mirror of
https://github.com/galaxyproject/galaxy.git
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Visualizations API: rough draft of index, show, create, and update; Browser tests: tests for visualizations API
This commit is contained in:
Carl Eberhard
@@ -1,28 +1,263 @@
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from galaxy import web
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from galaxy.web.base.controller import BaseController, BaseAPIController
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"""
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Visualizations resource control over the API.
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class VisualizationsController( BaseAPIController ):
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NOTE!: this is a work in progress and functionality and data structures
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may change often.
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"""
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import pkg_resources
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pkg_resources.require( 'SQLAlchemy >= 0.4' )
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from sqlalchemy import or_
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from galaxy import web, util
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from galaxy.web.base.controller import BaseAPIController, UsesVisualizationMixin
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from galaxy.model.item_attrs import UsesAnnotations
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from galaxy.exceptions import ( ItemAccessibilityException, ItemDeletionException, ItemOwnershipException,
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MessageException )
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from galaxy.web import url_for
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import logging
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log = logging.getLogger( __name__ )
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class VisualizationsController( BaseAPIController, UsesVisualizationMixin, UsesAnnotations ):
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"""
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RESTful controller for interactions with visualizations.
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"""
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@web.expose_api
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def index( self, trans, **kwds ):
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def index( self, trans, **kwargs ):
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"""
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GET /api/visualizations:
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"""
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pass
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#TODO: search for vizsesses that apply to an object (sending model class and id? - how to do this?)
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rval = []
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try:
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if not trans.user:
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raise ItemAccessibilityException( 'You must be logged in to access visualizations' )
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user = trans.user
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#TODO: search for: title, made by user, creation time range, type (vis name), dbkey, etc.
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#TODO: limit, offset, order_by
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#TODO: deleted
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# this is the default search - user's vis, vis shared with user, published vis
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visualizations = self.get_visualizations_by_user( trans, user )
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visualizations += self.get_visualizations_shared_with_user( trans, user )
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visualizations += self.get_published_visualizations( trans, exclude_user=user )
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#TODO: the admin case - everything
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for visualization in visualizations:
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item = self.get_visualization_summary_dict( visualization )
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item = trans.security.encode_dict_ids( item )
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item[ 'url' ] = web.url_for( 'visualization', id=item[ 'id' ] )
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rval.append( item )
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except ItemAccessibilityException, exception:
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trans.response.status = 403
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rval = { 'error': str( exception ) }
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if trans.debug:
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log.exception( str( exception ) )
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except Exception, exception:
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trans.response.status = 500
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rval = { 'error': str( exception ) }
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log.exception( 'visualizations index failed: %s' %( str( exception ) ) )
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return rval
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@web.json
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def show( self, trans, id, **kwd ):
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def show( self, trans, id, **kwargs ):
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"""
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GET /api/visualizations/{viz_id}
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"""
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pass
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#TODO: revisions should be a contents/nested controller like viz/xxx/r/xxx)?
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# the important thing is the config
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rval = {}
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#TODO:?? /api/visualizations/registry -> json of registry.listings?
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try:
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visualization = self.get_visualization( trans, id, check_ownership=False, check_accessible=True )
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dictionary = trans.security.encode_dict_ids( self.get_visualization_dict( visualization ) )
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dictionary[ 'url' ] = url_for( controller='visualization',
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action="display_by_username_and_slug", username=visualization.user.username, slug=visualization.slug )
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dictionary[ 'annotation' ] = self.get_item_annotation_str( trans.sa_session, trans.user, visualization )
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# need to encode ids in revisions as well
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encoded_revisions = []
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for revision in dictionary[ 'revisions' ]:
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#NOTE: does not encode ids inside the configs
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encoded_revisions.append( trans.security.encode_id( revision ) )
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dictionary[ 'revisions' ] = encoded_revisions
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dictionary[ 'latest_revision' ] = trans.security.encode_dict_ids( dictionary[ 'latest_revision' ] )
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rval = dictionary
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except ( ItemAccessibilityException, ItemDeletionException ), exception:
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trans.response.status = 403
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rval = { 'error': str( exception ) }
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if trans.debug:
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log.exception( 'visualization show forbidden (%s): %s' %( id, str( exception ) ) )
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except Exception, exception:
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trans.response.status = 500
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rval = { 'error': str( exception ) }
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log.exception( 'visualization show failed (%s): %s' %( id, str( exception ) ) )
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return rval
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@web.expose_api
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def create( self, trans, payload, **kwd ):
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def create( self, trans, payload, **kwargs ):
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"""
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POST /api/visualizations
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creates a new visualization using the given payload
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POST /api/visualizations?import_id={encoded_visualization_id}
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imports a copy of an existing visualization into the user's workspace
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"""
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pass
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rval = None
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try:
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if 'import_id' in payload:
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import_id = payload( 'import_id' )
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visualization = self.import_visualization( trans, import_id, user=trans.user )
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else:
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payload = self._validate_and_parse_payload( payload )
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payload[ 'save' ] = True
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# create needs defaults like wizard needs food - generate defaults - this will err if given a weird key?
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visualization = self.create_visualization( trans, **payload )
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rval = { 'id' : trans.security.encode_id( visualization.id ) }
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#TODO: exception boilerplate
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except ( ItemAccessibilityException, ItemDeletionException ), exception:
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trans.response.status = 403
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rval = { 'error': str( exception ) }
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if trans.debug:
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log.exception( str( exception ) )
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except ( ValueError, AttributeError ), exception:
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trans.response.status = 400
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rval = { 'error': str( exception ) }
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if trans.debug:
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log.exception( str( exception ) )
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except Exception, exception:
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trans.response.status = 500
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rval = { 'error': str( exception ) }
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log.exception( 'creation of visualization failed: %s' %( str( exception ) ) )
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return rval
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@web.expose_api
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def update( self, trans, id, payload, **kwargs ):
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"""
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PUT /api/visualizations/{encoded_visualization_id}
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"""
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rval = None
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try:
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payload = self._validate_and_parse_payload( payload )
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# there's a differentiation here between updating the visualiztion and creating a new revision
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# that needs to be handled clearly here
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# or alternately, using a different controller like PUT /api/visualizations/{id}/r/{id}
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#TODO: consider allowing direct alteration of revisions title (without a new revision)
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# only create a new revsion on a different config
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# only update owned visualizations
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visualization = self.get_visualization( trans, id, check_ownership=True )
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title = payload.get( 'title', visualization.latest_revision.title )
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dbkey = payload.get( 'dbkey', visualization.latest_revision.dbkey )
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config = payload.get( 'config', visualization.latest_revision.config )
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latest_config = visualization.latest_revision.config
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if( ( title != visualization.latest_revision.title )
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or ( dbkey != visualization.latest_revision.dbkey )
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or ( util.json.to_json_string( config ) != util.json.to_json_string( latest_config ) ) ):
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revision = self.add_visualization_revision( trans, visualization, config, title, dbkey )
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#TODO: need to somehow get what changed here?
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rval = { 'id' : revision.id }
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except ( ItemAccessibilityException, ItemDeletionException ), exception:
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trans.response.status = 403
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rval = { 'error': str( exception ) }
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if trans.debug:
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log.exception( str( exception ) )
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except ( ValueError, AttributeError ), exception:
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trans.response.status = 400
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rval = { 'error': str( exception ) }
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if trans.debug:
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log.exception( str( exception ) )
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except Exception, exception:
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trans.response.status = 500
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rval = { 'error': str( exception ) }
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log.exception( 'update of visualization (%s) failed: %s' %( id, str( exception ) ) )
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return rval
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def _validate_and_parse_payload( self, payload ):
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"""
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Validate and parse incomming data payload for a visualization.
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"""
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# This layer handles (most of the stricter idiot proofing):
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# - unknown/unallowed keys
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# - changing data keys from api key to attribute name
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# - protection against bad data form/type
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# - protection against malicious data content
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# all other conversions and processing (such as permissions, etc.) should happen down the line
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# keys listed here don't error when attempting to set, but fail silently
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# this allows PUT'ing an entire model back to the server without attribute errors on uneditable attrs
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valid_but_uneditable_keys = (
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'id', 'model_class'
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#TODO: fill out when we create get_api_value, get_dict, whatevs
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)
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#TODO: deleted
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#TODO: importable
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validated_payload = {}
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for key, val in payload.items():
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if key == 'config':
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if not isinstance( val, dict ):
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raise ValueError( '%s must be a dictionary (JSON): %s' %( key, str( type( val ) ) ) )
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elif key == 'annotation':
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if not ( isinstance( val, str ) or isinstance( val, unicode ) ):
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raise ValueError( '%s must be a string or unicode: %s' %( key, str( type( val ) ) ) )
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val = util.sanitize_html.sanitize_html( val, 'utf-8' )
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# these are keys that actually only be *updated* at the revision level and not here
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# (they are still valid for create, tho)
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elif key == 'title':
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if not ( isinstance( val, str ) or isinstance( val, unicode ) ):
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raise ValueError( '%s must be a string or unicode: %s' %( key, str( type( val ) ) ) )
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val = util.sanitize_html.sanitize_html( val, 'utf-8' )
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elif key == 'slug':
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if not isinstance( val, str ):
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raise ValueError( '%s must be a string: %s' %( key, str( type( val ) ) ) )
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val = util.sanitize_html.sanitize_html( val, 'utf-8' )
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elif key == 'type':
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if not isinstance( val, str ):
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raise ValueError( '%s must be a string: %s' %( key, str( type( val ) ) ) )
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val = util.sanitize_html.sanitize_html( val, 'utf-8' )
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#TODO: validate types in VALID_TYPES/registry names at the mixin/model level?
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elif key == 'dbkey':
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if not ( isinstance( val, str ) or isinstance( val, unicode ) ):
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raise ValueError( '%s must be a string or unicode: %s' %( key, str( type( val ) ) ) )
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val = util.sanitize_html.sanitize_html( val, 'utf-8' )
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elif key not in valid_but_uneditable_keys:
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raise AttributeError( 'unknown key: %s' %( str( key ) ) )
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validated_payload[ key ] = val
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return validated_payload
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#@web.expose_api
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#def delete( self, trans, id, **kwd ):
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# """
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# DELETE /api/visualizations/{encoded_history_id}
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# Deletes a visualization from the database
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# """
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# pass
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@@ -0,0 +1,282 @@
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/* Utility to load a specific page and output html, page text, or a screenshot
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* Optionally wait for some time, text, or dom selector
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*/
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try {
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//...if there's a better way - please let me know, universe
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var scriptDir = require( 'system' ).args[3]
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// remove the script filename
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.replace( /[\w|\.|\-|_]*$/, '' )
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// if given rel. path, prepend the curr dir
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.replace( /^(?!\/)/, './' ),
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spaceghost = require( scriptDir + 'spaceghost' ).create({
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// script options here (can be overridden by CLI)
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//verbose: true,
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//logLevel: debug,
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scriptDir: scriptDir
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});
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} catch( error ){
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console.debug( error );
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phantom.exit( 1 );
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}
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spaceghost.start();
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// =================================================================== SET UP
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var utils = require( 'utils' );
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var email = spaceghost.user.getRandomEmail(),
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password = '123456';
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if( spaceghost.fixtureData.testUser ){
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email = spaceghost.fixtureData.testUser.email;
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password = spaceghost.fixtureData.testUser.password;
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}
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spaceghost.user.loginOrRegisterUser( email, password );
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function hasKeys( object, keysArray ){
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if( !utils.isObject( object ) ){ return false; }
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for( var i=0; i<keysArray.length; i += 1 ){
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if( !object.hasOwnProperty( keysArray[i] ) ){
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spaceghost.debug( 'object missing key: ' + keysArray[i] );
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return false;
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}
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}
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return true;
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}
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function countKeys( object ){
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if( !utils.isObject( object ) ){ return 0; }
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var count = 0;
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for( var key in object ){
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if( object.hasOwnProperty( key ) ){ count += 1; }
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}
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return count;
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}
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function compareObjs( obj, compare_to, exclusionList ){
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exclusionList = exclusionList || [];
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for( var key in compare_to ){
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if( compare_to.hasOwnProperty( key ) && exclusionList.indexOf( key ) === -1 ){
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if( !obj.hasOwnProperty( key ) ){
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spaceghost.debug( 'obj missing key: ' + key );
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return false;
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}
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if( obj[ key ] !== compare_to[ key ] ){
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spaceghost.debug( 'obj value not equal. obj: ' + obj[ key ] + ', v.: ' + compare_to[ key ] );
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return false;
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}
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}
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}
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return true;
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}
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function assertRaises( fn, expectedCode, errMsgShouldContain, assertionMsg, debug ){
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//TODO: errMsgShouldContain optional, any old error
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assertionMsg = assertionMsg || 'create returned error';
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debug = debug || false;
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var errorReturned = {};
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try {
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fn.call( spaceghost );
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} catch( error ){
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errorReturned = error;
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}
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if( errorReturned ){
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if( debug ){ spaceghost.debug( 'error:\n' + spaceghost.jsonStr( errorReturned ) ); }
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var errorMsg = errorReturned.message || '';
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if( errorMsg ){
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try {
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errorMsg = JSON.parse( errorReturned.message ).error;
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} catch( parseErr ){
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spaceghost.warn( 'error parsing error.message' );
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}
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}
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var properCode = errorReturned.status === expectedCode,
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properMsg = errorMsg.indexOf( errMsgShouldContain ) !== -1;
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spaceghost.test.assert( properCode && properMsg,
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assertionMsg + ': (' + errorReturned.status + ') "' + errorMsg + '"' );
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if( !( properCode && properMsg ) ){
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throw errorReturned;
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}
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} else {
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spaceghost.test.fail( assertionMsg + ': (no error)' );
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}
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}
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// =================================================================== TESTS
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spaceghost.thenOpen( spaceghost.baseUrl ).then( function(){
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var ALWAYS_CREATE = true,
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indexKeys = [
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'id', 'title', 'type', 'dbkey', 'url'
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],
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showKeys = indexKeys.concat([
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'user_id', 'model_class', 'revisions', 'latest_revision', 'annotation'
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]),
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revisionKeys = [
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'id', 'title', 'visualization_id', 'dbkey', 'model_class', 'config'
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];
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// ------------------------------------------------------------------------------------------- set up
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var visualizationIndex = this.api.visualizations.index();
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if( ALWAYS_CREATE || !visualizationIndex.length ){
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// post a visualization
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this.info( 'creating new visualization for tests' );
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var testVisualization = this.api.visualizations.create({
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title : 'Test Visualization',
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// needs to be unique
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slug : 'test-visualization-' + Date.now(),
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type : 'test',
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dbkey : 'hg17',
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annotation : 'this is a test of the emergency visualization system',
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config : {
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x : 10,
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y : 12
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}
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});
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this.debug( this.jsonStr( testVisualization ) );
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}
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// ------------------------------------------------------------------------------------------- INDEX
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this.test.comment( 'index should get a list of visualizations' );
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visualizationIndex = this.api.visualizations.index();
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this.debug( this.jsonStr( visualizationIndex ) );
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this.test.assert( utils.isArray( visualizationIndex ),
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"index returned an array: length " + visualizationIndex.length );
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this.test.assert( visualizationIndex.length >= 1, 'Has at least one visualization' );
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var firstVisualization = visualizationIndex[0];
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this.test.assert( hasKeys( firstVisualization, indexKeys ), 'Has the proper keys' );
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this.test.assert( this.api.isEncodedId( firstVisualization.id ), 'Id appears well-formed' );
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//TODO: index searching
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//TODO: anon user
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//TODO: admin user
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// ------------------------------------------------------------------------------------------- SHOW
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this.test.comment( 'show should get a visualization details object' );
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var visualizationShow = this.api.visualizations.show( firstVisualization.id );
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this.debug( this.jsonStr( visualizationShow ) );
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this.test.assert( hasKeys( visualizationShow, showKeys ), 'Has the proper keys' );
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this.test.assert( visualizationShow.model_class === 'Visualization',
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'Has the proper model_class: ' + visualizationShow.model_class );
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this.test.comment( 'a visualization details object should contain an array of revision ids' );
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var revisions = visualizationShow.revisions;
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this.test.assert( utils.isArray( revisions ), 'revisions is an array' );
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this.test.assert( revisions.length >= 1, 'revisions has at least one entry' );
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var areIds = true;
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revisions.forEach( function( revision ){
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if( !spaceghost.api.isEncodedId( revision ) ){ areIds = false; }
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});
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this.test.assert( areIds, 'all revisions are ids' );
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this.test.comment( 'a visualization details object should contain a subobject of the latest revision' );
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var latestRevision = visualizationShow.latest_revision;
|
||||
this.test.assert( utils.isObject( latestRevision ), 'latestRevision is an object' );
|
||||
this.test.assert( hasKeys( latestRevision, revisionKeys ), 'latestRevision has the proper keys' );
|
||||
this.test.assert( latestRevision.model_class === 'VisualizationRevision',
|
||||
'Has the proper model_class: ' + latestRevision.model_class );
|
||||
this.test.assert( latestRevision.visualization_id === visualizationShow.id,
|
||||
'revision visualization_id matches containing visualization id: ' + latestRevision.visualization_id );
|
||||
this.test.assert( visualizationShow.revisions.indexOf( latestRevision.id ) !== -1,
|
||||
'found latest_revision id in revisions' );
|
||||
|
||||
this.test.comment( 'a visualization revision should contain a subobject for the config' );
|
||||
var config = latestRevision.config;
|
||||
this.test.assert( utils.isObject( config ), 'config is an object:\n' + this.jsonStr( config ) );
|
||||
|
||||
//TODO: url in visualizationIndex == show url
|
||||
//TODO: non existing id throws error
|
||||
//TODO: anon user
|
||||
//TODO: user1 has no permissions to show user2
|
||||
|
||||
// ------------------------------------------------------------------------------------------- CREATE
|
||||
this.test.comment( 'Calling create should create a new visualization and allow setting the name' );
|
||||
var visualizationData = {
|
||||
title : 'Created Visualization',
|
||||
// needs to be unique
|
||||
slug : 'created-visualization-' + Date.now(),
|
||||
type : 'test',
|
||||
dbkey : 'hg17',
|
||||
annotation : 'invisible visualization',
|
||||
config : {
|
||||
x : 10,
|
||||
y : 12
|
||||
}
|
||||
};
|
||||
var created = this.api.visualizations.create( visualizationData );
|
||||
this.debug( 'returned from create:\n' + this.jsonStr( created ) );
|
||||
this.test.assert( this.api.isEncodedId( created.id ), "create returned an id: " + created.id );
|
||||
|
||||
// check v. show
|
||||
visualizationShow = this.api.visualizations.show( created.id );
|
||||
this.debug( 'visualizationShow:\n' + this.jsonStr( visualizationShow ) );
|
||||
// config is re-located into a revision and won't be there
|
||||
this.test.assert( compareObjs( visualizationShow, visualizationData, [ 'config' ] ),
|
||||
"show results seem to match create data" );
|
||||
|
||||
// the following errors are produced within base.controller.UsesVisualizationsMixin._create_visualization
|
||||
this.test.comment( 'Calling create with a non-unique slug will cause an API error' );
|
||||
assertRaises( function(){
|
||||
created = this.api.visualizations.create( visualizationData );
|
||||
}, 400, 'visualization identifier must be unique' );
|
||||
|
||||
this.test.comment( 'Calling create with no title will cause an API error' );
|
||||
visualizationData.title = '';
|
||||
assertRaises( function(){
|
||||
created = this.api.visualizations.create( visualizationData );
|
||||
}, 400, 'visualization name is required' );
|
||||
visualizationData.title = 'Created Visualization';
|
||||
|
||||
this.test.comment( 'Calling create with improper characters in the slug will cause an API error' );
|
||||
var oldSlug = visualizationData.slug;
|
||||
visualizationData.slug = '123_()';
|
||||
assertRaises( function(){
|
||||
created = this.api.visualizations.create( visualizationData );
|
||||
}, 400, "visualization identifier must consist of only lowercase letters, numbers, and the '-' character" );
|
||||
visualizationData.slug = oldSlug;
|
||||
|
||||
this.test.comment( 'Calling create with an unrecognized key will cause an API error' );
|
||||
visualizationData.bler = 'blah';
|
||||
assertRaises( function(){
|
||||
created = this.api.visualizations.create( visualizationData );
|
||||
}, 400, 'unknown key: bler' );
|
||||
delete visualizationData.bler;
|
||||
|
||||
this.test.comment( 'Calling create with an unparsable JSON config will cause an API error' );
|
||||
visualizationData.config = '3 = nime';
|
||||
assertRaises( function(){
|
||||
created = this.api.visualizations.create( visualizationData );
|
||||
}, 400, 'config must be a dictionary (JSON)' );
|
||||
|
||||
// ------------------------------------------------------------------------------------------ UPDATE
|
||||
// ........................................................................................... idiot proofing
|
||||
this.test.comment( 'updating using a nonsense key should fail with an error' );
|
||||
assertRaises( function(){
|
||||
returned = this.api.visualizations.update( created.id, { bler : 'blah' });
|
||||
}, 400, 'unknown key: bler' );
|
||||
|
||||
this.test.comment( 'updating by attempting to change type should cause an error' );
|
||||
assertRaises( function(){
|
||||
returned = this.api.visualizations.update( created.id, { title : 30 });
|
||||
}, 400, 'title must be a string or unicode' );
|
||||
//TODO: the other types...
|
||||
|
||||
// ........................................................................................... title
|
||||
//this.test.comment( 'update should create a new visualization revision' );
|
||||
//
|
||||
//this.test.comment( 'updating with a new title should NOT change the visualization title...' );
|
||||
//latestRevision = this.api.visualizations.show( created.id ).latest_revision;
|
||||
//returned = this.api.visualizations.update( created.id, {
|
||||
// title : 'New title'
|
||||
//});
|
||||
//visualizationShow = this.api.visualizations.show( created.id );
|
||||
//this.debug( this.jsonStr( visualizationShow ) );
|
||||
//this.test.assert( visualizationShow.title === visualizationData.title,
|
||||
// "Title does not set via update: " + visualizationShow.title );
|
||||
|
||||
});
|
||||
|
||||
// ===================================================================
|
||||
spaceghost.run( function(){
|
||||
});
|
||||
@@ -24,6 +24,7 @@ var API = function API( spaceghost, apikey ){
|
||||
this.tools = new ToolsAPI( this );
|
||||
this.workflows = new WorkflowsAPI( this );
|
||||
this.users = new UsersAPI( this );
|
||||
this.visualizations = new VisualizationsAPI( this );
|
||||
};
|
||||
exports.API = API;
|
||||
|
||||
@@ -73,6 +74,7 @@ API.prototype._ajax = function _ajax( url, options ){
|
||||
if( resp.status !== 200 ){
|
||||
// grrr... this doesn't lose the \n\r\t
|
||||
//throw new APIError( resp.responseText.replace( /[\s\n\r\t]+/gm, ' ' ).replace( /"/, '' ) );
|
||||
this.spaceghost.debug( 'api error response status code: ' + resp.status );
|
||||
throw new APIError( resp.responseText, resp.status );
|
||||
}
|
||||
return JSON.parse( resp.responseText );
|
||||
@@ -490,3 +492,57 @@ UsersAPI.prototype.update = function create( id, payload ){
|
||||
};
|
||||
|
||||
|
||||
// =================================================================== HISTORIES
|
||||
var VisualizationsAPI = function VisualizationsAPI( api ){
|
||||
this.api = api;
|
||||
};
|
||||
VisualizationsAPI.prototype.toString = function toString(){
|
||||
return this.api + '.VisualizationsAPI';
|
||||
};
|
||||
|
||||
// -------------------------------------------------------------------
|
||||
VisualizationsAPI.prototype.urlTpls = {
|
||||
index : 'api/visualizations',
|
||||
show : 'api/visualizations/%s',
|
||||
create : 'api/visualizations',
|
||||
//delete_ : 'api/visualizations/%s',
|
||||
//undelete: 'api/visualizations/deleted/%s/undelete',
|
||||
update : 'api/visualizations/%s'
|
||||
};
|
||||
|
||||
VisualizationsAPI.prototype.index = function index(){
|
||||
this.api.spaceghost.info( 'visualizations.index' );
|
||||
|
||||
return this.api._ajax( this.urlTpls.index );
|
||||
};
|
||||
|
||||
VisualizationsAPI.prototype.show = function show( id ){
|
||||
this.api.spaceghost.info( 'visualizations.show' );
|
||||
|
||||
return this.api._ajax( utils.format( this.urlTpls.show, this.api.ensureId( id ) ) );
|
||||
};
|
||||
|
||||
VisualizationsAPI.prototype.create = function create( payload ){
|
||||
this.api.spaceghost.info( 'visualizations.create: ' + this.api.spaceghost.jsonStr( payload ) );
|
||||
|
||||
// py.payload <-> ajax.data
|
||||
payload = this.api.ensureObject( payload );
|
||||
return this.api._ajax( utils.format( this.urlTpls.create ), {
|
||||
type : 'POST',
|
||||
data : payload
|
||||
});
|
||||
};
|
||||
|
||||
VisualizationsAPI.prototype.update = function create( id, payload ){
|
||||
this.api.spaceghost.info( 'visualizations.update: ' + id + ',' + this.api.spaceghost.jsonStr( payload ) );
|
||||
|
||||
// py.payload <-> ajax.data
|
||||
id = this.api.ensureId( id );
|
||||
payload = this.api.ensureObject( payload );
|
||||
url = utils.format( this.urlTpls.update, id );
|
||||
|
||||
return this.api._ajax( url, {
|
||||
type : 'PUT',
|
||||
data : payload
|
||||
});
|
||||
};
|
||||
|
||||
Reference in New Issue
Block a user