Mercurial > repos > iuc > data_manager_metaphlan2_database_downloader
view data_manager/data_manager_metaphlan2_download.py @ 0:9c4ad82be5bd draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan2_database_downloader commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
author | iuc |
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date | Sat, 04 Mar 2017 12:11:20 -0500 |
parents | |
children | 83f07f40b200 |
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#!/usr/bin/env python # # Data manager for reference data for the 'humann2' Galaxy tools import json import optparse import os import subprocess import sys # Utility functions for interacting with Galaxy JSON def read_input_json(jsonfile): """Read the JSON supplied from the data manager tool Returns a tuple (param_dict,extra_files_path) 'param_dict' is an arbitrary dictionary of parameters input into the tool; 'extra_files_path' is the path to a directory where output files must be put for the receiving data manager to pick them up. NB the directory pointed to by 'extra_files_path' doesn't exist initially, it is the job of the script to create it if necessary. """ params = json.loads(open(jsonfile).read()) return (params['param_dict'], params['output_data'][0]['extra_files_path']) # Utility functions for creating data table dictionaries # # Example usage: # >>> d = create_data_tables_dict() # >>> add_data_table(d,'my_data') # >>> add_data_table_entry(dict(dbkey='hg19',value='human')) # >>> add_data_table_entry(dict(dbkey='mm9',value='mouse')) # >>> print str(json.dumps(d)) def create_data_tables_dict(): """Return a dictionary for storing data table information Returns a dictionary that can be used with 'add_data_table' and 'add_data_table_entry' to store information about a data table. It can be converted to JSON to be sent back to the data manager. """ d = {} d['data_tables'] = {} return d def add_data_table(d, table): """Add a data table to the data tables dictionary Creates a placeholder for a data table called 'table'. """ d['data_tables'][table] = [] def add_data_table_entry(d, table, entry): """Add an entry to a data table Appends an entry to the data table 'table'. 'entry' should be a dictionary where the keys are the names of columns in the data table. Raises an exception if the named data table doesn't exist. """ try: d['data_tables'][table].append(entry) except KeyError: raise Exception("add_data_table_entry: no table '%s'" % table) def download_metaphlan2_db(data_tables, build, table_name, target_dir): """Download MetaPhlAn2 database Creates references to the specified file(s) on the Galaxy server in the appropriate data table (determined from the file extension). The 'data_tables' dictionary should have been created using the 'create_data_tables_dict' and 'add_data_table' functions. Arguments: data_tables: a dictionary containing the data table info table_name: name of the table target_dir: directory to put copy or link to the data file """ cmd = "download_metaphlan2_db.py --output %s" % (target_dir) db_dir = os.path.join(target_dir, build) subprocess.check_call(cmd, shell=True) os.rename(os.path.join(target_dir, "db_v20"), db_dir) add_data_table_entry( data_tables, table_name, dict( dbkey=build, value="mpa_v20_m200", name="MetaPhlAn2 clade-specific marker genes", path=db_dir)) if __name__ == "__main__": print("Starting...") # Read command line parser = optparse.OptionParser(description='Download MetaPhlan2 database') parser.add_option('--database', help="Database name") options, args = parser.parse_args() print("args : %s" % args) # Check for JSON file if len(args) != 1: sys.stderr.write("Need to supply JSON file name") sys.exit(1) jsonfile = args[0] # Read the input JSON params, target_dir = read_input_json(jsonfile) # Make the target directory print("Making %s" % target_dir) os.mkdir(target_dir) # Set up data tables dictionary data_tables = create_data_tables_dict() add_data_table(data_tables, "metaphlan2_database") # Fetch data from specified data sources if options.database == "db_v20": download_metaphlan2_db( data_tables, "v20", "metaphlan2_database", target_dir) # Write output JSON print("Outputting JSON") print(str(json.dumps(data_tables))) with open(jsonfile, 'wb') as out: out.write(json.dumps(data_tables)) print("Done.")