style with black

Author: jdkent

store/neurostore/ingest/extracted_features.py

@@ -36,9 +36,13 @@ def ingest_feature(feature_directory):
             name=pipeline_info["name"],
             version=pipeline_info["version"],
             description=pipeline_info.get("description"),
-            study_dependent=True if pipeline_info.get("type", False) == "dependent" else False,
-            ace_compatible="ace" in pipeline_info.get("arguments", {}).get("input_sources", []),
-            pubget_compatible="pubget" in pipeline_info.get("arguments", {}).get("input_sources", []),
+            study_dependent=(
+                True if pipeline_info.get("type", False) == "dependent" else False
+            ),
+            ace_compatible="ace"
+            in pipeline_info.get("arguments", {}).get("input_sources", []),
+            pubget_compatible="pubget"
+            in pipeline_info.get("arguments", {}).get("input_sources", []),
             derived_from=pipeline_info.get("derived_from", None),
         )
         db.session.add(pipeline)

store/neurostore/models/data.py

@@ -596,7 +596,9 @@ class PipelineRunResultVote(BaseMixin, db.Model):
     __tablename__ = "pipeline_run_result_votes"
 
     run_result_id = db.Column(
-        db.Text, db.ForeignKey("pipeline_run_results.id", ondelete="CASCADE"), index=True
+        db.Text,
+        db.ForeignKey("pipeline_run_results.id", ondelete="CASCADE"),
+        index=True,
     )
     user_id = db.Column(db.Text, db.ForeignKey("users.external_id"), index=True)
     accurate = db.Column(db.Boolean)
@@ -605,6 +607,7 @@ class PipelineRunResultVote(BaseMixin, db.Model):
     )
     user = relationship("User", backref=backref("votes", passive_deletes=True))
 
+
 # from . import event_listeners  # noqa E402
 
 # del event_listeners

store/neurostore/resources/__init__.py

@@ -22,6 +22,7 @@
     PipelineRunResultsView,
     PipelineRunResultVotesView,
 )
+
 __all__ = [
     "StudysetsView",
     "AnnotationsView",

store/neurostore/resources/pipeline.py

@@ -1,9 +1,22 @@
 from flask import request, jsonify
-from neurostore.models.data import Pipeline, PipelineConfig, PipelineRun, PipelineRunResult, PipelineRunResultVote
-from neurostore.schemas.pipeline import PipelineSchema, PipelineConfigSchema, PipelineRunSchema, PipelineRunResultSchema, PipelineRunResultVoteSchema
+from neurostore.models.data import (
+    Pipeline,
+    PipelineConfig,
+    PipelineRun,
+    PipelineRunResult,
+    PipelineRunResultVote,
+)
+from neurostore.schemas.pipeline import (
+    PipelineSchema,
+    PipelineConfigSchema,
+    PipelineRunSchema,
+    PipelineRunResultSchema,
+    PipelineRunResultVoteSchema,
+)
 from neurostore.database import db
 from .base import ObjectView, ListView
 
+
 class PipelinesView(ObjectView, ListView):
     model = Pipeline
     schema = PipelineSchema
@@ -34,7 +47,7 @@ def delete(self, id):
         pipeline = self.model.query.get(id)
         db.session.delete(pipeline)
         db.session.commit()
-        return '', 204
+        return "", 204
 
 
 class PipelineConfigsView(ObjectView, ListView):
@@ -67,7 +80,7 @@ def delete(self, id):
         pipeline_config = self.model.query.get(id)
         db.session.delete(pipeline_config)
         db.session.commit()
-        return '', 204
+        return "", 204
 
 
 class PipelineRunsView(ObjectView, ListView):
@@ -100,7 +113,7 @@ def delete(self, pipeline_run_id):
         pipeline_run = self.model.query.get(pipeline_run_id)
         db.session.delete(pipeline_run)
         db.session.commit()
-        return '', 204
+        return "", 204
 
 
 class PipelineRunResultsView(ObjectView, ListView):
@@ -133,7 +146,7 @@ def delete(self, pipeline_run_result_id):
         pipeline_run_result = self.model.query.get(pipeline_run_result_id)
         db.session.delete(pipeline_run_result)
         db.session.commit()
-        return '', 204
+        return "", 204
 
 
 class PipelineRunResultVotesView(ObjectView, ListView):
@@ -166,4 +179,4 @@ def delete(self, pipeline_run_result_vote_id):
         pipeline_run_result_vote = self.model.query.get(pipeline_run_result_vote_id)
         db.session.delete(pipeline_run_result_vote)
         db.session.commit()
-        return '', 204
+        return "", 204

store/neurostore/schemas/pipeline.py

@@ -1,5 +1,12 @@
 from marshmallow import Schema, fields, post_load
-from neurostore.models.data import Pipeline, PipelineConfig, PipelineRun, PipelineRunResult, PipelineRunResultVote
+from neurostore.models.data import (
+    Pipeline,
+    PipelineConfig,
+    PipelineRun,
+    PipelineRunResult,
+    PipelineRunResultVote,
+)
+
 
 class PipelineSchema(Schema):
     id = fields.String(dump_only=True)

store/neurostore/tests/api/test_pipeline_resources.py

@@ -1,30 +1,47 @@
 import pytest
 from flask import url_for
-from neurostore.models.data import Pipeline, PipelineConfig, PipelineRun, PipelineRunResult, PipelineRunResultVote, BaseStudy
-from neurostore.schemas.pipeline import PipelineSchema, PipelineConfigSchema, PipelineRunSchema, PipelineRunResultSchema, PipelineRunResultVoteSchema
+from neurostore.models.data import (
+    Pipeline,
+    PipelineConfig,
+    PipelineRun,
+    PipelineRunResult,
+    PipelineRunResultVote,
+    BaseStudy,
+)
+from neurostore.schemas.pipeline import (
+    PipelineSchema,
+    PipelineConfigSchema,
+    PipelineRunSchema,
+    PipelineRunResultSchema,
+    PipelineRunResultVoteSchema,
+)
 from neurostore.database import db
 
+
 @pytest.fixture
 def pipeline(session, pipeline_payload):
     pipeline = Pipeline(**pipeline_payload)
     session.add(pipeline)
     session.commit()
     return pipeline
 
+
 @pytest.fixture
 def pipeline_config(session, pipeline_config_payload):
     pipeline_config = PipelineConfig(**pipeline_config_payload)
     session.add(pipeline_config)
     session.commit()
     return pipeline_config
 
+
 @pytest.fixture
 def pipeline_run(session, pipeline_run_payload):
     pipeline_run = PipelineRun(**pipeline_run_payload)
     session.add(pipeline_run)
     session.commit()
     return pipeline_run
 
+
 @pytest.fixture
 def pipeline_run_result(session, pipeline_run_result_payload):
     pipeline_run_result = PipelineRunResult(**pipeline_run_result_payload)
@@ -42,24 +59,23 @@ def pipeline_payload():
         "study_dependent": True,
         "ace_compatible": False,
         "pubget_compatible": True,
-        "derived_from": "Base Pipeline"
+        "derived_from": "Base Pipeline",
     }
 
+
 @pytest.fixture
 def pipeline_config_payload(pipeline):
     return {
         "pipeline_id": pipeline.id,
         "config": {"param1": "value1", "param2": "value2"},
-        "config_hash": "abc123"
+        "config_hash": "abc123",
     }
 
+
 @pytest.fixture
 def pipeline_run_payload(pipeline, pipeline_config):
-    return {
-        "pipeline_id": pipeline.id,
-        "config_id": pipeline_config.id,
-        "run_index": 1
-    }
+    return {"pipeline_id": pipeline.id, "config_id": pipeline_config.id, "run_index": 1}
+
 
 @pytest.fixture
 def pipeline_run_result_payload(pipeline_run):
@@ -71,135 +87,157 @@ def pipeline_run_result_payload(pipeline_run):
         "base_study_id": base_study.id,
         "date_executed": "2023-01-01T00:00:00Z",
         "data": {"result": "success"},
-        "file_inputs": {"input1": "file1"}
+        "file_inputs": {"input1": "file1"},
     }
 
 
 def test_create_pipeline(auth_client, pipeline_payload):
-    response = auth_client.post('/api/pipelines/', data=pipeline_payload)
+    response = auth_client.post("/api/pipelines/", data=pipeline_payload)
     assert response.status_code == 201
     data = response.json()
     assert data["name"] == pipeline_payload["name"]
 
+
 def test_get_pipeline(auth_client, pipeline_payload, session):
     pipeline = Pipeline(**pipeline_payload)
     db.session.add(pipeline)
     db.session.commit()
-    response = auth_client.get(f'/api/pipelines/{pipeline.id}')
+    response = auth_client.get(f"/api/pipelines/{pipeline.id}")
     assert response.status_code == 200
     data = response.json()
     assert data["name"] == pipeline_payload["name"]
 
+
 def test_update_pipeline(auth_client, pipeline_payload, session):
     pipeline = Pipeline(**pipeline_payload)
     db.session.add(pipeline)
     db.session.commit()
     updated_payload = {"name": "Updated Pipeline"}
-    response = auth_client.put(f'/api/pipelines/{pipeline.id}', data=updated_payload)
+    response = auth_client.put(f"/api/pipelines/{pipeline.id}", data=updated_payload)
     assert response.status_code == 200
     data = response.json()
     assert data["name"] == "Updated Pipeline"
 
+
 def test_delete_pipeline(auth_client, pipeline_payload):
     pipeline = Pipeline(**pipeline_payload)
     db.session.add(pipeline)
     db.session.commit()
-    response = auth_client.delete(f'/api/pipelines/{pipeline.id}')
+    response = auth_client.delete(f"/api/pipelines/{pipeline.id}")
     assert response.status_code == 204
 
 
 def test_create_pipeline_config(auth_client, pipeline_config_payload, session):
-    response = auth_client.post('/api/pipeline-configs/', data=pipeline_config_payload)
+    response = auth_client.post("/api/pipeline-configs/", data=pipeline_config_payload)
     assert response.status_code == 201
     data = response.json()
     assert data["config"] == pipeline_config_payload["config"]
 
+
 def test_get_pipeline_config(auth_client, pipeline_config_payload, session):
     pipeline_config = PipelineConfig(**pipeline_config_payload)
     db.session.add(pipeline_config)
     db.session.commit()
-    response = auth_client.get(f'/api/pipeline-configs/{pipeline_config.id}')
+    response = auth_client.get(f"/api/pipeline-configs/{pipeline_config.id}")
     assert response.status_code == 200
     data = response.json()
     assert data["config"] == pipeline_config_payload["config"]
 
+
 def test_update_pipeline_config(auth_client, pipeline_config_payload, session):
     pipeline_config = PipelineConfig(**pipeline_config_payload)
     db.session.add(pipeline_config)
     db.session.commit()
     updated_payload = {"config": {"param1": "new_value"}}
-    response = auth_client.put(f'/api/pipeline-configs/{pipeline_config.id}', data=updated_payload)
+    response = auth_client.put(
+        f"/api/pipeline-configs/{pipeline_config.id}", data=updated_payload
+    )
     assert response.status_code == 200
     data = response.json()
     assert data["config"] == {"param1": "new_value"}
 
+
 def test_delete_pipeline_config(auth_client, pipeline_config_payload, session):
     pipeline_config = PipelineConfig(**pipeline_config_payload)
     db.session.add(pipeline_config)
     db.session.commit()
-    response = auth_client.delete(f'/api/pipeline-configs/{pipeline_config.id}')
+    response = auth_client.delete(f"/api/pipeline-configs/{pipeline_config.id}")
     assert response.status_code == 204
 
+
 def test_create_pipeline_run(auth_client, pipeline_run_payload, session):
-    response = auth_client.post('/api/pipeline-runs/', data=pipeline_run_payload)
+    response = auth_client.post("/api/pipeline-runs/", data=pipeline_run_payload)
     assert response.status_code == 201
     data = response.json()
     assert data["pipeline_id"] == pipeline_run_payload["pipeline_id"]
 
+
 def test_get_pipeline_run(auth_client, pipeline_run_payload, session):
     pipeline_run = PipelineRun(**pipeline_run_payload)
     db.session.add(pipeline_run)
     db.session.commit()
-    response = auth_client.get(f'/api/pipeline-runs/{pipeline_run.id}')
+    response = auth_client.get(f"/api/pipeline-runs/{pipeline_run.id}")
     assert response.status_code == 200
     data = response.json()
     assert data["pipeline_id"] == pipeline_run_payload["pipeline_id"]
 
+
 def test_update_pipeline_run(auth_client, pipeline_run_payload, session):
     pipeline_run = PipelineRun(**pipeline_run_payload)
     db.session.add(pipeline_run)
     db.session.commit()
     updated_payload = {"run_index": 2}
-    response = auth_client.put(f'/api/pipeline-runs/{pipeline_run.id}', data=updated_payload)
+    response = auth_client.put(
+        f"/api/pipeline-runs/{pipeline_run.id}", data=updated_payload
+    )
     assert response.status_code == 200
     data = response.json()
     assert data["run_index"] == 2
 
+
 def test_delete_pipeline_run(auth_client, pipeline_run_payload, session):
     pipeline_run = PipelineRun(**pipeline_run_payload)
     db.session.add(pipeline_run)
     db.session.commit()
-    response = auth_client.delete(f'/api/pipeline-runs/{pipeline_run.id}')
+    response = auth_client.delete(f"/api/pipeline-runs/{pipeline_run.id}")
     assert response.status_code == 204
 
+
 def test_create_pipeline_run_result(auth_client, pipeline_run_result_payload, session):
-    response = auth_client.post('/api/pipeline-run-results/', data=pipeline_run_result_payload)
+    response = auth_client.post(
+        "/api/pipeline-run-results/", data=pipeline_run_result_payload
+    )
     assert response.status_code == 201
     data = response.json()
     assert data["run_id"] == pipeline_run_result_payload["run_id"]
 
+
 def test_get_pipeline_run_result(auth_client, pipeline_run_result_payload, session):
     pipeline_run_result = PipelineRunResult(**pipeline_run_result_payload)
     db.session.add(pipeline_run_result)
     db.session.commit()
-    response = auth_client.get(f'/api/pipeline-run-results/{pipeline_run_result.id}')
+    response = auth_client.get(f"/api/pipeline-run-results/{pipeline_run_result.id}")
     assert response.status_code == 200
     data = response.json()
     assert data["run_id"] == pipeline_run_result_payload["run_id"]
 
+
 def test_update_pipeline_run_result(auth_client, pipeline_run_result_payload, session):
     pipeline_run_result = PipelineRunResult(**pipeline_run_result_payload)
     db.session.add(pipeline_run_result)
     db.session.commit()
     updated_payload = {"data": {"result": "failure"}}
-    response = auth_client.put(f'/api/pipeline-run-results/{pipeline_run_result.id}', data=updated_payload)
+    response = auth_client.put(
+        f"/api/pipeline-run-results/{pipeline_run_result.id}", data=updated_payload
+    )
     assert response.status_code == 200
     data = response.json()
     assert data["data"] == {"result": "failure"}
 
+
 def test_delete_pipeline_run_result(auth_client, pipeline_run_result_payload, session):
     pipeline_run_result = PipelineRunResult(**pipeline_run_result_payload)
     db.session.add(pipeline_run_result)
     db.session.commit()
-    response = auth_client.delete(f'/api/pipeline-run-results/{pipeline_run_result.id}')
+    response = auth_client.delete(f"/api/pipeline-run-results/{pipeline_run_result.id}")
     assert response.status_code == 204

store/neurostore/tests/conftest.py

@@ -602,8 +602,8 @@ def create_demographic_features(session, ingest_neurosynth, tmp_path):
         "derived_from": None,
         "arguments": {
             "parallel": 1,
-            "inputs": ['text'],
-            "input_sources": ['pubget'],
+            "inputs": ["text"],
+            "input_sources": ["pubget"],
         },
     }
     with open(output_dir / "pipeline_info.json", "w") as f:

store/neurostore/tests/test_models.py

@@ -46,6 +46,7 @@ def test_Image():
 def test_Studyset():
     Studyset()
 
+
 def test_Pipeline():
     Pipeline()