changeset 3:1bde47139a8d draft

Deleted selected files

--- a/data_manager/add_ctat_ref_lib.py	Tue Dec 12 15:05:24 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,94 +0,0 @@
-#!/usr/bin/env python
-# ref: https://galaxyproject.org/admin/tools/data-managers/how-to/define/
-
-# Rewritten by H.E. Cicada Brokaw Dennis from source downloaded from the toolshed.
-# Eventually this should be modified to allow downloading of more than just the one library,
-# to let the user select what library/location to download, but that would require the
-# download tool to generate the list of libraries to download on the fly. Currently
-# we are only using the one library.
-# Users can create other ones locally and use this tool to add them if they don't want
-# to add them by hand.
-
-import argparse
-import os
-import tarfile
-import urllib
-
-from galaxy.util.json import from_json_string, to_json_string
-
-# The following was used by prior program to get input parameters from the json.
-# Just leaving here for reference.
-#def get_reference_id_name(params):
-#    genome_id = params['param_dict']['genome_id']
-#    genome_name = params['param_dict']['genome_name']
-#    return genome_id, genome_name
-#
-#def get_url(params):
-#    trained_url = params['param_dict']['trained_url']
-#    return trained_url
-
-def download_from_BroadInst(destination):
-    ctat_resource_lib = 'https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/GRCh38_gencode_v26_CTAT_lib_Nov012017.plug-n-play.tar.gz'
-    # FIX - Check that the download directory is empty if it exists. Also, can we check if there is enough space on the device as well?
-    # FIX - Also we want to make sure that destination is absolute fully specified path.
-    os.mkdir(destination)
-    full_filepath = os.path.join(destination, 'GRCh38_gencode_v26_CTAT_lib_Nov012017.plug-n-play.tar.gz')
-
-    #Download ref: https://dzone.com/articles/how-download-file-python
-    #f = urllib2.urlopen(ctat_resource_lib)
-    #data = f.read()
-    #with open(filepath, 'wb') as code:
-    #    code.write(data)
-
-    urllib.urlretrieve(url=ctat_resource_lib, filename=full_filepath)
-    # Put the following into a try statement, so that if there is a failure something can be printed about it before reraising exception.
-    tarfile.open(full_filepath, mode='r:*').extractall()
-    # FIX - There is additional processing that needs to happen for gmap-fusion to work.
-    # Get the root filename of the extracted file. 
-    # That directory is the actual destination that needs to be set as the ctat_genome_resource_library
-
-def main():
-    #Parse Command Line
-    parser = argparse.ArgumentParser()
-    parser.add_argument('-d', '--download', action="store_true", \
-        help='Do not use if you already have the CTAT Resource Library that this program downloads.')
-    parser.add_argument('-g', '--genome_name', default="GRCh38_gencode_v26", \
-        help='Is used as the selector text of the entry in the data table.')
-    parser.add_argument('-p', '--destination_path', \
-        help='Full path of the CTAT Resource Library location or destination.')
-    parser.add_argument('-o', '--output_filename', \
-        help='Name of the output file, where the json dictionary will be written.')
-    args = parser.parse_args()
-
-    # All of the input parameters are written by default to the output file prior to
-    # this program being called.
-    # But I do not get input values from the json file, but rather from command line.
-    # Just leaving the following code as a comment, in case it might be useful to someone later.
-    # params = from_json_string(open(filename).read())
-    # target_directory = params['output_data'][0]['extra_files_path']
-    # os.mkdir(target_directory)
-
-    if args.download:
-        ctat_genome_resource_lib_path = download_from_BroadInst(destination=args.destination_path)
-    else:
-        # FIX - probably should check if this is a valid path with an actual CTAT Genome Ref Lib there.
-        ctat_genome_resource_lib_path = args.destination_path
-
-    if (args.genome_name is None) or (args.genome_name == ""):
-        genome_name = "GRCh38_gencode_v26"
-    else:
-        genome_name = args.genome_name
-
-    data_manager_dict = {}
-    data_manager_dict['data_tables'] = {}
-    data_manager_dict['data_tables']['ctat_genome_ref_libs'] = []
-    data_table_entry = dict(value="CTAT_RESOURCE_LIB", name=genome_name, path=ctat_genome_resource_lib_path)
-    data_manager_dict['data_tables']['ctat_genome_ref_libs'].append(data_table_entry)
-
-    # Save info to json file. This is used to transfer data from the DataManager tool, to the data manager,
-    # which then puts it into the correct .loc file (I think).
-    open(args.output_filename, 'wb').write(to_json_string(data_manager_dict))
-
-if __name__ == "__main__":
-    main()
-