diff data_manager/gtdbtk_database_installer.py @ 0:629464b96c2e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/gtdbtk_database_installer.py	Thu Dec 08 19:26:49 2022 +0000
@@ -0,0 +1,84 @@
+#!/usr/bin/env python
+
+import argparse
+import json
+import os
+import shutil
+import sys
+import tarfile
+from urllib.parse import urlparse
+from urllib.request import Request
+from urllib.request import urlopen
+
+
+def url_download(url, target_directory):
+    url_parts = urlparse(url)
+    tarball = os.path.abspath(os.path.join(target_directory, os.path.basename(url_parts.path)))
+    src = None
+    dst = None
+    try:
+        req = Request(url)
+        src = urlopen(req)
+        with open(tarball, 'wb') as dst:
+            while True:
+                chunk = src.read(2**10)
+                if chunk:
+                    dst.write(chunk)
+                else:
+                    break
+    except Exception as e:
+        sys.exit(str(e))
+    finally:
+        if src is not None:
+            src.close()
+    if tarfile.is_tarfile(tarball):
+        fh = tarfile.open(tarball, 'r:*')
+    else:
+        return tarball
+    fh.extractall(target_directory)
+    fh.close()
+    os.remove(tarball)
+    # The tarball extraction will create a directory named
+    # something like release202 in the target_directory, so
+    # we need to move the items in that directory to the
+    # target directory.
+    subdir = next(os.walk(target_directory))[1][0]
+    subdir_path = os.path.join(target_directory, subdir)
+    items = os.listdir(subdir_path)
+    for item in items:
+        item_path = os.path.join(subdir_path, item)
+        shutil.move(item_path, target_directory)
+    os.rmdir(subdir_path)
+    return target_directory
+
+
+def download(database_id, database_name, url, out_file):
+
+    with open(out_file) as fh:
+        params = json.load(fh)
+
+    target_directory = params['output_data'][0]['extra_files_path']
+    os.makedirs(target_directory)
+    file_path = url_download(url, target_directory)
+
+    data_manager_json = {"data_tables": {}}
+    data_manager_entry = {}
+    data_manager_entry['value'] = database_id
+    data_manager_entry['name'] = database_name
+    data_manager_entry['path'] = file_path
+    data_manager_json["data_tables"]["gtdbtk_database"] = data_manager_entry
+
+    with open(out_file, 'w') as fh:
+        json.dump(data_manager_json, fh, sort_keys=True)
+
+
+parser = argparse.ArgumentParser()
+
+parser.add_argument('--database_name', dest='database_name', help='GTDB-Tk database display name')
+parser.add_argument('--database_id', dest='database_id', help='Unique GTDB-Tk database id')
+parser.add_argument('--url', dest='url', help='URL to download GTDB-Tk databse version')
+parser.add_argument('--out_file', dest='out_file', help='JSON output file')
+
+args = parser.parse_args()
+
+download(args.database_id, args.database_name, args.url, args.out_file)