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userName2NGIname_finder.py
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userName2NGIname_finder.py
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import os
import glob
import re
import sys
import socket
import couchdb
import logging
import argparse
import yaml
import json
import distance
import operator
try:
import ConfigParser
except ImportError:
import configparser
CONFIG = {}
logger = logging.getLogger(__name__)
def associete_samples(samples_name, mode):
couch = setupServer(CONFIG)
projects_db = couch['projects']
for doc_id in projects_db:
#perform sanity check on statusDB project database
if 'creation_time' not in projects_db[doc_id]:
continue
if 'details' not in projects_db[doc_id] or 'customer_project_reference' not in projects_db[doc_id]['details'] or \
'project_id' not in projects_db[doc_id]:
continue
project = projects_db[doc_id]
if 'samples' not in project:
continue
for sample in project['samples']:
if 'customer_name' in project['samples'][sample] and 'details' in project['samples'][sample] and \
'status_(manual)' in project['samples'][sample]['details']:
sample_user_name = project['samples'][sample]['customer_name']
sample_NGI_name = project['samples'][sample]['scilife_name']
status = project['samples'][sample]['details']['status_(manual)']
if mode == 'user2NGI':
if sample_user_name in samples_name:
print("{},{},{}".format(sample_user_name.encode('ascii', 'ignore'), sample_NGI_name, status))
else:
if sample_NGI_name in samples_name:
print("{},{},{}".format(sample_NGI_name, sample_user_name.encode('ascii', 'ignore'), status))
def associate_projects(projects_name, mode):
couch = setupServer(CONFIG)
projects_db = couch['projects']
user2NGI_samples_names = {}
NGI2user_samples_names = {}
for doc_id in projects_db:
#perform sanity check on statusDB project database
if 'creation_time' not in projects_db[doc_id]:
continue
if 'details' not in projects_db[doc_id] or 'customer_project_reference' not in projects_db[doc_id]['details'] or \
'project_id' not in projects_db[doc_id]:
continue
#check the projects
project = projects_db[doc_id]
user_project_name = projects_db[doc_id]['details']['customer_project_reference']
NGI_project_name = projects_db[doc_id]['project_id']
if project['project_id'] in projects_name:
for sample in project['samples']:
sample_user_name = project['samples'][sample]['customer_name']
sample_NGI_name = project['samples'][sample]['scilife_name']
status = project['samples'][sample]['details']['status_(manual)']
if sample_user_name not in user2NGI_samples_names:
user2NGI_samples_names[sample_user_name] = []
user2NGI_samples_names[sample_user_name].append([sample_NGI_name, status, user_project_name, NGI_project_name])
if sample_NGI_name not in NGI2user_samples_names:
NGI2user_samples_names[sample_NGI_name] = []
NGI2user_samples_names[sample_NGI_name].append([sample_user_name, status, user_project_name, NGI_project_name])
if mode == 'user2NGI':
for sample in user2NGI_samples_names:
print("{}".format(sample.encode('ascii', 'ignore')), end=' ') # handle unicode in sample names
for NGI_id in user2NGI_samples_names[sample]:
print(" --- {},{},{},{}".format(NGI_id[0].encode('ascii', 'ignore'),NGI_id[1],NGI_id[2],NGI_id[3]), end=' ')
print("")
else:
for sample in NGI2user_samples_names:
sys.stdout.write("{}".format(sample))
for user_id in NGI2user_samples_names[sample]:
sys.stdout.write(" --- {},{},{},{}".format(user_id[0].encode('ascii', 'ignore'),user_id[1],user_id[2],user_id[3]))
print("")
def setupServer(conf):
db_conf = conf['statusdb']
url="https://{0}:{1}@{2}".format(db_conf['username'], db_conf['password'], db_conf['url'])
return couchdb.Server(url)
def load_yaml_config(config_file):
"""Load YAML config file
:param str config_file: The path to the configuration file.
:returns: A dict of the parsed config file.
:rtype: dict
:raises IOError: If the config file cannot be opened.
"""
if type(config_file) is file:
CONFIG.update(yaml.load(config_file) or {})
return CONFIG
else:
try:
with open(config_file, 'r') as f:
content = yaml.load(f)
CONFIG.update(content)
return content
except IOError as e:
e.message = "Could not open configuration file \"{}\".".format(config_file)
raise e
def user2NGI(args):
if args.project is not None:
associate_projects(args.project, args.mode)
else:
associete_samples(args.sample, args.mode)
def main(args):
configuration_file = args.config
projects_name = args.project
load_yaml_config(configuration_file)
if args.project != None and args.sample != None: #Mutually exclusive arguments
sys.exit("Only one between --project and --sample can be specified")
if args.project is not None:
associate_projects(args.project, args.mode)
else:
associete_samples(args.sample, args.mode)
#findNGISampleNames("2014-02321")
#findNGISampleNames("2153-08D")
#findUserSampleNames(projects_name)
if __name__ == '__main__':
parser = argparse.ArgumentParser("""This scripts connects to project database in statusDB and tries to associate user names to NGI names and vice-versa""")
parser.add_argument('--config', help="cauchdb configuration file", type=str, required=True)
parser.add_argument('--mode', help="specifies if we want the user2NGI or the NGI2user convertion", required=True, choices=('user2NGI', 'NGI2user') )
parser.add_argument('--project', help="project name. If specified returns all samples associated to this project and the user-NGI convertion outputs also the status of the sample)", type=str, action='append')
parser.add_argument('--sample', help="Sample name. If specified returns a list of the samples the associated user/NGI names", type=str, action='append')
args = parser.parse_args()
main(args)