mirror of
https://github.com/galaxyproject/galaxy.git
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Refactor several methods in Galaxy's admin_toolshed controller in preparation for supporting installing tool shed repositories via the tool shed and Galaxy APIs.
This commit is contained in:
Greg Von Kuster
@@ -1,19 +1,35 @@
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import logging, os, shutil, tempfile, urllib2
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import logging
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import os
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import shutil
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import urllib2
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from admin import AdminGalaxy
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from galaxy import web, util, eggs, tools
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from galaxy.web.form_builder import SelectField, CheckboxField
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from galaxy.web.framework.helpers import iff, grids
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from galaxy import eggs
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from galaxy import web
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from galaxy import util
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from galaxy.web.form_builder import CheckboxField
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from galaxy.web.framework.helpers import grids
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from galaxy.web.framework.helpers import iff
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from galaxy.util import json
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from galaxy.model.orm import or_
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import tool_shed.util.shed_util_common as suc
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from tool_shed.util import common_install_util, data_manager_util, datatype_util, encoding_util, metadata_util
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from tool_shed.util import readme_util, repository_dependency_util, tool_dependency_util, tool_util, workflow_util
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from tool_shed.util import common_install_util
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from tool_shed.util import data_manager_util
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from tool_shed.util import datatype_util
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from tool_shed.util import encoding_util
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from tool_shed.util import metadata_util
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from tool_shed.util import readme_util
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from tool_shed.util import repository_dependency_util
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from tool_shed.util import tool_dependency_util
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from tool_shed.util import tool_util
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from tool_shed.util import workflow_util
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from tool_shed.galaxy_install import repository_util
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import tool_shed.galaxy_install.grids.admin_toolshed_grids as admin_toolshed_grids
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import pkg_resources
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eggs.require( 'mercurial' )
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from mercurial import hg, ui, commands
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from mercurial import commands
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from mercurial import hg
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from mercurial import ui
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pkg_resources.require( 'elementtree' )
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from elementtree import ElementTree
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@@ -520,96 +536,21 @@ class AdminToolshed( AdminGalaxy ):
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"""Install specified tool shed repositories."""
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shed_tool_conf = kwd.get( 'shed_tool_conf', '' )
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tool_path = kwd[ 'tool_path' ]
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includes_tool_dependencies = util.string_as_bool( kwd[ 'includes_tool_dependencies' ] )
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install_tool_dependencies = CheckboxField.is_checked( kwd.get( 'install_tool_dependencies', '' ) )
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# There must be a one-to-one mapping between items in the 3 lists:tool_shed_repositories, tool_panel_section_keys, repo_info_dicts.
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# There must be a one-to-one mapping between items in the 3 lists: tool_shed_repositories, tool_panel_section_keys, repo_info_dicts.
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tool_panel_section_keys = util.listify( kwd[ 'tool_panel_section_keys' ] )
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repo_info_dicts = util.listify( kwd[ 'repo_info_dicts' ] )
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for index, tool_shed_repository in enumerate( tool_shed_repositories ):
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repo_info_dict = repo_info_dicts[ index ]
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tool_panel_section_key = tool_panel_section_keys[ index ]
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if tool_panel_section_key:
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tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ]
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else:
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tool_section = None
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if isinstance( repo_info_dict, basestring ):
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repo_info_dict = encoding_util.tool_shed_decode( repo_info_dict )
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# Clone each repository to the configured location.
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suc.update_tool_shed_repository_status( trans.app, tool_shed_repository, trans.model.ToolShedRepository.installation_status.CLONING )
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repo_info_tuple = repo_info_dict[ tool_shed_repository.name ]
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description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = repo_info_tuple
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relative_clone_dir = suc.generate_tool_shed_repository_install_dir( repository_clone_url, tool_shed_repository.installed_changeset_revision )
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clone_dir = os.path.join( tool_path, relative_clone_dir )
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relative_install_dir = os.path.join( relative_clone_dir, tool_shed_repository.name )
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install_dir = os.path.join( tool_path, relative_install_dir )
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cloned_ok, error_message = suc.clone_repository( repository_clone_url, os.path.abspath( install_dir ), ctx_rev )
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if cloned_ok:
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if reinstalling:
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# Since we're reinstalling the repository we need to find the latest changeset revision to which is can be updated.
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changeset_revision_dict = repository_util.get_update_to_changeset_revision_and_ctx_rev( trans, tool_shed_repository )
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current_changeset_revision = changeset_revision_dict.get( 'changeset_revision', None )
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current_ctx_rev = changeset_revision_dict.get( 'ctx_rev', None )
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if current_ctx_rev != ctx_rev:
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repo = hg.repository( suc.get_configured_ui(), path=os.path.abspath( install_dir ) )
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repository_util.pull_repository( repo, repository_clone_url, current_changeset_revision )
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suc.update_repository( repo, ctx_rev=current_ctx_rev )
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repository_util.handle_repository_contents( trans,
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tool_shed_repository=tool_shed_repository,
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tool_path=tool_path,
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repository_clone_url=repository_clone_url,
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relative_install_dir=relative_install_dir,
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tool_shed=tool_shed_repository.tool_shed,
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tool_section=tool_section,
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shed_tool_conf=shed_tool_conf,
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reinstalling=reinstalling )
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trans.sa_session.refresh( tool_shed_repository )
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metadata = tool_shed_repository.metadata
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if 'tools' in metadata:
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# Get the tool_versions from the tool shed for each tool in the installed change set.
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suc.update_tool_shed_repository_status( trans.app,
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tool_shed_repository,
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trans.model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS )
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tool_shed_url = suc.get_url_from_tool_shed( trans.app, tool_shed_repository.tool_shed )
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url = suc.url_join( tool_shed_url,
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'/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s' % \
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( tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.changeset_revision ) )
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response = urllib2.urlopen( url )
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text = response.read()
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response.close()
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if text:
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tool_version_dicts = json.from_json_string( text )
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tool_util.handle_tool_versions( trans.app, tool_version_dicts, tool_shed_repository )
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else:
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message += "Version information for the tools included in the <b>%s</b> repository is missing. " % name
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message += "Reset all of this repository's metadata in the tool shed, then set the installed tool versions "
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message += "from the installed repository's <b>Repository Actions</b> menu. "
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status = 'error'
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if install_tool_dependencies and tool_shed_repository.tool_dependencies and 'tool_dependencies' in metadata:
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work_dir = tempfile.mkdtemp()
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# Install tool dependencies.
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suc.update_tool_shed_repository_status( trans.app,
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tool_shed_repository,
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trans.model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES )
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# Get the tool_dependencies.xml file from the repository.
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tool_dependencies_config = suc.get_config_from_disk( 'tool_dependencies.xml', install_dir )#relative_install_dir )
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installed_tool_dependencies = common_install_util.handle_tool_dependencies( app=trans.app,
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tool_shed_repository=tool_shed_repository,
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tool_dependencies_config=tool_dependencies_config,
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tool_dependencies=tool_shed_repository.tool_dependencies )
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try:
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shutil.rmtree( work_dir )
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except:
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pass
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suc.update_tool_shed_repository_status( trans.app, tool_shed_repository, trans.model.ToolShedRepository.installation_status.INSTALLED )
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else:
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# An error occurred while cloning the repository, so reset everything necessary to enable another attempt.
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self.set_repository_attributes( trans,
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tool_shed_repository,
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status=trans.model.ToolShedRepository.installation_status.ERROR,
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error_message=error_message,
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deleted=False,
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uninstalled=False,
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remove_from_disk=True )
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repository_util.install_tool_shed_repository( trans,
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tool_shed_repository,
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repo_info_dict,
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tool_panel_section_key,
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shed_tool_conf,
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tool_path,
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install_tool_dependencies,
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reinstalling=reinstalling )
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tsr_ids_for_monitoring = [ trans.security.encode_id( tsr.id ) for tsr in tool_shed_repositories ]
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return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
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action='monitor_repository_installation',
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@@ -844,7 +785,7 @@ class AdminToolshed( AdminGalaxy ):
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@web.expose
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@web.require_admin
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def prepare_for_install( self, trans, **kwd ):
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if not have_shed_tool_conf_for_install( trans ):
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if not suc.have_shed_tool_conf_for_install( trans ):
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message = 'The <b>tool_config_file</b> setting in <b>universe_wsgi.ini</b> must include at least one shed tool configuration file name with a '
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message += '<b><toolbox></b> tag that includes a <b>tool_path</b> attribute value which is a directory relative to the Galaxy installation '
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message += 'directory in order to automatically install tools from a Galaxy tool shed (e.g., the file name <b>shed_tool_conf.xml</b> whose '
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@@ -942,9 +883,9 @@ class AdminToolshed( AdminGalaxy ):
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return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
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action='manage_repositories',
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**kwd ) )
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shed_tool_conf_select_field = build_shed_tool_conf_select_field( trans )
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shed_tool_conf_select_field = tool_util.build_shed_tool_conf_select_field( trans )
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tool_path = suc.get_tool_path_by_shed_tool_conf_filename( trans, shed_tool_conf )
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tool_panel_section_select_field = build_tool_panel_section_select_field( trans )
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tool_panel_section_select_field = tool_util.build_tool_panel_section_select_field( trans )
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if len( repo_info_dicts ) == 1:
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# If we're installing a single repository, see if it contains a readme or dependencies that we can display.
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repo_info_dict = repo_info_dicts[ 0 ]
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@@ -1278,7 +1219,7 @@ class AdminToolshed( AdminGalaxy ):
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original_section_name = ''
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else:
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original_section_name = ''
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tool_panel_section_select_field = build_tool_panel_section_select_field( trans )
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tool_panel_section_select_field = tool_util.build_tool_panel_section_select_field( trans )
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no_changes_check_box = CheckboxField( 'no_changes', checked=True )
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if original_section_name:
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message += "The tools contained in your <b>%s</b> repository were last loaded into the tool panel section <b>%s</b>. " \
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@@ -1294,7 +1235,7 @@ class AdminToolshed( AdminGalaxy ):
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no_changes_check_box = None
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original_section_name = ''
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tool_panel_section_select_field = None
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shed_tool_conf_select_field = build_shed_tool_conf_select_field( trans )
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shed_tool_conf_select_field = tool_util.build_shed_tool_conf_select_field( trans )
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containers_dict = repository_util.populate_containers_dict_for_new_install( trans=trans,
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tool_shed_url=tool_shed_url,
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tool_path=tool_path,
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@@ -1398,13 +1339,13 @@ class AdminToolshed( AdminGalaxy ):
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"""An error occurred while cloning the repository, so reset everything necessary to enable another attempt."""
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repository = suc.get_installed_tool_shed_repository( trans, kwd[ 'id' ] )
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if kwd.get( 'reset_repository', False ):
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self.set_repository_attributes( trans,
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repository,
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status=trans.model.ToolShedRepository.installation_status.NEW,
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error_message=None,
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deleted=False,
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uninstalled=False,
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remove_from_disk=True )
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suc.set_repository_attributes( trans,
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repository,
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status=trans.model.ToolShedRepository.installation_status.NEW,
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error_message=None,
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deleted=False,
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uninstalled=False,
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remove_from_disk=True )
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new_kwd = {}
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new_kwd[ 'message' ] = "You can now attempt to install the repository named <b>%s</b> again." % repository.name
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new_kwd[ 'status' ] = "done"
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@@ -1415,20 +1356,6 @@ class AdminToolshed( AdminGalaxy ):
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action='manage_repository',
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**kwd ) )
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def set_repository_attributes( self, trans, repository, status, error_message, deleted, uninstalled, remove_from_disk=False ):
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if remove_from_disk:
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relative_install_dir = repository.repo_path( trans.app )
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if relative_install_dir:
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clone_dir = os.path.abspath( relative_install_dir )
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shutil.rmtree( clone_dir )
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log.debug( "Removed repository installation directory: %s" % str( clone_dir ) )
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repository.error_message = error_message
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repository.status = status
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repository.deleted = deleted
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repository.uninstalled = uninstalled
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trans.sa_session.add( repository )
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trans.sa_session.flush()
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@web.expose
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@web.require_admin
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def set_tool_versions( self, trans, **kwd ):
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@@ -1680,46 +1607,3 @@ class AdminToolshed( AdminGalaxy ):
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metadata=metadata,
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message=message,
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status=status )
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## ---- Utility methods -------------------------------------------------------
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def build_shed_tool_conf_select_field( trans ):
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"""Build a SelectField whose options are the keys in trans.app.toolbox.shed_tool_confs."""
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options = []
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for shed_tool_conf_dict in trans.app.toolbox.shed_tool_confs:
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shed_tool_conf_filename = shed_tool_conf_dict[ 'config_filename' ]
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if shed_tool_conf_filename != trans.app.config.migrated_tools_config:
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if shed_tool_conf_filename.startswith( './' ):
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option_label = shed_tool_conf_filename.replace( './', '', 1 )
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else:
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option_label = shed_tool_conf_filename
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options.append( ( option_label, shed_tool_conf_filename ) )
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select_field = SelectField( name='shed_tool_conf' )
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for option_tup in options:
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select_field.add_option( option_tup[0], option_tup[1] )
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return select_field
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def build_tool_panel_section_select_field( trans ):
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"""Build a SelectField whose options are the sections of the current in-memory toolbox."""
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options = []
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for k, v in trans.app.toolbox.tool_panel.items():
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if isinstance( v, tools.ToolSection ):
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options.append( ( v.name, v.id ) )
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select_field = SelectField( name='tool_panel_section', display='radio' )
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for option_tup in options:
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select_field.add_option( option_tup[0], option_tup[1] )
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return select_field
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def can_select_tool_panel_section():
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pass
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def have_shed_tool_conf_for_install( trans ):
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if not trans.app.toolbox.shed_tool_confs:
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return False
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migrated_tools_conf_path, migrated_tools_conf_name = os.path.split( trans.app.config.migrated_tools_config )
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for shed_tool_conf_dict in trans.app.toolbox.shed_tool_confs:
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shed_tool_conf = shed_tool_conf_dict[ 'config_filename' ]
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shed_tool_conf_path, shed_tool_conf_name = os.path.split( shed_tool_conf )
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if shed_tool_conf_name != migrated_tools_conf_name:
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return True
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return False
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@@ -1,12 +1,16 @@
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import logging
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import os
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import shutil
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import tempfile
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import threading
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import urllib2
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from galaxy import tools
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from galaxy.util import json
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from galaxy import web
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from galaxy.model.orm import or_
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from galaxy.webapps.tool_shed.util import container_util
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import tool_shed.util.shed_util_common as suc
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from tool_shed.util import common_install_util
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from tool_shed.util import data_manager_util
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from tool_shed.util import datatype_util
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from tool_shed.util import encoding_util
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@@ -63,7 +67,7 @@ def create_repo_info_dict( trans, repository_clone_url, changeset_revision, ctx_
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all_repository_dependencies=None,
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handled_key_rd_dicts=None,
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circular_repository_dependencies=None )
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tool_dependencies = metadata.get( 'tool_dependencies', None )
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tool_dependencies = metadata.get( 'tool_dependencies', {} )
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if tool_dependencies:
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new_tool_dependencies = {}
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for dependency_key, requirements_dict in tool_dependencies.items():
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@@ -347,6 +351,91 @@ def initiate_repository_installation( trans, installation_dict ):
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query = trans.sa_session.query( trans.model.ToolShedRepository ).filter( or_( *clause_list ) )
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return encoded_kwd, query, tool_shed_repositories, encoded_repository_ids
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def install_tool_shed_repository( trans, tool_shed_repository, repo_info_dict, tool_panel_section_key, shed_tool_conf, tool_path, install_tool_dependencies,
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reinstalling=False ):
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if tool_panel_section_key:
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tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ]
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else:
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tool_section = None
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if isinstance( repo_info_dict, basestring ):
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repo_info_dict = encoding_util.tool_shed_decode( repo_info_dict )
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# Clone each repository to the configured location.
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suc.update_tool_shed_repository_status( trans.app, tool_shed_repository, trans.model.ToolShedRepository.installation_status.CLONING )
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repo_info_tuple = repo_info_dict[ tool_shed_repository.name ]
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description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = repo_info_tuple
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relative_clone_dir = suc.generate_tool_shed_repository_install_dir( repository_clone_url, tool_shed_repository.installed_changeset_revision )
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clone_dir = os.path.join( tool_path, relative_clone_dir )
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relative_install_dir = os.path.join( relative_clone_dir, tool_shed_repository.name )
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install_dir = os.path.join( tool_path, relative_install_dir )
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cloned_ok, error_message = suc.clone_repository( repository_clone_url, os.path.abspath( install_dir ), ctx_rev )
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if cloned_ok:
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if reinstalling:
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# Since we're reinstalling the repository we need to find the latest changeset revision to which is can be updated.
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changeset_revision_dict = get_update_to_changeset_revision_and_ctx_rev( trans, tool_shed_repository )
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current_changeset_revision = changeset_revision_dict.get( 'changeset_revision', None )
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current_ctx_rev = changeset_revision_dict.get( 'ctx_rev', None )
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if current_ctx_rev != ctx_rev:
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repo = hg.repository( suc.get_configured_ui(), path=os.path.abspath( install_dir ) )
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pull_repository( repo, repository_clone_url, current_changeset_revision )
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suc.update_repository( repo, ctx_rev=current_ctx_rev )
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handle_repository_contents( trans,
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tool_shed_repository=tool_shed_repository,
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tool_path=tool_path,
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repository_clone_url=repository_clone_url,
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relative_install_dir=relative_install_dir,
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tool_shed=tool_shed_repository.tool_shed,
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tool_section=tool_section,
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shed_tool_conf=shed_tool_conf,
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reinstalling=reinstalling )
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trans.sa_session.refresh( tool_shed_repository )
|
||||
metadata = tool_shed_repository.metadata
|
||||
if 'tools' in metadata:
|
||||
# Get the tool_versions from the tool shed for each tool in the installed change set.
|
||||
suc.update_tool_shed_repository_status( trans.app,
|
||||
tool_shed_repository,
|
||||
trans.model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS )
|
||||
tool_shed_url = suc.get_url_from_tool_shed( trans.app, tool_shed_repository.tool_shed )
|
||||
url = suc.url_join( tool_shed_url,
|
||||
'/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s' % \
|
||||
( tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.changeset_revision ) )
|
||||
response = urllib2.urlopen( url )
|
||||
text = response.read()
|
||||
response.close()
|
||||
if text:
|
||||
tool_version_dicts = json.from_json_string( text )
|
||||
tool_util.handle_tool_versions( trans.app, tool_version_dicts, tool_shed_repository )
|
||||
else:
|
||||
message += "Version information for the tools included in the <b>%s</b> repository is missing. " % name
|
||||
message += "Reset all of this repository's metadata in the tool shed, then set the installed tool versions "
|
||||
message += "from the installed repository's <b>Repository Actions</b> menu. "
|
||||
status = 'error'
|
||||
if install_tool_dependencies and tool_shed_repository.tool_dependencies and 'tool_dependencies' in metadata:
|
||||
work_dir = tempfile.mkdtemp()
|
||||
# Install tool dependencies.
|
||||
suc.update_tool_shed_repository_status( trans.app,
|
||||
tool_shed_repository,
|
||||
trans.model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES )
|
||||
# Get the tool_dependencies.xml file from the repository.
|
||||
tool_dependencies_config = suc.get_config_from_disk( 'tool_dependencies.xml', install_dir )#relative_install_dir )
|
||||
installed_tool_dependencies = common_install_util.handle_tool_dependencies( app=trans.app,
|
||||
tool_shed_repository=tool_shed_repository,
|
||||
tool_dependencies_config=tool_dependencies_config,
|
||||
tool_dependencies=tool_shed_repository.tool_dependencies )
|
||||
try:
|
||||
shutil.rmtree( work_dir )
|
||||
except:
|
||||
pass
|
||||
suc.update_tool_shed_repository_status( trans.app, tool_shed_repository, trans.model.ToolShedRepository.installation_status.INSTALLED )
|
||||
else:
|
||||
# An error occurred while cloning the repository, so reset everything necessary to enable another attempt.
|
||||
suc.set_repository_attributes( trans,
|
||||
tool_shed_repository,
|
||||
status=trans.model.ToolShedRepository.installation_status.ERROR,
|
||||
error_message=error_message,
|
||||
deleted=False,
|
||||
uninstalled=False,
|
||||
remove_from_disk=True )
|
||||
|
||||
def merge_containers_dicts_for_new_install( containers_dicts ):
|
||||
"""
|
||||
When installing one or more tool shed repositories for the first time, the received list of containers_dicts contains a containers_dict for
|
||||
|
||||
@@ -0,0 +1,165 @@
|
||||
import os, sys, urllib, urllib2
|
||||
|
||||
new_path = [ os.path.join( os.path.dirname( __file__ ), '..', '..', '..', 'lib' ) ]
|
||||
new_path.extend( sys.path[ 1: ] )
|
||||
sys.path = new_path
|
||||
|
||||
from galaxy import eggs
|
||||
import pkg_resources
|
||||
|
||||
pkg_resources.require( "simplejson" )
|
||||
import simplejson
|
||||
|
||||
pkg_resources.require( "pycrypto" )
|
||||
from Crypto.Cipher import Blowfish
|
||||
from Crypto.Util.randpool import RandomPool
|
||||
from Crypto.Util import number
|
||||
|
||||
def encode_id( config_id_secret, obj_id ):
|
||||
# Utility method to encode ID's
|
||||
id_cipher = Blowfish.new( config_id_secret )
|
||||
# Convert to string
|
||||
s = str( obj_id )
|
||||
# Pad to a multiple of 8 with leading "!"
|
||||
s = ( "!" * ( 8 - len(s) % 8 ) ) + s
|
||||
# Encrypt
|
||||
return id_cipher.encrypt( s ).encode( 'hex' )
|
||||
|
||||
def delete( api_key, url, data, return_formatted=True ):
|
||||
# Sends an API DELETE request and acts as a generic formatter for the JSON response - 'data' will become the JSON payload read by Galaxy.
|
||||
try:
|
||||
url = make_url( api_key, url )
|
||||
req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = simplejson.dumps( data ))
|
||||
req.get_method = lambda: 'DELETE'
|
||||
r = simplejson.loads( urllib2.urlopen( req ).read() )
|
||||
except urllib2.HTTPError, e:
|
||||
if return_formatted:
|
||||
print e
|
||||
print e.read( 1024 )
|
||||
sys.exit( 1 )
|
||||
else:
|
||||
return 'Error. '+ str( e.read( 1024 ) )
|
||||
if not return_formatted:
|
||||
return r
|
||||
print 'Response'
|
||||
print '--------'
|
||||
print r
|
||||
|
||||
def display( api_key, url, return_formatted=True ):
|
||||
# Sends an API GET request and acts as a generic formatter for the JSON response.
|
||||
try:
|
||||
r = get( api_key, url )
|
||||
except urllib2.HTTPError, e:
|
||||
print e
|
||||
print e.read( 1024 ) # Only return the first 1K of errors.
|
||||
sys.exit( 1 )
|
||||
if type( r ) == unicode:
|
||||
print 'error: %s' % r
|
||||
return None
|
||||
if not return_formatted:
|
||||
return r
|
||||
elif type( r ) == list:
|
||||
# Response is a collection as defined in the REST style.
|
||||
print 'Collection Members'
|
||||
print '------------------'
|
||||
for n, i in enumerate(r):
|
||||
# All collection members should have a name and url in the response.
|
||||
print '#%d: %s' % (n+1, i.pop( 'url' ) )
|
||||
if 'name' in i:
|
||||
print ' name: %s' % i.pop( 'name' )
|
||||
for k, v in i.items():
|
||||
print ' %s: %s' % ( k, v )
|
||||
print ''
|
||||
print '%d element(s) in collection' % len( r )
|
||||
elif type( r ) == dict:
|
||||
# Response is an element as defined in the REST style.
|
||||
print 'Member Information'
|
||||
print '------------------'
|
||||
for k, v in r.items():
|
||||
print '%s: %s' % ( k, v )
|
||||
elif type( r ) == str:
|
||||
print r
|
||||
else:
|
||||
print 'response is unknown type: %s' % type( r )
|
||||
|
||||
def get( api_key, url ):
|
||||
# Do the actual GET.
|
||||
url = make_url( api_key, url )
|
||||
try:
|
||||
return simplejson.loads( urllib2.urlopen( url ).read() )
|
||||
except simplejson.decoder.JSONDecodeError, e:
|
||||
print "URL did not return JSON data"
|
||||
sys.exit(1)
|
||||
|
||||
def make_url( api_key, url, args=None ):
|
||||
# Adds the API Key to the URL if it's not already there.
|
||||
if args is None:
|
||||
args = []
|
||||
argsep = '&'
|
||||
if '?' not in url:
|
||||
argsep = '?'
|
||||
if '?key=' not in url and '&key=' not in url:
|
||||
args.insert( 0, ( 'key', api_key ) )
|
||||
return url + argsep + '&'.join( [ '='.join( t ) for t in args ] )
|
||||
|
||||
def post( api_key, url, data ):
|
||||
# Do the actual POST.
|
||||
url = make_url( api_key, url )
|
||||
req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = simplejson.dumps( data ) )
|
||||
return simplejson.loads( urllib2.urlopen( req ).read() )
|
||||
|
||||
def put( api_key, url, data ):
|
||||
# Do the actual PUT.
|
||||
url = make_url( api_key, url )
|
||||
req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = simplejson.dumps( data ))
|
||||
req.get_method = lambda: 'PUT'
|
||||
return simplejson.loads( urllib2.urlopen( req ).read() )
|
||||
|
||||
def submit( api_key, url, data, return_formatted=True ):
|
||||
# Sends an API POST request and acts as a generic formatter for the JSON response - 'data' will become the JSON payload read by Galaxy.
|
||||
try:
|
||||
r = post( api_key, url, data )
|
||||
except urllib2.HTTPError, e:
|
||||
if return_formatted:
|
||||
print e
|
||||
print e.read( 1024 )
|
||||
sys.exit( 1 )
|
||||
else:
|
||||
return 'Error. '+ str( e.read( 1024 ) )
|
||||
if not return_formatted:
|
||||
return r
|
||||
print 'Response'
|
||||
print '--------'
|
||||
if type( r ) == list:
|
||||
# Currently the only implemented responses are lists of dicts, because submission creates some number of collection elements.
|
||||
for i in r:
|
||||
if type( i ) == dict:
|
||||
if 'url' in i:
|
||||
print i.pop( 'url' )
|
||||
else:
|
||||
print '----'
|
||||
if 'name' in i:
|
||||
print ' name: %s' % i.pop( 'name' )
|
||||
for k, v in i.items():
|
||||
print ' %s: %s' % ( k, v )
|
||||
else:
|
||||
print i
|
||||
else:
|
||||
print r
|
||||
|
||||
def update( api_key, url, data, return_formatted=True ):
|
||||
# Sends an API PUT request and acts as a generic formatter for the JSON response - 'data' will become the JSON payload read by Galaxy.
|
||||
try:
|
||||
r = put( api_key, url, data )
|
||||
except urllib2.HTTPError, e:
|
||||
if return_formatted:
|
||||
print e
|
||||
print e.read( 1024 )
|
||||
sys.exit( 1 )
|
||||
else:
|
||||
return 'Error. '+ str( e.read( 1024 ) )
|
||||
if not return_formatted:
|
||||
return r
|
||||
print 'Response'
|
||||
print '--------'
|
||||
print r
|
||||
@@ -985,6 +985,17 @@ def handle_galaxy_url( trans, **kwd ):
|
||||
galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' )
|
||||
return galaxy_url
|
||||
|
||||
def have_shed_tool_conf_for_install( trans ):
|
||||
if not trans.app.toolbox.shed_tool_confs:
|
||||
return False
|
||||
migrated_tools_conf_path, migrated_tools_conf_name = os.path.split( trans.app.config.migrated_tools_config )
|
||||
for shed_tool_conf_dict in trans.app.toolbox.shed_tool_confs:
|
||||
shed_tool_conf = shed_tool_conf_dict[ 'config_filename' ]
|
||||
shed_tool_conf_path, shed_tool_conf_name = os.path.split( shed_tool_conf )
|
||||
if shed_tool_conf_name != migrated_tools_conf_name:
|
||||
return True
|
||||
return False
|
||||
|
||||
def open_repository_files_folder( trans, folder_path ):
|
||||
"""Return a list of dictionaries, each of which contains information for a file or directory contained within a directory in a repository file hierarchy."""
|
||||
try:
|
||||
@@ -1072,6 +1083,20 @@ def reversed_upper_bounded_changelog( repo, included_upper_bounds_changeset_revi
|
||||
"""Return a reversed list of changesets in the repository changelog up to and including the included_upper_bounds_changeset_revision."""
|
||||
return reversed_lower_upper_bounded_changelog( repo, INITIAL_CHANGELOG_HASH, included_upper_bounds_changeset_revision )
|
||||
|
||||
def set_repository_attributes( trans, repository, status, error_message, deleted, uninstalled, remove_from_disk=False ):
|
||||
if remove_from_disk:
|
||||
relative_install_dir = repository.repo_path( trans.app )
|
||||
if relative_install_dir:
|
||||
clone_dir = os.path.abspath( relative_install_dir )
|
||||
shutil.rmtree( clone_dir )
|
||||
log.debug( "Removed repository installation directory: %s" % str( clone_dir ) )
|
||||
repository.error_message = error_message
|
||||
repository.status = status
|
||||
repository.deleted = deleted
|
||||
repository.uninstalled = uninstalled
|
||||
trans.sa_session.add( repository )
|
||||
trans.sa_session.flush()
|
||||
|
||||
def strip_path( fpath ):
|
||||
"""Attempt to strip the path from a file name."""
|
||||
if not fpath:
|
||||
|
||||
@@ -1,12 +1,17 @@
|
||||
import filecmp, logging, os, shutil, tempfile
|
||||
import tool_shed.util.shed_util_common as suc
|
||||
from galaxy import util
|
||||
import filecmp
|
||||
import logging
|
||||
import os
|
||||
import shutil
|
||||
import tempfile
|
||||
import galaxy.tools
|
||||
from galaxy.tools.search import ToolBoxSearch
|
||||
from galaxy.model.orm import and_
|
||||
from galaxy import util
|
||||
from galaxy.datatypes import checkers
|
||||
from galaxy.model.orm import and_
|
||||
from galaxy.tools import parameters
|
||||
from galaxy.tools.parameters import dynamic_options
|
||||
from galaxy.tools.search import ToolBoxSearch
|
||||
from galaxy.web.form_builder import SelectField
|
||||
import tool_shed.util.shed_util_common as suc
|
||||
|
||||
from galaxy import eggs
|
||||
import pkg_resources
|
||||
@@ -79,6 +84,33 @@ def add_to_tool_panel( app, repository_name, repository_clone_url, changeset_rev
|
||||
app.toolbox.write_integrated_tool_panel_config_file()
|
||||
app.toolbox_search = ToolBoxSearch( app.toolbox )
|
||||
|
||||
def build_shed_tool_conf_select_field( trans ):
|
||||
"""Build a SelectField whose options are the keys in trans.app.toolbox.shed_tool_confs."""
|
||||
options = []
|
||||
for shed_tool_conf_dict in trans.app.toolbox.shed_tool_confs:
|
||||
shed_tool_conf_filename = shed_tool_conf_dict[ 'config_filename' ]
|
||||
if shed_tool_conf_filename != trans.app.config.migrated_tools_config:
|
||||
if shed_tool_conf_filename.startswith( './' ):
|
||||
option_label = shed_tool_conf_filename.replace( './', '', 1 )
|
||||
else:
|
||||
option_label = shed_tool_conf_filename
|
||||
options.append( ( option_label, shed_tool_conf_filename ) )
|
||||
select_field = SelectField( name='shed_tool_conf' )
|
||||
for option_tup in options:
|
||||
select_field.add_option( option_tup[ 0 ], option_tup[ 1 ] )
|
||||
return select_field
|
||||
|
||||
def build_tool_panel_section_select_field( trans ):
|
||||
"""Build a SelectField whose options are the sections of the current in-memory toolbox."""
|
||||
options = []
|
||||
for k, v in trans.app.toolbox.tool_panel.items():
|
||||
if isinstance( v, galaxy.tools.ToolSection ):
|
||||
options.append( ( v.name, v.id ) )
|
||||
select_field = SelectField( name='tool_panel_section', display='radio' )
|
||||
for option_tup in options:
|
||||
select_field.add_option( option_tup[ 0 ], option_tup[ 1 ] )
|
||||
return select_field
|
||||
|
||||
def can_use_tool_config_disk_file( trans, repository, repo, file_path, changeset_revision ):
|
||||
"""
|
||||
Determine if repository's tool config file on disk can be used. This method is restricted to tool config files since, with the
|
||||
|
||||
Reference in New Issue
Block a user