app.js

/*
 * Code specific to IslandCompare app
 * Contains functions for initialising state and populating ORM
 */
let stateFetched = false; // Prevent fetching more than once
let historyFetched = false; // Prevent fetching more than once
export let invocationsFetched = false;

import { api as galaxy } from 'galaxy-client'
import {workflow_tag, application_tag, workflow_owner} from "./app.config";
import {getOrCreateUUID, getAPIKey, setGlobalKey} from "./auth";

// Fetch all required state from api
export async function fetchState(createUUID = false) {
    if (stateFetched) return;  //Only fetch once across entire application for lifetime of window
    stateFetched = true;
    let key = '';
    if (createUUID) key= await getOrCreateUUID();
    else key = await getAPIKey();
    setGlobalKey(key);
    if (!key) {
        stateFetched = false;
        throw "No api key";
    }

    await galaxy.histories.History.fetch();
    await galaxy.workflows.StoredWorkflow.fetch({params: {show_published: true}});

    // Workflow inputs are not loaded in fetch, load them.
    const workflow = getConfiguredWorkflow();
    if (!workflow) throw("Failed to load workflow");
    if (Object.keys(workflow.inputs).length === 0) {
        workflow.reload(); //Get input details
    }

    // Fetch workflow invocations for histories that are not deleted
    const histories = galaxy.histories.History.query().where('deleted', false).where('tags', tags => tags.includes(application_tag) || tags.includes(workflow.id)).get();
    //Promise.all(histories.map(h=>galaxy.workflows.WorkflowInvocation.fetch({params: {view: "element", step_details: true, history_id: h.id}}))).then(() => invocationsFetched = true);
    Promise.all([workflow.fetch_invocations(histories),
        // Try to recover workflow id from history tags for jobs of an older workflow
        // Query must be done on workflow id as subworkflows will pollute the fetched invocations.
        // Queries for all invocations associated with a history is also very very slow.
        ...[...new Set(histories.map(h=>h.tags.find(t=>t !== application_tag && t !== workflow.id && t.length === 16)).filter(t=>t))].map(workflow_id=>{
        const w = new galaxy.workflows.StoredWorkflow();
        w.id = workflow_id;
        const hist = histories.filter(h=>h.tags.includes(workflow_id));
        return w.fetch_invocations(hist);
    })]).then(() => invocationsFetched = true);
}

export function makeUploadHistory(history) {
    history.name = "Unnamed project";
    history.tags.push('user_data');
    history.put(['name', 'tags']); // TODO https://github.com/galaxyproject/galaxy/issues/11679
    return history;
}

export async function fetchStateAndUploadHistories(createUUID = false) {
    await fetchState(createUUID);

    // Load or create the user_data histories and all its datasets
    let histories = getUploadHistories();
    if (!histories || histories.length === 0) {
        historyFetched = true;
        histories = [makeUploadHistory(await galaxy.histories.History.post())];
    } else if (histories && !historyFetched) {
        historyFetched = true;
        histories.forEach(h=>h.loadContents());
    }
    return histories;
}

export function getConfiguredWorkflow() {
    // Look for workflow with owner but fail back to any owner
    return galaxy.workflows.StoredWorkflow.query().where('owner', workflow_owner).where('tags', tags=>tags.includes(workflow_tag)).with('inputs|steps').first() ||
        galaxy.workflows.StoredWorkflow.query().where('tags', tags=>tags.includes(workflow_tag)).with('inputs|steps').first();
}

export function getInvocations(workflow) {
    return galaxy.workflows.WorkflowInvocation.query().whereHas('history', q => {
        q.where('deleted', false)
            .where('tags', tags=>tags.includes(application_tag) || tags.includes(workflow.id))
    }).with('history|workflow|steps.jobs').get();
}

export function getUploadHistories() {
    const histories = galaxy.histories.History.query().where('deleted', false).where('tags', tags=>tags.includes('user_data')).with('datasets.history').get();
    histories.sort((a,b)=>new Date(b.update_time)-new Date(a.update_time));
    return histories;
}

export async function onInvocation(invocation) {
    invocation = await invocation;
    const history = galaxy.histories.History.find(invocation.history_id);
    history.tags.push(application_tag);
    history.put(['tags']);
}