Fixed formatting issues

src/cromshell/submit/command.py

@@ -2,9 +2,9 @@
 import csv
 import json
 import logging
+import tempfile
 from datetime import datetime
 from pathlib import Path, PurePath
-import tempfile
 
 import click
 import requests
@@ -65,15 +65,23 @@ class WorkflowStatusError(Exception):
  help=".",
 )
 @click.pass_obj
-def main(config, wdl, wdl_json, options_json, dependencies_zip, no_validation, do_not_flatten_wdls):
+def main(
+ config,
+ wdl,
+ wdl_json,
+ options_json,
+ dependencies_zip,
+ no_validation,
+ do_not_flatten_wdls,
+):
  """Submit a workflow and arguments to the Cromwell Server"""
 
  LOGGER.info("submit")
 
  http_utils.assert_can_communicate_with_server(config=config)
 
  if not do_not_flatten_wdls and io_utils.has_nested_dependencies(wdl):
- tempdir = tempfile.TemporaryDirectory(prefix='cromshell_')
+ tempdir = tempfile.TemporaryDirectory(prefix="cromshell_")
 
  LOGGER.info(f"Flattening WDL structure to {tempdir.name}.")
 

src/cromshell/utilities/io_utils.py

@@ -1,13 +1,14 @@
 import json
 import logging
 import re
-#import os
+
+# import os
 import shutil
+import tempfile
 from contextlib import nullcontext
 from io import BytesIO
 from pathlib import Path
-import tempfile
-from typing import BinaryIO, List, Union, Tuple
+from typing import BinaryIO, List, Union
 from zipfile import ZIP_DEFLATED, ZipFile
 
 from pygments import formatters, highlight, lexers
@@ -106,30 +107,41 @@ def assert_path_is_not_empty(path: Union[str, Path], description: str) -> None:
 def has_nested_dependencies(wdl_path: str or Path) -> bool:
  """Determine if a WDL has any nested imports."""
 
- with open(wdl_path, 'r') as rf:
- for l in rf:
- if l.startswith('import'):
- m = re.match(r'import "(.+)"', l)
+ with open(wdl_path, "r") as rf:
+ for line in rf:
+ if line.startswith("import"):
+ m = re.match(r'import "(.+)"', line)
 
- if "../" in m.group(1):
+ imported_wdl_name = m.group(1)
+ if "../" in imported_wdl_name:
  return True
 
  return False
 
 
-def get_flattened_filename(tempdir: tempfile.TemporaryDirectory, wdl_path: str or Path) -> Path:
- """ Generate hyphen-separated path to use for flattened WDL file path.
- For example: 
+def get_flattened_filename(
+ tempdir: tempfile.TemporaryDirectory, wdl_path: str or Path
+) -> Path:
+ """Generate hyphen-separated path to use for flattened WDL file path.
+ For example:
  tempdir: /path/2/tempdir/ and wdl_path: /dir/path/2/wdl.wdl
  returns: /path/2/tempdir/dir-path-2-wdl.wdl
  """
 
  p = Path(wdl_path)
 
- return Path(tempdir.name + "/" + re.sub("^-", "", re.sub("/", "-", str(p.parent))) + '-' + str(p.name))
+ return Path(
+ tempdir.name
+ + "/"
+ + re.sub("^-", "", re.sub("/", "-", str(p.parent)))
+ + "-"
+ + str(p.name)
+ )
 
 
-def flatten_nested_dependencies(tempdir: tempfile.TemporaryDirectory, wdl_path: str or Path) -> Path:
+def flatten_nested_dependencies(
+ tempdir: tempfile.TemporaryDirectory, wdl_path: str or Path
+) -> Path:
  """Flatten a WDL directory structure and rewrite imports accordingly.
 
  Return string representing the filesystem location of the rewritten WDL.
@@ -140,22 +152,28 @@ def flatten_nested_dependencies(tempdir: tempfile.TemporaryDirectory, wdl_path:
 
  new_wdl_path = get_flattened_filename(tempdir, wdl_path)
 
- with open(wdl_path, 'r') as rf, open(new_wdl_path, 'w') as wf:
- for l in rf:
- if l.startswith('import'):
- m = re.match(r'import "(.+)"', l)
+ with open(wdl_path, "r") as rf, open(new_wdl_path, "w") as wf:
+ for line in rf:
+ if line.startswith("import"):
+ m = re.match(r'import "(.+)"', line)
  imported_wdl_name = m.group(1)
- imported_wdl_path = (Path(wdl_dir) / m.group(1)).absolute()
- import_line = re.sub(m.group(1), Path(get_flattened_filename(tempdir, imported_wdl_path)).name, l)
-
- if ' as ' in l:
+ imported_wdl_path = (Path(wdl_dir) / imported_wdl_name).absolute()
+ import_line = re.sub(
+ imported_wdl_name,
+ Path(get_flattened_filename(tempdir, imported_wdl_path)).name,
+ line,
+ )
+
+ if " as " in line:
  wf.write(import_line)
  else:
- wf.write(f'{import_line.strip()} as {re.sub(".wdl", "", Path(imported_wdl_path).name)}\n')
+ wf.write(
+ f'{import_line.strip()} as {re.sub(".wdl", "", Path(imported_wdl_path).name)}\n'
+ )
 
  flatten_nested_dependencies(tempdir, imported_wdl_path)
  else:
- wf.write(l)
+ wf.write(line)
 
  return new_wdl_path