Merge branch 'production' into issue-5138

.github/workflows/docker.yml

@@ -4,25 +4,29 @@ on:
   push:
   pull_request:
 
+env:
+  REGISTRY_IMAGE: specifyconsortium/specify7-service
+
 jobs:
-  dockerize:
+  build:
     runs-on: ubuntu-latest
     # "push" event is not triggered for forks, so need to listen for
     # pull_requests, but only for external ones, so as not to run the action
     # twice
     if:
       github.event_name != 'pull_request' ||
       github.event.pull_request.head.repo.fork == true
+    strategy:
+      fail-fast: false
+      matrix:
+        platform:
+          - linux/amd64
+          - linux/arm64
     steps:
-      - name: Checkout
-        uses: actions/checkout@v4
-
       - name: Prepare
         id: prep
-        env:
-          DEFAULT_BRANCH: ${{ github.event.repository.default_branch }}
         run: |
-          DOCKER_IMAGE=specifyconsortium/specify7-service
+          DOCKER_IMAGE=${{ env.REGISTRY_IMAGE }}
           VERSION=noop
           if [ "${{ github.event_name }}" = "schedule" ]; then
             VERSION=nightly
@@ -54,53 +58,80 @@ jobs:
           echo "version=${VERSION}" >> $GITHUB_OUTPUT
           echo "tags=${TAGS}" >> $GITHUB_OUTPUT
           echo "created=$(date -u +'%Y-%m-%dT%H:%M:%SZ')" >> $GITHUB_OUTPUT
-
-          # Determine the platforms based on the branch
-          PLATFORMS="linux/amd64"
-          REF_NAME=$(echo "${GITHUB_REF#refs/*/}")
-          if [[ $GITHUB_REF == refs/tags/* || "$REF_NAME" = "$DEFAULT_BRANCH" ]]; then
-            PLATFORMS="linux/amd64,linux/arm64"
-          elif [[ "$REF_NAME" == *arm ]]; then
-            PLATFORMS="linux/arm64"
-          fi
-          echo "platforms=${PLATFORMS}" >> $GITHUB_ENV
-
-      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
-
-      - name: Cache Docker layers
-        uses: actions/cache@v3
+      
+      - name: Docker meta
+        id: meta
+        uses: docker/metadata-action@v5
         with:
-          path: /tmp/.buildx-cache
-          key: ${{ runner.os }}-buildx-${{ github.sha }}
-          restore-keys: |
-            ${{ runner.os }}-buildx-
-
-      - name: Login to DockerHub
-        uses: docker/login-action@v2
+          images: ${{ env.REGISTRY_IMAGE }}
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Login to Docker Hub
+        uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Build and push by digest
+        id: build
+        uses: docker/build-push-action@v6
+        with:
+          platforms: ${{ matrix.platform }}
+          labels: ${{ steps.meta.outputs.labels }}
+          outputs: type=image,name=${{ env.REGISTRY_IMAGE }},push-by-digest=true,name-canonical=true,push=true
+
+      - name: Export digest
+        run: |
+          mkdir -p /tmp/digests
+          digest="${{ steps.build.outputs.digest }}"
+          touch "/tmp/digests/${digest#sha256:}"
+      
+      - name: Upload digest
+        uses: actions/upload-artifact@v4
+        with:
+          name: digests-${{ strategy.job-index }}
+          path: /tmp/digests/*
+          if-no-files-found: error
+          retention-days: 1
 
-      - name: Build and push
-        uses: docker/build-push-action@v3
+  merge:
+    runs-on: ubuntu-latest
+    needs:
+      - build
+    steps:
+      - name: Download digests
+        uses: actions/download-artifact@v4
+        with:
+          path: /tmp/digests
+          pattern: digests-*
+          merge-multiple: true
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Docker meta
+        id: meta
+        uses: docker/metadata-action@v5
         with:
-          context: .
-          file: ./Dockerfile
-          build-args: |
-            BUILD_VERSION=${{ steps.prep.outputs.version }}
-            GIT_SHA=${{ github.sha }}
-          push: true
-          cache-from: type=local,src=/tmp/.buildx-cache
-          cache-to: type=local,dest=/tmp/.buildx-cache
-          tags: ${{ steps.prep.outputs.tags }}
-          labels: |
-            org.opencontainers.image.title=${{ github.event.repository.name }}
-            org.opencontainers.image.description=${{ github.event.repository.description }}
-            org.opencontainers.image.url=${{ github.event.repository.html_url }}
-            org.opencontainers.image.source=${{ github.event.repository.clone_url }}
-            org.opencontainers.image.version=${{ steps.prep.outputs.version }}
-            org.opencontainers.image.created=${{ steps.prep.outputs.created }}
-            org.opencontainers.image.revision=${{ github.sha }}
-            org.opencontainers.image.licenses=${{ github.event.repository.license.spdx_id }}
-          platforms: ${{ env.platforms }}
+          images: ${{ env.REGISTRY_IMAGE }}
+
+      - name: Login to Docker Hub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Create manifest list and push
+        working-directory: /tmp/digests
+        run: |
+          docker buildx imagetools create $(jq -cr '.tags | map("-t " + .) | join(" ")' <<< "$DOCKER_METADATA_OUTPUT_JSON") \
+            $(printf '${{ env.REGISTRY_IMAGE }}@sha256:%s ' *)
+      
+      - name: Inspect image
+        run: |
+          docker buildx imagetools inspect ${{ env.REGISTRY_IMAGE }}:${{ steps.meta.outputs.version }}

specifyweb/barvis/views.py

@@ -1,29 +1,40 @@
 from django.http import HttpResponse
-
-from sqlalchemy.sql.expression import func, distinct
+from django.db.models import Count, Q
 
 from specifyweb.middleware.general import require_GET
 from specifyweb.specify.views import login_maybe_required
+from specifyweb.specify.filter_by_col import filter_by_collection
 from specifyweb.specify.api import toJson
-
-from specifyweb.stored_queries.models import Determination, Taxon
+from specifyweb.specify.models import Taxon
 
 from django.db import connection
 
+
 @require_GET
 @login_maybe_required
 def taxon_bar(request):
-    "Returns the data for creating a taxon tiles visualization."
-    cursor = connection.cursor()
-    cursor.execute("""
-    SELECT t.TaxonID,
-    t.RankID,
-    t.ParentID,
-    t.Name,
-    (SELECT COUNT(*) FROM determination d WHERE t.TaxonID = d.TaxonID AND d.IsCurrent = 1)
-    FROM taxon t
-    WHERE t.TaxonTreeDefID = %s
-    """, [request.specify_collection.discipline.taxontreedef_id])
+    # "Returns the data for creating a taxon tiles visualization."
+    # cursor = connection.cursor()
+    # cursor.execute("""
+    # SELECT t.TaxonID,
+    # t.RankID,
+    # t.ParentID,
+    # t.Name,
+    # (SELECT COUNT(*) FROM determination d WHERE t.TaxonID = d.TaxonID AND d.IsCurrent = 1)
+    # FROM taxon t
+    # WHERE t.TaxonTreeDefID = %s
+    # """, [request.specify_collection.discipline.taxontreedef_id])
+
+    # Implementing the previous SQL query in Django ORM:
+    taxons = (
+        Taxon.objects.annotate(
+            current_determination_count=Count(
+                'determinations', filter=Q(determinations__iscurrent=True))
+        )
+        .values_list("id", "rankid", "parent_id", "name", "current_determination_count")
+    )
+    filtered_taxons = filter_by_collection(taxons, request.specify_collection)
+    result = toJson(list(filtered_taxons))
 
     # SELECT d.TaxonID, COUNT(DISTINCT d.CollectionObjectID), t.ParentID
     # FROM determination d
@@ -33,7 +44,7 @@ def taxon_bar(request):
     # GROUP BY d.TaxonId
     # ORDER BY d.TaxonId
     # """, [request.specify_collection.id])
-    result = toJson(cursor.fetchall())
+    # result = toJson(cursor.fetchall())
     # session = Session()
     # query = session.query(
     #     Determination.TaxonID,

specifyweb/businessrules/rules/cogtype_rules.py

@@ -3,7 +3,7 @@
 from specifyweb.businessrules.orm_signal_handler import orm_signal_handler
 from specifyweb.specify.models import Picklist, Picklistitem
 
-@orm_signal_handler('pre_save', 'CollectionObjectGroupType')
+@orm_signal_handler('pre_save', 'Collectionobjectgrouptype')
 def cogtype_pre_save(cog_type):
 
     # Ensure the cog_type type is validated by being the picklist.

specifyweb/businessrules/rules/cojo_rules.py

@@ -1,8 +1,8 @@
 from specifyweb.businessrules.exceptions import BusinessRuleException
 from specifyweb.businessrules.orm_signal_handler import orm_signal_handler
-from specifyweb.specify.models import CollectionObjectGroupJoin
+from specifyweb.specify.models import Collectionobjectgroupjoin
 
-@orm_signal_handler('pre_save', 'CollectionObjectGroupJoin')
+@orm_signal_handler('pre_save', 'Collectionobjectgroupjoin')
 def cojo_pre_save(cojo):
     # Ensure the both the childcog and childco fields are not null.
     if cojo.childcog == None and cojo.childco == None:
@@ -16,12 +16,12 @@ def cojo_pre_save(cojo):
     # So when a record is saved with isPrimary set to True, we need to set all other records with the same parentcog
     # to isPrimary = False.
     if cojo.isprimary == True:
-        (CollectionObjectGroupJoin.objects
+        (Collectionobjectgroupjoin.objects
          .filter(parentcog=cojo.parentcog)
          .update(isprimary=False))
 
     if cojo.issubstrate == True:
-        (CollectionObjectGroupJoin.objects
+        (Collectionobjectgroupjoin.objects
          .filter(parentcog=cojo.parentcog)
          .update(issubstrate=False))
 

specifyweb/businessrules/tests/test_cog_type.py

@@ -1,13 +1,13 @@
 from specifyweb.businessrules.exceptions import BusinessRuleException
-from specifyweb.specify.models import CollectionObjectGroupType, Picklist, Picklistitem
+from specifyweb.specify.models import Collectionobjectgrouptype, Picklist, Picklistitem
 from specifyweb.specify.tests.test_api import DefaultsSetup
 from django.db import transaction
 
 # NOTE: Edit this test when a new COG type rule is decided upon.
 class COGTypeTest(DefaultsSetup):
     def test_cog_type_select_values(self):
-        CollectionObjectGroupType.objects.create(name='microscope slide', type='Discrete', collection=self.collection)
+        Collectionobjectgrouptype.objects.create(name='microscope slide', type='Discrete', collection=self.collection)
 
         with self.assertRaises(BusinessRuleException), transaction.atomic():
-            CollectionObjectGroupType.objects.create(name='whole rock', type='Burrito', collection=self.collection)
+            Collectionobjectgrouptype.objects.create(name='whole rock', type='Burrito', collection=self.collection)
 

specifyweb/businessrules/tests/test_cojo.py

@@ -1,56 +1,56 @@
-from specifyweb.specify.models import CollectionObjectGroup, CollectionObjectGroupJoin, CollectionObjectGroupType, Picklist, Picklistitem
+from specifyweb.specify.models import Collectionobjectgroup, Collectionobjectgroupjoin, Collectionobjectgrouptype, Picklist, Picklistitem
 from specifyweb.specify.tests.test_api import DefaultsSetup
 
 class CoJoTest(DefaultsSetup):
     def test_cojo_rules_enforcement(self):
-        cog_type = CollectionObjectGroupType.objects.create(name='microscope slide', type='Discrete', collection=self.collection)
-        cog_1 = CollectionObjectGroup.objects.create(
+        cog_type = Collectionobjectgrouptype.objects.create(name='microscope slide', type='Discrete', collection=self.collection)
+        cog_1 = Collectionobjectgroup.objects.create(
             collection=self.collection,
             cogtype=cog_type
         )
-        cog_2 = CollectionObjectGroup.objects.create(
+        cog_2 = Collectionobjectgroup.objects.create(
             collection=self.collection,
             cogtype=cog_type
         )
-        cog_3 = CollectionObjectGroup.objects.create(
+        cog_3 = Collectionobjectgroup.objects.create(
             collection=self.collection,
             cogtype=cog_type
         )
-        cojo_1 = CollectionObjectGroupJoin.objects.create(
+        cojo_1 = Collectionobjectgroupjoin.objects.create(
             parentcog=cog_1,
             childcog=cog_2,
             isprimary=True,
             issubstrate=True
         )
-        cojo_2 = CollectionObjectGroupJoin.objects.create(
+        cojo_2 = Collectionobjectgroupjoin.objects.create(
             parentcog=cog_1,
             childcog=cog_3,
             isprimary=True,
             issubstrate=True
         )
 
-        cojo_1 = CollectionObjectGroupJoin.objects.get(id=cojo_1.id)
-        cojo_2 = CollectionObjectGroupJoin.objects.get(id=cojo_2.id)
+        cojo_1 = Collectionobjectgroupjoin.objects.get(id=cojo_1.id)
+        cojo_2 = Collectionobjectgroupjoin.objects.get(id=cojo_2.id)
 
         self.assertFalse(cojo_1.isprimary)
         self.assertFalse(cojo_1.issubstrate)
         self.assertTrue(cojo_2.isprimary)
         self.assertTrue(cojo_2.issubstrate)
 
-        cog_4 = CollectionObjectGroup.objects.create(
+        cog_4 = Collectionobjectgroup.objects.create(
             collection=self.collection,
             cogtype=cog_type
         )
-        cojo_3 = CollectionObjectGroupJoin.objects.create(
+        cojo_3 = Collectionobjectgroupjoin.objects.create(
             parentcog=cog_1,
             childcog=cog_4,
             isprimary=False,
             issubstrate=False
         )
 
-        cojo_1 = CollectionObjectGroupJoin.objects.get(id=cojo_1.id)
-        cojo_2 = CollectionObjectGroupJoin.objects.get(id=cojo_2.id)
-        cojo_3 = CollectionObjectGroupJoin.objects.get(id=cojo_3.id)
+        cojo_1 = Collectionobjectgroupjoin.objects.get(id=cojo_1.id)
+        cojo_2 = Collectionobjectgroupjoin.objects.get(id=cojo_2.id)
+        cojo_3 = Collectionobjectgroupjoin.objects.get(id=cojo_3.id)
 
         self.assertFalse(cojo_1.isprimary)
         self.assertFalse(cojo_1.issubstrate)

specifyweb/businessrules/tests/test_collection.py

@@ -55,6 +55,6 @@ def test_collection_objects_block_delete(self):
         with self.assertRaises(ProtectedError):
             self.collection.delete()
 
-        models.CollectionObjectType.objects.filter(collection=self.collection).delete()
+        models.Collectionobjecttype.objects.filter(collection=self.collection).delete()
         models.Collectionobject.objects.filter(collection=self.collection).delete()
         self.collection.delete()

specifyweb/businessrules/tests/test_collectionobject.py

@@ -1,4 +1,4 @@
-from specifyweb.specify.models import Collection, Collectionobject, CollectionObjectType
+from specifyweb.specify.models import Collection, Collectionobject, Collectionobjecttype
 from specifyweb.specify.tests.test_api import ApiTests
 from ..exceptions import BusinessRuleException
 
@@ -15,7 +15,7 @@ def test_catalog_number_unique_in_collection(self):
             catalognumber=self.collectionobjects[0].catalognumber + 'foo')
 
     def test_default_collectionobjecttype(self):
-        default_type = CollectionObjectType.objects.create(
+        default_type = Collectionobjecttype.objects.create(
             name="default type",
             collection=self.collection,
             taxontreedef=self.discipline.taxontreedef