Get a list of filenames from a directory or a single file.
If a directory is provided, it will list all files in that directory
and in any subdirectory. If a file is provided, it will check if it
matches the prefix and extension.
This should handle the situation where the user provides a directory
that only contains a list of files, say from emodpy_workflow's download command.
This should also plot the files in a directory that contains subdirectories
created by the DownloadAnalyzer where each subdirectory contains the reports
from a simulation. Finally, this should also handle getting all of the files
in a suite or experiment directory created when using SLURM or Container platform
for the running of EMOD - the actual directories where the simulations are run.
Parameters:
| Name |
Type |
Description |
Default |
dir_or_filename
|
(string, required)
|
Directory or filename to search.
|
required
|
file_prefix
|
(string, required)
|
Prefix to filter files by.
|
required
|
file_extension
|
string
|
Extension to filter files by.
|
None
|
Returns:
List of filenames that match the criteria.
Source code in emodpy_malaria/plotting/helpers.py
| def get_filenames(dir_or_filename: str,
file_prefix: str,
file_extension: str = None):
"""
Get a list of filenames from a directory or a single file.
If a directory is provided, it will list all files in that directory
and in any subdirectory. If a file is provided, it will check if it
matches the prefix and extension.
This should handle the situation where the user provides a directory
that only contains a list of files, say from emodpy_workflow's download command.
This should also plot the files in a directory that contains subdirectories
created by the DownloadAnalyzer where each subdirectory contains the reports
from a simulation. Finally, this should also handle getting all of the files
in a suite or experiment directory created when using SLURM or Container platform
for the running of EMOD - the actual directories where the simulations are run.
Args:
dir_or_filename (string, required):
Directory or filename to search.
file_prefix (string, required):
Prefix to filter files by.
file_extension (string, optional):
Extension to filter files by.
Returns:
List of filenames that match the criteria.
"""
dir_filenames = []
# Check if the input is a directory or a file
if os.path.isdir(dir_or_filename):
# If it's a directory, list all files in the directory
for base_entry in os.listdir(dir_or_filename):
entry = os.path.join(dir_or_filename, base_entry)
if os.path.isdir(entry):
# If it's a subdirectory, recursively get filenames from it
sub_filenames = get_filenames(dir_or_filename=entry,
file_prefix=file_prefix,
file_extension=file_extension)
dir_filenames.extend(sub_filenames)
continue
if not os.path.isfile(entry):
continue
if file_prefix and not base_entry.startswith(file_prefix):
continue
if file_extension and not base_entry.endswith(file_extension):
continue
dir_filenames.append(entry)
elif os.path.isfile(dir_or_filename):
if (file_prefix and dir_or_filename.startswith(file_prefix)) or \
(file_extension and dir_or_filename.endswith(file_extension)):
dir_filenames.append(dir_or_filename)
elif file_prefix:
raise ValueError(f"'{dir_or_filename}' does not start with the specified prefix '{file_prefix}'.")
elif file_extension:
raise ValueError(f"'{dir_or_filename}' does not end with the specified extension '{file_extension}'.")
else:
dir_filenames.append(dir_or_filename)
else:
raise ValueError(f"'{dir_or_filename}' is neither a valid directory nor a file.")
dir_filenames = sorted(dir_filenames)
return dir_filenames
|