Commit 656b3c2f authored by John Chilton's avatar John Chilton
Browse files

Refactor dataset fetching in get/set dataset method in web controller.

parent 6feef2a2

lib/galaxy/webapps/galaxy/controllers/dataset.py

+31 −25
Original line number Diff line number Diff line
@@ -251,27 +251,11 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE 
    @web.expose_api_anonymous

    def get_edit(self, trans, dataset_id=None, **kwd):

        """Produces the input definitions available to modify dataset attributes"""

        message = None

        status = None

        if dataset_id is not None:

            id = self.decode_id(dataset_id)

            data = trans.sa_session.query(self.app.model.HistoryDatasetAssociation).get(id)

        else:

            trans.log_event("dataset_id is None, cannot load a dataset to edit.")

            return self.message_exception(trans, 'You must provide a dataset id to edit attributes.')

        if data is None:

            trans.log_event("Problem retrieving dataset id (%s)." % dataset_id)

            return self.message_exception(trans, 'The dataset id is invalid.')

        if dataset_id is not None and data.history.user is not None and data.history.user != trans.user:

            trans.log_event("User attempted to edit a dataset they do not own (encoded: %s, decoded: %s)." % (dataset_id, id))

            return self.message_exception(trans, 'The dataset id is invalid.')

        if data.history.user and not data.dataset.has_manage_permissions_roles(trans):

            # Permission setting related to DATASET_MANAGE_PERMISSIONS was broken for a period of time,

            # so it is possible that some Datasets have no roles associated with the DATASET_MANAGE_PERMISSIONS

            # permission.  In this case, we'll reset this permission to the hda user's private role.

            manage_permissions_action = trans.app.security_agent.get_action(trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS.action)

            permissions = {manage_permissions_action : [trans.app.security_agent.get_private_user_role(data.history.user)]}

            trans.app.security_agent.set_dataset_permission(data.dataset, permissions)

        data, message = self._get_dataset_for_edit(trans, dataset_id)

        if message:

            return message



        if self._can_access_dataset(trans, data):

            if data.state == trans.model.Dataset.states.UPLOAD:

                return self.message_exception(trans, 'Please wait until this dataset finishes uploading before attempting to edit its metadata.')
@@ -416,13 +400,13 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE 
                    return False

            return True



        message = None

        status = 'success'

        dataset_id = payload.get('dataset_id')

        operation = payload.get('operation')

        if dataset_id is not None:

            id = self.decode_id(dataset_id)

            data = trans.sa_session.query(self.app.model.HistoryDatasetAssociation).get(id)

        dataset_id = payload.get('dataset_id')

        data, message = self._get_dataset_for_edit(trans, dataset_id)

        if message:

            return message



        if operation == 'attributes':

            # The user clicked the Save button on the 'Edit Attributes' form

            data.name = payload.get('name')
@@ -510,6 +494,28 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE 
            return self.message_exception(trans, 'Invalid operation identifier (%s).' % operation)

        return {'status': status, 'message': sanitize_text(message)}



    def _get_dataset_for_edit(self, trans, dataset_id):

        if dataset_id is not None:

            id = self.decode_id(dataset_id)

            data = trans.sa_session.query(self.app.model.HistoryDatasetAssociation).get(id)

        else:

            trans.log_event("dataset_id is None, cannot load a dataset to edit.")

            return None, self.message_exception(trans, 'You must provide a dataset id to edit attributes.')

        if data is None:

            trans.log_event("Problem retrieving dataset id (%s)." % dataset_id)

            return None, self.message_exception(trans, 'The dataset id is invalid.')

        if dataset_id is not None and data.history.user is not None and data.history.user != trans.user:

            trans.log_event("User attempted to edit a dataset they do not own (encoded: %s, decoded: %s)." % (dataset_id, id))

            return None, self.message_exception(trans, 'The dataset id is invalid.')

        if data.history.user and not data.dataset.has_manage_permissions_roles(trans):

            # Permission setting related to DATASET_MANAGE_PERMISSIONS was broken for a period of time,

            # so it is possible that some Datasets have no roles associated with the DATASET_MANAGE_PERMISSIONS

            # permission.  In this case, we'll reset this permission to the hda user's private role.

            manage_permissions_action = trans.app.security_agent.get_action(trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS.action)

            permissions = {manage_permissions_action : [trans.app.security_agent.get_private_user_role(data.history.user)]}

            trans.app.security_agent.set_dataset_permission(data.dataset, permissions)

        return data, None



    @web.expose

    @web.json

    @web.require_login("see all available datasets")