playing arround how to create library automatically - not successfully

create_libraries.py

@@ -1,17 +1,52 @@
-import psycopg2
+#import psycopg2
 from bioblend import galaxy
-import sys
+import sys, os
 
 server_name = sys.argv[1]
 server = 'https://' + server_name
 api_key = sys.argv[2]
 gi = galaxy.GalaxyInstance(url=server, key=api_key)
 
 # Define library properties
-library_name = 'Test'
-library_description = 'Library for testing purpose'
+library_name = sys.argv[3] if sys.argv and len(sys.argv)>3 else "RCX-data"
+library_description = sys.argv[4] if sys.argv and len(sys.argv)>4 else "Recetox data from Sally"
 
 # Create library
-new_library = gi.libraries.create_library(name=library_name, description=library_description)
+if not library_name in [l['name'] for l in gi.libraries.get_libraries()]:
+  new_library = gi.libraries.create_library(name=library_name, description=library_description)
+  print("New library ID:", new_library['id'])
+else:
+  print("Library "+library_name+" already exists!")
+  for new_library in gi.libraries.get_libraries():
+    if library_name == new_library['name']:
+      break
+# populate library
+data_dir = sys.argv[5] if sys.argv and len(sys.argv) > 5 else '/mnt/sally/000020-Shares/rcx-da/umsa_test'
+root_folder_id = None
+for root, dirs, files in os.walk(data_dir):
+#  for item in dirs:
+#    if not any([dir.startswith('.') for dir in os.path.join(root,item).split(os.path.sep)]) and files:
+#      print('..importing folder '+os.path.join(root,item))
+#      new_ldda = gi.libraries.upload_file_from_server(library_id=new_library['id'], server_dir=os.path.join(os.path.relpath(root, '/mnt/sally/'),item), link_data_only='link_to_files', preserve_dirs=True)
 
-print("New library ID:", new_library['id'])
+  if not any([dir.startswith('.') for dir in root.split(os.path.sep)]):
+    if not os.path.basename(root) in [d['name'] for d in gi.libraries.get_folders(library_id=new_library['id'])]:
+      print('..creating folder '+root)
+      new_folder = gi.libraries.create_folder(library_id=new_library['id'], folder_name=os.path.basename(root), base_folder_id = root_folder_id)
+      root_folder_id = new_folder[0]['id']
+    else:
+      print('..skipping folder '+root+' because it already exists!')
+      for d in gi.libraries.get_folders(library_id=new_library['id']):
+        if os.path.basename(root) == d['name']:
+          root_folder_id = d['id']
+          break
+    for filename in files:
+      if not filename.startswith('.'):
+        print('..creating file '+filename)
+#        new_ldda = gi.libraries.upload_file_from_local_path(library_id=new_library['id'], file_local_path=os.path.join(root,filename), folder_id=root_folder_id)
+        new_ldda = gi.libraries.upload_from_galaxy_filesystem(library_id=new_library['id'], filesystem_paths=os.path.join(root,filename), folder_id=root_folder_id, link_data_only='link_to_files')
+  else:
+    print('..skipping folder '+root+' because it starts with a dot (i.e., most probably a hidden folder)!')
+
+#new_ldda = gi.libraries.upload_file_from_server(library_id=new_library['id'], server_dir=data_dir, link_data_only='link_to_files', preserve_dirs=True)
+print("Populating library "+new_library['id']+" with data from "+data_dir+" has finished!")