Coding on a plane and I want to use a local sqlite database...

... so lets add an option and make it setable in ~/.planemo.yml.

Author: jmchilton

planemo/galaxy_config.py

@@ -140,12 +140,13 @@ def config_join(*args):
         preseeded_database = True
         master_api_key = kwds.get("master_api_key", "test_key")
         dependency_dir = os.path.join(config_directory, "deps")
-
+        galaxy_sqlite_database = kwds.get("galaxy_sqlite_database", None)
         try:
             _download_database_template(
                 galaxy_root,
                 database_location,
-                latest=latest_galaxy
+                latest=latest_galaxy,
+                galaxy_sqlite_database=galaxy_sqlite_database,
             )
         except Exception as e:
             print(e)
@@ -358,7 +359,16 @@ def cleanup(self):
         shutil.rmtree(self.config_directory)
 
 
-def _download_database_template(galaxy_root, database_location, latest=False):
+def _download_database_template(
+    galaxy_root,
+    database_location,
+    latest=False,
+    galaxy_sqlite_database=None
+):
+    if galaxy_sqlite_database is not None:
+        shutil.copyfile(galaxy_sqlite_database, database_location)
+        return True
+
     if latest:
         template_url = DOWNLOADS_URL + urlopen(LATEST_URL).read()
         urlretrieve(template_url, database_location)

planemo/options.py

@@ -42,6 +42,15 @@ def galaxy_root_option():
     )
 
 
+def galaxy_sqlite_database_option():
+    return click.option(
+        "--galaxy_sqlite_database",
+        callback=get_default_callback(None, resolve_path=True),
+        type=click.Path(exists=True, file_okay=False, resolve_path=True),
+        help="Preseeded Galaxy sqlite database to target.",
+    )
+
+
 def galaxy_cwl_root_option():
     return click.option(
         "--cwl_galaxy_root",
@@ -521,6 +530,7 @@ def galaxy_config_options():
 def galaxy_target_options():
     return _compose(
         galaxy_root_option(),
+        galaxy_sqlite_database_option(),
         install_galaxy_option(),
         no_cache_galaxy_option(),
         no_cleanup_option(),