mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Remove more unused makos from tool shed.
This commit is contained in:
John Chilton
-94
@@ -1,94 +0,0 @@
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<%inherit file="/base.mako"/>
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<%namespace file="/admin/tool_shed_repository/repository_actions_menu.mako" import="*" />
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<%namespace file="/message.mako" import="render_msg" />
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<%namespace file="/webapps/tool_shed/common/common.mako" import="*" />
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<% import os %>
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${render_galaxy_repository_actions( repository )}
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%if message:
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${render_msg( message, status )}
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%endif
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<div class="warningmessage">
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<p>
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The updates to the <b>${repository.name}</b> repository require the following packages. Click the <b>Install</b> button to install them.
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Installing some packages may take a while, but you can continue to use Galaxy during installation.
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</p>
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</div>
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<div class="card">
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<div class="card-body">
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<form name="install_tool_dependencies_with_update" id="install_tool_dependencies_with_update" action="${h.url_for( controller='admin_toolshed', action='install_tool_dependencies_with_update' )}" method="post" >
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<input type="hidden" name="updating_repository_id" value="${updating_repository_id|h}"/>
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<input type="hidden" name="updating_to_ctx_rev" value="${updating_to_ctx_rev|h}"/>
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<input type="hidden" name="updating_to_changeset_revision" value="${updating_to_changeset_revision|h}"/>
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<input type="hidden" name="encoded_updated_metadata" value="${encoded_updated_metadata|h}"/>
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<input type="hidden" name="encoded_relative_install_dir" value="${encoded_relative_install_dir|h}"/>
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<input type="hidden" name="encoded_tool_dependencies_dict" value="${encoded_tool_dependencies_dict|h}"/>
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%if tool_dependencies_dict:
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%if install_tool_dependencies_check_box is not None:
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<div class="form-row">
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<label>Handle tool dependencies?</label>
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<% disabled = trans.app.tool_dependency_dir is None %>
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${render_checkbox(install_tool_dependencies_check_box, disabled=disabled)}
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<div class="toolParamHelp" style="clear: both;">
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%if disabled:
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Set the tool_dependency_dir configuration value in your Galaxy config to automatically handle tool dependencies.
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%else:
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Un-check to skip automatic handling of these tool dependencies.
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%endif
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</div>
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</div>
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<div style="clear: both"></div>
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%endif
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<div class="form-row">
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<table class="grid">
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<tr><td colspan="4" bgcolor="#D8D8D8"><b>New tool dependencies included in update</b></td></tr>
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<tr>
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<th>Name</th>
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<th>Version</th>
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<th>Install directory</th>
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</tr>
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%for key, requirements_dict in tool_dependencies_dict.items():
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<%
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readme_text = None
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if key == 'set_environment':
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key_name = ', '.join( [ environment_variable[ 'name' ] for environment_variable in requirements_dict ] )
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key_version = ''
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install_dir = ''
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else:
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key_items = key.split( '/' )
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key_name = key_items[ 0 ]
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key_version = key_items[ 1 ]
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readme_text = requirements_dict.get( 'readme', None )
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install_dir = os.path.join( trans.app.tool_dependency_dir,
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key_name,
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key_version,
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repository.owner,
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repository.name,
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repository.installed_changeset_revision )
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%>
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%if not os.path.exists( install_dir ):
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<tr>
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<td>${key_name|h}</td>
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<td>${key_version|h}</td>
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<td>${install_dir|h}</td>
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</tr>
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%if readme_text:
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<tr><td colspan="4" bgcolor="#FFFFCC">${key_name|h} ${key_version|h} requirements and installation information</td></tr>
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<tr><td colspan="4"><pre>${readme_text}</pre></td></tr>
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%endif
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%endif
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%endfor
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</table>
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<div style="clear: both"></div>
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</div>
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%endif
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<div class="form-row">
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<input type="submit" name="install_tool_dependencies_with_update_button" value="Install"/>
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</div>
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</form>
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</div>
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</div>
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-70
@@ -1,70 +0,0 @@
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<%inherit file="/base.mako"/>
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<%namespace file="/message.mako" import="render_msg" />
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<%namespace file="/admin/tool_shed_repository/common.mako" import="*" />
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<%def name="javascripts()">
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${parent.javascripts()}
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${repository_installation_status_updater()}
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${repository_installation_updater()}
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${self.repository_installation_javascripts()}
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</%def>
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<%def name="repository_installation_javascripts()">
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<script type="text/javascript">
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%if context.get("initiate_repository_installation_ids"):
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$(document).ready(function( ){
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initiate_repository_installation( "${initiate_repository_installation_ids}", "${encoded_kwd}", "${reinstalling}" );
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});
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%endif
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var initiate_repository_installation = function ( iri_ids, encoded_kwd, reinstalling ) {
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// Make ajax call
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$.ajax( {
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type: "POST",
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url: "${h.url_for( controller='admin_toolshed', action='install_repositories' )}",
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dataType: "html",
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data: { tool_shed_repository_ids: iri_ids, encoded_kwd: encoded_kwd, reinstalling: reinstalling },
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success : function ( data ) {
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console.log( "Initializing repository installation succeeded" );
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}
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});
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};
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</script>
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</%def>
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%if context.get("message"):
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${render_msg( message, status )}
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%endif
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%if tool_shed_repositories:
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<div class="card">
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<div class="card-header">Monitor installing tool shed repositories</div>
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<div class="card-body overflow-auto">
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<table class="grid">
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<tr>
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<td>Name</td>
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<td>Description</td>
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<td>Owner</td>
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<td>Revision</td>
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<td>Status</td>
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</tr>
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%for tool_shed_repository in tool_shed_repositories:
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<%
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encoded_repository_id = trans.security.encode_id( tool_shed_repository.id )
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ids_of_tool_dependencies_missing_or_being_installed = [ trans.security.encode_id( td.id ) for td in tool_shed_repository.tool_dependencies_missing_or_being_installed ]
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link_to_manage_tool_dependencies = tool_shed_repository.status in [ trans.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES ]
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%>
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<tr>
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<td>${tool_shed_repository.name|h}</td>
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<td>${tool_shed_repository.description}</td>
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<td>${tool_shed_repository.owner}</td>
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<td>${tool_shed_repository.changeset_revision}</td>
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<td><div id="RepositoryStatus-${encoded_repository_id}">${tool_shed_repository.status|h}</div></td>
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</tr>
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%endfor
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</table>
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<br clear="left"/>
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</div>
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</div>
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%else:
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${render_msg("There is no repository being installed.", "info")}
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%endif
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-74
@@ -1,74 +0,0 @@
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<%inherit file="/base.mako"/>
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<%namespace file="/message.mako" import="render_msg" />
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<%namespace file="/admin/tool_shed_repository/repository_actions_menu.mako" import="*" />
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<%def name="stylesheets()">
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${parent.stylesheets()}
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${h.css( "library" )}
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</%def>
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<%def name="javascripts()">
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${parent.javascripts()}
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</%def>
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${render_galaxy_repository_actions( repository )}
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%if message:
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${render_msg( message, status )}
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%endif
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<div class="warningmessage">
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<p>
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Purging the repository named <b>${repository.name|h}</b> will result in deletion of all records for the
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following associated items from the database. Click the <b>Purge</b> button to purge this repository
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and its associated items.
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</p>
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</div>
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<div class="card">
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<div class="card-header">Purge tool shed repository <b>${repository.name|h}</b></div>
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<form name="purge_repository" id="purge_repository" action="${h.url_for( controller='admin_toolshed', action='purge_repository', id=trans.security.encode_id( repository.id ) )}" method="post" >
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<%
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tool_versions = 0
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tool_dependencies = 0
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required_repositories = 0
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orphan_repository_repository_dependency_association_records = 0
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orphan_repository_dependency_records = 0
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# Count this repository's tool version lineage chain links that will be purged.
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for tool_version in repository.tool_versions:
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for tool_version_association in tool_version.parent_tool_association:
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tool_versions += 1
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for tool_version_association in tool_version.child_tool_association:
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tool_versions += 1
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tool_versions += 1
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# Count this repository's associated tool dependencies that will be purged.
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for tool_dependency in repository.tool_dependencies:
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tool_dependencies += 1
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# Count this repository's associated required repositories that will be purged.
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for rrda in repository.required_repositories:
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required_repositories += 1
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# Count any "orphan" repository_dependency records associated with the repository but not with any
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# repository_repository_dependency_association records that will be purged.
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for orphan_repository_dependency in \
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trans.sa_session.query( trans.app.install_model.RepositoryDependency ) \
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.filter( trans.app.install_model.RepositoryDependency.table.c.tool_shed_repository_id == repository.id ):
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for orphan_rrda in \
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trans.sa_session.query( trans.app.install_model.RepositoryRepositoryDependencyAssociation ) \
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.filter( trans.app.install_model.RepositoryRepositoryDependencyAssociation.table.c.repository_dependency_id == orphan_repository_dependency.id ):
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orphan_repository_repository_dependency_association_records += 1
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orphan_repository_dependency_records += 1
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%>
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<table class="grid">
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<tr><td>Tool version records</td><td>${tool_versions|h}</td><tr>
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<tr><td>Tool dependency records</td><td>${tool_dependencies|h}</td><tr>
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<tr><td>Repository dependency records</td><td>${required_repositories|h}</td><tr>
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<tr><td>Orphan repository_repository_dependency_association records</td><td>${orphan_repository_repository_dependency_association_records|h}</td><tr>
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<tr><td>Orphan repository_dependency records</td><td>${orphan_repository_dependency_records|h}</td><tr>
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</table>
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<div style="clear: both"></div>
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<div class="form-row">
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<input type="submit" name="purge_repository_button" value="Purge"/>
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</div>
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</form>
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</div>
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</div>
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-101
@@ -1,101 +0,0 @@
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<%inherit file="/base.mako"/>
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<%namespace file="/message.mako" import="render_msg" />
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<%namespace file="/admin/tool_shed_repository/common.mako" import="render_dependencies_section" />
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<%namespace file="/admin/tool_shed_repository/common.mako" import="render_readme_section" />
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<%namespace file="/webapps/tool_shed/repository/common.mako" import="*" />
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<%namespace file="/webapps/tool_shed/common/common.mako" import="*" />
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<%def name="stylesheets()">
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${parent.stylesheets()}
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${h.css( "library" )}
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</%def>
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<%def name="javascripts()">
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${parent.javascripts()}
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${container_javascripts()}
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</%def>
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%if message:
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${render_msg( message, status )}
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%endif
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<div class="card">
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<div class="card-body">
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<form name="reselect_tool_panel_section" id="reselect_tool_panel_section" action="${h.url_for( controller='admin_toolshed', action='reinstall_repository', id=trans.security.encode_id( repository.id ) )}" method="post" >
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<div class="form-row">
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<input type="hidden" name="repo_info_dict" value="${encoded_repo_info_dict}" />
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</div>
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<div style="clear: both"></div>
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<% readme_files_dict = containers_dict.get( 'readme_files', None ) %>
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%if readme_files_dict:
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<div class="form-row">
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<table class="colored" width="100%">
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<th bgcolor="#EBD9B2">Repository README files - may contain important installation or license information</th>
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</table>
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</div>
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${render_readme_section( containers_dict )}
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<div style="clear: both"></div>
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%endif
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%if has_repository_dependencies or includes_tool_dependencies:
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<div class="form-row">
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<table class="colored" width="100%">
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<th bgcolor="#EBD9B2">Confirm dependency installation</th>
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</table>
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</div>
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${render_dependencies_section( install_resolver_dependencies_check_box, install_repository_dependencies_check_box, install_tool_dependencies_check_box, containers_dict, revision_label=None, export=False )}
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%endif
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%if shed_tool_conf_select_field:
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<div class="form-row">
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<table class="colored" width="100%">
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<th bgcolor="#EBD9B2">Choose the configuration file whose tool_path setting will be used for installing repositories</th>
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</table>
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</div>
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<%
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if len( shed_tool_conf_select_field.options ) == 1:
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select_help = "Your Galaxy instance is configured with 1 shed-related tool configuration file, so repositories will be "
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select_help += "installed using its <b>tool_path</b> setting."
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else:
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select_help = "Your Galaxy instance is configured with %d shed-related tool configuration files, " % len( shed_tool_conf_select_field.options )
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select_help += "so select the file whose <b>tool_path</b> setting you want used for installing repositories."
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%>
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<div class="form-row">
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<label>Shed tool configuration file:</label>
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${render_select(shed_tool_conf_select_field)}
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<div class="toolParamHelp" style="clear: both;">
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${select_help|h}
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</div>
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</div>
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<div style="clear: both"></div>
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%else:
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<input type="hidden" name="shed_tool_conf" value="${shed_tool_conf|h}"/>
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%endif
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%if includes_tools_for_display_in_tool_panel:
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<div style="clear: both"></div>
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<div class="form-row">
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${render_checkbox(no_changes_check_box)}
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<label style="display: inline;">No changes</label>
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<div class="toolParamHelp" style="clear: both;">
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Uncheck and select a different tool panel section to load the tools into a different section in the tool panel.
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</div>
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</div>
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<div class="form-row">
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<label>Add new tool panel section:</label>
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<input name="new_tool_panel_section_label" type="textfield" value="" size="40"/>
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<div class="toolParamHelp" style="clear: both;">
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Add a new tool panel section to contain the installed tools (optional).
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</div>
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</div>
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<div class="form-row">
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<label>Select existing tool panel section:</label>
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${render_select(tool_panel_section_select_field)}
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<div class="toolParamHelp" style="clear: both;">
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Choose an existing section in your tool panel to contain the installed tools (optional).
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</div>
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</div>
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%endif
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<div class="form-row">
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<input type="submit" name="select_tool_panel_section_button" value="Install"/>
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</div>
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</form>
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</div>
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</div>
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Reference in New Issue
Block a user