Source code for galaxy.webapps.galaxy.api.visualizations

"""
Visualizations resource control over the API.

NOTE!: this is a work in progress and functionality and data structures
may change often.
"""
import json
import logging

from six import string_types

from galaxy import (
    exceptions,
    util,
    web
)
from galaxy.managers.visualizations import (
    VisualizationManager,
    VisualizationSerializer
)
from galaxy.model.item_attrs import UsesAnnotations
from galaxy.web import _future_expose_api as expose_api
from galaxy.web.base.controller import (
    BaseAPIController,
    SharableMixin,
    UsesVisualizationMixin
)

log = logging.getLogger(__name__)


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

[docs]    def __init__(self, app):
        super(VisualizationsController, self).__init__(app)
        self.manager = VisualizationManager(app)
        self.serializer = VisualizationSerializer(app)

[docs]    @expose_api
    def index(self, trans, **kwargs):
        """
        GET /api/visualizations:
        """
        rval = []
        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

        # 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)

        return rval

[docs]    @expose_api
    def show(self, trans, id, **kwargs):
        """
        GET /api/visualizations/{viz_id}
        """
        # TODO: revisions should be a contents/nested controller like viz/xxx/r/xxx)?
        # the important thing is the config
        # TODO:?? /api/visualizations/registry -> json of registry.listings?
        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)
        # 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'])
        if trans.app.visualizations_registry:
            visualization = trans.app.visualizations_registry.get_plugin(dictionary['type'])
            dictionary['plugin'] = visualization.to_dict()
        return dictionary

[docs]    @expose_api
    def create(self, trans, payload, **kwargs):
        """
        POST /api/visualizations
        creates a new visualization using the given payload

        POST /api/visualizations?import_id={encoded_visualization_id}
        imports a copy of an existing visualization into the user's workspace
        """
        rval = None

        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 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 as val_err:
                raise exceptions.RequestParameterMissingException(str(val_err))

        rval = {'id' : trans.security.encode_id(visualization.id)}

        return rval

[docs]    @expose_api
    def update(self, trans, id, payload, **kwargs):
        """
        PUT /api/visualizations/{encoded_visualization_id}
        """
        rval = None

        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}

        # TODO: consider allowing direct alteration of revisions title (without a new revision)
        #   only create a new revsion on a different config

        # 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)

        latest_config = visualization.latest_revision.config
        if((title != visualization.latest_revision.title) or
                (dbkey != visualization.latest_revision.dbkey) or
                (json.dumps(config) != json.dumps(latest_config))):
            revision = self.add_visualization_revision(trans, visualization, config, title, dbkey)
            rval = {'id' : id, 'revision' : revision.id}

        # allow updating vis title
        visualization.title = title
        trans.sa_session.flush()

        return rval

    def _validate_and_parse_payload(self, payload):
        """
        Validate and parse incomming data payload for a visualization.
        """
        # This layer handles (most of the stricter idiot proofing):
        #   - unknown/unallowed keys
        #   - changing data keys from api key to attribute name
        #   - protection against bad data form/type
        #   - protection against malicious data content
        # all other conversions and processing (such as permissions, etc.) should happen down the line

        # keys listed here don't error when attempting to set, but fail silently
        #   this allows PUT'ing an entire model back to the server without attribute errors on uneditable attrs
        valid_but_uneditable_keys = (
            'id', 'model_class'
            # TODO: fill out when we create to_dict, get_dict, whatevs
        )
        # 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, string_types):
                    raise ValidationError('%s must be a string or unicode: %s' % (key, str(type(val))))
                val = util.sanitize_html.sanitize_html(val)
            elif key == 'config':
                if not isinstance(val, dict):
                    raise ValidationError('%s must be a dictionary: %s' % (key, str(type(val))))

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

            # 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, string_types):
                    raise ValidationError('%s must be a string or unicode: %s' % (key, str(type(val))))
                val = util.sanitize_html.sanitize_html(val)
            elif key == 'slug':
                if not isinstance(val, string_types):
                    raise ValidationError('%s must be a string: %s' % (key, str(type(val))))
                val = util.sanitize_html.sanitize_html(val)
            elif key == 'dbkey':
                if not isinstance(val, string_types):
                    raise ValidationError('%s must be a string or unicode: %s' % (key, str(type(val))))
                val = util.sanitize_html.sanitize_html(val)

            elif key not in valid_but_uneditable_keys:
                continue
                # raise AttributeError( 'unknown key: %s' %( str( key ) ) )

            validated_payload[key] = val
        return validated_payload