Feature/components table

.github/workflows/ci_code.yml

@@ -103,6 +103,7 @@ jobs:
 
     - name: Unit Testing
       run: |
+        sqlite3 test.db "create table t(f int); drop table t;"
         make unit_testing pytest_arguments="--cov=superduper --cov-report=xml" SUPERDUPER_CONFIG=test/configs/${{ matrix.config }}
 
     - name: Usecase Testing

.github/workflows/ci_plugins.yaml

@@ -95,6 +95,9 @@ jobs:
       - name: Plugin Testing
         run: |
           export PYTHONPATH=./
+          if [ "${{ matrix.plugin }}" = "sql" ]; then
+            sqlite3 test.db "create table t(f int); drop table t;"
+          fi
           if [ -d "plugins/${{ matrix.plugin }}/plugin_test" ]; then
             pytest --cov=superduper --cov-report=xml plugins/${{ matrix.plugin }}/plugin_test
           else
@@ -103,6 +106,9 @@ jobs:
 
       - name: Optionally run the base testing
         run: |
+          if [ "${{ matrix.plugin }}" = "sql" ]; then
+            sqlite3 test.db "create table t(f int); drop table t;"
+          fi
           SUPERDUPER_CONFIG="plugins/${{ matrix.plugin }}/plugin_test/config.yaml"
           if [ -f "$SUPERDUPER_CONFIG" ]; then
             echo "Running the base testing..."

CHANGELOG.md

@@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Add assertion to verify directory copy in FileSystemArtifactStore
 - Batch the Qdrant requests and add a retry to the config of Qdrant
 - Add use_component_cache to config
+- Save data in the `Component` table instead of in individual tables
 
 ### Bug fixes
 

plugins/mongodb/superduper_mongodb/data_backend.py

@@ -6,6 +6,7 @@
 from bson.objectid import ObjectId
 from superduper import CFG, logging
 from superduper.backends.base.data_backend import BaseDataBackend
+from superduper.base.base import REGISTRY
 from superduper.base.query import Query
 from superduper.base.schema import Schema
 
@@ -171,24 +172,29 @@ def missing_outputs(self, query, predict_id: str):
     def select(self, query: Query):
         """Select data from the table."""
         if query.decomposition.outputs:
-            return self._outputs(query)
-
-        collection = self._database[query.table]
-
-        logging.debug(str(query))
-
-        limit = self._get_limit(query)
-        if limit:
-            native_query = collection.find(
-                self._mongo_filter(query), self._get_project(query)
-            ).limit(limit)
-            if skip := self._get_skip(query):
-                native_query = native_query.skip(skip)
-            return list(native_query)
-
-        return list(
-            collection.find(self._mongo_filter(query), self._get_project(query))
-        )
+            output = self._outputs(query)
+        else:
+            collection = self._database[query.table]
+
+            logging.debug(str(query))
+
+            limit = self._get_limit(query)
+            if limit:
+                native_query = collection.find(
+                    self._mongo_filter(query), self._get_project(query)
+                ).limit(limit)
+                if skip := self._get_skip(query):
+                    native_query = native_query.skip(skip)
+                output = list(native_query)
+            else:
+                output = list(
+                    collection.find(self._mongo_filter(query), self._get_project(query))
+                )
+        if query.table in REGISTRY and REGISTRY[query.table].primary_id != '_id':
+            for o in output:
+                if '_id' in o:
+                    del o['_id']
+        return output
 
     def to_id(self, id):
         """Convert the ID to the correct format."""

plugins/qdrant/superduper_qdrant/qdrant.py

@@ -160,7 +160,6 @@ def _do_scroll(offset):
 
         return ids
 
-
     def _create_collection(self):
         measure = (
             self.measure.name

plugins/sql/plugin_test/config.yaml

@@ -1,4 +1,4 @@
-data_backend: sqlite://
+data_backend: sqlite://./test.db
 auto_schema: false
 force_apply: true
 json_native: false

plugins/sql/plugin_test/test_query.py

@@ -1,3 +1,4 @@
+import typing as t
 from test.utils.setup.fake_data import add_listeners, add_models, add_random_data
 
 import numpy as np
@@ -44,7 +45,7 @@ def test_renamings(db):
     add_random_data(db, n=5)
     add_models(db)
     add_listeners(db)
-    t = db["documents"]
+    t = db["documentz"]
     listener_uuid = [db.load('Listener', k).outputs for k in db.show("Listener")][0]
     q = t.select("id", "x", "y").outputs(listener_uuid.split('__', 1)[-1])
     data = q.execute()
@@ -62,13 +63,13 @@ def test_serialize_query(db):
 
 def test_get_data(db):
     add_random_data(db, n=5)
-    db["documents"].limit(2)
-    db.metadata.get_component("Table", "documents")
+    db["documentz"].limit(2)
+    db.metadata.get_component("Table", "documentz")
 
 
 def test_insert_select(db):
     add_random_data(db, n=5)
-    q = db["documents"].select("id", "x", "y").limit(2)
+    q = db["documentz"].select("id", "x", "y").limit(2)
     r = q.execute()
 
     assert len(r) == 2
@@ -77,7 +78,7 @@ def test_insert_select(db):
 
 def test_filter(db):
     add_random_data(db, n=5)
-    t = db["documents"]
+    t = db["documentz"]
     q = t.select("id", "y")
     r = q.execute()
     ys = [x["y"] for x in r]
@@ -88,17 +89,18 @@ def test_filter(db):
     assert len(r) == uq[1][0]
 
 
-class documents(Base):
+class documents_plugin(Base):
+    primary_id: t.ClassVar[str] = 'id'
     this: 'str'
 
 
 def test_select_using_ids(db):
-    db.create(documents)
+    db.create(documents_plugin)
 
-    table = db["documents"]
+    table = db["documents_plugin"]
     table.insert([{"this": f"is a test {i}", "id": str(i)} for i in range(4)])
 
-    basic_select = db['documents'].select()
+    basic_select = db['documents_plugin'].select()
 
     assert len(basic_select.execute()) == 4
     assert len(basic_select.subset(['1', '2'])) == 2
@@ -112,16 +114,16 @@ def my_func(this: str):
 
     my_func = ObjectModel('my_func', object=my_func)
 
-    db.create(documents)
+    db.create(documents_plugin)
 
-    table = db["documents"]
+    table = db["documents_plugin"]
     table.insert([{"this": f"is a test {i}", "id": str(i)} for i in range(4)])
 
     listener = Listener(
         'test',
         model=my_func,
         key='this',
-        select=db['documents'].select(),
+        select=db['documents_plugin'].select(),
     )
     db.apply(listener)
 

plugins/sql/superduper_sql/data_backend.py

@@ -359,7 +359,10 @@ class SQLDatabackend(IbisDataBackend):
 
     def __init__(self, uri, plugin, flavour=None):
         super().__init__(uri, plugin, flavour)
-        self._create_sqlalchemy_engine()
+        if 'sqlite://./' in uri:
+            self._create_sqlalchemy_engine(uri.replace('./', '//'))
+        else:
+            self._create_sqlalchemy_engine(uri)
         self.sm = sessionmaker(bind=self.alchemy_engine)
 
     @property
@@ -374,6 +377,8 @@ def update(self, table, condition, key, value):
         with self.sm() as session:
             metadata = MetaData()
 
+            assert table in self.list_tables()
+
             metadata.reflect(bind=session.bind)
             table = Table(table, metadata, autoload_with=session.bind)
 
@@ -422,16 +427,16 @@ def delete(self, table, condition):
         except NoSuchTableError:
             raise exceptions.NotFound("Table", table)
 
-    def _create_sqlalchemy_engine(self):
+    def _create_sqlalchemy_engine(self, uri):
         with self.connection_manager.get_connection() as conn:
-            self.alchemy_engine = create_engine(self.uri, creator=lambda: conn.con)
+            self.alchemy_engine = create_engine(uri, creator=lambda: conn.con)
             if not self._test_engine():
                 logging.warn(
                     "Unable to reuse the ibis connection "
                     "to create the SQLAlchemy engine. "
                     "Creating a new connection with the URI."
                 )
-                self.alchemy_engine = create_engine(self.uri)
+                self.alchemy_engine = create_engine(uri)
 
     def _test_engine(self):
         """Test the engine."""