Enhance the galaxy API for the Tool Shed to retrieve the latest insta…

…llable revision from the Tool Shed from an installed repository, specifying a name and owner. Enhance the ~/scripts/api/install_tool_shed_repositories.py script to allow the changeset_revision to be optional, and if not specified, the latest installable revision will be installed for the repository specified by the name and owner.

lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py

@@ -66,6 +66,50 @@ def exported_workflows( self, trans, id, **kwd ):
             exported_workflows.append( display_dict )
         return exported_workflows
 
+    @web.expose_api
+    def get_latest_installable_revision( self, trans, payload, **kwd ):
+        """
+        POST /api/tool_shed_repositories/get_latest_installable_revision
+        Get the latest installable revision of a specified repository from a specified Tool Shed.
+
+        :param key: the current Galaxy admin user's API key
+
+        The following parameters are included in the payload.
+        :param tool_shed_url (required): the base URL of the Tool Shed from which to retrieve the Repository revision.
+        :param name (required): the name of the Repository
+        :param owner (required): the owner of the Repository
+        """
+        # Get the information about the repository to be installed from the payload.
+        tool_shed_url = payload.get( 'tool_shed_url', '' )
+        if not tool_shed_url:
+            raise HTTPBadRequest( detail="Missing required parameter 'tool_shed_url'." )
+        name = payload.get( 'name', '' )
+        if not name:
+            raise HTTPBadRequest( detail="Missing required parameter 'name'." )
+        owner = payload.get( 'owner', '' )
+        if not owner:
+            raise HTTPBadRequest( detail="Missing required parameter 'owner'." )
+        # Make sure the current user's API key proves he is an admin user in this Galaxy instance.
+        if not trans.user_is_admin():
+            raise HTTPForbidden( detail='You are not authorized to request the latest installable revision for a repository in this Galaxy instance.' )
+        params = '?name=%s&owner=%s' % ( name, owner )
+        url = common_util.url_join( tool_shed_url,
+                                    'api/repositories/get_ordered_installable_revisions%s' % params )
+        try:
+            raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url )
+        except Exception, e:
+            message = "Error attempting to retrieve the latest installable revision from tool shed %s for repository %s owned by %s: %s" % \
+                ( str( tool_shed_url ), str( name ), str( owner ), str( e ) )
+            log.debug( message )
+            return dict( status='error', error=message )
+        if raw_text:
+            # If successful, the response from get_ordered_installable_revisions will be a list of
+            # changeset_revision hash strings.
+            changeset_revisions = json.from_json_string( raw_text )
+            if len( changeset_revisions ) >= 1:
+                return changeset_revisions[ -1 ]
+        return suc.INITIAL_CHANGELOG_HASH
+
     def __get_value_mapper( self, trans, tool_shed_repository ):
         value_mapper={ 'id' : trans.security.encode_id( tool_shed_repository.id ),
                        'error_message' : tool_shed_repository.error_message or '' }

lib/galaxy/webapps/galaxy/buildapp.py

@@ -321,7 +321,8 @@ def app_factory( global_conf, **kwargs ):
                                      'exported_workflows' : 'GET',
                                      'import_workflow' : 'POST',
                                      'import_workflows' : 'POST' },
-                            collection={ 'reset_metadata_on_installed_repositories' : 'POST' },
+                            collection={ 'get_latest_installable_revision' : 'POST',
+                                         'reset_metadata_on_installed_repositories' : 'POST' },
                             controller='tool_shed_repositories',
                             name_prefix='tool_shed_repository_',
                             path_prefix='/api',

scripts/api/install_tool_shed_repositories.py

@@ -1,16 +1,20 @@
 #!/usr/bin/env python
 """
-Install a specified repository revision from a specified tool shed into Galaxy. This example demonstrates installation of a repository that contains
-valid tools, loading them into a section of the Galaxy tool panel or creating a new tool panel section.
-You can choose if tool dependencies or repository dependencies should be installed, use --repository-deps or --tool-deps.
+If a repository name, owner and revision are specified,install the revision from a specified tool shed into Galaxy.
+Specifying a revision is optional, if it is no specified, the latest installable revision will automatically be installed.
+However, the name and owner are required.
+
+This example demonstrates installation of a repository that contains valid tools, loading them into a section of the
+Galaxy tool panel or creating a new tool panel section.  You can choose if tool dependencies or repository dependencies
+should be installed, use --repository-deps or --tool-deps.
 
 This example requires a tool panel config file (e.g., tool_conf.xml, shed_tool_conf.xml, etc) to contain a tool panel section like the following:
 
 <section id="from_test_tool_shed" name="From Test Tool Shed" version="">
 </section>
 
 Here is a working example of how to use this script to install a repository from the test tool shed.
-./install_tool_shed_repositories.py --api <api key> --local <galaxy base url> --url http://testtoolshed.g2.bx.psu.edu --name gregs_filter --owner greg --revision f28d5018f9cb --tool-deps
+./install_tool_shed_repositories.py --api <api key> --local <galaxy base url> --url http://testtoolshed.g2.bx.psu.edu --name gregs_filter --owner greg --tool-deps
 """
 
 import os
@@ -25,7 +29,20 @@ def main( options ):
     data[ 'tool_shed_url' ] = options.tool_shed_url
     data[ 'name' ] = options.name
     data[ 'owner' ] = options.owner
-    data[ 'changeset_revision' ] = options.changeset_revision
+    if options.changeset_revision:
+        data[ 'changeset_revision' ] = options.changeset_revision
+    else:
+        # If the changeset_revision is not specified, default to the latest installable revision.
+        revision_data = {}
+        revision_data[ 'tool_shed_url' ] = options.tool_shed_url.rstrip( '/' )
+        revision_data[ 'name' ] = options.name
+        revision_data[ 'owner' ] = options.owner
+        revision_url = '%s%s' % ( options.local_url.rstrip( '/' ), '/api/tool_shed_repositories/get_latest_installable_revision' )
+        latest_installable_revision = submit( options.api,
+                                              revision_url,
+                                              revision_data,
+                                              return_formatted=False )
+        data[ 'changeset_revision' ] = latest_installable_revision
     if options.tool_panel_section_id:
         data[ 'tool_panel_section_id' ] = options.tool_panel_section_id
     elif options.new_tool_panel_section_label:
@@ -34,7 +51,7 @@ def main( options ):
         data[ 'install_repository_dependencies' ] = options.install_repository_dependencies
     if options.install_tool_dependencies:
         data[ 'install_tool_dependencies' ] = options.install_tool_dependencies
-    submit( options.api, '%s%s' % ( options.local_url.strip( '/' ), '/api/tool_shed_repositories/new/install_repository_revision' ), data )
+    submit( options.api, '%s%s' % ( options.local_url.rstrip( '/' ), '/api/tool_shed_repositories/new/install_repository_revision' ), data )
 
 if __name__ == '__main__':
     parser = argparse.ArgumentParser( description='Installation of tool shed repositories via the Galaxy API.' )
@@ -43,7 +60,7 @@ def main( options ):
     parser.add_argument( "-l", "--local", dest="local_url", required=True, help="URL of the galaxy instance." )
     parser.add_argument( "-n", "--name", required=True, help="Repository name." )
     parser.add_argument( "-o", "--owner", required=True, help="Repository owner." )
-    parser.add_argument( "-r", "--revision", dest="changeset_revision", required=True, help="Repository owner." )
+    parser.add_argument( "-r", "--revision", dest="changeset_revision", help="Repository revision." )
     parser.add_argument( "--panel-section-id", dest="tool_panel_section_id", help="Tool panel section id if you want to add your repository to an existing tool section." )
     parser.add_argument( "--panel-section-name", dest="new_tool_panel_section_label", help="New tool panel section label. If specified a new tool section will be created." )
     parser.add_argument( "--repository-deps", dest="install_repository_dependencies", action="store_true", default=False, help="Install repository dependencies. [False]")