1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/117db343f853/ Changeset: 117db343f853 User: carlfeberhard Date: 2015-02-02 21:38:30+00:00 Summary: API, visualizations: use _future_expose_api, some clean-up Affected #: 1 file

diff -r b9ec027d4b1e1b67f26632a55076dbf53e3225bd -r 117db343f853b815b6f584679c23d0f44277c07b lib/galaxy/webapps/galaxy/api/visualizations.py --- a/lib/galaxy/webapps/galaxy/api/visualizations.py +++ b/lib/galaxy/webapps/galaxy/api/visualizations.py @@ -5,68 +5,52 @@ may change often. """

-import pkg_resources -pkg_resources.require( 'SQLAlchemy >= 0.4' ) -from sqlalchemy import or_ +from galaxy.web.base.controller import BaseAPIController +from galaxy.web.base.controller import UsesVisualizationMixin +from galaxy.web.base.controller import SharableMixin +from galaxy.model.item_attrs import UsesAnnotations

-from galaxy import web, util -from galaxy.web.base.controller import BaseAPIController, UsesVisualizationMixin, SharableMixin -from galaxy.model.item_attrs import UsesAnnotations -from galaxy.exceptions import ( ItemAccessibilityException, ItemDeletionException, ItemOwnershipException, - MessageException ) - -from galaxy.web import url_for +from galaxy.web import _future_expose_api as expose_api +from galaxy import web +from galaxy import util +from galaxy import exceptions

import logging log = logging.getLogger( __name__ )

+ class VisualizationsController( BaseAPIController, UsesVisualizationMixin, SharableMixin, UsesAnnotations ): """ RESTful controller for interactions with visualizations. """

- @web.expose_api + @expose_api def index( self, trans, **kwargs ): """ GET /api/visualizations: """ - #TODO: search for vizsesses that apply to an object (sending model class and id? - how to do this?) rval = [] - try: - if not trans.user: - raise ItemAccessibilityException( 'You must be logged in to access visualizations' ) - user = trans.user + user = trans.user

- #TODO: search for: title, made by user, creation time range, type (vis name), dbkey, etc. - #TODO: limit, offset, order_by - #TODO: deleted + #TODO: search for: title, made by user, creation time range, type (vis name), dbkey, etc. + #TODO: limit, offset, order_by + #TODO: deleted

- # this is the default search - user's vis, vis shared with user, published vis - visualizations = self.get_visualizations_by_user( trans, user ) - visualizations += self.get_visualizations_shared_with_user( trans, user ) - visualizations += self.get_published_visualizations( trans, exclude_user=user ) - #TODO: the admin case - everything + # this is the default search - user's vis, vis shared with user, published vis + visualizations = self.get_visualizations_by_user( trans, user ) + visualizations += self.get_visualizations_shared_with_user( trans, user ) + visualizations += self.get_published_visualizations( trans, exclude_user=user ) + #TODO: the admin case - everything

- for visualization in visualizations: - item = self.get_visualization_summary_dict( visualization ) - item = trans.security.encode_dict_ids( item ) - item[ 'url' ] = web.url_for( 'visualization', id=item[ 'id' ] ) - rval.append( item ) - - except ItemAccessibilityException, exception: - trans.response.status = 403 - rval = { 'error': str( exception ) } - if trans.debug: - log.exception( str( exception ) ) - - except Exception, exception: - trans.response.status = 500 - rval = { 'error': str( exception ) } - log.exception( 'visualizations index failed: %s' %( str( exception ) ) ) + for visualization in visualizations: + item = self.get_visualization_summary_dict( visualization ) + item = trans.security.encode_dict_ids( item ) + item[ 'url' ] = web.url_for( 'visualization', id=item[ 'id' ] ) + rval.append( item )

return rval

- @web.json + @expose_api def show( self, trans, id, **kwargs ): """ GET /api/visualizations/{viz_id} @@ -75,37 +59,25 @@ # the important thing is the config rval = {} #TODO:?? /api/visualizations/registry -> json of registry.listings? - try: - visualization = self.get_visualization( trans, id, check_ownership=False, check_accessible=True ) - dictionary = trans.security.encode_dict_ids( self.get_visualization_dict( visualization ) ) - dictionary[ 'url' ] = url_for( controller='visualization', - action="display_by_username_and_slug", username=visualization.user.username, slug=visualization.slug ) - dictionary[ 'annotation' ] = self.get_item_annotation_str( trans.sa_session, trans.user, visualization )

- # need to encode ids in revisions as well - encoded_revisions = [] - for revision in dictionary[ 'revisions' ]: - #NOTE: does not encode ids inside the configs - encoded_revisions.append( trans.security.encode_id( revision ) ) - dictionary[ 'revisions' ] = encoded_revisions - dictionary[ 'latest_revision' ] = trans.security.encode_dict_ids( dictionary[ 'latest_revision' ] ) + visualization = self.get_visualization( trans, id, check_ownership=False, check_accessible=True ) + dictionary = trans.security.encode_dict_ids( self.get_visualization_dict( visualization ) ) + dictionary[ 'url' ] = web.url_for( controller='visualization', + action="display_by_username_and_slug", username=visualization.user.username, slug=visualization.slug ) + dictionary[ 'annotation' ] = self.get_item_annotation_str( trans.sa_session, trans.user, visualization )

- rval = dictionary + # need to encode ids in revisions as well + encoded_revisions = [] + for revision in dictionary[ 'revisions' ]: + #NOTE: does not encode ids inside the configs + encoded_revisions.append( trans.security.encode_id( revision ) ) + dictionary[ 'revisions' ] = encoded_revisions + dictionary[ 'latest_revision' ] = trans.security.encode_dict_ids( dictionary[ 'latest_revision' ] )

- except ( ItemAccessibilityException, ItemDeletionException ), exception: - trans.response.status = 403 - rval = { 'error': str( exception ) } - if trans.debug: - log.exception( 'visualization show forbidden (%s): %s' %( id, str( exception ) ) ) - - except Exception, exception: - trans.response.status = 500 - rval = { 'error': str( exception ) } - log.exception( 'visualization show failed (%s): %s' %( id, str( exception ) ) ) - + rval = dictionary return rval

- @web.expose_api + @expose_api def create( self, trans, payload, **kwargs ): """ POST /api/visualizations @@ -115,93 +87,61 @@ imports a copy of an existing visualization into the user's workspace """ rval = None - try: - if 'import_id' in payload: - import_id = payload( 'import_id' ) - visualization = self.import_visualization( trans, import_id, user=trans.user )

- else: - payload = self._validate_and_parse_payload( payload ) - # must have a type (I've taken this to be the visualization name) - if 'type' not in payload: - raise ValueError( "key/value 'type' is required" ) - vis_type = payload.pop( 'type', False ) + if 'import_id' in payload: + import_id = payload( 'import_id' ) + visualization = self.import_visualization( trans, import_id, user=trans.user )

- payload[ 'save' ] = True + else: + payload = self._validate_and_parse_payload( payload ) + # must have a type (I've taken this to be the visualization name) + if 'type' not in payload: + raise exceptions.RequestParameterMissingException( "key/value 'type' is required" ) + vis_type = payload.pop( 'type', False ) + + payload[ 'save' ] = True + try: # generate defaults - this will err if given a weird key? visualization = self.create_visualization( trans, vis_type, **payload ) + except ValueError, val_err: + raise exceptions.RequestParameterMissingException( str( val_err ) )

- rval = { 'id' : trans.security.encode_id( visualization.id ) } - - #TODO: exception boilerplate - except ( ItemAccessibilityException, ItemDeletionException ), exception: - trans.response.status = 403 - rval = { 'error': str( exception ) } - if trans.debug: - log.exception( str( exception ) ) - - except ( ValueError, AttributeError ), exception: - trans.response.status = 400 - rval = { 'error': str( exception ) } - if trans.debug: - log.exception( str( exception ) ) - - except Exception, exception: - trans.response.status = 500 - rval = { 'error': str( exception ) } - log.exception( 'creation of visualization failed: %s' %( str( exception ) ) ) + rval = { 'id' : trans.security.encode_id( visualization.id ) }

return rval

- @web.expose_api + @expose_api def update( self, trans, id, payload, **kwargs ): """ PUT /api/visualizations/{encoded_visualization_id} """ rval = None - try: - payload = self._validate_and_parse_payload( payload )

- # there's a differentiation here between updating the visualiztion and creating a new revision - # that needs to be handled clearly here - # or alternately, using a different controller like PUT /api/visualizations/{id}/r/{id} + payload = self._validate_and_parse_payload( payload )

- #TODO: consider allowing direct alteration of revisions title (without a new revision) - # only create a new revsion on a different config + # there's a differentiation here between updating the visualiztion and creating a new revision + # that needs to be handled clearly here + # or alternately, using a different controller like PUT /api/visualizations/{id}/r/{id}

- # only update owned visualizations - visualization = self.get_visualization( trans, id, check_ownership=True ) - title = payload.get( 'title', visualization.latest_revision.title ) - dbkey = payload.get( 'dbkey', visualization.latest_revision.dbkey ) - config = payload.get( 'config', visualization.latest_revision.config ) + #TODO: consider allowing direct alteration of revisions title (without a new revision) + # only create a new revsion on a different config

- latest_config = visualization.latest_revision.config - if( ( title != visualization.latest_revision.title ) - or ( dbkey != visualization.latest_revision.dbkey ) - or ( util.json.dumps( config ) != util.json.dumps( latest_config ) ) ): - revision = self.add_visualization_revision( trans, visualization, config, title, dbkey ) - rval = { 'id' : id, 'revision' : revision.id } + # only update owned visualizations + visualization = self.get_visualization( trans, id, check_ownership=True ) + title = payload.get( 'title', visualization.latest_revision.title ) + dbkey = payload.get( 'dbkey', visualization.latest_revision.dbkey ) + config = payload.get( 'config', visualization.latest_revision.config )

- # allow updating vis title - visualization.title = title - trans.sa_session.flush() + latest_config = visualization.latest_revision.config + if( ( title != visualization.latest_revision.title ) + or ( dbkey != visualization.latest_revision.dbkey ) + or ( util.json.dumps( config ) != util.json.dumps( latest_config ) ) ): + revision = self.add_visualization_revision( trans, visualization, config, title, dbkey ) + rval = { 'id' : id, 'revision' : revision.id }

- except ( ItemAccessibilityException, ItemDeletionException ), exception: - trans.response.status = 403 - rval = { 'error': str( exception ) } - if trans.debug: - log.exception( str( exception ) ) - - except ( ValueError, AttributeError ), exception: - trans.response.status = 400 - rval = { 'error': str( exception ) } - if trans.debug: - log.exception( str( exception ) ) - - except Exception, exception: - trans.response.status = 500 - rval = { 'error': str( exception ) } - log.exception( 'update of visualization (%s) failed: %s' %( id, str( exception ) ) ) + # allow updating vis title + visualization.title = title + trans.sa_session.flush()

return rval

@@ -224,36 +164,37 @@ ) #TODO: deleted #TODO: importable + ValidationError = exceptions.RequestParameterInvalidException

validated_payload = {} for key, val in payload.items(): #TODO: validate types in VALID_TYPES/registry names at the mixin/model level? if key == 'type': if not ( isinstance( val, str ) or isinstance( val, unicode ) ): - raise ValueError( '%s must be a string or unicode: %s' %( key, str( type( val ) ) ) ) + raise ValidationError( '%s must be a string or unicode: %s' %( key, str( type( val ) ) ) ) val = util.sanitize_html.sanitize_html( val, 'utf-8' ) elif key == 'config': if not isinstance( val, dict ): - raise ValueError( '%s must be a dictionary: %s' %( key, str( type( val ) ) ) ) + raise ValidationError( '%s must be a dictionary: %s' %( key, str( type( val ) ) ) )

elif key == 'annotation': if not ( isinstance( val, str ) or isinstance( val, unicode ) ): - raise ValueError( '%s must be a string or unicode: %s' %( key, str( type( val ) ) ) ) + raise ValidationError( '%s must be a string or unicode: %s' %( key, str( type( val ) ) ) ) val = util.sanitize_html.sanitize_html( val, 'utf-8' )

# these are keys that actually only be *updated* at the revision level and not here # (they are still valid for create, tho) elif key == 'title': if not ( isinstance( val, str ) or isinstance( val, unicode ) ): - raise ValueError( '%s must be a string or unicode: %s' %( key, str( type( val ) ) ) ) + raise ValidationError( '%s must be a string or unicode: %s' %( key, str( type( val ) ) ) ) val = util.sanitize_html.sanitize_html( val, 'utf-8' ) elif key == 'slug': if not ( isinstance( val, str ) or isinstance( val, unicode ) ): - raise ValueError( '%s must be a string: %s' %( key, str( type( val ) ) ) ) + raise ValidationError( '%s must be a string: %s' %( key, str( type( val ) ) ) ) val = util.sanitize_html.sanitize_html( val, 'utf-8' ) elif key == 'dbkey': if not ( isinstance( val, str ) or isinstance( val, unicode ) ): - raise ValueError( '%s must be a string or unicode: %s' %( key, str( type( val ) ) ) ) + raise ValidationError( '%s must be a string or unicode: %s' %( key, str( type( val ) ) ) ) val = util.sanitize_html.sanitize_html( val, 'utf-8' )

elif key not in valid_but_uneditable_keys: @@ -262,11 +203,3 @@

validated_payload[ key ] = val return validated_payload - - #@web.expose_api - #def delete( self, trans, id, **kwd ): - # """ - # DELETE /api/visualizations/{encoded_history_id} - # Deletes a visualization from the database - # """ - # pass

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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