annotate baric_archive.py @ 0:1ae6b80f1e03 draft default tip

"planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
author genouest
date Fri, 04 Mar 2022 11:16:34 +0000
parents
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1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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1 #!/usr/bin/env python
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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2 # Retrieves data from external data source applications and stores in a dataset file.
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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3 # Data source application parameters are temporarily stored in the dataset file.
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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4 import os
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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5 import socket
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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6 import sys
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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7 import urllib
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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8 from json import dumps, loads
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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9 from urllib.parse import urlparse
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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10 from urllib.request import urlopen
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
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11
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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12 from galaxy.datatypes import sniff
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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13 from galaxy.datatypes.registry import Registry
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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14 from galaxy.jobs import TOOL_PROVIDED_JOB_METADATA_FILE
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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15 from galaxy.util import get_charset_from_http_headers
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
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16
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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17 GALAXY_PARAM_PREFIX = 'GALAXY'
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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18 GALAXY_ROOT_DIR = os.path.realpath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir))
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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19 GALAXY_DATATYPES_CONF_FILE = os.path.join(GALAXY_ROOT_DIR, 'datatypes_conf.xml')
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
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20
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
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21
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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22 def stop_err(msg, json_file=None):
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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23 sys.stderr.write(msg)
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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24 # Need to write valid (but empty) json to avoid metadata collection failure
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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25 # leading to "unable to finish job" error with no logs
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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26 if json_file is not None:
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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27 json_file.write("%s\n" % dumps({}))
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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28 sys.exit(1)
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
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29
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
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30
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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31 def load_input_parameters(filename, erase_file=True):
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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32 datasource_params = {}
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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33 try:
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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34 json_params = loads(open(filename, 'r').read())
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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35 datasource_params = json_params.get('param_dict')
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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36 except Exception:
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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37 json_params = None
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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38 for line in open(filename, 'r'):
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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39 try:
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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40 line = line.strip()
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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41 fields = line.split('\t')
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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42 datasource_params[fields[0]] = fields[1]
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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43 except Exception:
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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44 continue
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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45 if erase_file:
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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46 open(filename, 'w').close() # open file for writing, then close, removes params from file
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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47 return json_params, datasource_params
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
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48
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
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49
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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50 def __main__():
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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51 filename = sys.argv[1]
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
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52
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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53 user_email = sys.argv[2]
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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54 user_id = sys.argv[3]
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
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55
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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56 try:
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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57 max_file_size = int(sys.argv[4])
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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58 except Exception:
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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59 max_file_size = 0
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
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60
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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61 job_params, params = load_input_parameters(filename)
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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62 if job_params is None: # using an older tabular file
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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63 enhanced_handling = False
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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64 job_params = dict(param_dict=params)
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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65 job_params['output_data'] = [dict(out_data_name='output',
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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66 ext='auto',
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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67 file_name=filename,
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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68 extra_files_path=None)]
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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69 job_params['job_config'] = dict(GALAXY_ROOT_DIR=GALAXY_ROOT_DIR, GALAXY_DATATYPES_CONF_FILE=GALAXY_DATATYPES_CONF_FILE, TOOL_PROVIDED_JOB_METADATA_FILE=TOOL_PROVIDED_JOB_METADATA_FILE)
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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70 else:
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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71 enhanced_handling = True
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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72 json_file = open(job_params['job_config']['TOOL_PROVIDED_JOB_METADATA_FILE'], 'w') # specially named file for output junk to pass onto set metadata
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
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73
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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74 datatypes_registry = Registry()
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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75 datatypes_registry.load_datatypes(root_dir=job_params['job_config']['GALAXY_ROOT_DIR'], config=job_params['job_config']['GALAXY_DATATYPES_CONF_FILE'])
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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76
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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77 URL = params.get('URL', None) # using exactly URL indicates that only one dataset is being downloaded
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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78 export = params.get('export', None)
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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79 userkey = params.get('userkey', 'none')
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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80 URL_method = params.get('URL_method', None)
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
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81
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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82 URL = URL + "&userkey=" + userkey + "&user_email=" + user_email + "&user_id=" + user_id
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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83
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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84 # The Python support for fetching resources from the web is layered. urllib uses the httplib
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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85 # library, which in turn uses the socket library. As of Python 2.3 you can specify how long
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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86 # a socket should wait for a response before timing out. By default the socket module has no
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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87 # timeout and can hang. Currently, the socket timeout is not exposed at the httplib or urllib2
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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88 # levels. However, you can set the default timeout ( in seconds ) globally for all sockets by
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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89 # doing the following.
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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90 socket.setdefaulttimeout(600)
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
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91
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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92 for data_dict in job_params['output_data']:
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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93 cur_filename = data_dict.get('file_name', filename)
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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94 cur_URL = params.get('%s|%s|URL' % (GALAXY_PARAM_PREFIX, data_dict['out_data_name']), URL)
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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95 if not cur_URL or urlparse(cur_URL).scheme not in ('http', 'https', 'ftp'):
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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96 open(cur_filename, 'w').write("")
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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97 stop_err('The remote data source application has not sent back a URL parameter in the request.', json_file)
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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98
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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99 # The following calls to urlopen() will use the above default timeout
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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100 try:
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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101 if not URL_method or URL_method == 'get':
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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102 page = urlopen(cur_URL)
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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103 elif URL_method == 'post':
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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104 page = urlopen(cur_URL, urllib.parse.urlencode(params).encode("utf-8"))
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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105 except Exception as e:
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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106 stop_err('The remote data source application may be off line, please try again later. Error: %s' % str(e), json_file)
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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107 if max_file_size:
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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108 file_size = int(page.info().get('Content-Length', 0))
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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109 if file_size > max_file_size:
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
parents:
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110 stop_err('The size of the data (%d bytes) you have requested exceeds the maximum allowed (%d bytes) on this server.' % (file_size, max_file_size), json_file)
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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111 # handle files available locally
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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112 if export:
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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diff changeset
113 try:
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
parents:
diff changeset
114 local_file = export + page.read()
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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115 os.remove(cur_filename)
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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116 os.symlink(local_file, cur_filename)
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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117 except Exception as e:
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
parents:
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118 stop_err('Unable to symlink %s to %s:\n%s' % (local_file, cur_filename, e), json_file)
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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119 else:
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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120 try:
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
parents:
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121 cur_filename = sniff.stream_to_open_named_file(page, os.open(cur_filename, os.O_WRONLY | os.O_CREAT), cur_filename, source_encoding=get_charset_from_http_headers(page.headers))
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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diff changeset
122 except Exception as e:
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
parents:
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123 stop_err('Unable to fetch %s:\n%s' % (cur_URL, e), json_file)
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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124
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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125 # here import checks that upload tool performs
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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126 if enhanced_handling:
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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127 try:
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
parents:
diff changeset
128 ext = sniff.handle_uploaded_dataset_file(filename, datatypes_registry, ext=data_dict['ext'])
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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129 except Exception as e:
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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diff changeset
130 stop_err(str(e), json_file)
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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diff changeset
131 info = dict(type='dataset',
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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diff changeset
132 dataset_id=data_dict['dataset_id'],
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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diff changeset
133 ext=ext)
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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diff changeset
134
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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diff changeset
135 json_file.write("%s\n" % dumps(info))
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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diff changeset
136
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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diff changeset
137
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
parents:
diff changeset
138 if __name__ == "__main__":
1ae6b80f1e03 "planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
genouest
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diff changeset
139 __main__()