diff data_manager/data_manager.py @ 2:ae5ddc5a6511 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit b63133897598f2881de7bad1f18fcd69d7d7e9df-dirty"

--- a/data_manager/data_manager.py	Sat Mar 21 15:32:06 2020 +0000
+++ b/data_manager/data_manager.py	Wed Dec 15 11:01:00 2021 +0000
@@ -12,7 +12,7 @@
 
 ZENODO = {
     "mitos": "2683856",
-    "mitos2": "3685310"
+    "mitos2": "4284483"
 }
 NAMES = {
     "mitos1-refdata": "RefSeq39 + MiTFi tRNA models",
@@ -53,11 +53,10 @@
         if src:
             src.close()
     with tarfile.open(tarfname, "r:bz2") as tar:
+        dirname = tar.getnames()[0]
         tar.extractall(workdir)
     os.remove(tarfname)
-    unzipped = os.listdir(workdir)
-    assert len(unzipped) == 1
-    return unzipped[0]
+    return dirname
 
 
 def main(tpe, db, outjson):
@@ -72,13 +71,14 @@
     data_manager_entry['path'] = path
     data_manager_json = dict(data_tables=dict(mitos=data_manager_entry))
 
-    params = json.loads(open(outjson).read())
+    with open(outjson) as fh:
+        params = json.load(fh)
     target_directory = params['output_data'][0]['extra_files_path']
     os.mkdir(target_directory)
     # output_path = os.path.abspath(os.path.join(os.getcwd(), 'mitos'))
     shutil.move(os.path.join(workdir, path), target_directory)
     with open(outjson, 'w') as fh:
-        fh.write(json.dumps(data_manager_json))
+        json.dump(data_manager_json, fh, sort_keys=True)
 
 
 if __name__ == '__main__':