, required=False
     )
-    organ = forms.ChoiceField(label='Organ', help_text='Select the body system.', choices=_organs)
+    organ = forms.ChoiceField(label='Organ', help_text='Select the body system.', choices=organ_choices)
     species = forms.ChoiceField(label='Species', help_text='Enter the species.', choices=_species)
     private = forms.BooleanField(required=False, label='Private Data', help_text='Check this box ↑ if this data collection is private.')
     access_groups = forms.CharField(

src/edrnsite.content/src/edrnsite/content/_spec_ref_set_form.py

@@ -13,7 +13,6 @@
 from wagtail.admin.panels import FieldPanel, FieldRowPanel, MultiFieldPanel
 from wagtail.contrib.forms.models import EmailFormMixin
 from wagtail.fields import RichTextField
-from django.utils.text import slugify
 
 
 _preamble_default = (

src/edrnsite.content/src/edrnsite/content/base_forms.py

@@ -4,12 +4,19 @@
 
 from django import forms
 from django.forms.utils import ErrorList
-from eke.knowledge.models import Site, Person
-
+from eke.knowledge.models import Site, Person, Protocol, BodySystem
 
 ALL_USERS_DN = 'cn=All Users,dc=edrn,dc=jpl,dc=nasa,dc=gov'
 
 
+def protocol_choices():
+    return [(i.identifier, f'{i.title} ({i.protocolID})') for i in Protocol.objects.all().order_by('title')]
+
+
+def organ_choices():
+    return [(i.identifier, i.title) for i in BodySystem.objects.all().order_by('title')]
+
+
 def institution_choices():
     '''Vocabulary for choices of institution in choice fields.'''
     return [(i.identifier, f'{i.title} ({i.dmccSiteID})') for i in Site.objects.all().order_by('title')]

src/edrnsite.content/src/edrnsite/content/base_models.py

@@ -93,4 +93,3 @@ class BaseEmailForm(Page):
     ]
     class Meta:
         abstract = True
-

src/edrnsite.content/src/edrnsite/content/forms.py

@@ -2,11 +2,13 @@
 
 '''😌 EDRN Site Content: Django forms.'''
 
-from ._metadata_collection_form import MetadataCollectionForm  # noqa
-from ._spec_ref_set_form import SpecimenReferenceSetRequestForm  # noqa
+from ._metadata_collection_form import MetadataCollectionForm  # noqa: F401
+from ._spec_ref_set_form import SpecimenReferenceSetRequestForm  # noqa: F401
+from ._biomarker_submission_form import BiomarklerSubmissionForm  # noqa: F401
 
 
 __all__ = (
+    BiomarklerSubmissionForm,
     MetadataCollectionForm,
     SpecimenReferenceSetRequestForm,
 )

src/edrnsite.content/src/edrnsite/content/migrations/0034_biomarkersubmissionformpage.py

@@ -0,0 +1,71 @@
+# Generated by Django 4.2.10 on 2024-03-08 20:22
+
+from django.db import migrations, models
+import django.db.models.deletion
+import wagtail.contrib.forms.models
+import wagtail.fields
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("wagtailcore", "0089_log_entry_data_json_null_to_object"),
+        ("edrnsitecontent", "0033_alter_homepage_body"),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name="BiomarkerSubmissionFormPage",
+            fields=[
+                (
+                    "page_ptr",
+                    models.OneToOneField(
+                        auto_created=True,
+                        on_delete=django.db.models.deletion.CASCADE,
+                        parent_link=True,
+                        primary_key=True,
+                        serialize=False,
+                        to="wagtailcore.page",
+                    ),
+                ),
+                (
+                    "to_address",
+                    models.CharField(
+                        blank=True,
+                        help_text="Optional - form submissions will be emailed to these addresses. Separate multiple addresses by comma.",
+                        max_length=255,
+                        validators=[wagtail.contrib.forms.models.validate_to_address],
+                        verbose_name="to address",
+                    ),
+                ),
+                (
+                    "from_address",
+                    models.EmailField(
+                        blank=True, max_length=255, verbose_name="from address"
+                    ),
+                ),
+                (
+                    "subject",
+                    models.CharField(
+                        blank=True, max_length=255, verbose_name="subject"
+                    ),
+                ),
+                (
+                    "intro",
+                    wagtail.fields.RichTextField(
+                        blank=True,
+                        help_text="Introductory text to appear above the form",
+                    ),
+                ),
+                (
+                    "outro",
+                    wagtail.fields.RichTextField(
+                        blank=True, help_text="Text to appear below the form"
+                    ),
+                ),
+            ],
+            options={
+                "abstract": False,
+            },
+            bases=("wagtailcore.page", models.Model),
+        ),
+    ]

src/edrnsite.content/src/edrnsite/content/models.py

@@ -3,6 +3,7 @@
 '''😌 EDRN site content's models.'''
 
 
+from ._biomarker_submission_form import BiomarkerSubmissionFormPage  # noqa: F401
 from ._dataset_metadata_form import DatasetMetadataFormPage  # noqa: F401
 from ._metadata_collection_form import MetadataCollectionFormPage  # noqa: F401
 from ._spec_ref_set_form import SpecimenReferenceSetRequestFormPage  # noqa: F401