Merge branch 'feature/preprints-affiliations' of https://github.com/C…

…enterForOpenScience/osf.io into clean-up-preprint-permissions

* 'feature/preprints-affiliations' of https://github.com/CenterForOpenScience/osf.io:
  add test confirming preprint affiliated institution data is sent to SHARE
  add tests for self link
  fix self link

.github/workflows/test-build.yml

@@ -21,7 +21,7 @@ jobs:
       uses: actions/cache@v2
       with:
         path: ~/.cache
-        key: reqs_${{ hashFiles('**/pyproject.toml') }}
+        key: reqs_${{ hashFiles('**/requirements.txt') }}
         restore-keys: reqs
     - run: |
         mkdir -p ~/.cache/downloads

addons/bitbucket/requirements.txt

@@ -0,0 +1 @@
+# no requirements

addons/boa/requirements.txt

@@ -0,0 +1,5 @@
+# Requirements for the boa add-on
+boa-api==0.1.14
+
+# Requirements for running asyncio in celery, using 3.4.1 for Python 3.6 compatibility
+asgiref==3.7.2

addons/box/requirements.txt

@@ -0,0 +1 @@
+boxsdk==3.9.2

addons/dataverse/requirements.txt

@@ -0,0 +1,3 @@
+# Allow for optional timeout parameter.
+# https://github.com/IQSS/dataverse-client-python/pull/27
+git+https://github.com/CenterForOpenScience/dataverse-client-python.git@2b3827578048e6df3818f82381c7ea9a2395e526 # branch is feature/dv-client-updates

addons/dropbox/requirements.txt

@@ -0,0 +1 @@
+dropbox==11.36.2

addons/figshare/requirements.txt

@@ -0,0 +1 @@
+

addons/github/requirements.txt

@@ -0,0 +1,3 @@
+cachecontrol==0.14.0
+github3.py==4.0.1
+uritemplate==4.1.1

addons/gitlab/requirements.txt

@@ -0,0 +1 @@
+python-gitlab==4.4.0

addons/mendeley/requirements.txt

@@ -0,0 +1,2 @@
+# up-to-date with mendeley's master + add folder support and future dep updates
+git+https://github.com/CenterForOpenScience/mendeley-python-sdk.git@be8a811fa6c3b105d9f5c656cabb6b1ba855ed5b # branch is feature/osf-dep-updates

addons/owncloud/requirements.txt

@@ -0,0 +1,2 @@
+# Requirements for the owncloud add-on
+pyocclient==0.6.0

addons/s3/requirements.txt

@@ -0,0 +1 @@
+boto3==1.34.60

addons/twofactor/requirements.txt

@@ -0,0 +1 @@
+pyotp==2.9.0

addons/wiki/requirements.txt

@@ -0,0 +1 @@
+pymongo==4.6.3

addons/zotero/requirements.txt

@@ -0,0 +1 @@
+Pyzotero==1.5.18

api/base/utils.py

@@ -1,5 +1,5 @@
 from furl import furl
-from urllib.parse import urlunsplit, urlsplit, parse_qs, urlencode
+from urllib.parse import urlunsplit, urlsplit, parse_qs, urlencode, quote
 from packaging.version import Version
 from hashids import Hashids
 
@@ -236,7 +236,7 @@ def waterbutler_api_url_for(node_id, provider, path='/', _internal=False, base_u
     # NOTE: furl encoding to be verified later
     url = furl(website_settings.WATERBUTLER_INTERNAL_URL if _internal else (base_url or website_settings.WATERBUTLER_URL))
     segments = ['v1', 'resources', node_id, 'providers', provider] + path.split('/')[1:]
-    url.add(path=segments)
+    url.add(path=[quote(x) for x in segments])
     url.args.update(kwargs)
     return url.url
 

api/preprints/serializers.py

@@ -209,7 +209,7 @@ class PreprintSerializer(TaxonomizableSerializerMixin, MetricsSerializerMixin, J
     affiliated_institutions = RelationshipField(
         related_view='preprints:preprints-institutions',
         related_view_kwargs={'preprint_id': '<_id>'},
-        self_view='preprints:preprints-institutions',
+        self_view='preprints:preprint-relationships-institutions',
         self_view_kwargs={'preprint_id': '<_id>'},
         read_only=False,
         required=False,

api_tests/preprints/views/test_preprint_detail.py

@@ -228,6 +228,8 @@ def test_return_affiliated_institutions(self, app, user, preprint, institution,
         assert res.status_code == 200
         relationship_link = res.json['data']['relationships']['affiliated_institutions']['links']['related']['href']
         assert f'/v2/preprints/{preprint._id}/institutions/' in relationship_link
+        relationship_link = res.json['data']['relationships']['affiliated_institutions']['links']['self']['href']
+        assert f'/v2/preprints/{preprint._id}/relationships/institutions/' in relationship_link
 
 
 @pytest.mark.django_db

api_tests/preprints/views/test_preprint_institutions_relationship.py

@@ -36,9 +36,8 @@ def institution_E(self):
     def institution_F(self):
         return InstitutionFactory()
 
-
     @pytest.fixture()
-    def admin_with_institutional_affiliation(self, institution_A, institution_B, institution_C,  preprint):
+    def admin_with_institutional_affiliation(self, institution_A, institution_B, institution_C, preprint):
         user = AuthUserFactory()
         preprint.add_contributor(user, permissions=ADMIN)
         user.add_or_update_affiliated_institution(institution_A)

api_tests/preprints/views/test_preprint_list.py

@@ -197,7 +197,8 @@ def test_return_affiliated_institutions(self):
         assert res.content_type == 'application/vnd.api+json'
         relationship_link = res.json['data'][0]['relationships']['affiliated_institutions']['links']['related']['href']
         assert f'/v2/preprints/{self.preprint._id}/institutions/' in relationship_link
-
+        relationship_link = res.json['data'][0]['relationships']['affiliated_institutions']['links']['self']['href']
+        assert f'/v2/preprints/{self.preprint._id}/relationships/institutions/' in relationship_link
 
 class TestPreprintsListFiltering(PreprintsListFilteringMixin):
 

docker-compose.yml

@@ -358,16 +358,15 @@ services:
       - /bin/bash
       - -c
       - python -m venv /tmp/venv
-        && /tmp/venv/bin/pip install poetry==1.8.3 &&
+        && /tmp/venv/bin/pip install poetry==1.8.0 &&
         /tmp/venv/bin/poetry install --no-root --without release --compile --sync &&
         rm -rf /python3.12/* &&
         cp -Rf -p /usr/local/lib/python3.12 /
     restart: 'no'
     environment:
       DJANGO_SETTINGS_MODULE: api.base.settings
     volumes:
-      - ./pyproject.toml:/code/pyproject.toml
-      - ./poetry.lock:/code/poetry.lock
+      - ./:/code:cached
       - osf_requirements_3_12_vol:/python3.12
 
   assets:

osf_tests/metadata/test_osf_gathering.py

@@ -538,6 +538,7 @@ def test_gather_affiliated_institutions(self):
         institution_iri = URIRef(institution.ror_uri)
         self.user__admin.add_or_update_affiliated_institution(institution)
         self.project.add_affiliated_institution(institution, self.user__admin)
+        self.preprint.add_affiliated_institution(institution, self.user__admin)
         assert_triples(osf_gathering.gather_affiliated_institutions(self.projectfocus), {
             (self.projectfocus.iri, OSF.affiliation, institution_iri),
             (institution_iri, RDF.type, DCTERMS.Agent),
@@ -559,6 +560,15 @@ def test_gather_affiliated_institutions(self):
         assert_triples(osf_gathering.gather_affiliated_institutions(self.registrationfocus), set())
         # focus: file
         assert_triples(osf_gathering.gather_affiliated_institutions(self.filefocus), set())
+        # focus: preprint
+        assert_triples(osf_gathering.gather_affiliated_institutions(self.preprintfocus), {
+            (self.preprintfocus.iri, OSF.affiliation, institution_iri),
+            (institution_iri, RDF.type, DCTERMS.Agent),
+            (institution_iri, RDF.type, FOAF.Organization),
+            (institution_iri, FOAF.name, Literal(institution.name)),
+            (institution_iri, DCTERMS.identifier, Literal(institution.identifier_domain)),
+            (institution_iri, DCTERMS.identifier, Literal(institution.ror_uri)),
+        })
 
     def test_gather_funding(self):
         # focus: project