Mercurial > repos > iuc > data_manager_mapseq

comparison data_manager_fetch_mapseq_db.py @ 3:a0d77af1d226 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit b6798b5213eca0d4b176ad3aeef81127dac6dcab
author iuc
date Tue, 03 Dec 2024 16:30:34 +0000
parents 23511530b8fd
children
comparison
equal deleted inserted replaced
2:23511530b8fd 3:a0d77af1d226
50 filename = wget.download(url, out=tmp_path) 50 filename = wget.download(url, out=tmp_path)
51 tarfile_path = os.path.join(tmp_path, filename) 51 tarfile_path = os.path.join(tmp_path, filename)
52 tar = tarfile.open(tarfile_path) 52 tar = tarfile.open(tarfile_path)
53 tar.extractall(extract_path) 53 tar.extractall(extract_path)
54 54
55 print(f"Content of folder: {extract_path}", os.listdir(extract_path))
56
57 # case for mapseq v6: all DB files are directly in the tar.gz file
58 # remove the VERSION.txt file since the tool can only handle on .txt file in the DB
55 if len(list(os.listdir(extract_path))) > 1: 59 if len(list(os.listdir(extract_path))) > 1:
56 print("More then one folder in zipped file, aborting !") 60 print(f"Found multiple files in {extract_path}. Copy the content.")
61 print(f"Copy data to {dest_path}")
62 version_file_path = os.path.join(extract_path, "VERSION.txt")
63 os.remove(version_file_path)
64 shutil.copytree(extract_path, dest_path)
65 print("Done !")
66
67 # case for mapseq v5: all files are in a subfolder in the tar.gz file
57 else: 68 else:
69 print(f"Found a folder in {extract_path}. Copy the content of the folder.")
58 for folder in os.listdir(extract_path): 70 for folder in os.listdir(extract_path):
59 folder_path = os.path.join(extract_path, folder) 71 folder_path = os.path.join(extract_path, folder)
60 72
61 print(f"Copy data to {dest_path}") 73 print(f"Copy data to {dest_path}")
62 shutil.copytree(folder_path, dest_path) 74 shutil.copytree(folder_path, dest_path)
67 79
68 def main(): 80 def main():
69 # Parse Command Line 81 # Parse Command Line
70 parser = argparse.ArgumentParser(description="Create data manager JSON.") 82 parser = argparse.ArgumentParser(description="Create data manager JSON.")
71 parser.add_argument("--out", dest="output", action="store", help="JSON filename") 83 parser.add_argument("--out", dest="output", action="store", help="JSON filename")
72 parser.add_argument("--version", dest="version", action="store", help="Version of the DB") 84 parser.add_argument(
73 parser.add_argument("--database-type", dest="db_type", action="store", help="Db type") 85 "--version", dest="version", action="store", help="Version of the DB"
86 )
87 parser.add_argument(
88 "--database-type", dest="db_type", action="store", help="Db type"
89 )
74 parser.add_argument( 90 parser.add_argument(
75 "--test", 91 "--test",
76 action="store_true", 92 action="store_true",
77 help="option to test the script with an lighted database", 93 help="option to test the script with an lighted database",
78 ) 94 )
82 # the output file of a DM is a json containing args that can be used by the DM 98 # the output file of a DM is a json containing args that can be used by the DM
83 # most tools mainly use these args to find the extra_files_path for the DM, which can be used 99 # most tools mainly use these args to find the extra_files_path for the DM, which can be used
84 # to store the DB data 100 # to store the DB data
85 with open(args.output) as fh: 101 with open(args.output) as fh:
86 params = json.load(fh) 102 params = json.load(fh)
87
88 print(params)
89 103
90 workdir = params["output_data"][0]["extra_files_path"] 104 workdir = params["output_data"][0]["extra_files_path"]
91 os.mkdir(workdir) 105 os.mkdir(workdir)
92 106
93 time = datetime.utcnow().strftime("%Y-%m-%d") 107 time = datetime.utcnow().strftime("%Y-%m-%d")