Change pixl schema so that it makes sense on multi-schema db

cli/tests/conftest.py

@@ -93,7 +93,7 @@ def db_engine(monkeymodule) -> Engine:
     :returns Engine: Engine for use in other setup fixtures
     """
     # SQLite doesnt support schemas, so remove pixl schema from engine options
-    execution_options = {"schema_translate_map": {"pipeline": None}}
+    execution_options = {"schema_translate_map": {"pixl_pipeline": None}}
     engine = create_engine(
         "sqlite:///:memory:",
         execution_options=execution_options,

pixl_core/src/core/db/models.py

@@ -27,7 +27,7 @@
 class Base(DeclarativeBase):
     """sqlalchemy base class"""
 
-    metadata = MetaData(schema="pipeline")
+    metadata = MetaData(schema="pixl_pipeline")
 
 
 class Extract(Base):

pixl_core/tests/conftest.py

@@ -118,7 +118,7 @@ def db_engine(monkeymodule) -> Generator[Engine, None, None]:
     :returns Engine: Engine for use in other setup fixtures
     """
     # SQLite doesnt support schemas, so remove pixl schema from engine options
-    execution_options = {"schema_translate_map": {"pipeline": None}}
+    execution_options = {"schema_translate_map": {"pixl_pipeline": None}}
     engine = create_engine(
         "sqlite:///:memory:",
         execution_options=execution_options,

pixl_dcmd/tests/conftest.py

@@ -153,7 +153,7 @@ def db_engine(monkeymodule) -> Generator[Engine, None, None]:
     :returns Engine: Engine for use in other setup fixtures
     """
     # SQLite doesnt support schemas, so remove pixl schema from engine options
-    execution_options = {"schema_translate_map": {"pipeline": None}}
+    execution_options = {"schema_translate_map": {"pixl_pipeline": None}}
     engine = create_engine(
         "sqlite:///:memory:",
         execution_options=execution_options,

pixl_imaging/alembic/versions/83dcb3812628_add_study_uid_column_to_image_table.py

@@ -36,11 +36,13 @@
 
 def upgrade() -> None:
     # ### commands auto generated by Alembic - please adjust! ###
-    op.add_column("image", sa.Column("study_uid", sa.String(), nullable=True), schema="pipeline")
+    op.add_column(
+        "image", sa.Column("study_uid", sa.String(), nullable=True), schema="pixl_pipeline"
+    )
     # ### end Alembic commands ###
 
 
 def downgrade() -> None:
     # ### commands auto generated by Alembic - please adjust! ###
-    op.drop_column("image", "study_uid", schema="pipeline")
+    op.drop_column("image", "study_uid", schema="pixl_pipeline")
     # ### end Alembic commands ###

pixl_imaging/alembic/versions/bcaef54e2bfe_create_extract_and_image_tables.py

@@ -39,7 +39,7 @@ def upgrade() -> None:
         sa.Column("extract_id", sa.Integer(), nullable=False),
         sa.Column("slug", sa.String(), nullable=False),
         sa.PrimaryKeyConstraint("extract_id"),
-        schema="pipeline",
+        schema="pixl_pipeline",
     )
     op.create_table(
         "image",
@@ -52,13 +52,13 @@ def upgrade() -> None:
         sa.Column("extract_id", sa.Integer(), nullable=False),
         sa.ForeignKeyConstraint(
             ["extract_id"],
-            ["pipeline.extract.extract_id"],
+            ["pixl_pipeline.extract.extract_id"],
         ),
         sa.PrimaryKeyConstraint("image_id"),
-        schema="pipeline",
+        schema="pixl_pipeline",
     )
 
 
 def downgrade() -> None:
-    op.drop_table("image", schema="pipeline")
-    op.drop_table("extract", schema="pipeline")
+    op.drop_table("image", schema="pixl_pipeline")
+    op.drop_table("extract", schema="pixl_pipeline")

pixl_imaging/alembic/versions/cb5ee12a6e20_replace_hashed_id_with_pseudo_study_uid.py

@@ -33,11 +33,11 @@
 
 def upgrade() -> None:
     op.alter_column(
-        "image", "hashed_identifier", new_column_name="pseudo_study_uid", schema="pipeline"
+        "image", "hashed_identifier", new_column_name="pseudo_study_uid", schema="pixl_pipeline"
     )
 
 
 def downgrade() -> None:
     op.alter_column(
-        "image", "pseudo_study_uid", new_column_name="hashed_identifier", schema="pipeline"
+        "image", "pseudo_study_uid", new_column_name="hashed_identifier", schema="pixl_pipeline"
     )

pixl_imaging/alembic/versions/d947cc715eb1_add_pseudo_patient_id_column_to_image_table.py

@@ -39,12 +39,12 @@ def upgrade() -> None:
     op.add_column(
         "image",
         sa.Column("pseudo_patient_id", sa.String(length=255), nullable=True),
-        schema="pipeline",
+        schema="pixl_pipeline",
     )
     # ### end Alembic commands ###
 
 
 def downgrade() -> None:
     # ### commands auto generated by Alembic - please adjust! ###
-    op.drop_column("image", "pseudo_patient_id", schema="pipeline")
+    op.drop_column("image", "pseudo_patient_id", schema="pixl_pipeline")
     # ### end Alembic commands ###

postgres/pixl-db_init.sh

@@ -16,4 +16,4 @@
 set -euxo pipefail
 
 # Create the pipeline schema for keeping track of images and extracts
-psql -U "${POSTGRES_USER}" --dbname "${POSTGRES_DB}" -c "CREATE SCHEMA pipeline AUTHORIZATION ${POSTGRES_USER}"
+psql -U "${POSTGRES_USER}" --dbname "${POSTGRES_DB}" -c "CREATE SCHEMA pixl_pipeline AUTHORIZATION ${POSTGRES_USER}"