Mercurial > repos > devteam > data_manager_rsync_g2

annotate data_manager/data_manager_rsync.py @ 1:8ff92bd7e2a3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
author iuc
date Tue, 04 Apr 2017 18:13:26 -0400
parents 0a3a6f862104
children e0329ab30f6d
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0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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1 #!/usr/bin/env python
1
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
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2 # Dan Blankenberg
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
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3 from __future__ import print_function
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0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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4
1
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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5 import datetime
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
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6 import logging
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0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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7 import optparse
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8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
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8 import os
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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9 import shutil
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0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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10 import subprocess
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8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
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11 import tempfile
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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12 from json import (
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
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13 dumps,
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
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14 loads
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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15 )
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0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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16 from os.path import basename
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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17 from xml.etree.ElementTree import tostring
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8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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18 try:
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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19 # For Python 3.0 and later
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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20 from urllib.request import urlopen
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
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21 except ImportError:
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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22 # Fall back to Python 2 imports
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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23 from urllib2 import urlopen
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0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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25 _log_name = __name__
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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26 if _log_name == '__builtin__':
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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27 _log_name = 'toolshed.installed.g2.rsync.data.manager'
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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28 log = logging.getLogger( _log_name )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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30 # Get the Data from the Galaxy Project rsync server
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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31 RSYNC_CMD = 'rsync'
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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32 RSYNC_SERVER = "rsync://datacache.g2.bx.psu.edu/"
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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33 LOCATION_DIR = "location"
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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34 INDEX_DIR = "indexes"
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0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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36 # Pull the Tool Data Table files from github
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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37 # FIXME: These files should be accessible from the rsync server directly.
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8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
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38 TOOL_DATA_TABLE_CONF_XML_URLS = {'main': "https://raw.githubusercontent.com/galaxyproject/usegalaxy-playbook/master/files/galaxy/usegalaxy.org/config/tool_data_table_conf.xml",
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
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39 'test': "https://raw.githubusercontent.com/galaxyproject/usegalaxy-playbook/master/files/galaxy/test.galaxyproject.org/config/tool_data_table_conf.xml" }
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0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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41 # Replace data table source entries with local temporary location
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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42 GALAXY_DATA_CANONICAL_PATH = "/galaxy/data/"
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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43 TOOL_DATA_TABLE_CONF_XML_REPLACE_SOURCE = '<file path="%slocation/' % ( GALAXY_DATA_CANONICAL_PATH )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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44 TOOL_DATA_TABLE_CONF_XML_REPLACE_TARGET = '<file path="%s/'
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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46 # Some basic Caching, so we don't have to reload and download everything every time
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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47 CACHE_TIME = datetime.timedelta( minutes=10 )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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48 TOOL_DATA_TABLES_LOADED_BY_URL = {}
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49
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50 # Entries will not be selected by default
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51 DEFAULT_SELECTED = False
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53 # Exclude data managers without 'path' column or that are in the manual exclude list
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54 PATH_COLUMN_NAMES = ['path']
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55 EXCLUDE_DATA_TABLES = []
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56 # TODO: Make additional handler actions available for tables that can't fit into the the basic
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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57 # "take the value of path" as a dir and copy contents.
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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58 # e.g. mafs. Although this maf table is goofy and doesn't have path defined in <table> def,
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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59 # but it does exit in the .loc.
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60
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61
0
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62 # --- These methods are called by/within the Galaxy Application
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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63 def exec_before_job( app, inp_data, out_data, param_dict, tool=None, **kwd ):
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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64 # Look for any data tables that haven't been defined for this data manager before and dynamically add them to Galaxy
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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65 param_dict = dict( **param_dict )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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66 param_dict['data_table_entries'] = param_dict.get( 'data_table_entries', [] )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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67 if not isinstance( param_dict['data_table_entries'], list ):
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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68 param_dict['data_table_entries'] = [param_dict['data_table_entries']]
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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69 param_dict['data_table_entries'] = ",".join( param_dict['data_table_entries'] )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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70 if tool:
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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71 tool_shed_repository = tool.tool_shed_repository
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72 else:
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73 tool_shed_repository = None
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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74 tdtm = None
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75 data_manager = app.data_managers.get_manager( tool.data_manager_id, None )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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76 data_table_entries = get_data_table_entries( param_dict )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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77 data_tables = load_data_tables_from_url( data_table_class=app.tool_data_tables.__class__ ).get( 'data_tables' )
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78 for data_table_name, entries in data_table_entries.items():
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79 # get data table managed by this data Manager
0
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80 has_data_table = app.tool_data_tables.get_tables().get( data_table_name )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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81 if has_data_table:
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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82 has_data_table = bool( has_data_table.get_filename_for_source( data_manager, None ) )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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83 if not has_data_table:
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84 if tdtm is None:
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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85 from tool_shed.tools import data_table_manager
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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86 tdtm = data_table_manager.ToolDataTableManager( app )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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87 target_dir, tool_path, relative_target_dir = tdtm.get_target_install_dir( tool_shed_repository )
1
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88 # Dynamically add this data table
0
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89 log.debug( "Attempting to dynamically create a missing Tool Data Table named %s." % data_table_name )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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90 data_table = data_tables[data_table_name]
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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91 repo_info = tdtm.generate_repository_info_elem_from_repository( tool_shed_repository, parent_elem=None )
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92 if repo_info is not None:
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93 repo_info = tostring( repo_info )
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94 tmp_file = tempfile.NamedTemporaryFile()
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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95 tmp_file.write( get_new_xml_definition( app, data_table, data_manager, repo_info, target_dir ) )
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96 tmp_file.flush()
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97 app.tool_data_tables.add_new_entries_from_config_file( tmp_file.name, None, app.config.shed_tool_data_table_config, persist=True )
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98 tmp_file.close()
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99
1
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100
0
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101 def galaxy_code_get_available_data_tables( trans ):
1
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102 # list of data tables
0
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103 found_tables = get_available_tables( trans )
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104 rval = [ ( x, x, DEFAULT_SELECTED ) for x in found_tables]
0
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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105 return rval
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106
1
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107
0
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108 def galaxy_code_get_available_data_tables_entries( trans, dbkey, data_table_names ):
1
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109 # available entries, optionally filtered by dbkey and table names
0
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110 if dbkey in [ None, '', '?' ]:
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111 dbkey = None
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112 if data_table_names in [ None, '', '?' ]:
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113 data_table_names = None
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114 found_tables = get_available_tables_for_dbkey( trans, dbkey, data_table_names )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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115 dbkey_text = '(%s) ' % ( dbkey ) if dbkey else ''
1
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116 rval = [( "%s%s" % ( dbkey_text, x[0] ), dumps( dict( name=x[0].split( ': ' )[0], entry=x[1] ) ).encode( 'base64' ).rstrip(), DEFAULT_SELECTED ) for x in found_tables.items()]
0
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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117 return rval
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118
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119 # --- End Galaxy called Methods ---
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120
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121
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122 def rsync_urljoin( base, url ):
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123 # urlparse.urljoin doesn't work correctly for our use-case
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124 # probably because it doesn't recognize the rsync scheme
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125 base = base.rstrip( '/' )
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126 url = url.lstrip( '/' )
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127 return "%s/%s" % ( base, url )
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128
1
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129
0
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130 def rsync_list_dir( server, dir=None, skip_names=[] ):
1
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131 # drwxr-xr-x 50 2014/05/16 20:58:11 .
0
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132 if dir:
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133 dir = rsync_urljoin( server, dir )
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134 else:
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135 dir = server
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136 rsync_response = tempfile.NamedTemporaryFile()
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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137 rsync_stderr = tempfile.NamedTemporaryFile()
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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138 rsync_cmd = [ RSYNC_CMD, '--list-only', dir ]
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139 return_code = subprocess.call( rsync_cmd, stdout=rsync_response, stderr=rsync_stderr )
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140 rsync_response.flush()
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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141 rsync_response.seek(0)
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142 rsync_stderr.flush()
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143 rsync_stderr.seek(0)
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144 if return_code:
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145 msg = "stdout:\n%s\nstderr:\n%s" % ( rsync_response.read(), rsync_stderr.read() )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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146 rsync_response.close()
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147 rsync_stderr.close()
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148 raise Exception( 'Failed to execute rsync command (%s), returncode=%s. Rsync_output:\n%s' % ( rsync_cmd, return_code, msg ) )
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149 rsync_stderr.close()
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150 rval = {}
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151 for line in rsync_response:
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152 perms, line = line.split( None, 1 )
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153 line = line.strip()
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154 size, line = line.split( None, 1 )
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155 line = line.strip()
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156 date, line = line.split( None, 1 )
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157 line = line.strip()
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158 time, line = line.split( None, 1 )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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159 name = line.strip()
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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160 if name in skip_names:
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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parents:
diff changeset
161 continue
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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162 size = line.strip()
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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163 rval[ name ] = dict( name=name, permissions=perms, bytes=size, date=date, time=time )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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164 rsync_response.close()
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165 return rval
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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166
1
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167
0
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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168 def rsync_sync_to_dir( source, target ):
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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169 rsync_response = tempfile.NamedTemporaryFile()
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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170 rsync_stderr = tempfile.NamedTemporaryFile()
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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171 rsync_cmd = [ RSYNC_CMD, '-avzP', source, target ]
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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172 return_code = subprocess.call( rsync_cmd, stdout=rsync_response, stderr=rsync_stderr )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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173 rsync_response.flush()
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174 rsync_response.seek(0)
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175 rsync_stderr.flush()
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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176 rsync_stderr.seek(0)
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177 if return_code:
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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178 msg = "stdout:\n%s\nstderr:\n%s" % ( rsync_response.read(), rsync_stderr.read() )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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179 rsync_response.close()
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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180 rsync_stderr.close()
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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181 raise Exception( 'Failed to execute rsync command (%s), returncode=%s. Rsync_output:\n%s' % ( rsync_cmd, return_code, msg ) )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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182 rsync_response.close()
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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183 rsync_stderr.close()
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184 return return_code
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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185
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186
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187 def data_table_needs_refresh( cached_data_table, url ):
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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188 if cached_data_table is None:
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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189 return True, {}
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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190 if datetime.datetime.now() - cached_data_table.get( 'time_loaded' ) > CACHE_TIME:
1
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191 data_table_text = urlopen( url ).read()
0
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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192 if cached_data_table.get( 'data_table_text', None ) != data_table_text:
1
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193 return True, {'data_table_text': data_table_text}
0
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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194 loc_file_attrs = rsync_list_dir( RSYNC_SERVER, LOCATION_DIR )
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195 if cached_data_table.get( 'loc_file_attrs', None ) != loc_file_attrs:
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
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196 return True, {'loc_file_attrs': loc_file_attrs}
0
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197 return False, {}
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198
1
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199
0
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200 def load_data_tables_from_url( url=None, site='main', data_table_class=None ):
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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201 if not url:
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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202 url = TOOL_DATA_TABLE_CONF_XML_URLS.get( site, None )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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203 assert url, ValueError( 'You must provide either a URL or a site=name.' )
1
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204
0
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205 cached_data_table = TOOL_DATA_TABLES_LOADED_BY_URL.get( url, None )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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206 refresh, attribs = data_table_needs_refresh( cached_data_table, url )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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207 if refresh:
1
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208 data_table_text = attribs.get( 'data_table_text' )or urlopen( url ).read()
0
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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209 loc_file_attrs = attribs.get( 'loc_file_attrs' ) or rsync_list_dir( RSYNC_SERVER, LOCATION_DIR )
1
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210
0
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211 tmp_dir = tempfile.mkdtemp( prefix='rsync_g2_' )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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212 tmp_loc_dir = os.path.join( tmp_dir, 'location' )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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213 os.mkdir( tmp_loc_dir )
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214 rsync_sync_to_dir( rsync_urljoin( RSYNC_SERVER, LOCATION_DIR ), os.path.abspath( tmp_loc_dir ) )
1
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215
0
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216 new_data_table_text = data_table_text.replace( TOOL_DATA_TABLE_CONF_XML_REPLACE_SOURCE, TOOL_DATA_TABLE_CONF_XML_REPLACE_TARGET % ( tmp_loc_dir ) )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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217 data_table_fh = tempfile.NamedTemporaryFile( dir=tmp_dir, prefix='rysnc_data_manager_data_table_conf_' )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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218 data_table_fh.write( new_data_table_text )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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219 data_table_fh.flush()
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220 tmp_data_dir = os.path.join( tmp_dir, 'tool-data' )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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221 os.mkdir( tmp_data_dir )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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222 data_tables = data_table_class( tmp_data_dir, config_filename=data_table_fh.name )
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diff changeset
223 for name, data_table in list(data_tables.data_tables.items()):
0
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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224 if name in EXCLUDE_DATA_TABLES or not data_table_has_path_column( data_table ):
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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225 log.debug( 'Removing data table "%s" because it is excluded by name or does not have a defined "path" column.', name )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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226 del data_tables.data_tables[name]
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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227 cached_data_table = { 'data_tables': data_tables, 'tmp_dir': tmp_dir, 'data_table_text': data_table_text, 'tmp_loc_dir': tmp_loc_dir, 'loc_file_attrs': loc_file_attrs, 'time_loaded': datetime.datetime.now() }
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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228 TOOL_DATA_TABLES_LOADED_BY_URL[ url ] = cached_data_table
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229 # delete the files
0
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230 data_table_fh.close()
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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231 cleanup_before_exit( tmp_dir )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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232 return cached_data_table
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233
1
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234
0
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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235 def data_table_has_path_column( data_table ):
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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236 col_names = data_table.get_column_name_list()
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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237 for name in PATH_COLUMN_NAMES:
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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238 if name in col_names:
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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239 return True
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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240 return False
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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241
1
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
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242
0
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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243 def get_available_tables( trans ):
1
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244 # list of data tables
0
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245 data_tables = load_data_tables_from_url( data_table_class=trans.app.tool_data_tables.__class__ )
1
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246 return list(data_tables.get( 'data_tables' ).get_tables().keys())
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
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247
0
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248
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249 def get_new_xml_definition( app, data_table, data_manager, repo_info=None, location_file_dir=None ):
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250 sub_dict = { 'table_name': data_table.name, 'comment_char': '', 'columns': '', 'file_path': '' }
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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251 sub_dict.update( data_manager.get_tool_shed_repository_info_dict() )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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252 if data_table.comment_char:
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253 sub_dict['comment_char'] = 'comment_char="%s"' % ( data_table.comment_char )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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254 for i, name in enumerate( data_table.get_column_name_list() ):
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255 if name is not None:
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256 sub_dict['columns'] = "%s\n%s" % ( sub_dict['columns'], '<column name="%s" index="%s" />' % ( name, i ) )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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257 location_file_dir = location_file_dir or app.config.galaxy_data_manager_data_path
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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258 for filename in data_table.filenames.keys():
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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259 sub_dict['file_path'] = basename( filename )
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260 sub_dict['file_path'] = os.path.join( location_file_dir, sub_dict['file_path'] ) # os.path.abspath?
0
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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261 if not os.path.exists( sub_dict['file_path'] ):
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262 # Create empty file
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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263 open( sub_dict['file_path'], 'wb+' ).close()
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264 break
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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265 sub_dict[ 'repo_info' ] = repo_info or ''
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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266 return """
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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267 <tables><table name="%(table_name)s" %(comment_char)s>
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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268 %(columns)s
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269 <file path="%(file_path)s" />
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270 %(repo_info)s
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271 </table></tables>
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272 """ % sub_dict
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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273
1
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274
0
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275 def get_available_tables_for_dbkey( trans, dbkey, data_table_names ):
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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276 data_tables = load_data_tables_from_url( data_table_class=trans.app.tool_data_tables.__class__ )
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277 rval = {}
1
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278 for name, data_table in data_tables.get( 'data_tables' ).get_tables().items():
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
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279 if ( not data_table_names or name in data_table_names ):
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280 # TODO: check that columns are similiar
0
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281 if not dbkey:
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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282 entry_getter = data_table.get_named_fields_list()
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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283 else:
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284 entry_getter = data_table.get_entries( 'dbkey', dbkey, None, default=[] )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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285 for entry in entry_getter:
1
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
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286 name = "%s: %s" % ( data_table.name, dumps( entry ) )
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
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287 rval[name] = entry
0
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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288 return rval
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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289
1
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290
0
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291 def split_path_all( path ):
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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292 rval = []
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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293 path = path.rstrip( '/' )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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294 while True:
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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295 head, tail = os.path.split( path )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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296 if tail:
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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297 rval.append( tail )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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298 path = head
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299 elif head:
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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300 rval.append( head )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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301 break
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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302 else:
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303 break
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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304 rval.reverse()
1
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305 return rval
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
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306
0
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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307
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308 def get_data_for_path( path, data_root_dir ):
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309 # We list dir with a /, but copy data without
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310 # listing with / gives a . entry when its a dir
1
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
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311 # cloning without the / will copy that whole directory into the target,
0
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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312 # instead of just that target's contents
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313 if path.startswith( GALAXY_DATA_CANONICAL_PATH ):
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314 path = path[ len( GALAXY_DATA_CANONICAL_PATH ):]
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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parents:
diff changeset
315 make_path = path
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
316 rsync_source = rsync_urljoin( rsync_urljoin( RSYNC_SERVER, INDEX_DIR ), path )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
317 if rsync_source.endswith( '/' ):
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
318 rsync_source = rsync_source[:-1]
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
319 try:
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
320 dir_list = rsync_list_dir( rsync_source + "/" )
1
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 0
diff changeset
321 except Exception:
0
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
322 dir_list = None
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
323 while not dir_list or '.' not in dir_list:
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
324 head, tail = os.path.split( make_path )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
325 if not head:
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
326 head = tail
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
327 make_path = head
1
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 0
diff changeset
328 rsync_source = rsync_urljoin( rsync_urljoin( RSYNC_SERVER, INDEX_DIR ), head ) # if we error here, likely due to a connection issue
0
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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parents:
diff changeset
329 if rsync_source.endswith( '/' ):
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
330 rsync_source = rsync_source[:-1]
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
331 dir_list = rsync_list_dir( rsync_source + "/" )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
332 split_path = split_path_all( make_path )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
333 target_path = data_root_dir
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
334 for p in split_path[:-1]:
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
335 target_path = os.path.join( target_path, p )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
336 if not os.path.exists( target_path ):
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
337 os.mkdir( target_path )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
338 rsync_sync_to_dir( rsync_source, target_path )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
339 return path
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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parents:
diff changeset
340
1
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 0
diff changeset
341
0
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
342 def get_data_and_munge_path( data_table_name, data_table_entry, data_root_dir ):
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
343 path_cols = []
1
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 0
diff changeset
344 for key, value in data_table_entry.items():
0
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
345 if key in PATH_COLUMN_NAMES:
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
346 path_cols.append( ( key, value ) )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
347 if path_cols:
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
348 for col_name, value in path_cols:
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
349 if value.startswith( GALAXY_DATA_CANONICAL_PATH ):
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
350 data_table_entry[col_name] = get_data_for_path( value, data_root_dir )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
351 else:
1
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 0
diff changeset
352 print('unable to determine location of rsync data for', data_table_name, data_table_entry)
0
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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parents:
diff changeset
353 return data_table_entry
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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diff changeset
354
1
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 0
diff changeset
355
0
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
356 def fulfill_data_table_entries( data_table_entries, data_manager_dict, data_root_dir ):
1
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 0
diff changeset
357 for data_table_name, entries in data_table_entries.items():
0
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
358 for entry in entries:
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
359 entry = get_data_and_munge_path( data_table_name, entry, data_root_dir )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
360 _add_data_table_entry( data_manager_dict, data_table_name, entry )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
361 return data_manager_dict
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
362
1
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 0
diff changeset
363
0
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
364 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
365 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
366 data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get( data_table_name, [] )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
367 data_manager_dict['data_tables'][data_table_name].append( data_table_entry )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
368 return data_manager_dict
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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parents:
diff changeset
369
1
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 0
diff changeset
370
0
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
371 def cleanup_before_exit( tmp_dir ):
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
372 if tmp_dir and os.path.exists( tmp_dir ):
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
373 shutil.rmtree( tmp_dir )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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diff changeset
374
1
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 0
diff changeset
375
0
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
376 def get_data_table_entries( params ):
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
377 rval = {}
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
378 data_table_entries = params.get( 'data_table_entries', None )
1
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 0
diff changeset
379 if data_table_entries:
0
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
380 for entry_text in data_table_entries.split( ',' ):
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
381 entry_text = entry_text.strip().decode( 'base64' )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
382 entry_dict = loads( entry_text )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
383 data_table_name = entry_dict['name']
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
384 data_table_entry = entry_dict['entry']
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
385 rval[ data_table_name ] = rval.get( data_table_name, [] )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
386 rval[ data_table_name ].append( data_table_entry )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
387 return rval
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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parents:
diff changeset
388
1
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 0
diff changeset
389
0
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
390 def main():
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
391 parser = optparse.OptionParser()
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
392 (options, args) = parser.parse_args()
1
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 0
diff changeset
393
0
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
394 filename = args[0]
1
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
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395
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0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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396 params = loads( open( filename ).read() )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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397 target_directory = params[ 'output_data' ][0]['extra_files_path']
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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398 os.mkdir( target_directory )
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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399 data_manager_dict = {}
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8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
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400
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0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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401 data_table_entries = get_data_table_entries( params['param_dict'] )
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8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
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402
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0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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403 # Populate the data Tables
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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404 data_manager_dict = fulfill_data_table_entries( data_table_entries, data_manager_dict, target_directory )
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8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
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405
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
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406 # save info to json file
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0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
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407 open( filename, 'wb' ).write( dumps( data_manager_dict ) )
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8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
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8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
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409
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
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410 if __name__ == "__main__":
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
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411 main()