Merge pull request #193 from pepkit/dev_sqllite_support

add sqlite option if included in config file

pipestat/pipestat.py

@@ -429,7 +429,11 @@ def initialize_dbbackend(self, record_identifier: str = None, show_db_logs: bool
             dbconf = self.cfg[CONFIG_KEY].exp[
                 CFG_DATABASE_KEY
             ]  # the .exp expands the paths before url construction
-            self.cfg[DB_URL] = construct_db_url(dbconf)
+            if "sqlite_url" in dbconf:
+                sqlite_url = f"sqlite:///{dbconf['sqlite_url']}"
+                self.cfg[DB_URL] = sqlite_url
+            else:
+                self.cfg[DB_URL] = construct_db_url(dbconf)
         except KeyError:
             raise PipestatDatabaseError(f"No database section ('{CFG_DATABASE_KEY}') in config")
         self._show_db_logs = show_db_logs

tests/conftest.py

@@ -82,6 +82,11 @@ def schema_file_path():
     return get_data_file_path("sample_output_schema.yaml")
 
 
+@pytest.fixture
+def schema_file_path_sqlite():
+    return get_data_file_path("sample_output_schema_sqlite.yaml")
+
+
 @pytest.fixture
 def highlight_schema_file_path():
     return get_data_file_path("sample_output_schema_highlight.yaml")

tests/data/sample_output_schema_sqlite.yaml

@@ -0,0 +1,14 @@
+title: An example Pipestat output schema
+description: A pipeline that uses pipestat to report sample and project level results.
+type: object
+properties:
+  pipeline_name: "default_pipeline_name"
+  samples:
+    type: object
+    properties:
+      number_of_things:
+        type: integer
+        description: "Number of things"
+      percentage_of_things:
+        type: number
+        description: "Percentage of things"

tests/test_db_only_mode.py

@@ -1,3 +1,5 @@
+from tempfile import NamedTemporaryFile
+
 import pytest
 
 from pipestat import SamplePipestatManager
@@ -132,3 +134,27 @@ def test_select_pagination(
             result = psm.select_records(cursor=offset, limit=limit)
             print(result)
             assert len(result["records"]) == min(max((psm.record_count - offset), 0), limit)
+
+
+class TestSQLLITE:
+    def test_manager_can_be_built_without_exception(self, schema_file_path_sqlite):
+
+        with NamedTemporaryFile() as f:
+            sqllite_url = f"sqlite:///{f.name}"
+            config_dict = {
+                "project_name": "test",
+                "record_identifier": "sample1",
+                "schema_path": "sample_output_schema_sqlite.yaml",
+                "database": {"sqlite_url": f.name},
+            }
+
+            with ContextManagerDBTesting(sqllite_url):
+                try:
+                    SamplePipestatManager(
+                        schema_path=schema_file_path_sqlite,
+                        record_identifier="irrelevant",
+                        database_only=True,
+                        config_dict=config_dict,
+                    )
+                except Exception as e:
+                    pytest.fail(f"Pipestat manager construction failed: {e})")