ENH: add alembic migration

.gitignore

@@ -24,6 +24,9 @@ target/
 .DS_Store
 *~
 
+#alembic
+alembic.ini
+
 #vim
 *.swp
 *.swo

CHANGELOG.md

@@ -8,6 +8,7 @@ Write the date in place of the "Unreleased" in the case a new version is release
 ### Added
 - Add method to `TableAdapter` which accepts a Python dictionary.
 - Added an `Arrow` adapter which supports reading/writing arrow tables via `RecordBatchFileReader`/`RecordBatchFileWriter`.
+- Add an alembic catalog migration script to rename `path` parameters of HDF5 nodes to `dataset`.
 
 ### Changed
 - Make `tiled.client` accept a Python dictionary when fed to `write_dataframe()`.

tiled/catalog/migrations/versions/562203c724c7_change_path_to_dataset_in_hdf5_assets.py

@@ -0,0 +1,47 @@
+"""Change 'path' to 'dataset' in HDF5 assets
+
+Revision ID: 562203c724c7
+Revises: ed3a4223a600
+Create Date: 2024-08-09 10:13:36.384838
+
+"""
+import sqlalchemy as sa
+from alembic import op
+
+from tiled.catalog.orm import JSONVariant
+
+# revision identifiers, used by Alembic.
+revision = "562203c724c7"
+down_revision = "ed3a4223a600"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    connection = op.get_bind()
+    nodes = sa.Table(
+        "nodes",
+        sa.MetaData(),
+        sa.Column("id", sa.Integer),
+        sa.Column("metadata", JSONVariant),
+    )
+
+    # Loop over all nodes that have 'parameters' field, choose and update those related to hdf5 files
+    cursor = connection.execute(
+        sa.select(nodes.c.id, nodes.c.metadata).select_from(nodes)
+    )
+    for _id, _md in cursor:
+        if "hdf5" in (_md.get("mimetype", "") + _md.get("spec", "")).lower():
+            if isinstance(_md.get("parameters"), dict) and (
+                "path" in _md["parameters"].keys()
+            ):
+                _md["parameters"]["dataset"] = _md["parameters"].pop("path")
+                connection.execute(
+                    nodes.update().where(nodes.c.id == _id).values(metadata=_md)
+                )
+
+
+def downgrade():
+    # This _could_ be implemented but we will wait for a need since we are
+    # still in alpha releases.
+    raise NotImplementedError

tiled/catalog/migrations/versions/83889e049ddc_add_table_to_structurefamily_enum.py

@@ -31,7 +31,7 @@ def upgrade():
     connection = op.get_bind()
 
     if connection.engine.dialect.name == "postgresql":
-        # This change must be committed befor ethe new 'table' enum value can be used.
+        # This change must be committed before the new 'table' enum value can be used.
         with op.get_context().autocommit_block():
             op.execute(
                 sa.text(