Mercurial > repos > iuc > data_manager_manual

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 09b56ef3e09ad6c5923c88616fea5cbd77d87616
author iuc
date Mon, 18 Dec 2023 09:36:28 +0000
parents 6a6a2e4cc222
children
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81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
iuc
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1 #!/usr/bin/env python
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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2 # Dan Blankenberg
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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4 import json
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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5 import logging
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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6 import optparse
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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7 import os
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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8 import shutil
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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9 import tempfile
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6524e573d9c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9e376934d399042eabcd4129e23beda60917273d
iuc
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10 from xml.etree.ElementTree import tostring
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81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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12 try:
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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13 # For Python 3.0 and later
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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14 from shutil import unpack_archive
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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15 except ImportError:
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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16 # Fall back to Python 2 import
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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17 from setuptools.archive_util import unpack_archive
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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19 try:
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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20 # For Python 3.0 and later
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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21 from urllib.request import urlretrieve
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1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
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22 from urllib.parse import urlsplit
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81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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23 except ImportError:
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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24 # Fall back to Python 2 imports
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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25 from urllib import urlretrieve
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26 from urlparse import urlsplit
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81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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28 _log_name = __name__
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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29 if _log_name == '__builtin__':
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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30 _log_name = 'toolshed.installed.manual.data.manager'
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31 log = logging.getLogger(_log_name)
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81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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34 # --- These methods are called by/within the Galaxy Application
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35 def exec_before_job(app, inp_data, out_data, param_dict, tool=None, **kwd):
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81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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36 # Look for any data tables that haven't been defined for this data manager before and dynamically add them to Galaxy
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1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
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37 param_dict = dict(**param_dict)
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
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38 data_tables_param = param_dict.get('data_tables', [])
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
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39 if not isinstance(data_tables_param, list):
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81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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40 data_tables_param = [data_tables_param]
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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41 if tool:
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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42 tool_shed_repository = tool.tool_shed_repository
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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43 else:
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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44 tool_shed_repository = None
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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45 tdtm = None
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46 data_manager = app.data_managers.get_manager(tool.data_manager_id, None)
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81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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47 for data_table_param in data_tables_param:
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48 data_table_name = data_table_param.get('data_table_name')
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49 if data_table_name:
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50 # the 'data_table_name' value in data_table_param is a SelectToolParameter,
31f44a9f507e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit a0d52600f3f1c622760362e255520b956dd48e6a"
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51 # to get the selected value we need to cast data_table_name to string
31f44a9f507e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit a0d52600f3f1c622760362e255520b956dd48e6a"
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52 data_table_name = str(data_table_name)
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53 # get data table managed by this data Manager
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54 data_table = app.tool_data_tables.get_tables().get(data_table_name)
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81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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55 if data_table:
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56 data_table_filename = data_table.get_filename_for_source(data_manager, None)
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57 if not data_table_filename:
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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58 if tdtm is None:
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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59 from tool_shed.tools import data_table_manager
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60 tdtm = data_table_manager.ToolDataTableManager(app)
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6a6a2e4cc222 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit dddd6cf3ff59f2a877d03930fcf0563240fb40d8"
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61 target_dir = tool_shed_repository.repo_path(app)
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62 # Dynamically add this data table
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63 log.debug("Attempting to dynamically create a missing Tool Data Table named %s." % data_table_name)
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
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64 repo_info = tdtm.generate_repository_info_elem_from_repository(tool_shed_repository, parent_elem=None)
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81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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65 if repo_info is not None:
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66 repo_info = tostring(repo_info)
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67 tmp_file = tempfile.NamedTemporaryFile(mode="w")
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68 tmp_file.write(__get_new_xml_definition(app, data_table, data_manager, repo_info, target_dir))
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81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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69 tmp_file.flush()
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70 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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81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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71 tmp_file.close()
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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72
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73
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74 def __get_new_xml_definition(app, data_table, data_manager, repo_info=None, location_file_dir=None):
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
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75 sub_dict = {'table_name': data_table.name, 'comment_char': '', 'columns': '', 'file_path': ''}
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
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76 sub_dict.update(data_manager.get_tool_shed_repository_info_dict())
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81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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77 if data_table.comment_char:
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1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
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78 sub_dict['comment_char'] = 'comment_char="%s"' % (data_table.comment_char)
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
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79 for i, name in enumerate(data_table.get_column_name_list()):
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81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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80 if name is not None:
2
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
iuc
parents: 1
diff changeset
81 sub_dict['columns'] = "%s\n%s" % (sub_dict['columns'], '<column name="%s" index="%s" />' % (name, i))
0
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
iuc
parents:
diff changeset
82 location_file_dir = location_file_dir or app.config.galaxy_data_manager_data_path
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
iuc
parents:
diff changeset
83 for filename in data_table.filenames.keys():
2
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
iuc
parents: 1
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84 sub_dict['file_path'] = os.path.basename(filename)
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
iuc
parents: 1
diff changeset
85 sub_dict['file_path'] = os.path.join(location_file_dir, sub_dict['file_path']) # os.path.abspath?
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
iuc
parents: 1
diff changeset
86 if not os.path.exists(sub_dict['file_path']):
0
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
iuc
parents:
diff changeset
87 # Create empty file
2
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
iuc
parents: 1
diff changeset
88 log.debug("Attempting to create a missing location file %s." % sub_dict['file_path'])
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
iuc
parents: 1
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89 open(sub_dict['file_path'], 'wb+').close()
0
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
iuc
parents:
diff changeset
90 break
2
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
iuc
parents: 1
diff changeset
91 sub_dict['repo_info'] = repo_info or ''
0
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
iuc
parents:
diff changeset
92 return """
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
iuc
parents:
diff changeset
93 <tables><table name="%(table_name)s" %(comment_char)s>
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
iuc
parents:
diff changeset
94 %(columns)s
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
iuc
parents:
diff changeset
95 <file path="%(file_path)s" />
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
iuc
parents:
diff changeset
96 %(repo_info)s
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
iuc
parents:
diff changeset
97 </table></tables>
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
iuc
parents:
diff changeset
98 """ % sub_dict
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
iuc
parents:
diff changeset
99
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
iuc
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100
2
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
iuc
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diff changeset
101 def galaxy_code_get_available_data_tables(trans):
0
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
iuc
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102 # list of data tables
2
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
iuc
parents: 1
diff changeset
103 return [(x, x, False) for x in trans.app.tool_data_tables.get_tables().keys()]
0
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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104
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
iuc
parents:
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105
2
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
iuc
parents: 1
diff changeset
106 def galaxy_code_get_available_data_table_columns(trans, data_table_name):
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
iuc
parents: 1
diff changeset
107 return [(x, x, True) for x in trans.app.tool_data_tables.get(data_table_name).get_column_name_list()]
0
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
iuc
parents:
diff changeset
108 # --- End Galaxy called Methods ---
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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diff changeset
109
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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110
2
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
iuc
parents: 1
diff changeset
111 def get_data_table_entries(params, galaxy_data_manager_data_path):
0
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
iuc
parents:
diff changeset
112 rval = {}
2
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
iuc
parents: 1
diff changeset
113 data_tables = params.get('data_tables', [])
0
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
iuc
parents:
diff changeset
114 for data_table in data_tables:
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
iuc
parents:
diff changeset
115 entry_dict = {}
2
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
iuc
parents: 1
diff changeset
116 for column in data_table.get('columns', []):
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
iuc
parents: 1
diff changeset
117 value = column.get('data_table_column_value', '')
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
iuc
parents: 1
diff changeset
118 if column.get('is_path', {}).get('is_path_selector') == 'yes' and column.get('is_path', {}).get('abspath') == 'abspath':
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
iuc
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diff changeset
119 value = os.path.abspath(os.path.join(galaxy_data_manager_data_path, value))
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
iuc
parents: 1
diff changeset
120 entry_dict[column.get('data_table_column_name', '')] = value
0
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
iuc
parents:
diff changeset
121 data_table_name = data_table['data_table_name']
2
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
iuc
parents: 1
diff changeset
122 rval[data_table_name] = rval.get(data_table_name, [])
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
iuc
parents: 1
diff changeset
123 rval[data_table_name].append(entry_dict)
0
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
iuc
parents:
diff changeset
124 return rval
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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125
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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126
2
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
iuc
parents: 1
diff changeset
127 def get_file_content(params, target_directory):
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
iuc
parents: 1
diff changeset
128 directory_content = params.get('directory_content', [])
0
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
iuc
parents:
diff changeset
129 for content in directory_content:
2
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
iuc
parents: 1
diff changeset
130 target_path = os.path.join(target_directory, content.get('subdir', ''))
0
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
iuc
parents:
diff changeset
131 try:
2
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
iuc
parents: 1
diff changeset
132 os.makedirs(target_path)
0
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
iuc
parents:
diff changeset
133 except OSError:
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
iuc
parents:
diff changeset
134 pass
2
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
iuc
parents: 1
diff changeset
135 if content.get('file_source', {}).get('file_source_selector') == 'URL':
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
iuc
parents: 1
diff changeset
136 (filename, headers) = urlretrieve(content.get('file_source', {}).get('file_URL'))
0
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
iuc
parents:
diff changeset
137 try:
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
iuc
parents:
diff changeset
138 bname = headers['Content-Disposition']
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
iuc
parents:
diff changeset
139 except KeyError:
2
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
iuc
parents: 1
diff changeset
140 bname = os.path.basename(urlsplit(content.get('file_source', {}).get('file_URL')).path)
0
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
iuc
parents:
diff changeset
141 else:
2
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
iuc
parents: 1
diff changeset
142 filename = content.get('file_source', {}).get('file_history')
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
iuc
parents: 1
diff changeset
143 bname = os.path.basename(filename)
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
iuc
parents: 1
diff changeset
144 file_action = content.get('file_action', {}).get('file_action_selector')
0
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
iuc
parents:
diff changeset
145 if file_action == 'unpack':
2
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
iuc
parents: 1
diff changeset
146 unpack_archive(filename, target_path)
0
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
iuc
parents:
diff changeset
147 else:
2
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
iuc
parents: 1
diff changeset
148 filename_override = content.get('file_action', {}).get('filename_override')
0
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
iuc
parents:
diff changeset
149 if filename_override:
2
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
iuc
parents: 1
diff changeset
150 target_path = os.path.join(target_path, filename_override)
0
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
iuc
parents:
diff changeset
151 else:
2
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
iuc
parents: 1
diff changeset
152 target_path = os.path.join(target_path, bname)
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
iuc
parents: 1
diff changeset
153 shutil.copyfile(filename, target_path)
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
iuc
parents: 1
diff changeset
154 return len(directory_content)
0
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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parents:
diff changeset
155
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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parents:
diff changeset
156
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
iuc
parents:
diff changeset
157 def main():
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
iuc
parents:
diff changeset
158 parser = optparse.OptionParser()
2
1c1e228884d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit f2ab0315fa6df9e3e917bbc112e29f384c3affba"
iuc
parents: 1
diff changeset
159 parser.add_option('', '--galaxy_data_manager_data_path', dest='galaxy_data_manager_data_path', default='', help='Root path for galaxy_data_manager_data_path')
0
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
iuc
parents:
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160 (options, args) = parser.parse_args()
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162 filename = args[0]
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163
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164 with open(filename) as fh:
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165 params = json.load(fh)
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166 target_directory = params['output_data'][0]['extra_files_path']
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167
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168 data_table_entries = get_data_table_entries(params['param_dict'], options.galaxy_data_manager_data_path)
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170 # save info to json file
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171 with open(filename, 'w') as fh:
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172 json.dump({"data_tables": data_table_entries}, fh, sort_keys=True)
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173
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174 get_file_content(params['param_dict'], target_directory)
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177 if __name__ == "__main__":
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178 main()