Merge branch 'main' into django/1to2

.github/workflows/main.yml

@@ -52,7 +52,7 @@ jobs:
  - name: Setup Node.js for use with actions
  uses: actions/setup-node@v1
  with:
- node-version: 12.x
+ node-version: 16.x
 
  - uses: actions/cache@v1
  with:

.gitignore

@@ -94,6 +94,7 @@ docs/_build/
 target/
 venv/
 metrics/
+.python-version
 
 # ignore Google Drive API secrets
 *secrets.json

conf/docker/Dockerfile

@@ -1,3 +1,12 @@
+FROM node:16 as node_build
+COPY package.json package-lock.json /designsafe/
+WORKDIR /designsafe
+RUN npm ci
+
+COPY . /designsafe/
+RUN npm run build
+
+
 FROM python:3.7-buster
 
 LABEL MAINTAINER="DesignSafe-CI <[email protected]>"
@@ -27,11 +36,7 @@ RUN apt-get update && apt-get install -y \
  git \
  vim
 
-# install node 12.x
-RUN curl -sL https://deb.nodesource.com/setup_12.x | bash -
-RUN apt-get install -y nodejs
-
-RUN pip install poetry==1.4.0
+RUN pip install poetry
 COPY poetry.lock pyproject.toml /srv/www/
 WORKDIR /srv/www
 RUN poetry config virtualenvs.create false && \
@@ -41,11 +46,10 @@ RUN poetry config virtualenvs.create false && \
 RUN groupadd --gid 816877 G-816877 && \
  useradd --uid 458981 --gid G-816877 -m --shell /bin/bash tg458981 -d /home/tg458981
 
-COPY . /srv/www/designsafe
-RUN chown -R tg458981:G-816877 /srv/www/designsafe
+COPY --from=node_build /designsafe/ /srv/www/designsafe
+RUN chown tg458981:G-816877 /srv/www/designsafe /srv/www/designsafe/*
+RUN chown -R tg458981:G-816877 /srv/www/designsafe/designsafe
 
 USER tg458981
 
-RUN echo "prefix=~/.npm-global" >> ~/.npmrc
-
 WORKDIR /srv/www/designsafe

designsafe/apps/api/users/views.py

@@ -9,11 +9,21 @@
 from django.core.exceptions import ObjectDoesNotExist
 from pytas.http import TASClient
 
-from designsafe.apps.data.models.elasticsearch import IndexedFile
+from designsafe.apps.data.models.elasticsearch import IndexedFile, IndexedPublication
+from designsafe.libs.elasticsearch.utils import new_es_client
 from elasticsearch_dsl import Q, Search
 
 logger = logging.getLogger(__name__)
 
+def check_public_availability(username):
+ es_client = new_es_client()
+ query = Q({'multi_match': {'fields': ['project.value.teamMembers', 
+ 'project.value.coPis', 
+ 'project.value.pi'], 
+ 'query': username}})
+ res = IndexedPublication.search(using=es_client).filter(query).execute()
+ return res.hits.total.value > 0
+
 
 class UsageView(SecureMixin, View):
 
@@ -56,6 +66,11 @@ def get(self, request):
  resp_fields = ['first_name', 'last_name', 'email', 'username']
  model = get_user_model()
  q = request.GET.get('username')
+
+ # Do not return user details if the user is not part of a public project.
+ if not request.user.is_authenticated and not check_public_availability(q):
+ return JsonResponse({})
+
  if q:
  try:
  user = model.objects.get(username=q)
@@ -95,6 +110,11 @@ def get(self, request):
  if role:
  logger.info(role)
  user_rs = user_rs.filter(groups__name=role)
+
+ # Prevent endpoint from returning unfiltered user list.
+ if not q and not role:
+ return HttpResponseNotFound()
+
  resp = [model_to_dict(u, fields=resp_fields) for u in user_rs]
  if len(resp):
  return JsonResponse(resp, safe=False)
@@ -113,6 +133,9 @@ def get(self, request):
  try:
  users = []
  for username in nl:
+ # Do not return user details if the user is not part of a public project.
+ if not request.user.is_authenticated and not check_public_availability(username):
+ continue
  try:
  users.append(model.objects.get(username=username))
  except model.DoesNotExist:

designsafe/apps/applications/templates/designsafe/apps/applications/index.j2

@@ -25,7 +25,6 @@
 <script type="text/javascript" src="{% static 'vendor/objectpath/lib/ObjectPath.js' %}"></script>
 <script type="text/javascript" src="{% static 'vendor/angular-schema-form/dist/schema-form.js' %}"></script>
 <script type="text/javascript" src="{% static 'vendor/angular-schema-form/dist/bootstrap-decorator.js' %}"></script>
-<script type="text/javascript" src="{% static 'vendor/angular-drag-and-drop-lists/angular-drag-and-drop-lists.js' %}"></script>
 <script type="text/javascript" src="{% static 'vendor/angular-xeditable/dist/js/xeditable.js' %}"></script>
 <script type="text/javascript" src="{% static 'vendor/codemirror/lib/codemirror.js' %}"></script>
 <script type="text/javascript" src="{% static 'vendor/angular-ui-codemirror/src/ui-codemirror.js' %}"></script>

designsafe/apps/notifications/admin.py

@@ -1,3 +1,6 @@
 from django.contrib import admin
+from designsafe.apps.notifications.models import SiteMessage
 
 # Register your models here.
+
+admin.site.register(SiteMessage)

designsafe/apps/notifications/migrations/0003_sitemessage.py

@@ -0,0 +1,23 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.29 on 2023-08-04 15:55
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('notifications', '0002_auto_20160301_2331'),
+ ]
+
+ operations = [
+ migrations.CreateModel(
+ name='SiteMessage',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('message', models.TextField(help_text='Text for the alert message')),
+ ('display', models.BooleanField()),
+ ],
+ ),
+ ]

designsafe/apps/notifications/models.py

@@ -52,3 +52,10 @@ def receive_notification(sender, **kwargs):
  notification.save()
 
  Event.send_event(event_type, event_users, event_data)
+
+
+#pylint: enable=invalid-name
+class SiteMessage(models.Model):
+ """Warning message to display on all pages."""
+ message = models.TextField(help_text='Text for the alert message')
+ display = models.BooleanField()

designsafe/apps/workspace/templates/designsafe/apps/workspace/index.j2

@@ -40,7 +40,6 @@
 <script type="text/javascript" src="{% static 'vendor/objectpath/lib/ObjectPath.js' %}"></script>
 <script type="text/javascript" src="{% static 'vendor/angular-schema-form/dist/schema-form.js' %}"></script>
 <script type="text/javascript" src="{% static 'vendor/angular-schema-form/dist/bootstrap-decorator.js' %}"></script>
-<script type="text/javascript" src="{% static 'vendor/angular-drag-and-drop-lists/angular-drag-and-drop-lists.js' %}"></script>
 <script type="text/javascript" src="{% static 'vendor/angular-xeditable/dist/js/xeditable.js' %}"></script>
 <script src="{% static 'vendor/angular-ui-codemirror/src/ui-codemirror.js' %}"></script>
 {% endaddtoblock %}

designsafe/libs/fedora/fedora_operations.py

@@ -686,7 +686,7 @@ def generate_manifest(walk_result, project_id, version=None):
  manifest.append({
  'parent_entity': entity['uuid'],
  'corral_path': file_path,
- 'rel_path': rel_path,
+ 'project_path': rel_path,
  'checksum': get_sha1_hash(file_path),
  'ffi': get_fido_output(fido_client, file_path)
  })
@@ -751,8 +751,8 @@ def generate_package(project_id):
 
  with ZipFile(archive_path, 'w') as zf:
  for file in manifest:
- print(file['rel_path'])
- zf.write(file['corral_path'], file['rel_path'])
+ print(file['project_path'])
+ zf.write(file['corral_path'], file['project_path'])
  zf.writestr('{}/manifest.json'.format(project_id), manifest_json)
  zf.writestr('{}/metadata.json'.format(project_id), report_json)
 

designsafe/libs/fedora/sim_operations.py

@@ -12,7 +12,7 @@
 from designsafe.apps.data.models.elasticsearch import IndexedPublication
 from django.contrib.auth import get_user_model
 from designsafe.apps.api.publications.operations import _get_user_by_username
-from designsafe.libs.fedora.fedora_operations import format_metadata_for_fedora, fedora_post, fedora_update, create_fc_version, upload_manifest, generate_manifest
+from designsafe.libs.fedora.fedora_operations import format_metadata_for_fedora, fedora_post, fedora_update, create_fc_version, upload_manifest, generate_manifest, generate_report_experimental
 import logging
 logger = logging.getLogger(__name__)
 
@@ -303,3 +303,21 @@ def ingest_project_sim(project_id, version=None, amend=False):
 
  if not amend:
  upload_manifest_sim(project_id, version=version)
+
+
+def generate_package_sim(project_id):
+ from zipfile import ZipFile
+ archive_path = '/corral-repl/tacc/NHERI/published/archives/{}.zip'.format(project_id)
+ walk_res = walk_sim(project_id)
+ manifest = generate_manifest(walk_res, project_id)
+ manifest_json = json.dumps(manifest, indent=4)
+ print(manifest_json)
+ report = generate_report_experimental(project_id)
+ report_json = json.dumps(report, indent=4)
+
+ with ZipFile(archive_path, 'w') as zf:
+ for file in manifest:
+ print(file['project_path'])
+ zf.write(file['corral_path'], file['project_path'])
+ zf.writestr('{}/manifest.json'.format(project_id), manifest_json)
+ zf.writestr('{}/metadata.json'.format(project_id), report_json)

designsafe/middleware.py

@@ -16,6 +16,7 @@
 from django.shortcuts import redirect
 from django.urls import reverse
 from django.utils.deprecation import MiddlewareMixin
+from designsafe.apps.notifications.models import SiteMessage
 
 logger = logging.getLogger(__name__)
 
@@ -63,6 +64,14 @@ def process_request(self, request):
  'Use is required for continued use of DesignSafe '
  'resources.' % accept_url)
  return None
+
+
+class SiteMessageMiddleware:
+ def process_request(self, request):
+ for message in SiteMessage.objects.filter(display=True):
+ if settings.SITE_ID == 1:
+ messages.warning(request, message.message)
+
 
 class RequestProfilingMiddleware(MiddlewareMixin):
  """Middleware to run cProfiler on each request"""

designsafe/settings/common_settings.py

@@ -30,6 +30,7 @@
 
 # SESSIONS
 SESSION_COOKIE_DOMAIN = os.environ.get('SESSION_COOKIE_DOMAIN')
+SESSION_COOKIE_SECURE = True
 SESSION_EXPIRE_AT_BROWSER_CLOSE = True
 SECURE_PROXY_SSL_HEADER = ('HTTP_X_FORWARDED_PROTO', 'https')
 # SECURITY WARNING: don't run with debug turned on in production!
@@ -148,6 +149,7 @@
  'impersonate.middleware.ImpersonateMiddleware',
  'designsafe.middleware.DesignSafeTermsMiddleware',
  'designsafe.middleware.DesignsafeProfileUpdateMiddleware',
+ 'designsafe.middleware.SiteMessageMiddleware',
 )
 
 ROOT_URLCONF = 'designsafe.urls'
@@ -254,7 +256,6 @@
  ('vendor/font-awesome', os.path.join(BASE_DIR, 'node_modules', 'font-awesome')),
  ('vendor/angular-toastr', os.path.join(BASE_DIR, 'node_modules', 'angular-toastr')),
  ('vendor/slick-carousel', os.path.join(BASE_DIR, 'node_modules', 'slick-carousel')),
- ('vendor/angular-drag-and-drop-lists', os.path.join(BASE_DIR, 'node_modules', 'angular-drag-and-drop-lists')),
  ('vendor/angular-xeditable', os.path.join(BASE_DIR, 'node_modules', 'angular-xeditable')),
  ('vendor/leaflet-measure', os.path.join(BASE_DIR, 'node_modules', 'leaflet-measure')),
  ('vendor/exif-js', os.path.join(BASE_DIR, 'node_modules', 'exif-js')),

designsafe/static/scripts/applications/app.js

@@ -1,6 +1,7 @@
 import $ from 'jquery';
 import angular from 'angular';
 import _ from 'underscore';
+import dndlists from 'angular-drag-and-drop-lists';
 
 import './services/apps-wizard-service';
 

designsafe/static/scripts/data-depot/components/modals/nees-doi-list.component.js

@@ -6,7 +6,7 @@ class NeesDoiListCtrl {
 
  $onInit() {
  this.project = this.resolve.project;
- this.experimentDois = this.project.metadata.experiments.map((exp)=> {
+ this.experimentDois = this.project.metadata.experiments.filter(exp => !!exp.doi).map((exp)=> {
  const authors = (exp.creators ? exp.creators.map((author) => `${author.lastName}, ${author.firstName}`).join('; ') : '')
  const year = exp.endDate.split('T')[0].split('-')[0];
  const doi = exp.doi;

designsafe/static/scripts/data-depot/components/projects/pipeline-amend/amend-citation.template.html

@@ -11,9 +11,7 @@
 <div class="pipeline-page">
  <div class="pipeline-header">
  <h3>Confirm Author Order</h3>
- <strong>You are required to confirm the list of Authors on your Citation(s) before continuing.</strong>
- Click Save to confirm.
- Your citation(s) will be updated to match what is shown in the preview.
+ Before proceeding, please review the list of authors and their order on your citation(s) and click "Save" to confirm. Your citation(s) will be updated accordingly.
  <div ng-if="$ctrl.ui.loading">
  <h3 class="text-center">
  <i class="fa fa-spinner fa-spin"></i> Loading...
@@ -70,7 +68,7 @@ <h3 class="text-center">
  <h5 style="font-family: Helvetica Neue">Citation Preview</h5>
  <div class="well" style="margin-bottom:20px; background-color: white;" ng-show="!$ctrl.ui.loading">
  <div>
- <ds-author-list format="hname" authors="$ctrl.authors[pubEnt.uuid]"></ds-author-list>
+ <ds-author-list format="citation" authors="$ctrl.authors[pubEnt.uuid]"></ds-author-list>
  <span>
  ({{ $ctrl.publishedDate }}) “{{ pubEnt.value.title }}”, in <i>{{ $ctrl.project.value.title }}</i>. DesignSafe-CI.
  <a href="{{'https://doi.org/' + $ctrl.pubEnt.value.dois[0]}}">{{'https://doi.org/' + $ctrl.pubEnt.value.dois[0]}}</a>.

designsafe/static/scripts/data-depot/components/projects/pipeline-amend/amend-experimental.template.html

@@ -42,12 +42,15 @@ <h3 class="text-center">
  <div ng-if="!$ctrl.ui.loading">
  <div class="pipeline-section">
  <ul>
- <li>Please review the preview of your amended publication carefully.</li>
- <li>Any acceptable changes you make from the project workspace are automatically imported to this preview.</li>
- <li>This preview shows what your publication will look like once it is amended.</li>
- <li>Categories may not be added or removed.</li>
- <li>Files related to any categories may not be modified.</li>
- <li>When you have finished proofreading your amended publication, click continue to move onto the next step.</li>
+ <li>Please review the amendable metadata carefully and make changes if necessary.</li>
+ <li>Any changes made in the project workspace are reflected in this preview.</li>
+ <li>Categories may not be added or removed and files related to any categories may not be modified.</li>
+ <li>When you have finished proofreading your amended publication, click "Continue to Authors".</li>
+ <li>If you need help, attend 
+ <a href="/facilities/virtual-office-hours/" target="_blank" aria-describedby="msg-open-new-window">
+ curation office hours
+ </a>.
+ </li>
  </ul>
  </div>
  <!-- Project Header Start -->
@@ -202,7 +205,7 @@ <h3 class="text-center">
  </div>
  </div>
  <div class="entity-meta-field" ng-if="experiment.value.referencedData.length">
- <div class="entity-meta-label-multi">Referenced Data</div>
+ <div class="entity-meta-label-multi">Referenced Data and Software</div>
  <div class="entity-meta-data">
  <div ng-repeat="reference in experiment.value.referencedData track by $index">
  <referenced-data></referenced-data>