Remove deprecated Tomogram.is_standardized field

chanzuckerberg · Oct 10, 2024 · a0f984c · a0f984c
1 parent eca7d59
commit a0f984c
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Showing 16 changed files with 62 additions and 133 deletions.
diff --git a/apiv2/database/migrations/versions/20241010_135050_autogenerated.py b/apiv2/database/migrations/versions/20241010_135050_autogenerated.py
diff --git a/apiv2/database/migrations/versions/20241010_153240_autogenerated.py b/apiv2/database/migrations/versions/20241010_153240_autogenerated.py
diff --git a/apiv2/database/models/tomogram.py b/apiv2/database/models/tomogram.py
diff --git a/apiv2/db_import/common/finders.py b/apiv2/db_import/common/finders.py
@@ -1,4 +1,3 @@
-
 import logging
 import re
 from abc import ABC, abstractmethod

diff --git a/apiv2/db_import/importers/frame.py b/apiv2/db_import/importers/frame.py
@@ -15,6 +15,7 @@
 #   s3_frame_path: str
 #   https_frame_path: str
 
+
 class FrameItem(ItemDBImporter):
     direct_mapped_fields = {}
     id_fields = ["run_id", "s3_frame_path"]

diff --git a/apiv2/db_import/importers/gain.py b/apiv2/db_import/importers/gain.py
@@ -10,6 +10,7 @@
 #   s3_file_path: str
 #   https_file_path: str
 
+
 class GainItem(ItemDBImporter):
     direct_mapped_fields = {}
     id_fields = ["run_id", "s3_file_path"]

diff --git a/apiv2/db_import/tests/test_frame_import.py b/apiv2/db_import/tests/test_frame_import.py
@@ -27,12 +27,22 @@ def expected_frames(http_prefix: str) -> list[dict[str, Any]]:
         },
     ]
 
+
 @write_data
 def populate_existing_frames(session: sa.orm.Session) -> models.Frame:
     populate_run(session)
-    stale_frame = models.Frame(run_id=RUN1_ID, deposition_id = DEPOSITION_ID1, https_frame_path="STALE_FRAME", s3_frame_path="STALE_FRAME")
+    stale_frame = models.Frame(
+        run_id=RUN1_ID, deposition_id=DEPOSITION_ID1, https_frame_path="STALE_FRAME", s3_frame_path="STALE_FRAME",
+    )
     session.add(stale_frame)
-    return models.Frame(id=333, run_id=RUN1_ID, deposition_id=DEPOSITION_ID1, s3_frame_path="s3://test-public-bucket/30001/RUN1/Frames/frame1", https_frame_path="https://foo.com/30001/RUN1/Frames/frame1")
+    return models.Frame(
+        id=333,
+        run_id=RUN1_ID,
+        deposition_id=DEPOSITION_ID1,
+        s3_frame_path="s3://test-public-bucket/30001/RUN1/Frames/frame1",
+        https_frame_path="https://foo.com/30001/RUN1/Frames/frame1",
+    )
+
 
 # Tests addition of new frames, and updating entries already existing in db
 def test_import_frames(
@@ -45,7 +55,7 @@ def test_import_frames(
     sync_db_session.commit()
     actual = verify_dataset_import(import_frames=True)
     expected_iter = iter(expected_frames)
-    for run in [run for run in actual.runs if run.name == 'RUN1']:
+    for run in [run for run in actual.runs if run.name == "RUN1"]:
         assert len(run.frames) == 2
         assert run.frames[0].id == 333
         for frame in run.frames:

diff --git a/apiv2/db_import/tests/test_gain_import.py b/apiv2/db_import/tests/test_gain_import.py
@@ -26,12 +26,19 @@ def expected_gains(http_prefix: str) -> list[dict[str, Any]]:
         },
     ]
 
+
 @write_data
 def populate_existing_gains(session: sa.orm.Session) -> models.GainFile:
     populate_run(session)
     stale_frame = models.GainFile(run_id=RUN1_ID, https_file_path="STALE_FRAME", s3_file_path="STALE_FRAME")
     session.add(stale_frame)
-    return models.GainFile(id=333, run_id=RUN1_ID, s3_file_path="s3://test-public-bucket/30001/RUN1/Frames/run1_gain.mrc", https_file_path="meep")
+    return models.GainFile(
+        id=333,
+        run_id=RUN1_ID,
+        s3_file_path="s3://test-public-bucket/30001/RUN1/Frames/run1_gain.mrc",
+        https_file_path="meep",
+    )
+
 
 # Tests addition of new gains, and updating entries already existing in db, and cleanup of old gains.
 def test_import_gains(
@@ -44,7 +51,7 @@ def test_import_gains(
     sync_db_session.commit()
     actual = verify_dataset_import(import_gains=True)
     expected_iter = iter(expected_gains)
-    for run in [run for run in actual.runs if run.name == 'RUN1']:
+    for run in [run for run in actual.runs if run.name == "RUN1"]:
         assert len(run.gain_files) == 2
         assert run.gain_files[0].id == 333
         for gain in run.gain_files:

diff --git a/apiv2/graphql_api/helpers/tomogram.py b/apiv2/graphql_api/helpers/tomogram.py
diff --git a/apiv2/graphql_api/schema.graphql b/apiv2/graphql_api/schema.graphql
diff --git a/apiv2/graphql_api/schema.json b/apiv2/graphql_api/schema.json