Add a confirmation page when purging installed repositories and include a fix for purging an installed repository that has a tool version lineage chain.

lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py

@@ -102,7 +102,6 @@ class AdminToolshed( AdminGalaxy ):
                                                                   action='reset_to_install',
                                                                   **kwd ) )
             if operation == "purge":
-                kwd[ 'purge_repository' ] = True
                 return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
                                                                   action='purge_repository',
                                                                   **kwd ) )
@@ -1269,18 +1268,25 @@ class AdminToolshed( AdminGalaxy ):
         new_kwd = {}
         if repository_id is not None:
             repository = suc.get_installed_tool_shed_repository( trans.app, repository_id )
-            if repository:
-                if kwd.get( 'purge_repository', False ):
-                    irm = trans.app.installed_repository_manager
-                    purge_status, purge_message = irm.purge_repository( trans.app, repository )
-                    if purge_status == 'ok':
-                        new_kwd[ 'status' ] = "done"
+            if repository.is_new:
+                if repository:
+                    if kwd.get( 'purge_repository_button', False ):
+                        irm = trans.app.installed_repository_manager
+                        purge_status, purge_message = irm.purge_repository( repository )
+                        if purge_status == 'ok':
+                            new_kwd[ 'status' ] = "done"
+                        else:
+                            new_kwd[ 'status' ] = 'error'
+                        new_kwd[ 'message' ] = purge_message
                     else:
-                        new_kwd[ 'status' ] = 'error'
-                    new_kwd[ 'message' ] = purge_message
+                        return trans.fill_template( 'admin/tool_shed_repository/purge_repository_confirmation.mako',
+                                                    repository=repository )
+                else:
+                    new_kwd[ 'status' ] = 'error'
+                    new_kwd[ 'message' ] = 'Cannot locate the database record for the repository with encoded id %s.' % str( repository_id )
             else:
                 new_kwd[ 'status' ] = 'error'
-                new_kwd[ 'message' ] = 'Cannot locate the database record for the repository with encoded id %s.' % str( repository_id )
+                new_kwd[ 'message' ] = 'Repositories must have a <b>New</b> status in order to be purged.'
         else:
             new_kwd[ 'status' ] = 'error'
             new_kwd[ 'message' ] = 'Invalid repository id value "None" received for repository to be purged.'

lib/tool_shed/galaxy_install/installed_repository_manager.py

@@ -718,7 +718,7 @@ class InstalledRepositoryManager( object ):
             if installed_repository_dict[ 'display_path' ]:
                 datatype_util.load_installed_display_applications( self.app, installed_repository_dict, deactivate=deactivate )
 
-    def purge_repository( self, app, repository ):
+    def purge_repository( self, repository ):
         """Purge a repository with status New (a white ghost) from the database."""
         sa_session = self.app.model.context.current
         status = 'ok'
@@ -732,24 +732,26 @@ class InstalledRepositoryManager( object ):
             # Purge this repository's associated tool versions.
             if repository.tool_versions:
                 for tool_version in repository.tool_versions:
-                    try:
-                        tool_version_association = tool_version.parent_tool_association
-                        sa_session.delete( tool_version_association )
-                        sa_session.flush()
-                    except Exception, e:
-                        status = 'error'
-                        message = 'Error attempting to purge tool_versions for the repository named %s with status %s: %s.' % \
-                            ( str( repository.name ), str( repository.status ), str( e ) )
-                        return status, message
-                    try:
-                        tool_version_association = tool_version.child_tool_association
-                        sa_session.delete( tool_version_association )
-                        sa_session.flush()
-                    except Exception, e:
-                        status = 'error'
-                        message = 'Error attempting to purge tool_versions for the repository named %s with status %s: %s.' % \
-                            ( str( repository.name ), str( repository.status ), str( e ) )
-                        return status, message
+                    if tool_version.parent_tool_association:
+                        for tool_version_association in tool_version.parent_tool_association:
+                            try:
+                                sa_session.delete( tool_version_association )
+                                sa_session.flush()
+                            except Exception, e:
+                                status = 'error'
+                                message = 'Error attempting to purge tool_versions for the repository named %s with status %s: %s.' % \
+                                    ( str( repository.name ), str( repository.status ), str( e ) )
+                                return status, message
+                    if tool_version.child_tool_association:
+                        for tool_version_association in tool_version.child_tool_association:
+                            try:
+                                sa_session.delete( tool_version_association )
+                                sa_session.flush()
+                            except Exception, e:
+                                status = 'error'
+                                message = 'Error attempting to purge tool_versions for the repository named %s with status %s: %s.' % \
+                                    ( str( repository.name ), str( repository.status ), str( e ) )
+                                return status, message
                     try:
                         sa_session.delete( tool_version )
                         sa_session.flush()

templates/admin/tool_shed_repository/purge_repository_confirmation.mako

@@ -0,0 +1,74 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+<%namespace file="/admin/tool_shed_repository/repository_actions_menu.mako" import="*" />
+
+<%def name="stylesheets()">
+    ${parent.stylesheets()}
+    ${h.css( "library" )}
+</%def>
+
+<%def name="javascripts()">
+    ${parent.javascripts()}
+</%def>
+
+${render_galaxy_repository_actions( repository )}
+
+%if message:
+    ${render_msg( message, status )}
+%endif
+
+<div class="warningmessage">
+    <p>
+        Purging the repository named <b>${repository.name}</b> will result in deletion of all records for the
+        following associated items from the database.  Click the <b>Purge</b> button to purge this repository
+        and its associated items.
+    </p>
+</div>
+
+<div class="toolForm">
+    <div class="toolFormTitle">Purge tool shed repository <b>${repository.name}</b></div>
+        <form name="purge_repository" id="purge_repository" action="${h.url_for( controller='admin_toolshed', action='purge_repository', id=trans.security.encode_id( repository.id ) )}" method="post" >
+            <%
+                tool_versions = 0
+                tool_dependencies = 0
+                required_repositories = 0
+                orphan_repository_repository_dependency_association_records = 0
+                orphan_repository_dependency_records = 0
+                # Count this repository's tool version lineage chain links that will be purged.
+                for tool_version in repository.tool_versions:
+                    for tool_version_association in tool_version.parent_tool_association:
+                        tool_versions += 1
+                    for tool_version_association in tool_version.child_tool_association:
+                        tool_versions += 1
+                    tool_versions += 1
+                # Count this repository's associated tool dependencies that will be purged.
+                for tool_dependency in repository.tool_dependencies:
+                    tool_dependencies += 1
+                # Count this repository's associated required repositories that will be purged.
+                for rrda in repository.required_repositories:
+                    required_repositories += 1
+                # Count any "orphan" repository_dependency records associated with the repository but not with any
+                # repository_repository_dependency_association records that will be purged.
+                for orphan_repository_dependency in \
+                    trans.sa_session.query( trans.app.install_model.RepositoryDependency ) \
+                                    .filter( trans.app.install_model.RepositoryDependency.table.c.tool_shed_repository_id == repository.id ):
+                    for orphan_rrda in \
+                        trans.sa_session.query( trans.app.install_model.RepositoryRepositoryDependencyAssociation ) \
+                                        .filter( trans.app.install_model.RepositoryRepositoryDependencyAssociation.table.c.repository_dependency_id == orphan_repository_dependency.id ):
+                        orphan_repository_repository_dependency_association_records += 1
+                    orphan_repository_dependency_records += 1
+            %>
+            <table class="grid">
+                <tr><td>Tool version records</td><td>${tool_versions}</td><tr>
+                <tr><td>Tool dependency records</td><td>${tool_dependencies}</td><tr>
+                <tr><td>Repository dependency records</td><td>${required_repositories}</td><tr>
+                <tr><td>Orphan repository_repository_dependency_association records</td><td>${orphan_repository_repository_dependency_association_records}</td><tr>
+                <tr><td>Orphan repository_dependency records</td><td>${orphan_repository_dependency_records}</td><tr>
+            </table>
+            <div style="clear: both"></div>
+            <div class="form-row">
+                <input type="submit" name="purge_repository_button" value="Purge"/>
+            </div>
+        </form>
+    </div>
+</div>