Merge pull request #728 from hms-dbmi/development

Development

Author: b32147

CHANGELOG.md

@@ -1,3 +1,13 @@
+## [1.2.1-rc.1](https://github.com/hms-dbmi/hypatio-app/compare/v1.2.0...v1.2.1-rc.1) (2025-01-07)
+
+
+### Bug Fixes
+
+* **manage:** Checks for existing pending applications that might be linked to an agreement form from an institutional signer when granting access ([e096de7](https://github.com/hms-dbmi/hypatio-app/commit/e096de7870aff3667d029a899656fcffe1e913d4))
+* **projects:** Added a method to SignedAgreementForm to determine whether it's for an institutional signer or not ([ecf5f01](https://github.com/hms-dbmi/hypatio-app/commit/ecf5f017c7d6fcdea5f15229dc0924246e60e1b0))
+* **projects:** Set to use method on SignedAgreementForm to determine when to handle SignedAgreementForms from institutional signers ([48b4802](https://github.com/hms-dbmi/hypatio-app/commit/48b4802abb5b04c3834a94ab784ee8dfa93a8067))
+* **requirements:** Updated Python requirements ([b04f0ec](https://github.com/hms-dbmi/hypatio-app/commit/b04f0ecd0174558dcba327e473fe0887fcafa18b))
+
 # [1.2.0](https://github.com/hms-dbmi/hypatio-app/compare/v1.1.2...v1.2.0) (2024-10-17)
 
 

app/manage/api.py

@@ -41,6 +41,7 @@
 from projects.models import TeamComment
 from projects.serializers import HostedFileSerializer, HostedFileDownloadSerializer
 from projects.models import AGREEMENT_FORM_TYPE_MODEL, AGREEMENT_FORM_TYPE_FILE
+from projects.models import InstitutionalOfficial
 
 # Get an instance of a logger
 logger = logging.getLogger(__name__)
@@ -1157,6 +1158,54 @@ def grant_view_permission(request, project_key, user_email):
         participant = project.participant_set.get(user__email=user_email)
         participant.permission = 'VIEW'
         participant.save()
+
+        # Check if this project allows institutional signers
+        if project.institutional_signers:
+
+            # Check if this is a signing official
+            try:
+                official = InstitutionalOfficial.objects.get(
+                    project=project,
+                    user=participant.user,
+                )
+
+                # Iterate linked members
+                for member_email in official.member_emails:
+
+                    logger.debug(f"Institutional signer/{participant.user.email}: Checking for existing linked member '{member_email}'")
+
+                    # Check if a participant exists for this email with no VIEW permission
+                    if Participant.objects.filter(project=project, user__email=member_email).exclude(permission="VIEW").exists():
+
+                        # Fetch them
+                        member_participant = Participant.objects.get(project=project, user__email=member_email)
+
+                        # Approve signed agreement forms
+                        for signed_agreement_form in SignedAgreementForm.objects.filter(project=project, user=member_participant.user):
+
+                            # If allows institutional signers, auto-approve
+                            if signed_agreement_form.agreement_form.institutional_signers:
+
+                                signed_agreement_form.status = "A"
+                                signed_agreement_form.save()
+
+                        # Grant this user access immediately if all agreement forms are accepted
+                        for agreement_form in project.agreement_forms.all():
+                            if not SignedAgreementForm.objects.filter(
+                                agreement_form=agreement_form,
+                                project=project,
+                                user=member_participant.user,
+                                status="A"
+                                ):
+                                break
+                        else:
+
+                            # Call this method to process the access
+                            grant_view_permission(request, project_key, member_email)
+
+            except ObjectDoesNotExist:
+                pass
+
     except Exception as e:
         logger.exception(
             '[HYPATIO][DEBUG][grant_view_permission] User {user} could not have permission added to project {project_key}: {e}'.format(
@@ -1226,6 +1275,26 @@ def remove_view_permission(request, project_key, user_email):
         participant = project.participant_set.get(user__email=user_email)
         participant.permission = None
         participant.save()
+
+        # Check if this project allows institutional signers
+        if project.institutional_signers:
+
+            # Check if this is a signing official
+            try:
+                official = InstitutionalOfficial.objects.get(
+                    project=project,
+                    user=participant.user,
+                )
+
+                # Iterate linked members
+                for member_email in official.member_emails:
+
+                    # Remove their access
+                    remove_view_permission(request, project_key, member_email)
+
+            except ObjectDoesNotExist:
+                pass
+
     except Exception as e:
         logger.exception(
             '[HYPATIO][ERROR][grant_view_permission] User {user} could not have permission remove from project {project_key}: {e}'.format(

app/projects/models.py

@@ -2,6 +2,7 @@
 import re
 import importlib
 from datetime import datetime
+from typing import Optional, Tuple
 
 import boto3
 from botocore.exceptions import ClientError
@@ -489,6 +490,37 @@ class Meta:
         verbose_name_plural = 'Signed Agreement Forms'
 
 
+    def get_institutional_signer_details(self) -> Optional[Tuple[str, str, list[str]]]:
+        """
+        Checks the SignedAgreementForm to see if it has been signed by an institutional official.
+        If so, it returns the name of the institution and email of the institutional official along with a list of
+        emails for the members they are representing.
+
+        :returns: A tuple containing the institution name, official email, and a list of member emails if this is an
+                  institutional signer; otherwise tuple of None, None, None
+        :rtype: Optional[Tuple[str, str, list[str]]], defaults to Tuple[None, None, None]
+        """
+        if self.agreement_form.institutional_signers:
+
+            # Fields should contain whether this is an institutional official or not
+            if self.fields and self.fields.get("registrant_is", "").lower() == "official":
+
+                # Ensure member emails is a list
+                member_emails = self.fields.get("member_emails", [])
+                if isinstance(member_emails, str):
+                    member_emails = [member_emails]
+                elif not isinstance(member_emails, list):
+                    raise ValidationError(f"Unhandled state of 'member_emails' field: {type(member_emails)}/{member_emails}")
+
+                # Cleanup emails to remove whitespace, if any
+                member_emails = [email.strip() for email in member_emails]
+
+                # Return values
+                return self.fields["institute_name"], self.user.email, member_emails
+
+        return None, None, None
+
+
 class DataUseReportRequest(models.Model):
     """
     This model describes a request for a participant to report on data use.

app/projects/signals.py

@@ -133,16 +133,22 @@ def signed_agreement_form_pre_save_handler(sender, **kwargs):
     logger.debug(f"Pre-save: {instance}")
 
     # Check for specific types of forms that require additional handling
-    if instance.status == "A" and instance.agreement_form.short_name == "4ce-dua" \
-        and instance.fields.get("registrant-is") == "official":
-        logger.debug(f"Pre-save institutional official: {instance}")
-
-        # Create official and member objects
-        official = InstitutionalOfficial.objects.create(
-            user=instance.user,
-            institution=instance.fields["institute-name"],
-            project=instance.project,
-            signed_agreement_form=instance,
-            member_emails=instance.fields["member-emails"],
-        )
-        official.save()
+    institute_name, official_email, member_emails = instance.get_institutional_signer_details()
+    if instance.status == "A" and institute_name and official_email and member_emails:
+        logger.debug(f"Pre-save institutional official AgreementForm: {instance}")
+
+        # Ensure they don't already exist
+        if InstitutionalOfficial.objects.filter(user=instance.user, project=instance.project).exists():
+            logger.debug(f"InstitutionalOfficial already exists for {instance.user}/{instance.project}")
+
+        else:
+
+            # Create official and member objects
+            official = InstitutionalOfficial.objects.create(
+                user=instance.user,
+                institution=institute_name,
+                project=instance.project,
+                signed_agreement_form=instance,
+                member_emails=member_emails,
+            )
+            official.save()

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "dbmi-data-portal"
-version = "1.2.0"
+version = "1.2.1-rc.1"
 description = "A portal for hosting and managing access to DBMI-provided datasets"
 readme = "README.md"
 requires-python = ">=3.9"