| Previous changeset 2:23511530b8fd (2024-09-30) Next changeset 4:19ef193d1316 (2024-12-06) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit b6798b5213eca0d4b176ad3aeef81127dac6dcab |
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modified:
data_manager_fetch_mapseq_db.py mapseq_db_fetcher.xml |
| b |
| diff -r 23511530b8fd -r a0d77af1d226 data_manager_fetch_mapseq_db.py --- a/data_manager_fetch_mapseq_db.py Mon Sep 30 10:08:03 2024 +0000 +++ b/data_manager_fetch_mapseq_db.py Tue Dec 03 16:30:34 2024 +0000 |
| [ |
| @@ -52,9 +52,21 @@ tar = tarfile.open(tarfile_path) tar.extractall(extract_path) + print(f"Content of folder: {extract_path}", os.listdir(extract_path)) + + # case for mapseq v6: all DB files are directly in the tar.gz file + # remove the VERSION.txt file since the tool can only handle on .txt file in the DB if len(list(os.listdir(extract_path))) > 1: - print("More then one folder in zipped file, aborting !") + print(f"Found multiple files in {extract_path}. Copy the content.") + print(f"Copy data to {dest_path}") + version_file_path = os.path.join(extract_path, "VERSION.txt") + os.remove(version_file_path) + shutil.copytree(extract_path, dest_path) + print("Done !") + + # case for mapseq v5: all files are in a subfolder in the tar.gz file else: + print(f"Found a folder in {extract_path}. Copy the content of the folder.") for folder in os.listdir(extract_path): folder_path = os.path.join(extract_path, folder) @@ -69,8 +81,12 @@ # Parse Command Line parser = argparse.ArgumentParser(description="Create data manager JSON.") parser.add_argument("--out", dest="output", action="store", help="JSON filename") - parser.add_argument("--version", dest="version", action="store", help="Version of the DB") - parser.add_argument("--database-type", dest="db_type", action="store", help="Db type") + parser.add_argument( + "--version", dest="version", action="store", help="Version of the DB" + ) + parser.add_argument( + "--database-type", dest="db_type", action="store", help="Db type" + ) parser.add_argument( "--test", action="store_true", @@ -85,8 +101,6 @@ with open(args.output) as fh: params = json.load(fh) - print(params) - workdir = params["output_data"][0]["extra_files_path"] os.mkdir(workdir) |
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| diff -r 23511530b8fd -r a0d77af1d226 mapseq_db_fetcher.xml --- a/mapseq_db_fetcher.xml Mon Sep 30 10:08:03 2024 +0000 +++ b/mapseq_db_fetcher.xml Tue Dec 03 16:30:34 2024 +0000 |
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| @@ -17,8 +17,8 @@ </command> <inputs> <!-- <param name="test_data_manager" type="hidden" /> --> - <param name="test_data_manager_v5" type="boolean" truevalue="--test" falsevalue="" checked="False" label="Download minimal test DB and create mock data table entry." /> - <param name="test_data_manager_v6" type="boolean" truevalue="--test" falsevalue="" checked="False" label="Download minimal test DB and create mock data table entry." /> + <param name="test_data_manager_v5" type="boolean" truevalue="--test" falsevalue="" checked="False" label="Download minimal test DB and create mock data table entry for v5." /> + <param name="test_data_manager_v6" type="boolean" truevalue="--test" falsevalue="" checked="False" label="Download minimal test DB and create mock data table entry for v6." /> <param name="database_type" type="select" multiple="false" label="Database Type"> <option value="mgnify_v6_lsu">MGnify LSU (v6.0)</option> |