WIP: DandiExport logger 10

src/spyglass/utils/dj_graph.py

@@ -1,6 +1,10 @@
+from pathlib import Path
+from subprocess import run as subprocess_run
+from tempfile import NamedTemporaryFile
 from typing import Dict, List
 
 from datajoint import FreeTable
+from datajoint import config as dj_config
 from datajoint.condition import make_condition
 from datajoint.table import Table
 
@@ -271,7 +275,47 @@ def as_dict(self) -> List[Dict[str, str]]:
             if self._get_restr(table)
         ]
 
-    def export(self):
-        raise NotImplementedError("Export to file not implemented")
-        # for table in self._all_ft:
-        #     where = table.where_clause()
+    def _write_sql_cnf(self):
+        """Write SQL cnf file to avoid password prompt"""
+        cnf_path = ".my.cnf"
+        if Path(cnf_path).exists():
+            logger.error(f"File {cnf_path} already exists. Not overwriting.")
+            return
+        thisuser = dj_config["database.user"]
+        thispass = dj_config["database.password"]
+        thishost = dj_config["database.host"]
+        credenials = (
+            f"[client]\nuser={thisuser}\npassword={thispass}\nhost={thishost}\n"
+        )
+        with open(".my.cnf", "w") as file:
+            file.write(credenials)
+
+    def _write_mysqldump(
+        self, dump_fname: str, docker_id=None
+    ) -> NamedTemporaryFile:
+        """Write mysqlmdump to a temporary file and return the file object"""
+        # TODO: How do we want to organize outputs?
+        #       Separate sql files for each schema?
+        #       Do they live in a new SPYGLASS_EXPORT_DIR ?
+        prefix = f"docker exec -i {docker_id}" if docker_id else ""
+        file = NamedTemporaryFile(mode="w")
+        file.write("#!/bin/bash\n")
+        for table in self._all_ft:
+            full_name = table.full_table_name
+            if not (where := table.where_clause()):
+                continue
+            database, table_name = full_name.split(".")
+            cmd = (
+                f"{prefix}mysqldump {database} {table_name} "
+                + f'--where="{where}" >> {dump_fname}\n'
+            )
+            file.write(cmd)
+        file.flush()
+
+        return file
+
+    def export(self, dump_fname: str = "./temp_export.sql", docker_id=None):
+        self._write_sql_cnf()
+        dump_file = self._write_mysqldump(dump_fname, docker_id)
+        subprocess_run(["chmod", "+x", dump_file.name])
+        return subprocess_run([dump_file.name])