#!/usr/bin/env python
-from ConfigParser import SafeConfigParser
+from configparser import SafeConfigParser
import fnmatch
from glob import glob
import json
import os
from pprint import pprint, pformat
import shlex
-from StringIO import StringIO
+from io import StringIO
import stat
import sys
import time
import types
-import urllib
-import urllib2
-import urlparse
+import urllib.request, urllib.parse, urllib.error
+import urllib.request, urllib.error, urllib.parse
+import urllib.parse
from zipfile import ZipFile
import RDF
model = get_model(opts.model, opts.db_path)
mapper = None
if opts.name:
- mapper = GEOSubmission(opts.name, model)
- if opts.library_url is not None:
- mapper.library_url = opts.library_url
+ mapper = GEOSubmission(opts.name, model, host=opts.host)
submission_uri = get_submission_uri(opts.name)
results = ResultMap()
for a in args:
- results.add_results_from_file(a)
+ if os.path.exists(a):
+ results.add_results_from_file(a)
+ else:
+ logger.warn("File %s doesn't exist.", a)
if opts.make_tree_from is not None:
results.make_tree_from(opts.make_tree_from)
if opts.fastq:
- extractor = CondorFastqExtract(opts.host, apidata, opts.sequence,
+ logger.info("Building fastq extraction scripts")
+ flowcells = os.path.join(opts.sequence, 'flowcells')
+ extractor = CondorFastqExtract(opts.host, flowcells,
+ model=opts.model,
force=opts.force)
extractor.create_scripts(results)
if opts.scan_submission:
+ if opts.name is None:
+ parser.error("Please define a submission name")
mapper.scan_submission_dirs(results)
if opts.make_soft:
if opts.print_rdf:
writer = get_serializer()
- print writer.serialize_model_to_string(model)
+ print(writer.serialize_model_to_string(model))
def make_parser():