workflows.py

"""
API operations for Workflows
"""
from __future__ import absolute_import

import io
import json
import logging
import os

import requests
from gxformat2._yaml import ordered_dump
from markupsafe import escape
from sqlalchemy import desc, false, or_, true
from sqlalchemy.orm import joinedload

from galaxy import (
    exceptions,
    model,
    util
)
from galaxy.managers import (
    histories,
    workflows
)
from galaxy.managers.jobs import fetch_job_states, invocation_job_source_iter
from galaxy.model.item_attrs import UsesAnnotations
from galaxy.tool_shed.galaxy_install.install_manager import InstallRepositoryManager
from galaxy.tools import recommendations
from galaxy.tools.parameters import populate_state
from galaxy.tools.parameters.basic import workflow_building_modes
from galaxy.util.sanitize_html import sanitize_html
from galaxy.web import (
    expose_api,
    expose_api_anonymous_and_sessionless,
    expose_api_raw,
    format_return_as_json,
)
from galaxy.webapps.base.controller import (
    BaseAPIController,
    SharableMixin,
    url_for,
    UsesStoredWorkflowMixin
)
from galaxy.workflow.extract import extract_workflow
from galaxy.workflow.modules import module_factory
from galaxy.workflow.reports import generate_report
from galaxy.workflow.run import invoke, queue_invoke
from galaxy.workflow.run_request import build_workflow_run_configs

log = logging.getLogger(__name__)


class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnnotations, SharableMixin):

    def __init__(self, app):
        super(WorkflowsAPIController, self).__init__(app)
        self.history_manager = histories.HistoryManager(app)
        self.workflow_manager = workflows.WorkflowsManager(app)
        self.workflow_contents_manager = workflows.WorkflowContentsManager(app)
        self.tool_recommendations = recommendations.ToolRecommendations()

    def __get_full_shed_url(self, url):
        for name, shed_url in self.app.tool_shed_registry.tool_sheds.items():
            if url in shed_url:
                return shed_url
        return None

    @expose_api_anonymous_and_sessionless
    def index(self, trans, **kwd):
        """
        GET /api/workflows
        """
        return self.get_workflows_list(trans, kwd)

    @expose_api
    def get_workflow_menu(self, trans, **kwd):
        """
        Get workflows present in the tools panel
        GET /api/workflows/menu
        """
        user = trans.get_user()
        ids_in_menu = [x.stored_workflow_id for x in user.stored_workflow_menu_entries]
        return {
            'ids_in_menu': ids_in_menu,
            'workflows': self.get_workflows_list(trans, kwd)
        }

    @expose_api
    def set_workflow_menu(self, trans, **kwd):
        """
        Save workflow menu to be shown in the tool panel
        PUT /api/workflows/menu
        """
        payload = kwd.get('payload')
        user = trans.get_user()
        workflow_ids = payload.get('workflow_ids')
        if workflow_ids is None:
            workflow_ids = []
        elif type(workflow_ids) != list:
            workflow_ids = [workflow_ids]
        workflow_ids_decoded = []
        # Decode the encoded workflow ids
        for ids in workflow_ids:
            workflow_ids_decoded.append(trans.security.decode_id(ids))
        sess = trans.sa_session
        # This explicit remove seems like a hack, need to figure out
        # how to make the association do it automatically.
        for m in user.stored_workflow_menu_entries:
            sess.delete(m)
        user.stored_workflow_menu_entries = []
        q = sess.query(model.StoredWorkflow)
        # To ensure id list is unique
        seen_workflow_ids = set()
        for wf_id in workflow_ids_decoded:
            if wf_id in seen_workflow_ids:
                continue
            else:
                seen_workflow_ids.add(wf_id)
            m = model.StoredWorkflowMenuEntry()
            m.stored_workflow = q.get(wf_id)
            user.stored_workflow_menu_entries.append(m)
        sess.flush()
        message = "Menu updated."
        trans.set_message(message)
        return {'message': message, 'status': 'done'}

    def get_workflows_list(self, trans, kwd):
        """
        Displays a collection of workflows.

        :param  show_published:      if True, show also published workflows
        :type   show_published:      boolean
        :param  missing_tools:       if True, include a list of missing tools per workflow
        :type   missing_tools:       boolean
        """
        missing_tools = util.string_as_bool(kwd.get('missing_tools', 'False'))
        rval = []
        filter1 = (trans.app.model.StoredWorkflow.user == trans.user)
        user = trans.get_user()
        if user is None:
            show_published = util.string_as_bool(kwd.get('show_published', 'True'))
        else :
            show_published = util.string_as_bool(kwd.get('show_published', 'False'))
        if show_published:
            filter1 = or_(filter1, (trans.app.model.StoredWorkflow.published == true()))
        for wf in trans.sa_session.query(trans.app.model.StoredWorkflow).options(
                joinedload("annotations")).options(
                joinedload("latest_workflow").undefer("step_count").lazyload("steps")).options(
                joinedload("tags")).filter(
                    filter1, trans.app.model.StoredWorkflow.table.c.deleted == false()).order_by(
                    desc(trans.app.model.StoredWorkflow.table.c.update_time)).all():
            item = wf.to_dict(value_mapper={'id': trans.security.encode_id})
            encoded_id = trans.security.encode_id(wf.id)
            item['annotations'] = [x.annotation for x in wf.annotations]
            item['url'] = url_for('workflow', id=encoded_id)
            item['owner'] = wf.user.username
            item['number_of_steps'] = wf.latest_workflow.step_count
            item['show_in_tool_panel'] = False
            if user is not None:
                item['show_in_tool_panel'] = wf.show_in_tool_panel(user_id=user.id)
            rval.append(item)
        for wf_sa in trans.sa_session.query(model.StoredWorkflowUserShareAssociation).join(
                model.StoredWorkflowUserShareAssociation.stored_workflow).options(
                joinedload("stored_workflow").joinedload("annotations")).options(
                joinedload("stored_workflow").joinedload("latest_workflow").undefer("step_count").lazyload("steps")).options(
                joinedload("stored_workflow").joinedload("user")).options(
                joinedload("stored_workflow").joinedload("tags")).filter(model.StoredWorkflowUserShareAssociation.user == trans.user).filter(
                model.StoredWorkflow.deleted == false()).order_by(
                desc(model.StoredWorkflow.update_time)).all():
            item = wf_sa.stored_workflow.to_dict(value_mapper={'id': trans.security.encode_id})
            encoded_id = trans.security.encode_id(wf_sa.stored_workflow.id)
            item['annotations'] = [x.annotation for x in wf_sa.stored_workflow.annotations]
            item['url'] = url_for('workflow', id=encoded_id)
            item['slug'] = wf_sa.stored_workflow.slug
            item['owner'] = wf_sa.stored_workflow.user.username
            item['number_of_steps'] = wf_sa.stored_workflow.latest_workflow.step_count
            item['show_in_tool_panel'] = False
            if user is not None:
                item['show_in_tool_panel'] = wf_sa.stored_workflow.show_in_tool_panel(user_id=user.id)
            rval.append(item)
        if missing_tools:
            workflows_missing_tools = []
            workflows = []
            workflows_by_toolshed = dict()
            for key, value in enumerate(rval):
                tool_ids = []
                workflow_details = self.workflow_contents_manager.workflow_to_dict(trans, self.__get_stored_workflow(trans, value['id']), style='instance')
                if 'steps' in workflow_details:
                    for step in workflow_details['steps']:
                        tool_id = workflow_details['steps'][step].get('tool_id')
                        if tool_id and tool_id not in tool_ids and self.app.toolbox.is_missing_shed_tool(tool_id):
                            tool_ids.append(tool_id)
                if len(tool_ids) > 0:
                    value['missing_tools'] = tool_ids
                    workflows_missing_tools.append(value)
            for workflow in workflows_missing_tools:
                for tool_id in workflow['missing_tools']:
                    toolshed, _, owner, name, tool, version = tool_id.split('/')
                    shed_url = self.__get_full_shed_url(toolshed)
                    repo_identifier = '/'.join((toolshed, owner, name))
                    if repo_identifier not in workflows_by_toolshed:
                        workflows_by_toolshed[repo_identifier] = dict(shed=shed_url.rstrip('/'), repository=name, owner=owner, tools=[tool_id], workflows=[workflow['name']])
                    else:
                        if tool_id not in workflows_by_toolshed[repo_identifier]['tools']:
                            workflows_by_toolshed[repo_identifier]['tools'].append(tool_id)
                        if workflow['name'] not in workflows_by_toolshed[repo_identifier]['workflows']:
                            workflows_by_toolshed[repo_identifier]['workflows'].append(workflow['name'])
            for repo_tag in workflows_by_toolshed:
                workflows.append(workflows_by_toolshed[repo_tag])
            return workflows
        return rval

    @expose_api_anonymous_and_sessionless
    def show(self, trans, id, **kwd):
        """
        GET /api/workflows/{encoded_workflow_id}

        :param  instance:                 true if fetch by Workflow ID instead of StoredWorkflow id, false
                                          by default.
        :type   instance:                 boolean

        Displays information needed to run a workflow.
        """
        stored_workflow = self.__get_stored_workflow(trans, id, **kwd)
        if stored_workflow.importable is False and stored_workflow.user != trans.user and not trans.user_is_admin:
            if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0:
                message = "Workflow is neither importable, nor owned by or shared with current user"
                raise exceptions.ItemAccessibilityException(message)
        if kwd.get("legacy", False):
            style = "legacy"
        else:
            style = "instance"
        version = kwd.get('version')
        return self.workflow_contents_manager.workflow_to_dict(trans, stored_workflow, style=style, version=version)

    @expose_api
    def show_versions(self, trans, workflow_id, **kwds):
        """
        GET /api/workflows/{encoded_workflow_id}/versions

        :param  instance:                 true if fetch by Workflow ID instead of StoredWorkflow id, false
                                          by default.
        :type   instance:                 boolean

        Lists all versions of this workflow.
        """
        stored_workflow = self.workflow_manager.get_stored_accessible_workflow(trans, workflow_id, **kwds)
        return [{'version': i, 'update_time': str(w.update_time), 'steps': len(w.steps)} for i, w in enumerate(reversed(stored_workflow.workflows))]

    @expose_api
    def create(self, trans, payload, **kwd):
        """
        POST /api/workflows

        Run or create workflows from the api.

        .. tip:: When executing a workflow externally (e.g. from a script) it is
            recommended to use the :func:`galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController.invoke` method below instead.

        If installed_repository_file or from_history_id is specified a new
        workflow will be created for this user. Otherwise, workflow_id must be
        specified and this API method will cause a workflow to execute.

        :param  installed_repository_file    The path of a workflow to import. Either workflow_id, installed_repository_file or from_history_id must be specified
        :type   installed_repository_file    str

        :param  workflow_id:                 An existing workflow id. Either workflow_id, installed_repository_file or from_history_id must be specified
        :type   workflow_id:                 str

        :param  parameters:                  If workflow_id is set - see _step_parameters() in lib/galaxy/workflow/run_request.py
        :type   parameters:                  dict

        :param  ds_map:                      If workflow_id is set - a dictionary mapping each input step id to a dictionary with 2 keys: 'src' (which can be 'ldda', 'ld' or 'hda') and 'id' (which should be the id of a LibraryDatasetDatasetAssociation, LibraryDataset or HistoryDatasetAssociation respectively)
        :type   ds_map:                      dict

        :param  no_add_to_history:           If workflow_id is set - if present in the payload with any value, the input datasets will not be added to the selected history
        :type   no_add_to_history:           str

        :param  history:                     If workflow_id is set - optional history where to run the workflow, either the name of a new history or "hist_id=HIST_ID" where HIST_ID is the id of an existing history. If not specified, the workflow will be run a new unnamed history
        :type   history:                     str

        :param  replacement_params:          If workflow_id is set - an optional dictionary used when renaming datasets
        :type   replacement_params:          dict

        :param  from_history_id:             Id of history to extract a workflow from. Either workflow_id, installed_repository_file or from_history_id must be specified
        :type   from_history_id:             str

        :param  job_ids:                     If from_history_id is set - optional list of jobs to include when extracting a workflow from history
        :type   job_ids:                     str

        :param  dataset_ids:                 If from_history_id is set - optional list of HDA `hid`s corresponding to workflow inputs when extracting a workflow from history
        :type   dataset_ids:                 str

        :param  dataset_collection_ids:      If from_history_id is set - optional list of HDCA `hid`s corresponding to workflow inputs when extracting a workflow from history
        :type   dataset_collection_ids:      str

        :param  workflow_name:               If from_history_id is set - name of the workflow to create when extracting a workflow from history
        :type   workflow_name:               str

        :param  allow_tool_state_corrections:  If set to True, any Tool parameter changes will not prevent running workflow, defaults to False
        :type   allow_tool_state_corrections:  bool

        :param use_cached_job:               If set to True galaxy will attempt to find previously executed steps for all workflow steps with the exact same parameter combinations
                                             and will copy the outputs of the previously executed step.
        """
        ways_to_create = {
            'archive_source',
            'workflow_id',
            'installed_repository_file',
            'from_history_id',
            'from_path',
            'shared_workflow_id',
            'workflow',
        }

        if len(ways_to_create.intersection(payload)) == 0:
            message = "One parameter among - %s - must be specified" % ", ".join(ways_to_create)
            raise exceptions.RequestParameterMissingException(message)

        if len(ways_to_create.intersection(payload)) > 1:
            message = "Only one parameter among - %s - must be specified" % ", ".join(ways_to_create)
            raise exceptions.RequestParameterInvalidException(message)

        if 'installed_repository_file' in payload:
            if not trans.user_is_admin:
                raise exceptions.AdminRequiredException()
            installed_repository_file = payload.get('installed_repository_file', '')
            if not os.path.exists(installed_repository_file):
                raise exceptions.RequestParameterInvalidException("Workflow file '%s' not found" % installed_repository_file)
            elif os.path.getsize(os.path.abspath(installed_repository_file)) > 0:
                with io.open(installed_repository_file, encoding='utf-8') as f:
                    workflow_data = f.read()
                return self.__api_import_from_archive(trans, workflow_data)
            else:
                raise exceptions.MessageException("You attempted to open an empty file.")

        if 'archive_source' in payload:
            archive_source = payload['archive_source']
            archive_file = payload.get('archive_file')
            archive_data = None
            if archive_source:
                if archive_source.startswith("file://"):
                    if not trans.user_is_admin:
                        raise exceptions.AdminRequiredException()
                    workflow_src = {"src": "from_path", "path": archive_source[len("file://"):]}
                    payload["workflow"] = workflow_src
                    return self.__api_import_new_workflow(trans, payload, **kwd)
                else:
                    try:
                        archive_data = requests.get(archive_source).text
                    except Exception:
                        raise exceptions.MessageException("Failed to open URL '%s'." % escape(archive_source))
            elif hasattr(archive_file, 'file'):
                uploaded_file = archive_file.file
                uploaded_file_name = uploaded_file.name
                if os.path.getsize(os.path.abspath(uploaded_file_name)) > 0:
                    archive_data = util.unicodify(uploaded_file.read())
                else:
                    raise exceptions.MessageException("You attempted to upload an empty file.")
            else:
                raise exceptions.MessageException("Please provide a URL or file.")
            return self.__api_import_from_archive(trans, archive_data, "uploaded file")

        if 'from_history_id' in payload:
            from_history_id = payload.get('from_history_id')
            from_history_id = self.decode_id(from_history_id)
            history = self.history_manager.get_accessible(from_history_id, trans.user, current_history=trans.history)

            job_ids = [self.decode_id(_) for _ in payload.get('job_ids', [])]
            dataset_ids = payload.get('dataset_ids', [])
            dataset_collection_ids = payload.get('dataset_collection_ids', [])
            workflow_name = payload['workflow_name']
            stored_workflow = extract_workflow(
                trans=trans,
                user=trans.get_user(),
                history=history,
                job_ids=job_ids,
                dataset_ids=dataset_ids,
                dataset_collection_ids=dataset_collection_ids,
                workflow_name=workflow_name,
            )
            item = stored_workflow.to_dict(value_mapper={'id': trans.security.encode_id})
            item['url'] = url_for('workflow', id=item['id'])
            return item

        if 'from_path' in payload:
            from_path = payload.get('from_path')
            object_id = payload.get("object_id")
            workflow_src = {"src": "from_path", "path": from_path}
            if object_id is not None:
                workflow_src["object_id"] = object_id
            payload["workflow"] = workflow_src
            return self.__api_import_new_workflow(trans, payload, **kwd)

        if 'shared_workflow_id' in payload:
            workflow_id = payload['shared_workflow_id']
            return self.__api_import_shared_workflow(trans, workflow_id, payload)

        if 'workflow' in payload:
            return self.__api_import_new_workflow(trans, payload, **kwd)

        workflow_id = payload.get('workflow_id', None)
        if not workflow_id:
            message = "Invalid workflow_id specified."
            raise exceptions.RequestParameterInvalidException(message)

        # Get workflow + accessibility check.
        stored_workflow = self.__get_stored_accessible_workflow(trans, workflow_id)
        workflow = stored_workflow.latest_workflow

        run_configs = build_workflow_run_configs(trans, workflow, payload)
        assert len(run_configs) == 1
        run_config = run_configs[0]
        history = run_config.target_history

        # invoke may throw MessageExceptions on tool erors, failure
        # to match up inputs, etc...
        outputs, invocation = invoke(
            trans=trans,
            workflow=workflow,
            workflow_run_config=run_config,
            populate_state=True,
        )
        trans.sa_session.flush()

        # Build legacy output - should probably include more information from
        # outputs.
        rval = {}
        rval['history'] = trans.security.encode_id(history.id)
        rval['outputs'] = []
        if outputs:
            # Newer outputs don't necessarily fill outputs (?)
            for step in workflow.steps:
                if step.type == 'tool' or step.type is None:
                    for v in outputs[step.id].values():
                        rval['outputs'].append(trans.security.encode_id(v.id))

        # Newer version of this API just returns the invocation as a dict, to
        # facilitate migration - produce the newer style response and blend in
        # the older information.
        invocation_response = self.__encode_invocation(invocation, **kwd)
        invocation_response.update(rval)
        return invocation_response

    @expose_api_raw
    def workflow_dict(self, trans, workflow_id, **kwd):
        """
        GET /api/workflows/{encoded_workflow_id}/download

        Returns a selected workflow.

        :type   style:  str
        :param  style:  Style of export. The default is 'export', which is the meant to be used
                        with workflow import endpoints. Other formats such as 'instance', 'editor',
                        'run' are more tied to the GUI and should not be considered stable APIs.
                        The default format for 'export' is specified by the
                        admin with the `default_workflow_export_format` config
                        option. Style can be specified as either 'ga' or 'format2' directly
                        to be explicit about which format to download.

        :param  instance:                 true if fetch by Workflow ID instead of StoredWorkflow id, false
                                          by default.
        :type   instance:                 boolean
        """
        stored_workflow = self.__get_stored_accessible_workflow(trans, workflow_id, **kwd)

        style = kwd.get("style", "export")
        download_format = kwd.get('format')
        version = kwd.get('version')
        ret_dict = self.workflow_contents_manager.workflow_to_dict(trans, stored_workflow, style=style, version=version)
        if download_format == 'json-download':
            sname = stored_workflow.name
            sname = ''.join(c in util.FILENAME_VALID_CHARS and c or '_' for c in sname)[0:150]
            if ret_dict.get("format-version", None) == "0.1":
                extension = "ga"
            else:
                extension = "gxwf.json"
            trans.response.headers["Content-Disposition"] = 'attachment; filename="Galaxy-Workflow-%s.%s"' % (sname, extension)
            trans.response.set_content_type('application/galaxy-archive')

        if style == "format2" and download_format != 'json-download':
            return ordered_dump(ret_dict)
        else:
            return format_return_as_json(ret_dict, pretty=True)

    @expose_api
    def delete(self, trans, id, **kwd):
        """
        DELETE /api/workflows/{encoded_workflow_id}
        Deletes a specified workflow
        Author: rpark

        copied from galaxy.web.controllers.workflows.py (delete)
        """
        workflow_id = id

        try:
            stored_workflow = trans.sa_session.query(self.app.model.StoredWorkflow).get(self.decode_id(workflow_id))
        except Exception as e:
            trans.response.status = 400
            return ("Workflow with ID='%s' can not be found\n Exception: %s") % (workflow_id, util.unicodify(e))

        # check to see if user has permissions to selected workflow
        if stored_workflow.user != trans.user and not trans.user_is_admin:
            trans.response.status = 403
            return("Workflow is not owned by current user")

        # Mark a workflow as deleted
        stored_workflow.deleted = True
        trans.sa_session.flush()

        # TODO: Unsure of response message to let api know that a workflow was successfully deleted
        return ("Workflow '%s' successfully deleted" % stored_workflow.name)

    @expose_api
    def import_new_workflow_deprecated(self, trans, payload, **kwd):
        """
        POST /api/workflows/upload
        Importing dynamic workflows from the api. Return newly generated workflow id.
        Author: rpark

        # currently assumes payload['workflow'] is a json representation of a workflow to be inserted into the database

        Deprecated in favor to POST /api/workflows with encoded 'workflow' in
        payload the same way.
        """
        return self.__api_import_new_workflow(trans, payload, **kwd)

    @expose_api
    def update(self, trans, id, payload, **kwds):
        """
        * PUT /api/workflows/{id}
            updates the workflow stored with ``id``

        :type   id:      str
        :param  id:      the encoded id of the workflow to update
        :param  instance:                 true if fetch by Workflow ID instead of StoredWorkflow id, false
                                          by default.
        :type   instance:                 boolean
        :type   payload: dict
        :param  payload: a dictionary containing any or all the
            * workflow   the json description of the workflow as would be
                         produced by GET workflows/<id>/download or
                         given to `POST workflows`

                         The workflow contents will be updated to target
                         this.

            * name       optional string name for the workflow, if not present in payload,
                         name defaults to existing name
            * annotation optional string annotation for the workflow, if not present in payload,
                         annotation defaults to existing annotation
            * menu_entry optional boolean marking if the workflow should appear in the user's menu,
                         if not present, workflow menu entries are not modified
            * from_tool_form True iff encoded state coming in is encoded for the tool form.

        :rtype:     dict
        :returns:   serialized version of the workflow
        """
        stored_workflow = self.__get_stored_workflow(trans, id, **kwds)
        workflow_dict = payload.get('workflow') or payload
        if workflow_dict:
            raw_workflow_description = self.__normalize_workflow(trans, workflow_dict)
            workflow_dict = raw_workflow_description.as_dict
            new_workflow_name = workflow_dict.get('name')
            if new_workflow_name and new_workflow_name != stored_workflow.name:
                sanitized_name = sanitize_html(new_workflow_name)
                workflow = stored_workflow.latest_workflow.copy()
                workflow.stored_workflow = stored_workflow
                workflow.name = sanitized_name
                stored_workflow.name = sanitized_name
                stored_workflow.latest_workflow = workflow
                trans.sa_session.add(workflow, stored_workflow)
                trans.sa_session.flush()

            if 'annotation' in workflow_dict:
                newAnnotation = sanitize_html(workflow_dict['annotation'])
                self.add_item_annotation(trans.sa_session, trans.get_user(), stored_workflow, newAnnotation)
                trans.sa_session.flush()

            if 'menu_entry' in workflow_dict or 'show_in_tool_panel' in workflow_dict:
                if workflow_dict.get('menu_entry') or workflow_dict.get('show_in_tool_panel'):
                    menuEntry = model.StoredWorkflowMenuEntry()
                    menuEntry.stored_workflow = stored_workflow
                    trans.get_user().stored_workflow_menu_entries.append(menuEntry)
                else:
                    # remove if in list
                    entries = {x.stored_workflow_id: x for x in trans.get_user().stored_workflow_menu_entries}
                    if trans.security.decode_id(id) in entries:
                        trans.get_user().stored_workflow_menu_entries.remove(entries[trans.security.decode_id(id)])
            # set tags
            if 'tags' in workflow_dict:
                trans.app.tag_handler.set_tags_from_list(user=trans.user, item=stored_workflow, new_tags_list=workflow_dict['tags'])

            if 'steps' in workflow_dict:
                try:
                    from_dict_kwds = self.__import_or_update_kwds(payload)
                    workflow, errors = self.workflow_contents_manager.update_workflow_from_raw_description(
                        trans,
                        stored_workflow,
                        raw_workflow_description,
                        **from_dict_kwds
                    )
                except workflows.MissingToolsException:
                    raise exceptions.MessageException("This workflow contains missing tools. It cannot be saved until they have been removed from the workflow or installed.")
        else:
            message = "Updating workflow requires dictionary containing 'workflow' attribute with new JSON description."
            raise exceptions.RequestParameterInvalidException(message)
        return self.workflow_contents_manager.workflow_to_dict(trans, stored_workflow, style="instance")

    @expose_api
    def build_module(self, trans, payload={}):
        """
        POST /api/workflows/build_module
        Builds module models for the workflow editor.
        """
        inputs = payload.get('inputs', {})
        trans.workflow_building_mode = workflow_building_modes.ENABLED
        module = module_factory.from_dict(trans, payload, from_tool_form=True)
        if 'tool_state' not in payload:
            module_state = {}
            populate_state(trans, module.get_inputs(), inputs, module_state, check=False)
            module.recover_state(module_state, from_tool_form=True)
        return {
            'label'             : inputs.get('__label', ''),
            'annotation'        : inputs.get('__annotation', ''),
            'name'              : module.get_name(),
            'tool_state'        : module.get_state(),
            'inputs'            : module.get_all_inputs(connectable_only=True),
            'outputs'           : module.get_all_outputs(),
            'config_form'       : module.get_config_form(),
            'post_job_actions'  : module.get_post_job_actions(inputs)
        }

    @expose_api
    def get_tool_predictions(self, trans, payload, **kwd):
        """
        POST /api/workflows/get_tool_predictions
        Fetch predicted tools for a workflow
        :type   payload: dict
        :param  payload: a dictionary containing two parameters:
                         'tool_sequence' - comma separated sequence of tool ids
                         'remote_model_url' - (optional) path to the deep learning model
        """
        remote_model_url = payload.get('remote_model_url', trans.app.config.tool_recommendation_model_path)
        tool_sequence = payload.get('tool_sequence', "")
        if 'tool_sequence' not in payload or remote_model_url is None:
            return
        tool_sequence, recommended_tools = self.tool_recommendations.get_predictions(trans, tool_sequence, remote_model_url)
        return {
            "current_tool": tool_sequence,
            "predicted_data": recommended_tools
        }

    #
    # -- Helper methods --
    #
    def __api_import_from_archive(self, trans, archive_data, source=None):
        try:
            data = json.loads(archive_data)
        except Exception:
            if "GalaxyWorkflow" in archive_data:
                data = {"yaml_content": archive_data}
            else:
                raise exceptions.MessageException("The data content does not appear to be a valid workflow.")
        if not data:
            raise exceptions.MessageException("The data content is missing.")
        raw_workflow_description = self.__normalize_workflow(trans, data)
        workflow, missing_tool_tups = self._workflow_from_dict(trans, raw_workflow_description, source=source)
        workflow = workflow.latest_workflow
        if workflow.has_errors:
            return {"message": "Imported, but some steps in this workflow have validation errors.", "status": "error"}
        elif len(workflow.steps) == 0:
            return {"message": "Imported, but this workflow has no steps.", "status": "error"}
        elif workflow.has_cycles:
            return {"message": "Imported, but this workflow contains cycles.", "status": "error"}
        return {"message": "Workflow '%s' imported successfully." % escape(workflow.name), "status": "success"}

    def __api_import_new_workflow(self, trans, payload, **kwd):
        data = payload['workflow']
        raw_workflow_description = self.__normalize_workflow(trans, data)
        data = raw_workflow_description.as_dict
        import_tools = util.string_as_bool(payload.get("import_tools", False))
        if import_tools and not trans.user_is_admin:
            raise exceptions.AdminRequiredException()

        from_dict_kwds = self.__import_or_update_kwds(payload)

        publish = util.string_as_bool(payload.get("publish", False))
        # If 'publish' set, default to importable.
        importable = util.string_as_bool(payload.get("importable", publish))

        if publish and not importable:
            raise exceptions.RequestParameterInvalidException("Published workflow must be importable.")

        from_dict_kwds["publish"] = publish
        workflow, missing_tool_tups = self._workflow_from_dict(trans, raw_workflow_description, **from_dict_kwds)
        if importable:
            self._make_item_accessible(trans.sa_session, workflow)
            trans.sa_session.flush()
        # galaxy workflow newly created id
        workflow_id = workflow.id
        # api encoded, id
        encoded_id = trans.security.encode_id(workflow_id)
        item = workflow.to_dict(value_mapper={'id': trans.security.encode_id})
        item['annotations'] = [x.annotation for x in workflow.annotations]
        item['url'] = url_for('workflow', id=encoded_id)
        item['owner'] = workflow.user.username
        item['number_of_steps'] = len(workflow.latest_workflow.steps)
        if import_tools:
            tools = {}
            for key in data['steps']:
                item = data['steps'][key]
                if item is not None:
                    if 'tool_shed_repository' in item:
                        tool_shed_repository = item['tool_shed_repository']
                        if 'owner' in tool_shed_repository and 'changeset_revision' in tool_shed_repository and 'name' in tool_shed_repository and 'tool_shed' in tool_shed_repository:
                            toolstr = tool_shed_repository['owner'] \
                                + tool_shed_repository['changeset_revision'] \
                                + tool_shed_repository['name'] \
                                + tool_shed_repository['tool_shed']
                            tools[toolstr] = tool_shed_repository
            irm = InstallRepositoryManager(self.app)
            for k in tools:
                item = tools[k]
                tool_shed_url = 'https://' + item['tool_shed'] + '/'
                name = item['name']
                owner = item['owner']
                changeset_revision = item['changeset_revision']
                irm.install(tool_shed_url,
                            name,
                            owner,
                            changeset_revision,
                            payload)
        return item

    def __import_or_update_kwds(self, payload):
        # Galaxy will try to upgrade tool versions that don't match exactly during import,
        # this prevents that.
        exact_tools = util.string_as_bool(payload.get("exact_tools", True))

        # Fill in missing tool state for hand built so the workflow can run, default of this
        # should become True at some point in the future I imagine.
        fill_defaults = util.string_as_bool(payload.get("fill_defaults", False))
        from_tool_form = payload.get("from_tool_form", False)
        return {
            'exact_tools': exact_tools,
            'fill_defaults': fill_defaults,
            'from_tool_form': from_tool_form,
        }

    def __normalize_workflow(self, trans, as_dict):
        return self.workflow_contents_manager.normalize_workflow_format(trans, as_dict)

    @expose_api
    def import_shared_workflow_deprecated(self, trans, payload, **kwd):
        """
        POST /api/workflows/import
        Import a workflow shared by other users.

        :param  workflow_id:      the workflow id (required)
        :type   workflow_id:      str

        :raises: exceptions.MessageException, exceptions.ObjectNotFound
        """
        # Pull parameters out of payload.
        workflow_id = payload.get('workflow_id', None)
        if workflow_id is None:
            raise exceptions.ObjectAttributeMissingException("Missing required parameter 'workflow_id'.")
        self.__api_import_shared_workflow(trans, workflow_id, payload)

    def __api_import_shared_workflow(self, trans, workflow_id, payload, **kwd):
        try:
            stored_workflow = self.get_stored_workflow(trans, workflow_id, check_ownership=False)
        except Exception:
            raise exceptions.ObjectNotFound("Malformed workflow id ( %s ) specified." % workflow_id)
        if stored_workflow.importable is False:
            raise exceptions.ItemAccessibilityException('The owner of this workflow has disabled imports via this link.')
        elif stored_workflow.deleted:
            raise exceptions.ItemDeletionException("You can't import this workflow because it has been deleted.")
        imported_workflow = self._import_shared_workflow(trans, stored_workflow)
        item = imported_workflow.to_dict(value_mapper={'id': trans.security.encode_id})
        encoded_id = trans.security.encode_id(imported_workflow.id)
        item['url'] = url_for('workflow', id=encoded_id)
        return item

    @expose_api
    def invoke(self, trans, workflow_id, payload, **kwd):
        """
        POST /api/workflows/{encoded_workflow_id}/invocations

        Schedule the workflow specified by `workflow_id` to run.

        .. note:: This method takes the same arguments as
            :func:`galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController.create` above.
        """
        # Get workflow + accessibility check.
        stored_workflow = self.__get_stored_accessible_workflow(trans, workflow_id)
        workflow = stored_workflow.latest_workflow
        run_configs = build_workflow_run_configs(trans, workflow, payload)
        is_batch = payload.get('batch')
        if not is_batch and len(run_configs) != 1:
            raise exceptions.RequestParameterInvalidException("Must specify 'batch' to use batch parameters.")

        invocations = []
        for run_config in run_configs:
            workflow_scheduler_id = payload.get('scheduler', None)
            # TODO: workflow scheduler hints
            work_request_params = dict(scheduler=workflow_scheduler_id)
            workflow_invocation = queue_invoke(
                trans=trans,
                workflow=workflow,
                workflow_run_config=run_config,
                request_params=work_request_params
            )
            invocation = self.encode_all_ids(trans, workflow_invocation.to_dict(), recursive=True)
            invocations.append(invocation)

        if is_batch:
            return invocations
        else:
            return invocations[0]

    @expose_api
    def index_invocations(self, trans, workflow_id=None, **kwd):
        """
        GET /api/workflows/{workflow_id}/invocations
        GET /api/invocations

        Get the list of a user's workflow invocations. If workflow_id is supplied
        (either via URL or query parameter) it should be an encoded StoredWorkflow id
        and returned invocations will be restricted to that workflow. history_id (an encoded
        History id) can be used to further restrict the query. If neither a workflow_id or
        history_id is supplied, all the current user's workflow invocations will be indexed
        (as determined by the invocation being executed on one of the user's histories).

        :param  workflow_id:      an encoded stored workflow id to restrict query to
        :type   workflow_id:      str

        :param  history_id:       an encoded history id to restrict query to
        :type   history_id:       str

        :param  user_id:          an encoded user id to restrict query to, must be own id if not admin user
        :type   user_id:          str

        :param  view:             level of detail to return per invocation 'element' or 'collection'.
        :type   view:             str

        :param  step_details:     If 'view' is 'element', also include details on individual steps.
        :type   step_details:     bool

        :raises: exceptions.MessageException, exceptions.ObjectNotFound
        """
        if workflow_id is not None:
            stored_workflow_id = self.__get_stored_workflow(trans, workflow_id).id
        else:
            stored_workflow_id = None

        encoded_history_id = kwd.get("history_id", None)
        if encoded_history_id:
            history = self.history_manager.get_accessible(self.decode_id(encoded_history_id), trans.user, current_history=trans.history)
            history_id = history.id
        else:
            history_id = None

        encoded_user_id = kwd.get("user_id", None)
        if encoded_user_id:
            target_user_id = self.decode_id(encoded_user_id)
        else:
            target_user_id = None

        if not trans.user_is_admin:
            # We restrict the query to the current users' invocations
            user_id = trans.user.id
            if target_user_id and user_id != target_user_id:
                raise exceptions.AdminRequiredException("Only admins can index the invocations of others")
        else:
            # Get all invocation if user is admin
            user_id = target_user_id

        include_terminal = util.string_as_bool(kwd.get("include_terminal", True))
        limit = kwd.get("limit", None)
        if limit is not None:
            limit = int(limit)
        invocations = self.workflow_manager.build_invocations_query(
            trans, stored_workflow_id=stored_workflow_id, history_id=history_id, user_id=user_id, include_terminal=include_terminal, limit=limit
        )
        return self.workflow_manager.serialize_workflow_invocations(invocations, **kwd)

    @expose_api
    def show_invocation(self, trans, invocation_id, **kwd):
        """
        GET /api/workflows/{workflow_id}/invocations/{invocation_id}
        GET /api/invocations/{invocation_id}

        Get detailed description of workflow invocation

        :param  invocation_id:      the invocation id (required)
        :type   invocation_id:      str

        :param  step_details:       fetch details about individual invocation steps
                                    and populate a steps attribute in the resulting
                                    dictionary. Defaults to false.
        :type   step_details:       bool

        :param  legacy_job_state:   If step_details is true, and this is set to true
                                    populate the invocation step state with the job state
                                    instead of the invocation step state. This will also
                                    produce one step per job in mapping jobs to mimic the
                                    older behavior with respect to collections. Partially
                                    scheduled steps may provide incomplete information
                                    and the listed steps outputs are the mapped over
                                    step outputs but the individual job outputs
                                    when this is set - at least for now.
        :type   legacy_job_state:   bool

        :raises: exceptions.MessageException, exceptions.ObjectNotFound
        """
        decoded_workflow_invocation_id = self.decode_id(invocation_id)
        workflow_invocation = self.workflow_manager.get_invocation(trans, decoded_workflow_invocation_id)
        if workflow_invocation:
            step_details = util.string_as_bool(kwd.get('step_details', 'False'))
            legacy_job_state = util.string_as_bool(kwd.get('legacy_job_state', 'False'))
            return self.__encode_invocation(workflow_invocation, step_details=step_details, legacy_job_state=legacy_job_state)
        return None

    @expose_api
    def cancel_invocation(self, trans, invocation_id, **kwd):
        """
        DELETE /api/workflows/{workflow_id}/invocations/{invocation_id}
        DELETE /api/invocations/{invocation_id}
        Cancel the specified workflow invocation.

        :param  invocation_id:      the usage id (required)
        :type   invocation_id:      str

        :raises: exceptions.MessageException, exceptions.ObjectNotFound
        """
        decoded_workflow_invocation_id = self.decode_id(invocation_id)
        workflow_invocation = self.workflow_manager.cancel_invocation(trans, decoded_workflow_invocation_id)
        return self.__encode_invocation(workflow_invocation, **kwd)

    @expose_api
    def show_invocation_report(self, trans, invocation_id, **kwd):
        """
        GET /api/workflows/{workflow_id}/invocations/{invocation_id}/report
        GET /api/invocations/{invocation_id}/report

        Get JSON summarizing invocation for reporting.
        """
        kwd["format"] = "json"
        return self._generate_report(trans, invocation_id, **kwd)

    @expose_api_raw
    def show_invocation_report_pdf(self, trans, invocation_id, **kwd):
        """
        GET /api/workflows/{workflow_id}/invocations/{invocation_id}/report.pdf
        GET /api/invocations/{invocation_id}/report.pdf

        Get JSON summarizing invocation for reporting.
        """
        kwd["format"] = "pdf"
        trans.response.set_content_type("application/pdf")
        return self._generate_report(trans, invocation_id, **kwd)

    def _generate_report(self, trans, invocation_id, **kwd):
        decoded_workflow_invocation_id = self.decode_id(invocation_id)
        workflow_invocation = self.workflow_manager.get_invocation(trans, decoded_workflow_invocation_id)
        generator_plugin_type = kwd.get("generator_plugin_type")
        runtime_report_config_json = kwd.get("runtime_report_config_json")
        invocation_markdown = kwd.get("invocation_markdown", None)
        target_format = kwd.get("format", "json")
        if invocation_markdown:
            runtime_report_config_json = {"markdown": invocation_markdown}
        return generate_report(
            trans, workflow_invocation,
            runtime_report_config_json=runtime_report_config_json,
            plugin_type=generator_plugin_type,
            target_format=target_format,
        )

    @expose_api
    def invocation_step(self, trans, invocation_id, step_id, **kwd):
        """
        GET /api/workflows/{workflow_id}/invocations/{invocation_id}/steps/{step_id}
        GET /api/invocations/{invocation_id}/steps/{step_id}

        :param  invocation_id:      the invocation id (required)
        :type   invocation_id:      str

        :param  step_id:      encoded id of the WorkflowInvocationStep (required)
        :type   step_id:      str

        :param  payload:       payload containing update action information
                               for running workflow.

        :raises: exceptions.MessageException, exceptions.ObjectNotFound
        """
        decoded_invocation_step_id = self.decode_id(step_id)
        invocation_step = self.workflow_manager.get_invocation_step(
            trans,
            decoded_invocation_step_id
        )
        return self.__encode_invocation_step(trans, invocation_step)

    @expose_api_anonymous_and_sessionless
    def invocation_step_jobs_summary(self, trans, invocation_id, **kwd):
        """
        * GET /api/workflows/{workflow_id}/invocations/{invocation_id}/step_jobs_summary
          GET /api/invocations/{invocation_id}/step_jobs_summary
            return job state summary info aggregated across per step of the workflow invocation

        Warning: We allow anyone to fetch job state information about any object they
        can guess an encoded ID for - it isn't considered protected data. This keeps
        polling IDs as part of state calculation for large histories and collections as
        efficient as possible.

        :param  invocation_id:    the invocation id (required)
        :type   invocation_id:    str

        :rtype:     dict[]
        :returns:   an array of job summary object dictionaries for each step
        """
        decoded_invocation_id = self.decode_id(invocation_id)
        ids = []
        types = []
        for (job_source_type, job_source_id, _) in invocation_job_source_iter(trans.sa_session, decoded_invocation_id):
            ids.append(job_source_id)
            types.append(job_source_type)
        return [self.encode_all_ids(trans, s) for s in fetch_job_states(trans.sa_session, ids, types)]

    @expose_api_anonymous_and_sessionless
    def invocation_jobs_summary(self, trans, invocation_id, **kwd):
        """
        * GET /api/workflows/{workflow_id}/invocations/{invocation_id}/jobs_summary
          GET /api/invocations/{invocation_id}/jobs_summary
            return job state summary info aggregated across all current jobs of workflow invocation

        Warning: We allow anyone to fetch job state information about any object they
        can guess an encoded ID for - it isn't considered protected data. This keeps
        polling IDs as part of state calculation for large histories and collections as
        efficient as possible.

        :param  invocation_id:    the invocation id (required)
        :type   invocation_id:    str

        :rtype:     dict
        :returns:   a job summary object merged for all steps in workflow invocation
        """
        ids = [self.decode_id(invocation_id)]
        types = ["WorkflowInvocation"]
        return [self.encode_all_ids(trans, s) for s in fetch_job_states(trans.sa_session, ids, types)][0]

    @expose_api
    def update_invocation_step(self, trans, invocation_id, step_id, payload, **kwd):
        """
        PUT /api/workflows/{workflow_id}/invocations/{invocation_id}/steps/{step_id}
        PUT /api/invocations/{invocation_id}/steps/{step_id}

        Update state of running workflow step invocation - still very nebulous
        but this would be for stuff like confirming paused steps can proceed
        etc....

        :param  invocation_id:      the usage id (required)
        :type   invocation_id:      str

        :param  step_id:      encoded id of the WorkflowInvocationStep (required)
        :type   step_id:      str

        :raises: exceptions.MessageException, exceptions.ObjectNotFound
        """
        decoded_invocation_step_id = self.decode_id(step_id)
        action = payload.get("action", None)

        invocation_step = self.workflow_manager.update_invocation_step(
            trans,
            decoded_invocation_step_id,
            action=action,
        )
        return self.__encode_invocation_step(trans, invocation_step)

    def __encode_invocation_step(self, trans, invocation_step):
        return self.encode_all_ids(
            trans,
            invocation_step.to_dict('element'),
            True
        )

    def __get_stored_accessible_workflow(self, trans, workflow_id, **kwd):
        instance = util.string_as_bool(kwd.get("instance", "false"))
        return self.workflow_manager.get_stored_accessible_workflow(trans, workflow_id, by_stored_id=not instance)

    def __get_stored_workflow(self, trans, workflow_id, **kwd):
        instance = util.string_as_bool(kwd.get("instance", "false"))
        return self.workflow_manager.get_stored_workflow(trans, workflow_id, by_stored_id=not instance)

    def __encode_invocation(self, invocation, **kwd):
        return self.workflow_manager.serialize_workflow_invocation(invocation, **kwd)