From 85ae464bc0157a7c1cb94347f5eb794b1747ff69 Mon Sep 17 00:00:00 2001 From: Adrienne Stilp Date: Tue, 25 Jun 2024 10:53:44 -0700 Subject: [PATCH 01/10] Add button to update dbGaPApplication collaborators Add a button on the dbGaPApplicationDetail view to update the collaborators for that application. --- primed/dbgap/tests/test_views.py | 4 ++++ primed/templates/dbgap/dbgapapplication_detail.html | 1 + 2 files changed, 5 insertions(+) diff --git a/primed/dbgap/tests/test_views.py b/primed/dbgap/tests/test_views.py index 10c698dd..dad3f2f3 100644 --- a/primed/dbgap/tests/test_views.py +++ b/primed/dbgap/tests/test_views.py @@ -1452,6 +1452,7 @@ def test_staff_edit_links(self): self.assertContains( response, reverse("anvil_consortium_manager:managed_groups:detail", args=[self.obj.anvil_access_group.name]) ) + self.assertContains(response, reverse("dbgap:dbgap_applications:update", args=[self.obj.dbgap_project_id])) def test_staff_view_links(self): """No edit links if staff user only has view permission.""" @@ -1475,6 +1476,7 @@ def test_staff_view_links(self): self.assertContains( response, reverse("anvil_consortium_manager:managed_groups:detail", args=[self.obj.anvil_access_group.name]) ) + self.assertNotContains(response, reverse("dbgap:dbgap_applications:update", args=[self.obj.dbgap_project_id])) def test_links_pi(self): """Links seen by PI are correct.""" @@ -1500,6 +1502,7 @@ def test_links_pi(self): self.assertNotContains( response, reverse("anvil_consortium_manager:managed_groups:detail", args=[self.obj.anvil_access_group.name]) ) + self.assertNotContains(response, reverse("dbgap:dbgap_applications:update", args=[self.obj.dbgap_project_id])) def test_links_collaborators(self): """Links seen by collaborators are correct.""" @@ -1526,6 +1529,7 @@ def test_links_collaborators(self): self.assertNotContains( response, reverse("anvil_consortium_manager:managed_groups:detail", args=[self.obj.anvil_access_group.name]) ) + self.assertNotContains(response, reverse("dbgap:dbgap_applications:update", args=[self.obj.dbgap_project_id])) def test_table_classes(self): """The table classes are correct.""" diff --git a/primed/templates/dbgap/dbgapapplication_detail.html b/primed/templates/dbgap/dbgapapplication_detail.html index dd3363fe..37cf6b86 100644 --- a/primed/templates/dbgap/dbgapapplication_detail.html +++ b/primed/templates/dbgap/dbgapapplication_detail.html @@ -99,6 +99,7 @@

{% if show_acm_edit_links %} Update data access requests + Update collaborators {% endif %} {% if show_acm_view_links %} Audit workspace access From ca73be30e2848e0d63fcd5917f03b72f3d88d742 Mon Sep 17 00:00:00 2001 From: Adrienne Stilp Date: Tue, 25 Jun 2024 11:01:38 -0700 Subject: [PATCH 02/10] Update example data scripts so both CDSA and dbGaP ones can be added Instead of just creating a Study or StudySite, first check if it exists and get the object if it does. This means that the dbgap example script can be run, and then the CDSA example script can be run afterward, or vice versa. --- add_cdsa_example_data.py | 47 ++++++++++++++++++++++++++------------- add_dbgap_example_data.py | 15 ++++++++++--- 2 files changed, 44 insertions(+), 18 deletions(-) diff --git a/add_cdsa_example_data.py b/add_cdsa_example_data.py index eb26c72d..105233ba 100644 --- a/add_cdsa_example_data.py +++ b/add_cdsa_example_data.py @@ -37,11 +37,28 @@ dum = DataUseModifier.objects.get(abbreviation="NPU") # Create some study sites. -StudySiteFactory.create(short_name="CC", full_name="Coordinating Center") -StudySiteFactory.create(short_name="CARDINAL", full_name="CARDINAL") +try: + cc = StudySite.objects.get(short_name="CC") +except StudySite.DoesNotExist: + cc = StudySiteFactory.create(short_name="CC", full_name="Coordinating Center") +try: + cardinal = StudySite.objects.get(short_name="CARDINAL") +except StudySite.DoesNotExist: + cardinal = StudySiteFactory.create(short_name="CARDINAL", full_name="CARDINAL") + # Create some studies. -StudyFactory.create(short_name="Amish", full_name="Amish") -StudyFactory.create(short_name="MESA", full_name="MESA") +try: + amish = Study.objects.get(short_name="Amish") +except Study.DoesNotExist: + amish = StudyFactory.create(short_name="Amish", full_name="Amish") +try: + mesa = Study.objects.get(short_name="MESA") +except Study.DoesNotExist: + mesa = StudyFactory.create(short_name="MESA", full_name="MESA") +try: + aric = Study.objects.get(short_name="ARIC") +except Study.DoesNotExist: + aric = Study.objects.create(short_name="ARIC", full_name="Atherosclerosis Risk in Communities") # Create some CDSAs cdsa_1001 = factories.MemberAgreementFactory.create( @@ -51,7 +68,7 @@ signed_agreement__representative_role="Contact PI", is_primary=True, signed_agreement__version=v10, - study_site=StudySite.objects.get(short_name="CC"), + study_site=cc, ) GroupGroupMembershipFactory.create(parent_group=cdsa_group, child_group=cdsa_1001.signed_agreement.anvil_access_group) @@ -62,7 +79,7 @@ signed_agreement__representative_role="Contact PI", is_primary=True, signed_agreement__version=v10, - study_site=StudySite.objects.get(short_name="CARDINAL"), + study_site=cardinal, ) GroupGroupMembershipFactory.create(parent_group=cdsa_group, child_group=cdsa_1002.signed_agreement.anvil_access_group) @@ -73,7 +90,7 @@ signed_agreement__representative_role="Co-PI", is_primary=False, signed_agreement__version=v10, - study_site=StudySite.objects.get(short_name="CARDINAL"), + study_site=cardinal, ) GroupGroupMembershipFactory.create(parent_group=cdsa_group, child_group=cdsa_1003.signed_agreement.anvil_access_group) @@ -84,7 +101,7 @@ signed_agreement__representative_role="Co-I", is_primary=False, signed_agreement__version=v11, - study_site=StudySite.objects.get(short_name="CARDINAL"), + study_site=cardinal, ) GroupGroupMembershipFactory.create(parent_group=cdsa_group, child_group=cdsa_1004.signed_agreement.anvil_access_group) @@ -93,7 +110,7 @@ signed_agreement__representative=User.objects.get(name="Brackie Mitchell"), signed_agreement__signing_institution="UMaryland", signed_agreement__representative_role="Study PI", - study=Study.objects.get(short_name="Amish"), + study=amish, signed_agreement__version=v10, ) GroupGroupMembershipFactory.create(parent_group=cdsa_group, child_group=cdsa_1005.signed_agreement.anvil_access_group) @@ -103,7 +120,7 @@ signed_agreement__representative=UserFactory.create(name="Robyn"), signed_agreement__representative_role="DCC PI", signed_agreement__signing_institution="UW", - study=Study.objects.get(short_name="MESA"), + study=mesa, signed_agreement__version=v10, additional_limitations="This data can only be used for testing the app.", requires_study_review=True, @@ -116,7 +133,7 @@ signed_agreement__signing_institution="JHU", signed_agreement__representative_role="Field Center PI", is_primary=False, - study=Study.objects.get(short_name="MESA"), + study=mesa, signed_agreement__version=v10, ) GroupGroupMembershipFactory.create(parent_group=cdsa_group, child_group=cdsa_1007.signed_agreement.anvil_access_group) @@ -127,7 +144,7 @@ signed_agreement__signing_institution="Lundquist", signed_agreement__representative_role="Analysis Center PI", is_primary=False, - study=Study.objects.get(short_name="MESA"), + study=mesa, signed_agreement__version=v10, ) GroupGroupMembershipFactory.create(parent_group=cdsa_group, child_group=cdsa_1008.signed_agreement.anvil_access_group) @@ -209,7 +226,7 @@ cdsa_workspace_1 = factories.CDSAWorkspaceFactory.create( workspace__billing_project__name="demo-primed-cdsa", workspace__name="DEMO_PRIMED_CDSA_MESA_1", - study=Study.objects.get(short_name="MESA"), + study=mesa, data_use_permission=dup, ) GroupGroupMembershipFactory.create( @@ -222,7 +239,7 @@ cdsa_workspace_2 = factories.CDSAWorkspaceFactory.create( workspace__billing_project__name="demo-primed-cdsa", workspace__name="DEMO_PRIMED_CDSA_MESA_2", - study=Study.objects.get(short_name="MESA"), + study=mesa, data_use_permission=dup, additional_limitations="Additional limitations for workspace.", ) @@ -233,6 +250,6 @@ cdsa_workspace_3 = factories.CDSAWorkspaceFactory.create( workspace__billing_project__name="demo-primed-cdsa", workspace__name="DEMO_PRIMED_CDSA_ARIC_1", - study=Study.objects.create(short_name="ARIC", full_name="Atherosclerosis Risk in Communities"), + study=aric, data_use_permission=dup, ) diff --git a/add_dbgap_example_data.py b/add_dbgap_example_data.py index 20a1054b..854fa973 100644 --- a/add_dbgap_example_data.py +++ b/add_dbgap_example_data.py @@ -9,9 +9,18 @@ from primed.users.tests.factories import UserFactory # Studies -fhs = StudyFactory.create(short_name="FHS", full_name="Framingham Heart Study") -mesa = StudyFactory.create(short_name="MESA", full_name="Multi-Ethnic Study of Atherosclerosis") -aric = StudyFactory.create(short_name="ARIC", full_name="Atherosclerosis Risk in Communities") +try: + fhs = models.Study.objects.get(short_name="FHS") +except models.Study.DoesNotExist: + fhs = StudyFactory.create(short_name="FHS", full_name="Framingham Heart Study") +try: + mesa = models.Study.objects.get(short_name="MESA") +except models.Study.DoesNotExist: + mesa = StudyFactory.create(short_name="MESA", full_name="Multi-Ethnic Study of Atherosclerosis") +try: + aric = models.Study.objects.get(short_name="ARIC") +except models.Study.DoesNotExist: + aric = StudyFactory.create(short_name="ARIC", full_name="Atherosclerosis Risk in Communities") # dbGaP study accessions dbgap_study_accession_fhs = factories.dbGaPStudyAccessionFactory.create(dbgap_phs=7, studies=[fhs]) From 2f9e1d1e1d0295d7dd77d759d6df54af0978dab2 Mon Sep 17 00:00:00 2001 From: Adrienne Stilp Date: Tue, 25 Jun 2024 11:09:59 -0700 Subject: [PATCH 03/10] Add collaborators in example data to get dbGaP auditing --- add_dbgap_example_data.py | 27 ++++++++++++++++++++++++++- 1 file changed, 26 insertions(+), 1 deletion(-) diff --git a/add_dbgap_example_data.py b/add_dbgap_example_data.py index 854fa973..232b0790 100644 --- a/add_dbgap_example_data.py +++ b/add_dbgap_example_data.py @@ -1,7 +1,11 @@ # Temporary script to create some test data. # Run with: python manage.py shell < add_cdsa_example_data.py -from anvil_consortium_manager.tests.factories import GroupGroupMembershipFactory +from anvil_consortium_manager.tests.factories import ( + AccountFactory, + GroupAccountMembershipFactory, + GroupGroupMembershipFactory, +) from primed.dbgap import models from primed.dbgap.tests import factories @@ -133,3 +137,24 @@ parent_group=workspace_fhs_1.workspace.authorization_domains.first(), child_group=dbgap_application_1.anvil_access_group, ) + +# Add the PI to the access group for the first application. +GroupAccountMembershipFactory.create( + group=dbgap_application_1.anvil_access_group, + account__user=dbgap_application_1.principal_investigator, +) +# Add some collaborators for the first application. +users = UserFactory.create_batch(3) +dbgap_application_1.collaborators.add(users[0]) +GroupAccountMembershipFactory.create( + group=dbgap_application_1.anvil_access_group, + account__user=users[0], +) +# # Do not add as an collaborator so we can check auditing. +# dbgap_application_1.collaborators.add(users[1]) +GroupAccountMembershipFactory.create( + group=dbgap_application_1.anvil_access_group, + account__user=users[1], +) +dbgap_application_1.collaborators.add(users[2]) +AccountFactory.create(user=users[2], verified=True) From fd807d5732f472da5eeeec646f294f8187e3db4f Mon Sep 17 00:00:00 2001 From: Adrienne Stilp Date: Tue, 25 Jun 2024 11:10:28 -0700 Subject: [PATCH 04/10] Add new template for dbGaP collaborator update --- primed/dbgap/views.py | 3 +- ...dbgapapplication_update_collaborators.html | 49 +++++++++++++++++++ 2 files changed, 51 insertions(+), 1 deletion(-) create mode 100644 primed/templates/dbgap/dbgapapplication_update_collaborators.html diff --git a/primed/dbgap/views.py b/primed/dbgap/views.py index 403d2ef3..8cb4f4a2 100644 --- a/primed/dbgap/views.py +++ b/primed/dbgap/views.py @@ -246,7 +246,8 @@ class dbGaPApplicationUpdate(AnVILConsortiumManagerStaffEditRequired, SuccessMes model = models.dbGaPApplication form_class = forms.dbGaPApplicationUpdateForm - success_message = "dbGaP application successfully updated." + success_message = "dbGaP collaborators successfully updated." + template_name = "dbgap/dbgapapplication_update_collaborators.html" def get_object(self, queryset=None): queryset = self.get_queryset() diff --git a/primed/templates/dbgap/dbgapapplication_update_collaborators.html b/primed/templates/dbgap/dbgapapplication_update_collaborators.html new file mode 100644 index 00000000..0f77c4a0 --- /dev/null +++ b/primed/templates/dbgap/dbgapapplication_update_collaborators.html @@ -0,0 +1,49 @@ +{% extends "anvil_consortium_manager/__object_detail.html" %} +{% load crispy_forms_tags %} + +{% block title %}New dbGaP application{% endblock %} + + +{% block panel %} +

+
dbGaP PI
+ + {{ object.principal_investigator.name }} + +
+
dbGaP Project ID
{{ object.dbgap_project_id }}
+
AnVIL access Group
+ {% if show_acm_view_links %} + {{ object.anvil_access_group }} + {% else %} + {{ object.anvil_access_group }} + {% endif %} + +
+
Date created
{{ object.created }}
+
Date modified
{{ object.modified }}
+
Last DAR update
+ {% if latest_snapshot %} + {{ latest_snapshot.created }} + {% else %} + — + {% endif %} +
+
+{% endblock panel %} + +{% block after_panel %} +
+ + {% csrf_token %} + {{ form|crispy }} + + +
+ +{% endblock after_panel %} + + +{% block inline_javascript %} + {{ form.media }} +{% endblock inline_javascript %} From c62fe029e50bc1bf8f7407ff34a6a633f05d9d3c Mon Sep 17 00:00:00 2001 From: Adrienne Stilp Date: Tue, 25 Jun 2024 11:22:19 -0700 Subject: [PATCH 05/10] Fix title and remove some details from template --- ...dbgapapplication_update_collaborators.html | 19 +------------------ 1 file changed, 1 insertion(+), 18 deletions(-) diff --git a/primed/templates/dbgap/dbgapapplication_update_collaborators.html b/primed/templates/dbgap/dbgapapplication_update_collaborators.html index 0f77c4a0..a0e43812 100644 --- a/primed/templates/dbgap/dbgapapplication_update_collaborators.html +++ b/primed/templates/dbgap/dbgapapplication_update_collaborators.html @@ -1,7 +1,7 @@ {% extends "anvil_consortium_manager/__object_detail.html" %} {% load crispy_forms_tags %} -{% block title %}New dbGaP application{% endblock %} +{% block title %}Update dbGaP collaborators{% endblock %} {% block panel %} @@ -12,23 +12,6 @@
dbGaP Project ID
{{ object.dbgap_project_id }}
-
AnVIL access Group
- {% if show_acm_view_links %} - {{ object.anvil_access_group }} - {% else %} - {{ object.anvil_access_group }} - {% endif %} - -
-
Date created
{{ object.created }}
-
Date modified
{{ object.modified }}
-
Last DAR update
- {% if latest_snapshot %} - {{ latest_snapshot.created }} - {% else %} - — - {% endif %} -
{% endblock panel %} From d60977866233be5f6736fdc92699c9ffd0bf6bb4 Mon Sep 17 00:00:00 2001 From: Adrienne Stilp Date: Fri, 28 Jun 2024 10:46:32 -0700 Subject: [PATCH 06/10] Show representative CDSAs on user detail page Show CDSAs where the user is the representative on the user detail page. Previously it was just showing accessors and uploaders. --- primed/templates/users/user_detail.html | 5 +++++ primed/users/tests/test_views.py | 13 +++++++++++++ primed/users/views.py | 2 +- 3 files changed, 19 insertions(+), 1 deletion(-) diff --git a/primed/templates/users/user_detail.html b/primed/templates/users/user_detail.html index c8e903fc..0261598e 100644 --- a/primed/templates/users/user_detail.html +++ b/primed/templates/users/user_detail.html @@ -124,6 +124,11 @@

{% if object == request.user %}My{% el
  • Consortium data sharing agreements
    • {% if signed_agreements %} {% for agreement in signed_agreements %} + {% if object == agreement.representative %} +
  • + Representative: {{ agreement }} +
    • + {% endif %} {% if object in agreement.accessors.all %}
  • Accessor: {{ agreement }} diff --git a/primed/users/tests/test_views.py b/primed/users/tests/test_views.py index 25720612..98e9d6b3 100644 --- a/primed/users/tests/test_views.py +++ b/primed/users/tests/test_views.py @@ -329,6 +329,19 @@ def test_cdsa_no_signed_agreements(self): self.assertEqual(response.status_code, 200) self.assertContains(response, "No CDSAs") + def test_cdsa_representative(self): + agreement = MemberAgreementFactory.create(signed_agreement__representative=self.user) + self.client.force_login(self.user) + response = self.client.get(self.user.get_absolute_url()) + self.assertEqual(response.status_code, 200) + self.assertContains(response, "Representative", count=1) + self.assertNotContains(response, "No CDSAs") + self.assertContains(response, agreement.signed_agreement.cc_id) + self.assertContains(response, agreement.get_absolute_url()) + self.assertIn("signed_agreements", response.context) + self.assertEqual(len(response.context["signed_agreements"]), 1) + self.assertIn(agreement.signed_agreement, response.context["signed_agreements"]) + def test_cdsa_accessor_on_one_member_agreement(self): agreement = MemberAgreementFactory.create() agreement.signed_agreement.accessors.add(self.user) diff --git a/primed/users/views.py b/primed/users/views.py index 8631101a..26458b59 100644 --- a/primed/users/views.py +++ b/primed/users/views.py @@ -26,7 +26,7 @@ def get_context_data(self, **kwargs): Q(principal_investigator=self.object) | Q(collaborators=self.object) ).distinct() context["signed_agreements"] = SignedAgreement.objects.filter( - Q(accessors=self.object) | Q(dataaffiliateagreement__uploaders=self.object) + Q(representative=self.object) | Q(accessors=self.object) | Q(dataaffiliateagreement__uploaders=self.object) ).distinct() return context From cec812ae203f50266d2020c55ad3a736533d8060 Mon Sep 17 00:00:00 2001 From: Adrienne Stilp Date: Fri, 28 Jun 2024 10:52:41 -0700 Subject: [PATCH 07/10] Update templates for investigator viewers Change the spacing in the details box such that the definition list has a better appearance. Add alert boxes to the accessors, uploaders, and collaborators tables indicating that the a can contact the CDSA if changes need to be made. --- .../cdsa/dataaffiliateagreement_detail.html | 34 ++++++++++--------- .../cdsa/memberagreement_detail.html | 27 ++++++++------- .../nondataaffiliateagreement_detail.html | 25 +++++++------- .../dbgap/dbgapapplication_detail.html | 3 +- 4 files changed, 47 insertions(+), 42 deletions(-) diff --git a/primed/templates/cdsa/dataaffiliateagreement_detail.html b/primed/templates/cdsa/dataaffiliateagreement_detail.html index 11756028..40ac0363 100644 --- a/primed/templates/cdsa/dataaffiliateagreement_detail.html +++ b/primed/templates/cdsa/dataaffiliateagreement_detail.html @@ -14,51 +14,51 @@ {% block panel %}
    -
    Coordinating Center ID
    {{ object.signed_agreement.cc_id }}
    -
    Representative
    +
    Coordinating Center ID
    {{ object.signed_agreement.cc_id }}
    +
    Representative
    {% if perms.anvil_consortium_manager.anvil_consortium_manager_staff_view %} {{ object.signed_agreement.representative.name }} {% else %} {{ object.signed_agreement.representative.name }} {% endif %}
    -
    Representative role
    {{ object.signed_agreement.representative_role }}
    -
    Signing institution
    {{ object.signed_agreement.signing_institution }}
    -
    Primary?
    +
    Representative role
    {{ object.signed_agreement.representative_role }}
    +
    Signing institution
    {{ object.signed_agreement.signing_institution }}
    +
    Primary?
    {% if object.is_primary %} Yes {% else %} No {% endif %}
    -
    Study review required?
    +
    Study review required?
    {% if object.requires_study_review %} Yes {% else %} No {% endif %}
    -
    Agreement version
    +
    Agreement version
    {% if perms.anvil_consortium_manager.anvil_consortium_manager_staff_view %} {{ object.signed_agreement.version }} {% else %} {{ object.signed_agreement.version }} {% endif %}
    -
    Status
    {{ object.signed_agreement.get_status_display }}
    -
    Date signed
    {{ object.signed_agreement.date_signed }}
    +
    Status
    {{ object.signed_agreement.get_status_display }}
    +
    Date signed
    {{ object.signed_agreement.date_signed }}
    -
    Study
    +
    Study
    {{ object.study }}
    -
    AnVIL access group
    +
    AnVIL access group
    {% if perms.anvil_consortium_manager.anvil_consortium_manager_staff_view %} {{ object.signed_agreement.anvil_access_group }} {% else %} {{ object.signed_agreement.anvil_access_group }} {% endif %}
    -
    AnVIL upload group
    +
    AnVIL upload group
    {% if perms.anvil_consortium_manager.anvil_consortium_manager_staff_view %} {{ object.anvil_upload_group }} {% else %} @@ -68,8 +68,8 @@ {% if perms.anvil_consortium_manager.anvil_consortium_manager_staff_view %}
    -
    Date created
    {{ object.created }}
    -
    Date modified
    {{ object.modified }}
    +
    Date created
    {{ object.created }}
    +
    Date modified
    {{ object.modified }}
    {% endif %}
    @@ -112,11 +112,12 @@

    This table shows accessors named for this signed agreement, their AnVIL account (if linked), and whether or not they are a member of the access group on AnVIL. Only accessors who are PRIMED members are included. An accessor must have linked their AnVIL account to be granted access to data on AnVIL. - If changes need to be made, please contact the CC.

    {% render_table tables.0 %} +

    If accessors need to be added or removed, please contact the CC at {{ DCC_CONTACT_EMAIL }}

    + @@ -140,11 +141,12 @@

    This table shows uploaders named for this signed agreement, their AnVIL account (if linked), and whether or not they are a member of the upload group on AnVIL. Only uploaders who are PRIMED members are included. An uploaders must have linked their AnVIL account to be granted access to data on AnVIL. - If changes need to be made, please contact the CC.

    {% render_table tables.1 %} +

    If uploaders need to be added or removed, please contact the CC at {{ DCC_CONTACT_EMAIL }}

    + diff --git a/primed/templates/cdsa/memberagreement_detail.html b/primed/templates/cdsa/memberagreement_detail.html index 277481ed..0d3e7f2d 100644 --- a/primed/templates/cdsa/memberagreement_detail.html +++ b/primed/templates/cdsa/memberagreement_detail.html @@ -14,41 +14,41 @@ {% block panel %}
    -
    Coordinating Center ID
    {{ object.signed_agreement.cc_id }}
    -
    Representative
    +
    Coordinating Center ID
    {{ object.signed_agreement.cc_id }}
    +
    Representative
    {% if perms.anvil_consortium_manager.anvil_consortium_manager_staff_view %} {{ object.signed_agreement.representative.name }} {% else %} {{ object.signed_agreement.representative.name }} {% endif %}
    -
    Representative role
    {{ object.signed_agreement.representative_role }}
    -
    Signing institution
    {{ object.signed_agreement.signing_institution }}
    -
    Primary?
    +
    Representative role
    {{ object.signed_agreement.representative_role }}
    +
    Signing institution
    {{ object.signed_agreement.signing_institution }}
    +
    Primary?
    {% if object.is_primary %} Yes {% else %} No {% endif %}
    -
    Agreement version
    +
    Agreement version
    {% if perms.anvil_consortium_manager.anvil_consortium_manager_staff_view %} {{ object.signed_agreement.version }} {% else %} {{ object.signed_agreement.version }} {% endif %}
    -
    Status
    {{ object.signed_agreement.get_status_display }}
    -
    Date signed
    {{ object.signed_agreement.date_signed }}
    +
    Status
    {{ object.signed_agreement.get_status_display }}
    +
    Date signed
    {{ object.signed_agreement.date_signed }}
    -
    Study site
    +
    Study site
    {% if perms.anvil_consortium_manager.anvil_consortium_manager_staff_view %} {{ object.study_site }} {% else %} {{ object.study_site }} {% endif %}
    -
    AnVIL access group
    +
    AnVIL access group
    {% if perms.anvil_consortium_manager.anvil_consortium_manager_staff_view %} {{ object.signed_agreement.anvil_access_group }} {% else %} @@ -58,8 +58,8 @@ {% if perms.anvil_consortium_manager.anvil_consortium_manager_staff_view %}
    -
    Date created
    {{ object.created }}
    -
    Date modified
    {{ object.modified }}
    +
    Date created
    {{ object.created }}
    +
    Date modified
    {{ object.modified }}
    {% endif %}
    @@ -83,11 +83,12 @@

    This table shows accessors named for this signed agreement, their AnVIL account (if linked), and whether or not they are a member of the access group on AnVIL. Only accessors who are PRIMED members are included. An accessor must have linked their AnVIL account to be granted access to data on AnVIL. - If changes need to be made, please contact the CC.

    {% render_table table %} +

    If accessors need to be added or removed, please contact the CC at {{ DCC_CONTACT_EMAIL }}

    + diff --git a/primed/templates/cdsa/nondataaffiliateagreement_detail.html b/primed/templates/cdsa/nondataaffiliateagreement_detail.html index 0988060e..d89a9ba4 100644 --- a/primed/templates/cdsa/nondataaffiliateagreement_detail.html +++ b/primed/templates/cdsa/nondataaffiliateagreement_detail.html @@ -14,28 +14,28 @@ {% block panel %}
    -
    Coordinating Center ID
    {{ object.signed_agreement.cc_id }}
    -
    Representative
    +
    Coordinating Center ID
    {{ object.signed_agreement.cc_id }}
    +
    Representative
    {% if perms.anvil_consortium_manager.anvil_consortium_manager_staff_view %} {{ object.signed_agreement.representative.name }} {% else %} {{ object.signed_agreement.representative.name }} {% endif %}
    -
    Representative role
    {{ object.signed_agreement.representative_role }}
    -
    Signing institution
    {{ object.signed_agreement.signing_institution }}
    -
    Agreement version
    +
    Representative role
    {{ object.signed_agreement.representative_role }}
    +
    Signing institution
    {{ object.signed_agreement.signing_institution }}
    +
    Agreement version
    {% if perms.anvil_consortium_manager.anvil_consortium_manager_staff_view %} {{ object.signed_agreement.version }} {% else %} {{ object.signed_agreement.version }} {% endif %}
    -
    Status
    {{ object.signed_agreement.get_status_display }}
    -
    Date signed
    {{ object.signed_agreement.date_signed }}
    +
    Status
    {{ object.signed_agreement.get_status_display }}
    +
    Date signed
    {{ object.signed_agreement.date_signed }}
    -
    Affiliation
    {{ object.affiliation }}
    -
    AnVIL access group
    +
    Affiliation
    {{ object.affiliation }}
    +
    AnVIL access group
    {% if perms.anvil_consortium_manager.anvil_consortium_manager_staff_view %} {{ object.signed_agreement.anvil_access_group }} {% else %} @@ -45,8 +45,8 @@ {% if perms.anvil_consortium_manager.anvil_consortium_manager_staff_view %}
    -
    Date created
    {{ object.created }}
    -
    Date modified
    {{ object.modified }}
    +
    Date created
    {{ object.created }}
    +
    Date modified
    {{ object.modified }}
    {% endif %}
    @@ -71,11 +71,12 @@

    This table shows accessors named for this signed agreement, their AnVIL account (if linked), and whether or not they are a member of the access group on AnVIL. Only accessors who are PRIMED members are included. An accessor must have linked their AnVIL account to be granted access to data on AnVIL. - If changes need to be made, please contact the CC.

    {% render_table table %} +

    If accessors need to be added or removed, please contact the CC at {{ DCC_CONTACT_EMAIL }}

    + diff --git a/primed/templates/dbgap/dbgapapplication_detail.html b/primed/templates/dbgap/dbgapapplication_detail.html index 37cf6b86..51e0ab2a 100644 --- a/primed/templates/dbgap/dbgapapplication_detail.html +++ b/primed/templates/dbgap/dbgapapplication_detail.html @@ -50,7 +50,6 @@

    This table shows collaborators named for this dbGaP application, their AnVIL account (if linked), and whether or not they are a member of the access group on AnVIL. Only collaborators who are PRIMED members are included. A collaborator must have linked their AnVIL account to be granted access to data on AnVIL. - If changes need to be made, please contact the CC.

    It is the PI's responsibility to ensure that all collaborators meet the dbGaP definition of internal collaborators or trainees/postdocs @@ -58,6 +57,8 @@

    {% render_table tables.1 %} +

    If collaborators need to be added or removed, please contact the CC at {{ DCC_CONTACT_EMAIL }}

    + From f6059c7d95d7c3962d0cef6920c42194e9cfeaaf Mon Sep 17 00:00:00 2001 From: Adrienne Stilp Date: Fri, 28 Jun 2024 13:45:04 -0700 Subject: [PATCH 08/10] Whitespace changes to get pre-commit.ci to run again It failed with what looks like some sort of server error somewhere. --- primed/templates/cdsa/memberagreement_detail.html | 1 + primed/templates/dbgap/dbgapapplication_detail.html | 3 ++- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/primed/templates/cdsa/memberagreement_detail.html b/primed/templates/cdsa/memberagreement_detail.html index 0d3e7f2d..342cb9b0 100644 --- a/primed/templates/cdsa/memberagreement_detail.html +++ b/primed/templates/cdsa/memberagreement_detail.html @@ -96,6 +96,7 @@

    {% endblock after_panel %} + {% block action_buttons %} {% if show_update_button %}

    diff --git a/primed/templates/dbgap/dbgapapplication_detail.html b/primed/templates/dbgap/dbgapapplication_detail.html index 51e0ab2a..f92ed40a 100644 --- a/primed/templates/dbgap/dbgapapplication_detail.html +++ b/primed/templates/dbgap/dbgapapplication_detail.html @@ -94,7 +94,8 @@

    {% endif %} - {% endblock after_panel %} +{% endblock after_panel %} + {% block action_buttons %}

    From 6dbdc89c164bf71edcd8ff23714a11aab107cd61 Mon Sep 17 00:00:00 2001 From: Adrienne Stilp Date: Fri, 28 Jun 2024 14:03:57 -0700 Subject: [PATCH 09/10] Update tests for definition list format change --- primed/cdsa/tests/test_views.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/primed/cdsa/tests/test_views.py b/primed/cdsa/tests/test_views.py index eb5a2290..bb498028 100644 --- a/primed/cdsa/tests/test_views.py +++ b/primed/cdsa/tests/test_views.py @@ -2879,7 +2879,7 @@ def test_response_is_primary(self): self.assertContains(response, "Primary?") self.assertContains( response, - """

    Primary?
    Yes
    """, # noqa: E501 + """
    Primary?
    Yes
    """, # noqa: E501 html=True, ) instance.is_primary = False @@ -2888,7 +2888,7 @@ def test_response_is_primary(self): self.assertContains(response, "Primary?") self.assertContains( response, - """
    Primary?
    No
    """, # noqa: E501 + """
    Primary?
    No
    """, # noqa: E501 html=True, ) @@ -4698,7 +4698,7 @@ def test_response_is_primary(self): self.assertContains(response, "Primary?") self.assertContains( response, - """
    Primary?
    Yes
    """, # noqa: E501 + """
    Primary?
    Yes
    """, # noqa: E501 html=True, ) instance.is_primary = False @@ -4707,7 +4707,7 @@ def test_response_is_primary(self): self.assertContains(response, "Primary?") self.assertContains( response, - """
    Primary?
    No
    """, # noqa: E501 + """
    Primary?
    No
    """, # noqa: E501 html=True, ) From 267deec64d33240f3d3b7f9ba6adcb2bca24e44a Mon Sep 17 00:00:00 2001 From: Adrienne Stilp Date: Fri, 28 Jun 2024 14:48:23 -0700 Subject: [PATCH 10/10] Fix additional definition list test --- primed/cdsa/tests/test_views.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/primed/cdsa/tests/test_views.py b/primed/cdsa/tests/test_views.py index bb498028..6015197d 100644 --- a/primed/cdsa/tests/test_views.py +++ b/primed/cdsa/tests/test_views.py @@ -4720,7 +4720,7 @@ def test_response_requires_study_review(self): # import ipdb; ipdb.set_trace() self.assertContains( response, - """
    Study review required?
    Yes
    """, # noqa: E501 + """
    Study review required?
    Yes
    """, # noqa: E501 html=True, ) instance.requires_study_review = False @@ -4729,7 +4729,7 @@ def test_response_requires_study_review(self): self.assertContains(response, "Study review required?") self.assertContains( response, - """
    Study review required?
    No
    """, # noqa: E501 + """
    Study review required?
    No
    """, # noqa: E501 html=True, )