def _save_uploaded_file_list(samples, file_list_work, out_dir):
""" Fixes all absolute work-rooted paths to relative final-rooted paths
For CWL, prepare paths relative to output directory.
"""
if not utils.file_exists(file_list_work):
return None
if any([cwlutils.is_cwl_run(d) for d in samples]):
upload_paths = []
with open(file_list_work) as f:
for p in (l.strip() for l in f.readlines() if os.path.exists(l.strip())):
if p.startswith(out_dir):
upload_paths.append(p.replace(out_dir + "/", ""))
else:
upload_path_mapping = dict()
for sample in samples:
upload_path_mapping.update(get_all_upload_paths_from_sample(sample))
if not upload_path_mapping:
return None
with open(file_list_work) as f:
paths = [l.strip() for l in f.readlines() if os.path.exists(l.strip())]
upload_paths = [p for p in [
_work_path_to_rel_final_path(path, upload_path_mapping, samples[0]["upload"]["dir"])
for path in paths
] if p]
if not upload_paths:
return None
file_list_final = os.path.join(out_dir, "list_files_final.txt")
with open(file_list_final, "w") as f:
for path in upload_paths:
f.write(path + '\n')
return file_list_final
def _save_uploaded_file_list(samples, file_list_work, out_dir):
""" Fixes all absolute work-rooted paths to relative final-rooted paths
"""
if not utils.file_exists(file_list_work):
return None
upload_path_mapping = dict()
for sample in samples:
upload_path_mapping.update(get_all_upload_paths_from_sample(sample))
if not upload_path_mapping:
return None
with open(file_list_work) as f:
paths = [l.strip() for l in f.readlines() if os.path.exists(l.strip())]
upload_paths = [
p for p in [
_work_path_to_rel_final_path(path, upload_path_mapping, samples[0]
["upload"]["dir"]) for path in paths
] if p
]
if not upload_paths:
return None
file_list_final = os.path.join(out_dir, "list_files_final.txt")
with open(file_list_final, "w") as f:
for path in upload_paths:
f.write(path + '\n')
return file_list_final
def _save_uploaded_file_list(samples, file_list_work, out_dir):
""" Fixes all absolute work-rooted paths to relative final-rooted paths
For CWL, prepare paths relative to output directory.
"""
if not utils.file_exists(file_list_work):
return None
if any([cwlutils.is_cwl_run(d) for d in samples]):
upload_paths = []
with open(file_list_work) as f:
for p in (l.strip() for l in f.readlines() if os.path.exists(l.strip())):
if p.startswith(out_dir):
upload_paths.append(p.replace(out_dir + "/", ""))
else:
upload_path_mapping = dict()
for sample in samples:
upload_path_mapping.update(get_all_upload_paths_from_sample(sample))
if not upload_path_mapping:
return None
with open(file_list_work) as f:
paths = [l.strip() for l in f.readlines() if os.path.exists(l.strip())]
upload_paths = [p for p in [
_work_path_to_rel_final_path(path, upload_path_mapping, samples[0]["upload"]["dir"])
for path in paths
] if p]
if not upload_paths:
return None
file_list_final = os.path.join(out_dir, "list_files_final.txt")
with open(file_list_final, "w") as f:
for path in upload_paths:
f.write(path + '\n')
return file_list_final
def _save_uploaded_data_json(samples, data_json_work, out_dir):
""" Fixes all absolute work-rooted paths to relative final-rooted paths
"""
if not utils.file_exists(data_json_work):
return None
upload_path_mapping = dict()
for sample in samples:
upload_path_mapping.update(get_all_upload_paths_from_sample(sample))
if not upload_path_mapping:
return data_json_work
with open(data_json_work) as f:
data = json.load(f, object_pairs_hook=OrderedDict)
upload_base = samples[0]["upload"]["dir"]
data = walk_json(data, lambda s: _work_path_to_rel_final_path(s, upload_path_mapping, upload_base))
data_json_final = os.path.join(out_dir, "multiqc_data_final.json")
with open(data_json_final, "w") as f:
json.dump(data, f, indent=4)
return data_json_final
def _save_uploaded_data_json(samples, data_json_work, out_dir):
""" Fixes all absolute work-rooted paths to relative final-rooted paths
"""
if not utils.file_exists(data_json_work):
return None
upload_path_mapping = dict()
for sample in samples:
upload_path_mapping.update(get_all_upload_paths_from_sample(sample))
if not upload_path_mapping:
return data_json_work
with open(data_json_work) as f:
data = json.load(f, object_pairs_hook=OrderedDict)
upload_base = samples[0]["upload"]["dir"]
data = walk_json(data, lambda s: _work_path_to_rel_final_path(s, upload_path_mapping, upload_base))
data_json_final = os.path.join(out_dir, "multiqc_data_final.json")
with open(data_json_final, "w") as f:
json.dump(data, f, indent=4)
return data_json_final
def _save_uploaded_file_list(samples, file_list_work, out_dir):
if not utils.file_exists(file_list_work):
return None
file_list_final = os.path.join(out_dir, "list_files_final.txt")
upload_path_mapping = dict()
for sample in samples:
upload_path_mapping.update(get_all_upload_paths_from_sample(sample))
if not upload_path_mapping:
return None
with open(file_list_work) as f:
paths = [l.strip() for l in f.readlines() if os.path.exists(l.strip())]
upload_paths = []
for path in paths:
if path in upload_path_mapping:
upload_path = upload_path_mapping[path]
upload_base = samples[0]["upload"]["dir"]
upload_relpath = os.path.relpath(upload_path, upload_base)
upload_paths.append(upload_relpath)
if not upload_paths:
return None
with open(file_list_final, "w") as f:
for path in upload_paths:
f.write(path + '\n')
return file_list_final
def _save_uploaded_file_list(samples, file_list_work, out_dir):
if not utils.file_exists(file_list_work):
return None
file_list_final = os.path.join(out_dir, "list_files_final.txt")
upload_path_mapping = dict()
for sample in samples:
upload_path_mapping.update(get_all_upload_paths_from_sample(sample))
if not upload_path_mapping:
return None
with open(file_list_work) as f:
paths = [l.strip() for l in f.readlines() if os.path.exists(l.strip())]
upload_paths = []
for path in paths:
if path in upload_path_mapping:
upload_path = upload_path_mapping[path]
upload_base = samples[0]["upload"]["dir"]
upload_relpath = os.path.relpath(upload_path, upload_base)
upload_paths.append(upload_relpath)
if not upload_paths:
return None
with open(file_list_final, "w") as f:
for path in upload_paths:
f.write(path + '\n')
return file_list_final
