- {% render_table tables.4 %}
+
+
+
+
+
+
+ {% render_table tables.2 %}
+
+
+
-
Partner upload workspaces
-
- {% render_table tables.5 %}
+
+
+
+
+
+
+ {% render_table tables.5 %}
+
+
+
+{% endif %}
{% endblock after_panel %}
@@ -68,6 +159,7 @@
Partner upload workspaces
{% endif %}
+{% if perms.anvil_consortium_manager.anvil_consortium_manager_staff_view %}
Audit upload workspace sharing
@@ -76,4 +168,5 @@ Partner upload workspaces
Audit upload workspace auth domains
+{% endif %}
{% endblock action_buttons %}
diff --git a/gregor_django/templates/gregor_anvil/uploadcycle_list.html b/gregor_django/templates/gregor_anvil/uploadcycle_list.html
index cce9063a..c3a4f8b8 100644
--- a/gregor_django/templates/gregor_anvil/uploadcycle_list.html
+++ b/gregor_django/templates/gregor_anvil/uploadcycle_list.html
@@ -6,6 +6,12 @@
{% block content %}
Upload Cycles
+
+ The following table shows all GREGoR upload cycles to date.
+ Click on an upload cycle number to view more details about and workspaces associated with that cycle.
+
+
+
{% render_table table %}
{% endblock content %}
diff --git a/gregor_django/templates/gregor_anvil/uploadworkspace_detail.html b/gregor_django/templates/gregor_anvil/uploadworkspace_detail.html
index f4646b7b..b16bd688 100644
--- a/gregor_django/templates/gregor_anvil/uploadworkspace_detail.html
+++ b/gregor_django/templates/gregor_anvil/uploadworkspace_detail.html
@@ -3,8 +3,20 @@
{% block workspace_data %}
- - Research Center
- {{ workspace_data_object.research_center }}
- - Consent group
- {{ workspace_data_object.consent_group }}
+ - Research Center
-
+ {% if perms.anvil_consortium_manager.anvil_consortium_manager_staff_view %}
+ {{ workspace_data_object.research_center }}
+ {% else %}
+ {{ workspace_data_object.research_center }}
+ {% endif %}
+
+ - Consent group
-
+ {% if perms.anvil_consortium_manager.anvil_consortium_manager_staff_view %}
+ {{ workspace_data_object.consent_group }}
+ {% else %}
+ {{ workspace_data_object.consent_group }}
+ {% endif %}
+
- Upload cycle
- {{ workspace_data_object.upload_cycle }}
- Date QC completed
-
{% if workspace_data_object.date_qc_completed %}
@@ -39,7 +51,7 @@
Audit consortium sharing
diff --git a/gregor_django/templates/gregor_anvil/uploadworkspace_list.html b/gregor_django/templates/gregor_anvil/uploadworkspace_list.html
new file mode 100644
index 00000000..4c4b0a91
--- /dev/null
+++ b/gregor_django/templates/gregor_anvil/uploadworkspace_list.html
@@ -0,0 +1,42 @@
+{% extends "anvil_consortium_manager/base.html" %}
+{% load static %}
+
+{% load render_table from django_tables2 %}
+{% load crispy_forms_tags %}
+
+{% block title %}{{workspace_type_display_name}}s{% endblock %}
+
+{% block content %}
+
+
+
+
+
{{workspace_type_display_name}}s
+
+
+
+ This page lists all available workspaces that contain data uploaded by Research Centers (RCs) in a given upload cycle.
+ Upload workspaces are unique to an RC, consent group (GRU or HMB), and upload cycle.
+
+
+ Current upload cycle workspaces are accessible to an RC's members who are approved by their PI for uploader and/or reader access.
+ Previous upload cycles workspaces are accessible to all GREGoR members who are approved for reader access.
+
+
+ Learn more about Accessing Consortium Data.
+
+
+
+
+
+ {% crispy filter.form %}
+
+
+ {% render_table table %}
+
+
+
+
+
+
+{% endblock content %}
diff --git a/gregor_django/templates/pages/home.html b/gregor_django/templates/pages/home.html
index 94d9808c..5cb63ad8 100644
--- a/gregor_django/templates/pages/home.html
+++ b/gregor_django/templates/pages/home.html
@@ -1 +1,54 @@
{% extends "base.html" %}
+
+{% block content %}
+
+
+
+
+
GREGoR AnVIL app
+
+ The GREGoR Consortium leverages the NHGRI Analysis Visualization and Informatics Lab (AnVIL) for rapid Consortium data sharing and release to the broader scientific community.
+ Consortium members upload data to workspaces on the AnVIL platform every calendar quarter (“upload cycle”).
+ Uploaded data are combined into a Consortium dataset after each upload cycle, and the dataset is shared with Consortium members.
+ The Data Coordinating Center (DCC) developed and utilizes this app, the AnVIL Consortium Manager, to manage various workspace types that facilitate the data uploading process, as well as subsequent data processing and synthesis procedures.
+ More information about Consortium data, including how to access and how to get started with working with the data, can be found on the GREGoR website.
+
+
+
+
+
+
+
+
+
+
+
+
View the list of all GREGoR upload cycles to date.
+
+
+
+
+
+
+
+
+
+
Browse the current set of GREGoR workspaces on AnVIL.
+
+
+
+
+
+
+
+
+
+{% endblock content %}
diff --git a/pytest.ini b/pytest.ini
index 3b3a2e8c..d954c9a2 100644
--- a/pytest.ini
+++ b/pytest.ini
@@ -1,5 +1,5 @@
[pytest]
-addopts = --ds=config.settings.test --reuse-db -n auto
+addopts = --ds=config.settings.test --reuse-db -n auto --maxprocesses 4
python_files = tests.py test_*.py
filterwarnings =
# Convert all warnings to errors.
diff --git a/requirements/dev-requirements.txt b/requirements/dev-requirements.txt
index 21e1b81e..ca4dd453 100644
--- a/requirements/dev-requirements.txt
+++ b/requirements/dev-requirements.txt
@@ -150,7 +150,7 @@ requests==2.32.3
# -c requirements/requirements.txt
# -c requirements/test-requirements.txt
# sphinx
-ruff==0.7.2
+ruff==0.8.1
# via -r requirements/dev-requirements.in
six==1.16.0
# via
@@ -233,7 +233,7 @@ wcwidth==0.2.13
# via prompt-toolkit
websockets==12.0
# via sphinx-autobuild
-werkzeug==3.1.2
+werkzeug==3.1.3
# via -r requirements/dev-requirements.in
# The following packages are considered to be unsafe in a requirements file:
diff --git a/requirements/requirements.in b/requirements/requirements.in
index e39662ee..25aa98f9 100644
--- a/requirements/requirements.in
+++ b/requirements/requirements.in
@@ -35,7 +35,7 @@ django-extensions # https://github.com/django-extensions/django-extensions
# Bootstrap5 templates for crispy-forms
crispy-bootstrap5 # https://github.com/django-crispy-forms/crispy-bootstrap5
-django-anvil-consortium-manager @ git+https://github.com/UW-GAC/django-anvil-consortium-manager.git@v0.25
+django-anvil-consortium-manager @ git+https://github.com/UW-GAC/django-anvil-consortium-manager.git@v0.26.1
# Simple history - model history tracking
django-simple-history
diff --git a/requirements/requirements.txt b/requirements/requirements.txt
index cac76c2f..e1600082 100644
--- a/requirements/requirements.txt
+++ b/requirements/requirements.txt
@@ -32,7 +32,7 @@ crispy-bootstrap5==2024.10
# via
# -r requirements/requirements.in
# django-anvil-consortium-manager
-cryptography==43.0.3
+cryptography==44.0.0
# via -r requirements/requirements.in
django==4.2.16
# via
@@ -50,9 +50,9 @@ django==4.2.16
# django-picklefield
# django-simple-history
# django-tables2
-django-allauth==65.1.0
+django-allauth==65.3.0
# via -r requirements/requirements.in
-django-anvil-consortium-manager @ git+https://github.com/UW-GAC/django-anvil-consortium-manager.git@v0.25
+django-anvil-consortium-manager @ git+https://github.com/UW-GAC/django-anvil-consortium-manager.git@v0.26.1
# via -r requirements/requirements.in
django-autocomplete-light==3.11.0
# via django-anvil-consortium-manager
@@ -97,7 +97,7 @@ idna==3.7
# via requests
jsonapi-requests==0.8.0
# via -r requirements/requirements.in
-mysqlclient==2.2.5
+mysqlclient==2.2.6
# via -r requirements/requirements.in
networkx==3.1
# via django-anvil-consortium-manager
@@ -123,7 +123,7 @@ pyasn1-modules==0.3.0
# via google-auth
pycparser==2.21
# via cffi
-pyjwt==2.9.0
+pyjwt==2.10.1
# via -r requirements/requirements.in
pyproject-hooks==1.0.0
# via
diff --git a/requirements/test-requirements.txt b/requirements/test-requirements.txt
index 2f6f4a10..52cbfef8 100644
--- a/requirements/test-requirements.txt
+++ b/requirements/test-requirements.txt
@@ -49,7 +49,7 @@ packaging==23.2
# pytest-sugar
pluggy==1.5.0
# via pytest
-pytest==8.3.3
+pytest==8.3.4
# via
# -r requirements/test-requirements.in
# pytest-cov