Merge pull request #48 from CAVEconnectome/fix_migrations

feat: check if tables or columns already exist

dynamicannotationdb/migration/alembic/versions/309cf493a1e2_adding_warning_field.py

@@ -9,6 +9,8 @@
 import sqlalchemy as sa
 
 from sqlalchemy.dialects import postgresql
+from sqlalchemy import engine_from_config
+from sqlalchemy.engine import reflection
 
 # revision identifiers, used by Alembic.
 revision = '309cf493a1e2'
@@ -17,10 +19,20 @@
 depends_on = None
 
 
+def _table_has_column(table, column):
+    config = op.get_context().config
+    engine = engine_from_config(
+        config.get_section(config.config_ini_section), prefix="sqlalchemy."
+    )
+
+    insp = reflection.Inspector.from_engine(engine)
+    return any(column in col["name"] for col in insp.get_columns(table))
+
+
+
 def upgrade():
-    # ### commands auto generated by Alembic - please adjust! ###
-    op.add_column('annotation_table_metadata', sa.Column('notice_text', sa.Text(), nullable=True))
-    # ### end Alembic commands ###
+    if not _table_has_column('annotation_table_metadata', 'notice_text'):
+        op.add_column('annotation_table_metadata', sa.Column('notice_text', sa.Text(), nullable=True))
 
 
 def downgrade():

dynamicannotationdb/migration/alembic/versions/5a1d7c0ad006_add_status_column.py

@@ -8,32 +8,43 @@
 from alembic import op
 import sqlalchemy as sa
 from sqlalchemy.dialects import postgresql
+from sqlalchemy import engine_from_config
+from sqlalchemy.engine import reflection
 
 # revision identifiers, used by Alembic.
 revision = "5a1d7c0ad006"
 down_revision = "7c79eff751b4"
 branch_labels = None
 depends_on = None
 
+def _table_has_column(table, column):
+    config = op.get_context().config
+    engine = engine_from_config(
+        config.get_section(config.config_ini_section), prefix="sqlalchemy."
+    )
+
+    insp = reflection.Inspector.from_engine(engine)
+    return any(column in col["name"] for col in insp.get_columns(table))
 
 def upgrade():
     status_enum = postgresql.ENUM(
         "AVAILABLE", "RUNNING", "FAILED", "EXPIRED", name="version_status"
     )
     status_enum.create(op.get_bind())
-    op.add_column(
-        "analysisversion",
-        sa.Column(
-            "status",
-            postgresql.ENUM(
-                "AVAILABLE", "RUNNING", "FAILED", "EXPIRED", name="version_status"
-            ),
-            nullable=True,
+    if not _table_has_column("analysisversion", "status"):
+        op.add_column(
+            "analysisversion",
+            sa.Column(
+                "status",
+                postgresql.ENUM(
+                    "AVAILABLE", "RUNNING", "FAILED", "EXPIRED", name="version_status"
+                ),
+                nullable=True,
 
-        ),
-    )
-    op.execute("UPDATE analysisversion SET status = 'EXPIRED'")
-    op.alter_column('analysisversion', 'status', nullable=False)
+            ),
+        )
+        op.execute("UPDATE analysisversion SET status = 'EXPIRED'")
+        op.alter_column('analysisversion', 'status', nullable=False)
 
 
 def downgrade():

dynamicannotationdb/migration/alembic/versions/6e7f580ff680_add_error_msg.py

@@ -9,6 +9,8 @@
 import sqlalchemy as sa
 
 from sqlalchemy.dialects import postgresql
+from sqlalchemy import engine_from_config
+from sqlalchemy.engine import reflection
 
 # revision identifiers, used by Alembic.
 revision = '6e7f580ff680'
@@ -17,8 +19,18 @@
 depends_on = None
 
 
+def _table_has_column(table, column):
+    config = op.get_context().config
+    engine = engine_from_config(
+        config.get_section(config.config_ini_section), prefix="sqlalchemy."
+    )
+
+    insp = reflection.Inspector.from_engine(engine)
+    return any(column in col["name"] for col in insp.get_columns(table))
+
 def upgrade():
-    op.add_column('version_error', sa.Column('exception', sa.String(), nullable=True))
+    if not _table_has_column("version_error", "exception"):
+        op.add_column('version_error', sa.Column('exception', sa.String(), nullable=True))
 
 
 def downgrade():

dynamicannotationdb/migration/alembic/versions/7c79eff751b4_add_parent_version_column.py

@@ -29,14 +29,16 @@ def _table_has_column(table, column):
 
 
 def upgrade():
-    with op.batch_alter_table("analysisversion", schema=None) as batch_op:
-        op.add_column(
-            "analysisversion",
-            sa.Column("parent_version", sa.Integer(), nullable=True),
-        )
-        op.create_foreign_key(
-            None, "analysisversion", "analysisversion", ["parent_version"], ["id"]
-        )
+    if not _table_has_column("analysisversion", "parent_version"):  
+
+        with op.batch_alter_table("analysisversion", schema=None) as batch_op:
+            op.add_column(
+                "analysisversion",
+                sa.Column("parent_version", sa.Integer(), nullable=True),
+            )
+            op.create_foreign_key(
+                None, "analysisversion", "analysisversion", ["parent_version"], ["id"]
+            )
 
 
 def downgrade():

dynamicannotationdb/migration/alembic/versions/814d72d74e3b_add_version_error_table.py

@@ -9,34 +9,46 @@
 import sqlalchemy as sa
 
 from sqlalchemy.dialects import postgresql
+from sqlalchemy import engine_from_config
+from sqlalchemy.engine import reflection
 
 # revision identifiers, used by Alembic.
 revision = "814d72d74e3b"
 down_revision = "975a79461cab"
 branch_labels = None
 depends_on = None
 
+def get_tables():
+    config = op.get_context().config
+    engine = engine_from_config(
+        config.get_section(config.config_ini_section), prefix="sqlalchemy."
+    )
+    inspector = reflection.Inspector.from_engine(engine)
+    return inspector.get_table_names()
+
 
 def upgrade():
-    op.create_table(
-        "version_error",
-        sa.Column("id", sa.INTEGER(), autoincrement=True, nullable=False),
-        sa.Column(
-            "error",
-            postgresql.JSON(astext_type=sa.Text()),
-            autoincrement=False,
-            nullable=True,
-        ),
-        sa.Column(
-            "analysisversion_id", sa.INTEGER(), autoincrement=False, nullable=True
-        ),
-        sa.ForeignKeyConstraint(
-            ["analysisversion_id"],
-            ["analysisversion.id"],
-            name="version_error_analysisversion_id_fkey",
-        ),
-        sa.PrimaryKeyConstraint("id", name="version_error_pkey"),
-    )
+    tables = get_tables()
+    if "version_error" not in tables:
+        op.create_table(
+            "version_error",
+            sa.Column("id", sa.INTEGER(), autoincrement=True, nullable=False),
+            sa.Column(
+                "error",
+                postgresql.JSON(astext_type=sa.Text()),
+                autoincrement=False,
+                nullable=True,
+            ),
+            sa.Column(
+                "analysisversion_id", sa.INTEGER(), autoincrement=False, nullable=True
+            ),
+            sa.ForeignKeyConstraint(
+                ["analysisversion_id"],
+                ["analysisversion.id"],
+                name="version_error_analysisversion_id_fkey",
+            ),
+            sa.PrimaryKeyConstraint("id", name="version_error_pkey"),
+        )
 
 
 def downgrade():

dynamicannotationdb/migration/alembic/versions/8fdc843fc202_adding_permission_and_last_modified.py

@@ -9,51 +9,64 @@
 import sqlalchemy as sa
 
 from sqlalchemy.dialects import postgresql
+from sqlalchemy import engine_from_config
+from sqlalchemy.engine import reflection
 
 # revision identifiers, used by Alembic.
 revision = "8fdc843fc202"
 down_revision = "6e7f580ff680"
 branch_labels = None
 depends_on = None
 
+def _table_has_column(table, column):
+    config = op.get_context().config
+    engine = engine_from_config(
+        config.get_section(config.config_ini_section), prefix="sqlalchemy."
+    )
+
+    insp = reflection.Inspector.from_engine(engine)
+    return any(column in col["name"] for col in insp.get_columns(table))
+
 
 def upgrade():
-    # ### commands auto generated by Alembic - please adjust! ###
     permission_enum = postgresql.ENUM(
         "PRIVATE", "GROUP", "PUBLIC", name="readwrite_permission"
     )
-    permission_enum.create(op.get_bind())
-
-    op.add_column(
-        "annotation_table_metadata",
-        sa.Column(
-            "write_permission",
-            postgresql.ENUM("PRIVATE", "GROUP", "PUBLIC", name="readwrite_permission"),
-            nullable=True,
-        ),
-    )
-    op.add_column(
-        "annotation_table_metadata",
-        sa.Column(
-            "read_permission",
-            postgresql.ENUM("PRIVATE", "GROUP", "PUBLIC", name="readwrite_permission"),
-            nullable=True,
-        ),
-    )
-    op.add_column(
-        "annotation_table_metadata",
-        sa.Column("last_modified", sa.DateTime(), nullable=True),
-    )
-    # ### end Alembic commands ###
-    op.execute("UPDATE annotation_table_metadata SET read_permission = 'PUBLIC'")
-    op.execute("UPDATE annotation_table_metadata SET write_permission = 'PRIVATE'")
-    op.execute("UPDATE annotation_table_metadata SET last_modified = current_timestamp")
+    permission_enum.create(op.get_bind())   
+
+    if not _table_has_column("annotation_table_metadata", "write_permission"):
+        op.add_column(
+            "annotation_table_metadata",
+            sa.Column(
+                "write_permission",
+                postgresql.ENUM("PRIVATE", "GROUP", "PUBLIC", name="readwrite_permission"),
+                nullable=True,
+            ),
+        )
+        op.execute("UPDATE annotation_table_metadata SET write_permission = 'PRIVATE'")
+        op.alter_column("annotation_table_metadata", "write_permission", nullable=False)
 
-    op.alter_column("annotation_table_metadata", "write_permission", nullable=False)
-    op.alter_column("annotation_table_metadata", "read_permission", nullable=False)
-    op.alter_column("annotation_table_metadata", "last_modified", nullable=False)
+    if not _table_has_column("annotation_table_metadata", "read_permission"):
+        op.add_column(
+            "annotation_table_metadata",
+            sa.Column(
+                "read_permission",
+                postgresql.ENUM("PRIVATE", "GROUP", "PUBLIC", name="readwrite_permission"),
+                nullable=True,
+            ),
+        )
+        op.execute("UPDATE annotation_table_metadata SET read_permission = 'PUBLIC'")
+        op.alter_column("annotation_table_metadata", "read_permission", nullable=False)
 
+    if not _table_has_column("annotation_table_metadata", "last_modified"):
+        op.add_column(
+            "annotation_table_metadata",
+            sa.Column("last_modified", sa.DateTime(), nullable=True),
+        )
 
+        op.execute("UPDATE annotation_table_metadata SET last_modified = current_timestamp")
+        op.alter_column("annotation_table_metadata", "last_modified", nullable=False)
+
 def downgrade():
     # ### commands auto generated by Alembic - please adjust! ###
     op.drop_column("annotation_table_metadata", "last_modified")

dynamicannotationdb/migration/alembic/versions/975a79461cab_add_is_merged.py

@@ -9,23 +9,34 @@
 import sqlalchemy as sa
 
 from sqlalchemy.dialects import postgresql
+from sqlalchemy import engine_from_config
+from sqlalchemy.engine import reflection
 
 # revision identifiers, used by Alembic.
 revision = "975a79461cab"
 down_revision = "5a1d7c0ad006"
 branch_labels = None
 depends_on = None
 
+def _table_has_column(table, column):
+    config = op.get_context().config
+    engine = engine_from_config(
+        config.get_section(config.config_ini_section), prefix="sqlalchemy."
+    )
 
-def upgrade():
+    insp = reflection.Inspector.from_engine(engine)
+    return any(column in col["name"] for col in insp.get_columns(table))
 
-    op.add_column(
-        "analysisversion",
-        sa.Column("is_merged", sa.Boolean(), nullable=True, default=True),
-    )
 
-    op.execute("UPDATE analysisversion SET is_merged = True")
-    op.alter_column('analysisversion', 'is_merged', nullable=False)
+def upgrade():
+    if not _table_has_column("analysisversion", "is_merged"):
+        op.add_column(
+            "analysisversion",
+            sa.Column("is_merged", sa.Boolean(), nullable=True, default=True),
+        )
+
+        op.execute("UPDATE analysisversion SET is_merged = True")
+        op.alter_column('analysisversion', 'is_merged', nullable=False)
 
 def downgrade():
     op.drop_column("analysisversion", "is_merged")

dynamicannotationdb/migration/alembic/versions/fac66b439033_add_view_model.py

@@ -9,28 +9,40 @@
 import sqlalchemy as sa
 
 from sqlalchemy.dialects import postgresql
+from sqlalchemy.engine import reflection
+from sqlalchemy import engine_from_config
 
 # revision identifiers, used by Alembic.
 revision = "fac66b439033"
 down_revision = "309cf493a1e2"
 branch_labels = None
 depends_on = None
 
+def get_tables():
+    config = op.get_context().config
+    engine = engine_from_config(
+        config.get_section(config.config_ini_section), prefix="sqlalchemy."
+    )
+    inspector = reflection.Inspector.from_engine(engine)
+    return inspector.get_table_names()
+
 
 def upgrade():
-    op.create_table(
-        "analysisviews",
-        sa.Column("id", sa.Integer(), nullable=False),
-        sa.Column("table_name", sa.String(length=100), nullable=False),
-        sa.Column("description", sa.Text(), nullable=False),
-        sa.Column("datastack_name", sa.String(length=100), nullable=False),
-        sa.Column("voxel_resolution_x", sa.Float(), nullable=False),
-        sa.Column("voxel_resolution_y", sa.Float(), nullable=False),
-        sa.Column("voxel_resolution_z", sa.Float(), nullable=False),
-        sa.Column("notice_text", sa.Text(), nullable=True),
-        sa.Column("live_compatible", sa.Boolean(), nullable=False),
-        sa.PrimaryKeyConstraint("id"),
-    )
+    tables = get_tables()
+    if "analysisviews" not in tables:
+        op.create_table(
+            "analysisviews",
+            sa.Column("id", sa.Integer(), nullable=False),
+            sa.Column("table_name", sa.String(length=100), nullable=False),
+            sa.Column("description", sa.Text(), nullable=False),
+            sa.Column("datastack_name", sa.String(length=100), nullable=False),
+            sa.Column("voxel_resolution_x", sa.Float(), nullable=False),
+            sa.Column("voxel_resolution_y", sa.Float(), nullable=False),
+            sa.Column("voxel_resolution_z", sa.Float(), nullable=False),
+            sa.Column("notice_text", sa.Text(), nullable=True),
+            sa.Column("live_compatible", sa.Boolean(), nullable=False),
+            sa.PrimaryKeyConstraint("id"),
+        )
 
 
 def downgrade():