import { RUN_PROCESS_BASIC_FORM, RunProcessBasicFormData } from "views/run-process-panel/run-process-basic-form";
import { RunProcessAdvancedFormData, RUN_PROCESS_ADVANCED_FORM } from "views/run-process-panel/run-process-advanced-form";
import { MOUNT_PATH_CWL_WORKFLOW, MOUNT_PATH_CWL_INPUT } from 'models/process';
-import { getWorkflow, getWorkflowInputs } from "models/workflow";
+import { CommandInputParameter, getWorkflow, getWorkflowInputs, getWorkflowOutputs } from "models/workflow";
import { ProjectResource } from "models/project";
import { UserResource } from "models/user";
+import { CommandOutputParameter } from "cwlts/mappings/v1.0/CommandOutputParameter";
export const loadProcess = (containerRequestUuid: string) =>
async (dispatch: Dispatch, getState: () => RootState, services: ServiceRepository): Promise<Process> => {
const containerRequest = await services.containerRequestService.get(containerRequestUuid);
dispatch<any>(updateResources([containerRequest]));
+ if (containerRequest.outputUuid) {
+ const collection = await services.collectionService.get(containerRequest.outputUuid);
+ dispatch<any>(updateResources([collection]));
+ }
+
if (containerRequest.containerUuid) {
const container = await services.containerService.get(containerRequest.containerUuid);
dispatch<any>(updateResources([container]));
}
};
-const getInputs = (data: any) => {
+/*
+ * Fetches raw inputs from containerRequest mounts with fallback to properties
+ */
+export const getRawInputs = (data: any): CommandInputParameter[] | undefined => {
+ if (!data) { return undefined; }
+ const mountInput = data.mounts?.[MOUNT_PATH_CWL_INPUT]?.content;
+ const propsInput = data.properties?.cwl_input;
+ if (!mountInput && !propsInput) { return undefined; }
+ return (mountInput || propsInput);
+}
+
+export const getInputs = (data: any): CommandInputParameter[] => {
if (!data || !data.mounts || !data.mounts[MOUNT_PATH_CWL_WORKFLOW]) { return []; }
+ const content = getRawInputs(data) as any;
+ if (!content) { return []; }
+
const inputs = getWorkflowInputs(data.mounts[MOUNT_PATH_CWL_WORKFLOW].content);
return inputs ? inputs.map(
(it: any) => (
type: it.type,
id: it.id,
label: it.label,
- default: data.mounts[MOUNT_PATH_CWL_INPUT].content[it.id],
+ default: content[it.id],
+ value: content[it.id.split('/').pop()] || [],
+ doc: it.doc
+ }
+ )
+ ) : [];
+};
+
+/*
+ * Fetches raw outputs from containerRequest properties
+ */
+export const getRawOutputs = (data: any): CommandInputParameter[] | undefined => {
+ if (!data || !data.properties || !data.properties.cwl_output) { return undefined; }
+ return (data.properties.cwl_output);
+}
+
+export type InputCollectionMount = {
+ path: string;
+ pdh: string;
+}
+
+export const getInputCollectionMounts = (data: any): InputCollectionMount[] => {
+ if (!data || !data.mounts) { return []; }
+ return Object.keys(data.mounts)
+ .map(key => ({
+ ...data.mounts[key],
+ path: key,
+ }))
+ .filter(mount => mount.kind === 'collection' &&
+ mount.portable_data_hash &&
+ mount.path)
+ .map(mount => ({
+ path: mount.path,
+ pdh: mount.portable_data_hash,
+ }));
+};
+
+export const getOutputParameters = (data: any): CommandOutputParameter[] => {
+ if (!data || !data.mounts || !data.mounts[MOUNT_PATH_CWL_WORKFLOW]) { return []; }
+ const outputs = getWorkflowOutputs(data.mounts[MOUNT_PATH_CWL_WORKFLOW].content);
+ return outputs ? outputs.map(
+ (it: any) => (
+ {
+ type: it.type,
+ id: it.id,
+ label: it.label,
doc: it.doc
}
)