Wrong error message for set scratch

utilix/batchq.py

@@ -38,8 +38,9 @@ def get_server_type():
 # for non-dali hosts, SCRATCH_DIR must have write permission
 if not os.access(SCRATCH_DIR, os.W_OK) and SERVER != "Dali":
     raise ValueError(
-        f"SCRATCH_DIR {SCRATCH_DIR} does not have write permission. "
-        "You may need to set SCRATCH_DIR manually in your .bashrc or .bash_profile."
+        f"SCRATCH {SCRATCH_DIR} does not have write permission. "
+        "You may need to set SCRATCH manually in your .bashrc or .bash_profile using"
+        "export SCRATCH=/path/to/your/scratch"
     )
 
 PARTITIONS: List[str] = [

utilix/mongo_storage.py

@@ -107,7 +107,6 @@ def __init__(
             (only deactivate if you are using a brand new database)!
 
         """
-
         if collection is None:
             if not readonly:
                 # We want admin access to start writing data!
@@ -169,14 +168,11 @@ def config_exists(self, config):
         return self.collection.count_documents(query) > 0
 
     def md5_stored(self, abs_path):
-        """
-        NB: RAM intensive operation!
-        Carefully compare if the MD5 identifier is the same as the file
-        as stored under abs_path.
+        """NB: RAM intensive operation! Carefully compare if the MD5 identifier is the same as the
+        file as stored under abs_path.
 
         :param abs_path: str, absolute path to the file name
-        :return: bool, returns if the exact same file is already stored
-            in the database
+        :return: bool, returns if the exact same file is already stored in the database
 
         """
         if not os.path.exists(abs_path):
@@ -205,12 +201,11 @@ def list_files(self):
 
     @staticmethod
     def compute_md5(abs_path):
-        """
-        NB: RAM intensive operation!
-        Get the md5 hash of a file stored under abs_path
+        """NB: RAM intensive operation! Get the md5 hash of a file stored under abs_path.
 
         :param abs_path: str, absolute path to a file
         :return: str, the md5-hash of the requested file
+
         """
         # This function is copied from:
         # stackoverflow.com/questions/3431825/generating-an-md5-checksum-of-a-file

utilix/rundb.py

@@ -272,7 +272,6 @@ def get_doc(self, identifier):
         takes place automatically.
 
         """
-
         # map from all kinds of types (int, np int, ...)
         identifier = str(identifier)
 
@@ -290,7 +289,6 @@ def get_data(self, identifier, **filters):
         automatically.
 
         """
-
         # map from all kinds of types (int, np int, ...)
         identifier = str(identifier)
 
@@ -321,7 +319,6 @@ def update_data(self, identifier, datum):
         Identifier can be run number of name.
 
         """
-
         datum = cleanup_datadict(datum)
 
         # map from all kinds of types (int, np int, ...)
@@ -337,7 +334,6 @@ def update_data(self, identifier, datum):
 
     def delete_data(self, identifier, datum):
         """Updates a datum for a document with a matching identifier (name or run number)"""
-
         # map from all kinds of types (int, np int, ...)
         identifier = str(identifier)
 
@@ -519,7 +515,6 @@ def get_file_md5(self, filename):
 
 class PyMongoCannotConnect(Exception):
     """Raise error when we cannot connect to the pymongo client."""
-
     pass
 
 

utilix/scripts/xefind.py

@@ -96,7 +96,6 @@ def get_runs_from_source(science_run, source):
         list: A list of run numbers matching the given science run and source.
 
     """
-
     query = SCIENCE_RUNS[science_run]
     query["source"] = source
     # end is lt now in GMT time
@@ -153,7 +152,6 @@ def get_lineage_hash_from_version(context, versions, data_type):
         str or None: The lineae hash if found, None otherwise.
 
     """
-
     ctxs = xent_collection(collection="contexts")
 
     if context == "xenonnt_online":
@@ -229,7 +227,6 @@ def check_runs_available(data_type, run_ids, extra_location="", livetime=False):
         pandas.DataFrame: A DataFrame containing the availability information for each run ID.
 
     """
-
     if not run_ids:
         raise ValueError("No run_ids found")
 
@@ -300,7 +297,6 @@ def get_runs_from_db(run_ids, data_type, lineage_hash, location=None):
         list: A list of run IDs matching the criteria.
 
     """
-
     coll = xent_collection(collection="runs")
     run_ids = [int(run_id) for run_id in run_ids]
 
@@ -323,9 +319,9 @@ def parse_args():
         argparse.Namespace: The parsed command line arguments.
 
     """
-
     parser = argparse.ArgumentParser(
-        description="""
+        description=\
+                    """
         Check if the data is available for a given list of runs,
         or for a given source and science run.
         You can provide a file with the run_ids,

utilix/tarball.py

@@ -8,7 +8,6 @@
 
 def filter_tarinfo(tarinfo, git_ignored_files, tarball_ignore_patterns=None):
     """Custom filter for tarfile to exclude Git-ignored files and .tarballignore patterns."""
-
     # Exclude Git-ignored files
     if any(f in tarinfo.name for f in git_ignored_files):
         return None
@@ -47,7 +46,6 @@ def tarball_path(self):
 
     def create_tarball(self, overwrite=False):
         """Create the tarball of package."""
-
         if os.path.exists(self.tarball_path) and not overwrite:
             raise RuntimeError(f"{self.tarball_path} already exists!")