Merge pull request #51 from chanzuckerberg/jgadling/new_anno_author_f…

…ield chore: Make a new `annotation_authors.primary_author_status` field
chanzuckerberg · Apr 22, 2024 · 60fe5b4 · 60fe5b4
2 parents 105753b + 253debb
commit 60fe5b4
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Showing 11 changed files with 31 additions and 18 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,10 +1,10 @@
 repos:
 - repo: https://github.com/psf/black-pre-commit-mirror
-  rev: 23.9.1
+  rev: 24.4.0
   hooks:
   - id: black
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.0.292
+  rev: v0.4.1
   hooks:
   - id: ruff
     args:

diff --git a/api_server/metadata/databases/cryoetdataportal/tables/public_annotation_authors.yaml b/api_server/metadata/databases/cryoetdataportal/tables/public_annotation_authors.yaml
@@ -20,6 +20,7 @@ select_permissions:
         - name
         - orcid
         - primary_annotator_status
+        - primary_author_status
       filter: {}
       allow_aggregations: true
       query_root_fields:

diff --git a/...956764128_alter_table_public_annotation_authors_add_column_primary_author_status/down.sql b/...956764128_alter_table_public_annotation_authors_add_column_primary_author_status/down.sql
@@ -0,0 +1 @@
+alter table "public"."annotation_authors" drop column "primary_author_status";
diff --git a/...12956764128_alter_table_public_annotation_authors_add_column_primary_author_status/up.sql b/...12956764128_alter_table_public_annotation_authors_add_column_primary_author_status/up.sql
@@ -0,0 +1,3 @@
+alter table "public"."annotation_authors" add column "primary_author_status" boolean
+ null;
+UPDATE "public"."annotation_authors" SET primary_author_status = primary_annotator_status;
diff --git a/ingestion_tools/Dockerfile b/ingestion_tools/Dockerfile
@@ -17,7 +17,7 @@ ENV IMOD_DIR /usr/local/IMOD
 
 # Get our packaging house in order
 RUN pip install --upgrade pip
-ENV POETRY_VERSION=1.7
+ENV POETRY_VERSION=1.8.2
 RUN python3 -m pip install --no-cache-dir poetry==$POETRY_VERSION
 
 # Install our dependencies

diff --git a/ingestion_tools/pyproject.toml b/ingestion_tools/pyproject.toml
@@ -50,6 +50,10 @@ line-length = 120
 target_version = ['py311']
 
 [tool.ruff]
+line-length = 120
+target-version = "py39"
+
+[tool.ruff.lint]
 select = [
     "E", "W",  # pycodestyle
     "F",  # pyflakes
@@ -72,17 +76,15 @@ ignore = [
     "DTZ007", # Datetime objects without timezones.
     "DTZ005", # More datetimes without timezones.
 ]
-line-length = 120
-target-version = "py39"
 
 [tool.ruff.lint.per-file-ignores]
 # Ignore `SIM115` (not using open() in a context manager) since all calls to this method *do* use a context manager.
 "scripts/common/fs.py" = ["SIM115"]
 
-[tool.ruff.isort]
+[tool.ruff.lint.isort]
 known-first-party =["common"]
 
-[tool.ruff.flake8-quotes]
+[tool.ruff.lint.flake8-quotes]
 docstring-quotes = "double"
 
 [tool.mypy]

diff --git a/ingestion_tools/scripts/common/db_models.py b/ingestion_tools/scripts/common/db_models.py
@@ -206,6 +206,7 @@ class Meta:
     orcid = CharField(null=True)
     corresponding_author_status = BooleanField(default=False)
     primary_annotator_status = BooleanField(default=False)
+    primary_author_status = BooleanField(default=False)
     email = CharField(null=True)
     affiliation_name = CharField(null=True)
     affiliation_address = CharField(null=True)

diff --git a/ingestion_tools/scripts/importers/db/annotation.py b/ingestion_tools/scripts/importers/db/annotation.py
@@ -147,6 +147,7 @@ def update_data_map(self, data_map: dict[str, Any], metadata: dict[str, Any], in
         data_map = super().update_data_map(data_map, metadata, index)
         primary_author_status = {
             "primary_annotator_status": metadata.get("primary_annotator_status", metadata.get("primary_author_status")),
+            "primary_author_status": metadata.get("primary_annotator_status", metadata.get("primary_author_status")),
         }
         return {**data_map, **primary_author_status}
 

diff --git a/ingestion_tools/scripts/tests/db_import/test_db_annotation_import.py b/ingestion_tools/scripts/tests/db_import/test_db_annotation_import.py
@@ -84,20 +84,23 @@ def expected_annotation_authors() -> list[dict[str, Any]]:
             "name": "Jane Smith",
             "corresponding_author_status": False,
             "primary_annotator_status": True,
+            "primary_author_status": True,
             "author_list_order": 1,
         },
         {
             "annotation_id": ANNOTATION_ID,
             "name": "J Carpenter",
             "corresponding_author_status": False,
             "primary_annotator_status": True,
+            "primary_author_status": True,
             "author_list_order": 2,
         },
         {
             "annotation_id": ANNOTATION_ID,
             "name": "John Doe",
             "corresponding_author_status": False,
             "primary_annotator_status": False,
+            "primary_author_status": False,
             "orcid": "0000-0000-1234-0000",
             "email": "jdoe@test.com",
             "author_list_order": 3,

diff --git a/test_infra/sql/schema.sql b/test_infra/sql/schema.sql
@@ -116,7 +116,8 @@ CREATE TABLE public.annotation_authors (
     affiliation_name character varying,
     affiliation_address character varying,
     affiliation_identifier character varying,
-    author_list_order integer
+    author_list_order integer,
+    primary_author_status boolean
 );
 
 

diff --git a/test_infra/sql/seed_db_data.sql b/test_infra/sql/seed_db_data.sql
@@ -29,16 +29,16 @@ INSERT INTO public.annotations VALUES (43, 's3://test-public-bucket/20002/RUN001
 INSERT INTO public.annotations VALUES (44, 's3://test-public-bucket/20002/RUN002/TomogramVoxelSpacing13.48/Annotations/author4-ribosome-1.0.json', 'http://localhost:4444/20002/RUN002/TomogramVoxelSpacing13.48/Annotations/author4-ribosome-1.0.json', '2023-04-01', '2023-06-01', '2023-06-01', 'EMPIAR-77777', 'Manual', true, 'Ribosome', 'GO:000000A', NULL, NULL, 16, NULL, NULL, NULL, 7, NULL, true);
 INSERT INTO public.annotations VALUES (45, 's3://test-public-bucket/20002/RUN002/TomogramVoxelSpacing13.48/Annotations/author4-spike-1.0.json', 'http://localhost:4444/20002/RUN002/TomogramVoxelSpacing13.48/Annotations/author4-spike-1.0.json', '2023-04-01', '2023-06-01', '2023-06-01', 'EMPIAR-77777', 'Manual', true, 'Spike Protein', 'GO:000000A', NULL, NULL, 16, NULL, NULL, NULL, 7, NULL, true);
 
-INSERT INTO public.annotation_authors VALUES (50, 40, 'Author 1', '0000-0000-0000-0007', false, true, NULL, NULL, NULL, NULL, NULL);
-INSERT INTO public.annotation_authors VALUES (51, 40, 'Author 2', '0000-0000-0000-0008', false, true, NULL, NULL, NULL, NULL, NULL);
-INSERT INTO public.annotation_authors VALUES (52, 41, 'Author 1', '0000-0000-0000-0007', false, true, NULL, NULL, NULL, NULL, NULL);
-INSERT INTO public.annotation_authors VALUES (53, 41, 'Author 2', '0000-0000-0000-0008', false, true, NULL, NULL, NULL, NULL, NULL);
-INSERT INTO public.annotation_authors VALUES (54, 42, 'Author 3', '0000-0000-0000-0039', false, true, NULL, NULL, NULL, NULL, NULL);
-INSERT INTO public.annotation_authors VALUES (55, 42, 'Author 4', '0000-0000-0000-0049', false, true, NULL, NULL, NULL, NULL, NULL);
-INSERT INTO public.annotation_authors VALUES (56, 43, 'Author 5', '0000-0000-0000-0059', false, true, NULL, NULL, NULL, NULL, NULL);
-INSERT INTO public.annotation_authors VALUES (57, 44, 'Author 6', '0000-0000-0000-0069', false, true, NULL, NULL, NULL, NULL, NULL);
-INSERT INTO public.annotation_authors VALUES (58, 45, 'Author 7', '0000-0000-0000-0079', false, true, NULL, NULL, NULL, NULL, NULL);
-INSERT INTO public.annotation_authors VALUES (59, 45, 'Author 8', '0000-0000-0000-0089', false, true, NULL, NULL, NULL, NULL, NULL);
+INSERT INTO public.annotation_authors VALUES (50, 40, 'Author 1', '0000-0000-0000-0007', false, true, NULL, NULL, NULL, NULL, NULL, true);
+INSERT INTO public.annotation_authors VALUES (51, 40, 'Author 2', '0000-0000-0000-0008', false, NULL, NULL, NULL, NULL, NULL, NULL, NULL);
+INSERT INTO public.annotation_authors VALUES (52, 41, 'Author 1', '0000-0000-0000-0007', false, true, NULL, NULL, NULL, NULL, NULL, true);
+INSERT INTO public.annotation_authors VALUES (53, 41, 'Author 2', '0000-0000-0000-0008', true,  NULL, NULL, NULL, NULL, NULL, NULL  NULL);
+INSERT INTO public.annotation_authors VALUES (54, 42, 'Author 3', '0000-0000-0000-0039', false, true, NULL, NULL, NULL, NULL, NULL, true);
+INSERT INTO public.annotation_authors VALUES (55, 42, 'Author 4', '0000-0000-0000-0049', true, false, NULL, NULL, NULL, NULL, NULL, false);
+INSERT INTO public.annotation_authors VALUES (56, 43, 'Author 5', '0000-0000-0000-0059', false, true, NULL, NULL, NULL, NULL, NULL, true);
+INSERT INTO public.annotation_authors VALUES (57, 44, 'Author 6', '0000-0000-0000-0069', false, true, NULL, NULL, NULL, NULL, NULL, true);
+INSERT INTO public.annotation_authors VALUES (58, 45, 'Author 7', '0000-0000-0000-0079', false, true, NULL, NULL, NULL, NULL, NULL, true);
+INSERT INTO public.annotation_authors VALUES (59, 45, 'Author 8', '0000-0000-0000-0089', false, true, NULL, NULL, NULL, NULL, NULL, true);
 
 
 INSERT INTO public.annotation_files VALUES (70, 40, 'OrientedPoint', 'ndjson', 'http://localhost:4444/20001/RUN1/TomogramVoxelSpacing13.48/Annotations/mitochondria.ndjson', 's3://test-public-bucket/20001/RUN1/TomogramVoxelSpacing13.48/Annotations/mitochondria.ndjson');