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galaxy/scripts/api/load_data_with_metadata.py
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2.6 KiB
Python
Executable File

#!/usr/bin/env python
"""
This script scans a directory for files with companion '.json' files, then loads
the data from the file, and attaches the .json contents using the 'extended_metadata'
system in the library
Sample call:
python load_data_with_metadata.py <api_key> <api_url> /data/folder "API Imports"
NOTE: The upload method used requires the data library filesystem upload allow_library_path_paste
"""
import os
import shutil
import sys
import json
import time
sys.path.insert( 0, os.path.dirname( __file__ ) )
from common import submit, display
def main(api_key, api_url, in_folder, data_library):
# Find/Create data library with the above name. Assume we're putting datasets in the root folder '/'
libs = display(api_key, api_url + 'libraries', return_formatted=False)
library_id = None
for library in libs:
if library['name'] == data_library:
library_id = library['id']
if not library_id:
lib_create_data = {'name':data_library}
library = submit(api_key, api_url + 'libraries', lib_create_data, return_formatted=False)
library_id = library[0]['id']
folders = display(api_key, api_url + "libraries/%s/contents" % library_id, return_formatted = False)
for f in folders:
if f['name'] == "/":
library_folder_id = f['id']
if not library_id or not library_folder_id:
print "Failure to configure library destination."
sys.exit(1)
for fname in os.listdir(in_folder):
fullpath = os.path.join(in_folder, fname)
if os.path.isfile(fullpath) and os.path.exists(fullpath + ".json"):
print "Loading", fullpath
data = {}
data['folder_id'] = library_folder_id
data['file_type'] = 'auto'
data['dbkey'] = ''
data['upload_option'] = 'upload_paths'
data['filesystem_paths'] = fullpath
data['create_type'] = 'file'
data['link_data_only'] = 'link_to_files'
handle = open( fullpath + ".json" )
smeta = handle.read()
handle.close()
data['extended_metadata'] = json.loads(smeta)
libset = submit(api_key, api_url + "libraries/%s/contents" % library_id, data, return_formatted = True)
print libset
if __name__ == '__main__':
try:
api_key = sys.argv[1]
api_url = sys.argv[2]
in_folder = sys.argv[3]
data_library = sys.argv[4]
except IndexError:
print 'usage: %s key url in_folder data_library' % os.path.basename( sys.argv[0] )
sys.exit( 1 )
main(api_key, api_url, in_folder, data_library )