release commit

biocypher/output/write/relational/_sqlite.py

@@ -0,0 +1,51 @@
+from biocypher.output.write.relational._postgresql import _PostgreSQLBatchWriter
+
+
+class _SQLiteBatchWriter(_PostgreSQLBatchWriter):
+    """
+    Class for writing node and edge representations to a SQLite database.
+    It uses the _PostgreSQLBatchWriter class under the hood, which already
+    implements the logic to write the nodes/edges to a relational DBMS.
+    Only the import bash script differs between PostgreSQL and SQLite
+    and is therefore implemented in this class.
+
+    - _construct_import_call
+    """
+
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+
+    def _construct_import_call(self) -> str:
+        """
+        Function to construct the import call detailing folder and
+        individual node and edge headers and data files, as well as
+        delimiters and database name. Built after all data has been
+        processed to ensure that nodes are called before any edges.
+
+        Returns:
+            str: a bash command for sqlite import
+        """
+        import_call = ""
+
+        # create tables
+        # At this point, csv files of nodes and edges do not require differentiation
+        for import_file_path in [
+            *self.import_call_nodes,
+            *self.import_call_edges,
+        ]:
+            import_call += f'echo "Setup {import_file_path}..."\n'
+            import_call += f"{self.import_call_bin_prefix}sqlite3 {self.db_name} < {import_file_path}"
+            import_call += '\necho "Done!"\n'
+            import_call += "\n"
+
+        for command in self._copy_from_csv_commands:
+            table_name = command.split(" ")[1]
+            table_part = command.split(" ")[3].replace("'", "")
+            import_call += f'echo "Importing {table_part}..."\n'
+            separator = self.delim
+            import_part = f".import {table_part} {table_name}"
+            import_call += f"{self.import_call_bin_prefix}sqlite3 -separator $'{separator}' {self.db_name} \"{import_part}\""
+            import_call += '\necho "Done!"\n'
+            import_call += "\n"
+
+        return import_call