sqla2.0 (#17)

* migrate to SQLAlchemy 2.0
chembl · Jan 27, 2023 · 1305063 · 1305063
1 parent 8733f47
commit 1305063
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Showing 4 changed files with 37 additions and 39 deletions.
diff --git a/cbl_migrator/migrator.py b/cbl_migrator/migrator.py
@@ -97,7 +97,7 @@ def fill_table(o_eng_conn, d_eng_conn, table, chunk_size):
                 res = connr.execute(q)
                 data = res.all()
                 if len(data):
-                    last_id = data[-1].__getitem__(pk.name)
+                    last_id = getattr(data[-1], pk.name)
                     with d_eng.begin() as conn:
                         conn.execute(
                             table.insert(),
@@ -225,7 +225,7 @@ def __copy_schema(self):
                 col = self.__fix_column_type(col, o_eng.name, d_eng.name)
                 col.autoincrement = False
                 new_metadata_cols.add(col)
-            table.columns = new_metadata_cols.as_immutable()
+            table.columns = new_metadata_cols.as_readonly()
             new_metadata_tables[table_name] = table
         metadata.tables = immutabledict(new_metadata_tables)
         metadata.create_all(d_eng)

diff --git a/cbl_migrator/test/schema.py b/cbl_migrator/test/schema.py
@@ -1,4 +1,4 @@
-from sqlalchemy.ext.declarative import declarative_base
+from sqlalchemy.orm import declarative_base
 from sqlalchemy import Column, ForeignKey, CheckConstraint
 from sqlalchemy.types import String, Integer, Float, Text
 

diff --git a/cbl_migrator/test/test_migration.py b/cbl_migrator/test/test_migration.py
@@ -1,4 +1,4 @@
-from sqlalchemy import MetaData, create_engine, inspect
+from sqlalchemy import MetaData, create_engine, inspect, insert
 from .schema import Base, Compound, CompoundStructure, CompoundProperties
 from .. import DbMigrator
 import unittest
@@ -97,40 +97,38 @@ def __gen_test_data(self):
         engine = create_engine(self.origin)
         Base.metadata.create_all(bind=engine)
 
-        # compound data
-        stmt = Compound.__table__.insert(
-            [
-                {"cid": i, "structure_type": "MOL", "compound_name": "chemblone"}
-                for i in range(1, 42)
-            ]
-        )
-        engine.execute(stmt)
-
-        # structure data
-        structure_data = []
-        for i in range(1, 42):
-            smiles = "CC(=O)Oc1ccccc1C(=O)O"
-            inchi_key = inchis[i - 1]
-            structure_data.append(
-                {
-                    "sid": i,
-                    "cid": i,
-                    "smiles": smiles,
-                    "molblock": molblock,
-                    "inchi_key": inchi_key,
-                }
+        com_stmt = insert(Compound)
+        com_struct_stmt = insert(CompoundStructure)
+        com_props_stmt = insert(CompoundProperties)
+
+        with engine.begin() as conn:
+            conn.execute(
+                com_stmt,
+                [
+                    {"cid": i, "structure_type": "MOL", "compound_name": "chemblone"}
+                    for i in range(1, 42)
+                ],
+            )
+            conn.execute(
+                com_struct_stmt,
+                [
+                    {
+                        "sid": i,
+                        "cid": i,
+                        "smiles": "CC(=O)Oc1ccccc1C(=O)O",
+                        "molblock": molblock,
+                        "inchi_key": inchis[i - 1],
+                    }
+                    for i in range(1, 42)
+                ],
+            )
+            conn.execute(
+                com_props_stmt,
+                [
+                    {"pid": i, "cid": i, "mw": random.random(), "logp": random.random()}
+                    for i in range(1, 42)
+                ],
             )
-        stmt = CompoundStructure.__table__.insert(structure_data)
-        engine.execute(stmt)
-
-        # properties data
-        stmt = CompoundProperties.__table__.insert(
-            [
-                {"pid": i, "cid": i, "mw": random.random(), "logp": random.random()}
-                for i in range(1, 42)
-            ]
-        )
-        engine.execute(stmt)
 
     def __get_tables_insp(self):
         o_eng = create_engine(self.origin)

diff --git a/setup.py b/setup.py
@@ -3,7 +3,7 @@
 if __name__ == "__main__":
     setup(
         name="cbl_migrator",
-        version="0.3.4",
+        version="0.3.5",
         author="Eloy Félix",
         author_email="eloyfelix@gmail.com",
         description="Migrates Oracle dbs to PostgreSQL, MySQL and SQLite",
@@ -12,7 +12,7 @@
         packages=["cbl_migrator", "cbl_migrator.bin"],
         long_description=open("README.md", encoding="utf-8").read(),
         long_description_content_type="text/markdown",
-        install_requires=["SQLAlchemy~=1.4"],
+        install_requires=["SQLAlchemy~=2.0"],
         tests_require=["pytest"],
         entry_points={
             "console_scripts": ["cbl-migrator=cbl_migrator.bin.run_migrator:main"],