From c5e0387f02ebde8b2531fd42a5891614d0200d8f Mon Sep 17 00:00:00 2001 From: Anibal Date: Wed, 27 Sep 2023 11:51:52 -0500 Subject: [PATCH 01/10] fix: bunch of stuff, will detail on the PR description --- .dockerignore | 7 +- .env.dev | 6 + .gitignore | 1 + .stignore | 2 - Dockerfile | 9 - README.md | 16 +- api/.dockerignore | 1 + api/Dockerfile | 17 + api/config.js | 13 - api/config.js.map | 1 - api/controllers.js | 236 - api/controllers.js.map | 1 - api/controllers.ts | 50 +- api/dev.sh | 4 - api/ezbids.js | 58 - api/ezbids.js.map | 1 - api/ezbids.ts | 45 +- api/models.js.map | 1 - api/models.ts | 16 +- api/package-lock.json | 6422 ++++++++++++++++++++++++++++ package.json => api/package.json | 14 +- api/start.sh | 11 - api/tsconfig.json | 4 +- dev.sh | 8 +- docker-compose.yml | 55 +- handler/.dockerignore | 1 + handler/Dockerfile | 41 +- handler/convert.js | 419 -- handler/convert.js.map | 1 - handler/convert.ts | 449 -- handler/handler.js | 217 - handler/handler.js.map | 1 - handler/handler.ts | 7 +- api/models.js => handler/models.ts | 78 +- handler/package-lock.json | 3965 +++++++++++++++++ handler/package.json | 22 + handler/tsconfig.json | 3 +- package-lock.json | 3117 -------------- test/run.sh | 3 - ui/Dockerfile | 4 +- ui/package-lock.json | 345 +- ui/package.json | 58 +- 42 files changed, 10944 insertions(+), 4786 deletions(-) create mode 100644 .env.dev delete mode 100644 .stignore delete mode 100644 Dockerfile create mode 100644 api/.dockerignore create mode 100644 api/Dockerfile delete mode 100644 api/config.js delete mode 100644 api/config.js.map delete mode 100644 api/controllers.js delete mode 100644 api/controllers.js.map delete mode 100755 api/dev.sh delete mode 100644 api/ezbids.js delete mode 100644 api/ezbids.js.map delete mode 100644 api/models.js.map create mode 100644 api/package-lock.json rename package.json => api/package.json (61%) delete mode 100755 api/start.sh create mode 100644 handler/.dockerignore delete mode 100755 handler/convert.js delete mode 100644 handler/convert.js.map delete mode 100755 handler/convert.ts delete mode 100644 handler/handler.js delete mode 100644 handler/handler.js.map rename api/models.js => handler/models.ts (60%) create mode 100644 handler/package-lock.json create mode 100644 handler/package.json delete mode 100644 package-lock.json delete mode 100644 test/run.sh diff --git a/.dockerignore b/.dockerignore index 2eb7c9f9..6482b7f7 100644 --- a/.dockerignore +++ b/.dockerignore @@ -1,5 +1,2 @@ -ui -handler -workdir -test -bids-specification +node_modules +volumes \ No newline at end of file diff --git a/.env.dev b/.env.dev new file mode 100644 index 00000000..250383fc --- /dev/null +++ b/.env.dev @@ -0,0 +1,6 @@ +MONGO_URL=mongodb://mongodb:27017/ezbids +MONGOOSE_DEBUG=true +UPLOAD_DIR=/app/volumes/upload +WORK_DIR=/app/volumes/ezbids-workdir +HOST=0.0.0.0 +PORT=8082 \ No newline at end of file diff --git a/.gitignore b/.gitignore index 297f5805..89a5570b 100644 --- a/.gitignore +++ b/.gitignore @@ -1,5 +1,6 @@ .DS_Store node_modules +volumes # local env files .env.local diff --git a/.stignore b/.stignore deleted file mode 100644 index 8257f570..00000000 --- a/.stignore +++ /dev/null @@ -1,2 +0,0 @@ -testdata -testdata/* diff --git a/Dockerfile b/Dockerfile deleted file mode 100644 index 42a875fc..00000000 --- a/Dockerfile +++ /dev/null @@ -1,9 +0,0 @@ -FROM node:16 - -COPY . /app - -WORKDIR /app -RUN npm install -g pm2 typescript - -RUN npm install - diff --git a/README.md b/README.md index 9861dae1..27d9a440 100644 --- a/README.md +++ b/README.md @@ -98,19 +98,11 @@ brainlife.io is publicly funded and for the sustainability of the project it is ### Citations We ask that you the following articles when publishing papers that used data, code or other resources created by the brainlife.io community. -1. Levias, D. et al. **In review** - -### This repo was bootstrapped by - -``` -npm init vite@latest ui2 -- --template vue-ts -``` +1. Levitas, D. et al. **In review** ### Development Environment -A local development instance of ezBIDS can be launched by first git cloning this repo, then running `./dev.sh` on a docker enabled machine. When everything is built/running, you should be able to reach the dev instance at http://localhost:3000/ - - - -Copyright © 2022 brainlife.io at University of Texas at Austin +A local development instance of ezBIDS can be launched by first git cloning this repo, then running `./dev.sh` on a docker enabled machine. +When everything is built/running, you should be able to reach the dev instance at http://localhost:3000/ +Copyright © 2022 brainlife.io at University of Texas at Austin \ No newline at end of file diff --git a/api/.dockerignore b/api/.dockerignore new file mode 100644 index 00000000..b512c09d --- /dev/null +++ b/api/.dockerignore @@ -0,0 +1 @@ +node_modules \ No newline at end of file diff --git a/api/Dockerfile b/api/Dockerfile new file mode 100644 index 00000000..3b4c355f --- /dev/null +++ b/api/Dockerfile @@ -0,0 +1,17 @@ +FROM node:16 + +ARG USER=docker +ARG UID +ARG GID + +RUN groupadd -g "${GID}" ${USER} || true +RUN useradd --create-home --no-log-init -u "${UID}" -g "${GID}" ${USER} || true + +COPY . /app +RUN chown -R ${UID}:${GID} /app +WORKDIR /app/api +RUN npm install + +USER ${UID}:${GID} + +CMD [ "npm", "run", "dev" ] diff --git a/api/config.js b/api/config.js deleted file mode 100644 index 9b8b468c..00000000 --- a/api/config.js +++ /dev/null @@ -1,13 +0,0 @@ -'use strict'; -exports.mongodb = "mongodb://mongodb:27017/ezbids"; -exports.mongoose_debug = true; -//multer incoming upload directory -exports.multer = { - dest: "/tmp/upload", -} -//directory to copy uploaded files (it needs to be on the same filesystem as multer incoming dir) -exports.workdir = "/tmp/ezbids-workdir", -exports.express = { - host: "0.0.0.0", - port: 8082, -} \ No newline at end of file diff --git a/api/config.js.map b/api/config.js.map deleted file mode 100644 index 9c9f9877..00000000 --- a/api/config.js.map +++ /dev/null @@ -1 +0,0 @@ -{"version":3,"file":"config.js","sourceRoot":"","sources":["config.ts"],"names":[],"mappings":"AAAA,YAAY,CAAC;AAEb,OAAO,CAAC,OAAO,GAAG,kCAAkC,CAAC;AACrD,OAAO,CAAC,cAAc,GAAG,IAAI,CAAC;AAE9B,kCAAkC;AAClC,OAAO,CAAC,MAAM,GAAG;IACb,IAAI,EAAE,wBAAwB;CACjC,CAAA;AACD,iGAAiG;AACjG,OAAO,CAAC,OAAO,GAAG,4BAA4B;IAE9C,OAAO,CAAC,OAAO,GAAG;QACd,IAAI,EAAE,WAAW;QACjB,IAAI,EAAE,KAAK;KACd,CAAA"} \ No newline at end of file diff --git a/api/controllers.js b/api/controllers.js deleted file mode 100644 index c7484dfc..00000000 --- a/api/controllers.js +++ /dev/null @@ -1,236 +0,0 @@ -"use strict"; -var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) { - function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); } - return new (P || (P = Promise))(function (resolve, reject) { - function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } } - function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } } - function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); } - step((generator = generator.apply(thisArg, _arguments || [])).next()); - }); -}; -Object.defineProperty(exports, "__esModule", { value: true }); -const express = require("express"); -const multer = require("multer"); -const path = require("path"); -const fs = require("fs"); -const mkdirp = require("mkdirp"); -const archiver = require("archiver"); -const async = require("async"); -const config = require("./config"); -const models = require("./models"); -console.debug(config.multer); -const upload = multer(config.multer); -const router = express.Router(); -router.get('/health', (req, res, next) => { - let status = "ok"; - let message = ""; - //check to see if we can access the workdir - try { - fs.writeFileSync(config.workdir + '/health.txt', "test"); - } - catch (err) { - status = "failed"; - message = err; - } - res.json({ status, message, date: new Date() }); -}); -router.post('/session', (req, res, next) => { - req.body.status = "created"; - req.body.request_headers = req.headers; - let session = new models.Session(req.body); - session.save().then(_session => { - res.json(_session); - }).catch(err => { - next(err); - }); -}); -router.get('/session/:session_id', (req, res, next) => { - models.Session.findById(req.params.session_id).then(session => { - res.json(session); - }).catch(err => { - next(err); - }); -}); -router.post('/session/:session_id/deface', (req, res, next) => { - models.Session.findById(req.params.session_id).then(session => { - if (!session) - return next("no such session"); - fs.writeFile(config.workdir + "/" + session._id + "/deface.json", JSON.stringify(req.body), err => { - session.status = "deface"; - session.status_msg = "Waiting to be defaced"; - session.save().then(() => { - res.send("ok"); - }); - }); - }); -}); -router.post('/session/:session_id/canceldeface', (req, res, next) => { - models.Session.findById(req.params.session_id).then(session => { - if (!session) - return next("no such session"); - //request deface.cancel by writing out "deface.cancel" file - console.debug("writing .cancel"); - fs.writeFile(config.workdir + "/" + session._id + "/.cancel", "", err => { - if (err) - console.error(err); - session.status_msg = "requested to cancel defacing"; - //handler should set the status when the job is killed so this shouldn't - //be necessary.. but right not kill() doesn't work.. so - session.deface_begin_date = undefined; - session.status = "analyzed"; - session.save().then(() => { - res.send("ok"); - }); - }); - }); -}); -router.post('/session/:session_id/resetdeface', (req, res, next) => { - models.Session.findById(req.params.session_id).then(session => { - if (!session) - return next("no such session"); - try { - const workdir = config.workdir + "/" + session._id; - console.log("removing deface output"); - if (fs.existsSync(workdir + "/deface.finished")) { - fs.unlinkSync(workdir + "/deface.finished"); - } - if (fs.existsSync(workdir + "/deface.failed")) { - fs.unlinkSync(workdir + "/deface.failed"); - } - session.status = "analyzed"; - session.status_msg = "reset defacing"; - session.deface_begin_date = undefined; - session.deface_finish_date = undefined; - session.save().then(() => { - res.send("ok"); - }); - } - catch (err) { - console.error(err); - res.send(err); - } - }); -}); -router.post('/session/:session_id/finalize', (req, res, next) => { - models.Session.findById(req.params.session_id).then(session => { - if (!session) - return next("no such session"); - fs.writeFile(config.workdir + "/" + session._id + "/finalized.json", JSON.stringify(req.body), err => { - models.ezBIDS.findOneAndUpdate({ _session_id: req.params.session_id }, { $set: { - //TODO - store this somewhere for book keeping - //updated: req.body, //finalized.json could exceed 16MB - update_date: new Date(), - } }).then(err => { - session.status = "finalized"; - session.status_msg = "Waiting to be finalized"; - session.save().then(() => { - res.send("ok"); - }); - }); - }); - }); -}); -//download finalized(updated) content -router.get('/session/:session_id/updated', (req, res, next) => { - models.ezBIDS.findOne({ _session_id: req.params.session_id }).then(ezbids => { - if (!ezbids) - return next("no such session or ezbids not finalized"); - if (!ezbids.updated) - return next("not yet finalized"); - res.json(ezbids.updated); - }); -}); -//let user download files within session (like the .png image generated by analyzer) -router.get('/download/:session_id/*', (req, res, next) => { - models.Session.findById(req.params.session_id).then(session => { - const basepath = config.workdir + "/" + session._id; - //validate path so it will be inside the basepath - const fullpath = path.resolve(basepath + "/" + req.params[0]); - if (!fullpath.startsWith(basepath)) - return next("invalid path"); - //TODO - if requested path is a file, thenstream - const stats = fs.lstatSync(fullpath); - if (stats.isFile()) { - res.setHeader('Content-disposition', 'attachment; filename=' + path.basename(fullpath)); - fs.createReadStream(fullpath).pipe(res); - } - else if (stats.isDirectory()) { - res.setHeader('Content-disposition', 'attachment; filename=' + path.basename(fullpath) + ".zip"); - const archive = archiver('zip', { - zlib: { level: 0 } - }); - archive.directory(fullpath, 'bids'); - archive.finalize(); - archive.pipe(res); - } - else - next("weird file"); - }).catch(err => { - next(err); - }); -}); -router.post('/upload-multi/:session_id', upload.any(), (req, res, next) => { - //when a single file is uploaded paths becomes just a string. convert it to an array of 1 - let paths = req.body["paths"]; - if (!Array.isArray(paths)) - paths = [paths]; - //same for mtimes - let mtimes = req.body["mtimes"]; - if (!Array.isArray(mtimes)) - mtimes = [mtimes]; - models.Session.findById(req.params.session_id).then((session) => __awaiter(void 0, void 0, void 0, function* () { - let idx = -1; - async.eachSeries(req.files, (file, next_file) => { - idx++; - const src_path = file.path; - /* //file -11|ezbids- | { -11|ezbids- | fieldname: 'files', -11|ezbids- | originalname: 'i1848324.MRDC.82', -11|ezbids- | encoding: '7bit', -11|ezbids- | mimetype: 'application/octet-stream', -11|ezbids- | destination: '/mnt/ezbids/upload', -11|ezbids- | filename: '2d682c5694b0fb8da2beeea3e670350a', -11|ezbids- | path: '/mnt/ezbids/upload/2d682c5694b0fb8da2beeea3e670350a', -11|ezbids- | size: 147882 -11|ezbids- | } - */ - const dirty_path = config.workdir + "/" + req.params.session_id + "/" + paths[idx]; - const dest_path = path.resolve(dirty_path); - const mtime = mtimes[idx] / 1000; //browser uses msec.. filesystem uses sec since epoch - if (!dest_path.startsWith(config.workdir)) - return next_file("invalid path:", dest_path); - const destdir = path.dirname(dest_path); - //move the file over to workdir - const made = mkdirp.sync(destdir); - fs.renameSync(src_path, dest_path); - if (mtime) - fs.utimesSync(dest_path, mtime, mtime); - next_file(); - }, err => { - if (err) - return next(err); - res.send("ok"); - }); - })).catch(err => { - console.error(err); - next(err); - }); -}); -//done uploading. -router.patch('/session/uploaded/:session_id', (req, res, next) => { - models.Session.findByIdAndUpdate(req.params.session_id, { - status: "uploaded", - status_msg: "Waiting in the queue..", - upload_finish_date: new Date() - }).then(session => { - if (!session) - return next("no such session"); - res.send("ok"); - }).catch(err => { - console.error(err); - next(err); - }); -}); -module.exports = router; -//# sourceMappingURL=controllers.js.map \ No newline at end of file diff --git a/api/controllers.js.map b/api/controllers.js.map deleted file mode 100644 index fefd7687..00000000 --- a/api/controllers.js.map +++ /dev/null @@ -1 +0,0 @@ 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\ No newline at end of file diff --git a/api/controllers.ts b/api/controllers.ts index e3ca6198..82f98a3e 100644 --- a/api/controllers.ts +++ b/api/controllers.ts @@ -1,21 +1,19 @@ - -import express = require('express'); -import multer = require('multer'); -import path = require('path'); -import fs = require('fs'); -import mkdirp = require('mkdirp'); -import archiver = require('archiver'); -import async = require('async'); - -import config = require('./config'); -import models = require('./models'); -import { isFunction } from 'util'; -import { fstat } from 'fs'; - -import rangeStream = require('range-stream'); - -console.debug(config.multer); -const upload = multer(config.multer); +import * as express from 'express'; +import multer from 'multer'; +import path from 'path'; +import fs from 'fs'; +import mkdirp from 'mkdirp'; +import archiver from 'archiver'; +import async from 'async'; + +import * as models from './models'; + +const upload = multer({ + dest: process.env.UPLOAD_DIR, +}); +if (!fs.existsSync(process.env.WORK_DIR)) { + fs.mkdirSync(process.env.WORK_DIR); +} const router = express.Router(); @@ -25,7 +23,7 @@ router.get('/health', (req, res, next) => { //check to see if we can access the workdir try { - fs.writeFileSync(config.workdir+'/health.txt', "test") + fs.writeFileSync(process.env.WORK_DIR + '/health.txt', "test") } catch (err) { status = "failed"; message = err; @@ -56,7 +54,7 @@ router.post('/session/:session_id/deface', (req, res, next)=>{ models.Session.findById(req.params.session_id).then(session=>{ if(!session) return next("no such session"); - fs.writeFile(config.workdir+"/"+session._id+"/deface.json", JSON.stringify(req.body), err=>{ + fs.writeFile(process.env.WORK_DIR + "/"+session._id+"/deface.json", JSON.stringify(req.body), err=>{ session.status = "deface"; session.status_msg = "Waiting to be defaced"; session.save().then(()=>{ @@ -72,7 +70,7 @@ router.post('/session/:session_id/canceldeface', (req, res, next)=>{ //request deface.cancel by writing out "deface.cancel" file console.debug("writing .cancel"); - fs.writeFile(config.workdir+"/"+session._id+"/.cancel", "", err=>{ + fs.writeFile(process.env.WORK_DIR + "/"+session._id+"/.cancel", "", err=>{ if(err) console.error(err); session.status_msg = "requested to cancel defacing"; @@ -92,7 +90,7 @@ router.post('/session/:session_id/resetdeface', (req, res, next)=>{ models.Session.findById(req.params.session_id).then(session=>{ if(!session) return next("no such session"); try { - const workdir = config.workdir+"/"+session._id; + const workdir = process.env.WORK_DIR + "/"+session._id; console.log("removing deface output"); if(fs.existsSync(workdir+"/deface.finished")) { fs.unlinkSync(workdir+"/deface.finished"); @@ -117,7 +115,7 @@ router.post('/session/:session_id/resetdeface', (req, res, next)=>{ router.post('/session/:session_id/finalize', (req, res, next)=>{ models.Session.findById(req.params.session_id).then(session=>{ if(!session) return next("no such session"); - fs.writeFile(config.workdir+"/"+session._id+"/finalized.json", JSON.stringify(req.body), err=>{ + fs.writeFile(process.env.WORK_DIR + "/"+session._id+"/finalized.json", JSON.stringify(req.body), err=>{ models.ezBIDS.findOneAndUpdate({_session_id: req.params.session_id}, {$set: { //TODO - store this somewhere for book keeping @@ -147,7 +145,7 @@ router.get('/session/:session_id/updated', (req, res, next)=>{ //let user download files within session (like the .png image generated by analyzer) router.get('/download/:session_id/*', (req, res, next)=>{ models.Session.findById(req.params.session_id).then(session=>{ - const basepath = config.workdir+"/"+session._id; + const basepath = process.env.WORK_DIR + "/"+session._id; //validate path so it will be inside the basepath const fullpath = path.resolve(basepath+"/"+req.params[0]); @@ -199,11 +197,11 @@ router.post('/upload-multi/:session_id', upload.any(), (req:any, res, next)=>{ 11|ezbids- | size: 147882 11|ezbids- | } */ - const dirty_path = config.workdir+"/"+req.params.session_id+"/"+paths[idx]; + const dirty_path = process.env.WORK_DIR + "/"+req.params.session_id+"/"+paths[idx]; const dest_path = path.resolve(dirty_path); const mtime = mtimes[idx]/1000; //browser uses msec.. filesystem uses sec since epoch - if(!dest_path.startsWith(config.workdir)) return next_file("invalid path:", dest_path); + if(!dest_path.startsWith(process.env.WORK_DIR ) ) return next_file("invalid path:", dest_path); const destdir = path.dirname(dest_path); //move the file over to workdir diff --git a/api/dev.sh b/api/dev.sh deleted file mode 100755 index e06d183b..00000000 --- a/api/dev.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -tsc --watch & -pm2 start ezbids.js --attach --watch --ignore-watch="*.log test *.sh ui bin example .git **/*.ts" diff --git a/api/ezbids.js b/api/ezbids.js deleted file mode 100644 index 2f2c6082..00000000 --- a/api/ezbids.js +++ /dev/null @@ -1,58 +0,0 @@ -#!/usr/bin/node -"use strict"; -Object.defineProperty(exports, "__esModule", { value: true }); -const express = require("express"); -const bodyParser = require("body-parser"); -const compression = require("compression"); -const cors = require("cors"); -const nocache = require("nocache"); -const models = require("./models"); -const config = require("./config"); -//import sendSeekable = require('send-seekable'); -//init express -const app = express(); -app.use(cors({ origin: '*' })); -app.use(compression()); -app.use(nocache()); -//app.use(sendSeekable); -app.disable('x-powered-by'); //for better security? -app.use(bodyParser.urlencoded({ - limit: '50gb', - extended: true -})); -app.use(bodyParser.json({ - limit: '50mb', - type: "application/json", -})); -app.use('/', require('./controllers')); -//error handling -//app.use(expressWinston.errorLogger(config.logger.winston)); -app.use(function (err, req, res, next) { - if (typeof err == "string") - err = { message: err }; - if (!err.name || err.name != "UnauthorizedError") { - console.error(err); - } - if (err.stack) - err.stack = "hidden"; //don't sent call stack to UI - for security reason - res.status(err.status || 500); - res.json(err); -}); -process.on('uncaughtException', err => { - //TODO report this to somewhere! - console.error((new Date).toUTCString() + ' uncaughtException:', err.message); - console.error(err.stack); -}); -models.connect(err => { - if (err) - throw err; - var port = process.env.PORT || config.express.port || '8081'; - var host = process.env.HOST || config.express.host || 'localhost'; - var server = app.listen(port, host, function () { - console.log("warehouse api service running on %s:%d in %s mode", host, port, app.settings.env); - }); -}); -//increase timeout for dataset download .. 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\ No newline at end of file diff --git a/api/models.ts b/api/models.ts index d73dbeb4..69d91e6e 100644 --- a/api/models.ts +++ b/api/models.ts @@ -1,12 +1,10 @@ +import mongoose from "mongoose"; -import mongoose = require("mongoose"); -import config = require("./config"); - -if(config.mongoose_debug) mongoose.set("debug", true); +if (process.env.MONGOOSE_DEBUG === 'true') mongoose.set("debug", true); export function connect(cb) { console.debug("connecting to mongo"); - mongoose.connect(config.mongodb, { + mongoose.connect(process.env.MONGO_URL, { /* this really screwed up warehouse db.. readPreference: 'nearest', @@ -35,7 +33,7 @@ export function disconnect(cb) { // upload sessions // -var sessionSchema = mongoose.Schema({ +const sessionSchema = mongoose.Schema({ create_date: { type: Date, default: Date.now }, update_date: { type: Date, default: Date.now }, @@ -88,9 +86,9 @@ sessionSchema.pre('save', function(next) { this.update_date = Date.now(); next(); }); -export let Session = mongoose.model("Session", sessionSchema); +export const Session = mongoose.model("Session", sessionSchema); -var ezbidsSchema = mongoose.Schema({ +const ezbidsSchema = mongoose.Schema({ _session_id: mongoose.Schema.Types.ObjectId, original: mongoose.Schema.Types.Mixed, @@ -99,6 +97,6 @@ var ezbidsSchema = mongoose.Schema({ create_date: { type: Date, default: Date.now }, update_date: { type: Date }, }); -export let ezBIDS = mongoose.model("ezBIDS", ezbidsSchema); +export const ezBIDS = mongoose.model("ezBIDS", ezbidsSchema); diff --git a/api/package-lock.json b/api/package-lock.json new file mode 100644 index 00000000..1c22e189 --- /dev/null +++ b/api/package-lock.json @@ -0,0 +1,6422 @@ +{ + "name": "ezbids", + "version": "1.0.0", + "lockfileVersion": 2, + "requires": true, + "packages": { + "": { + "name": "ezbids", + "version": "1.0.0", + "license": "MIT", + "dependencies": { + "@types/express": "^4.17.13", + "archiver": "^5.3.0", + "async": "^3.2.3", + "body-parser": "^1.19.2", + 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"^4.0.6", + "lodash.union": "^4.6.0", + "normalize-path": "^3.0.0", + "readable-stream": "^3.6.0" + } + } + } + } + } +} diff --git a/package.json b/api/package.json similarity index 61% rename from package.json rename to api/package.json index 6a44092c..10c9ed92 100644 --- a/package.json +++ b/api/package.json @@ -1,15 +1,10 @@ { "name": "ezbids", - "version": "1.1.0", + "version": "1.0.0", "description": "", - "main": "index.js", "scripts": { - "uidev": "cd ui && lite-server", - "tsc": "tsc", - "dev": "ts-node-dev --respawn --transpileOnly ./api/ezbids.ts", - "prod": "tsc && node ./build/ezbids.js", - "deploy": "ssh -t hayashis@test.brainlife.io \"sudo su - -c 'cd /root/docker/ezbids && ./update.sh'\"", - "deploy-prod": "ssh -t -J hayashis@brainlife.io ubuntu@ezbids \"sudo su - -c 'cd /root/docker/ezbids && ./update.sh'\"" + "dev": "ts-node-dev --respawn --transpile-only ezbids.ts", + "prod": "tsc && node ./build/ezbids.js" }, "author": "", "license": "MIT", @@ -20,6 +15,7 @@ "body-parser": "^1.19.2", "compression": "^1.7.4", "cors": "^2.8.5", + "dotenv": "^16.3.1", "express": "^4.17.3", "express-fileupload": "^1.3.1", "mkdirp": "^1.0.4", @@ -35,6 +31,8 @@ "@types/async": "^3.2.12", "@types/cors": "^2.8.12", "@types/node": "^16.11.26", + "ts-node": "^10.9.1", + "ts-node-dev": "^2.0.0", "typescript": "^4.7.2" } } diff --git a/api/start.sh b/api/start.sh deleted file mode 100755 index 2f9840c1..00000000 --- a/api/start.sh +++ /dev/null @@ -1,11 +0,0 @@ -#!/bin/bash - -# start server components - -pm2 delete ezbids-api -pm2 start ezbids.js --name ezbids-api --watch --ignore-watch="*.log test *.sh ui bin example .git" - -pm2 delete ezbids-tsc -pm2 start tsc.sh --name ezbids-tsc - -pm2 save diff --git a/api/tsconfig.json b/api/tsconfig.json index 930d602e..a634c35f 100644 --- a/api/tsconfig.json +++ b/api/tsconfig.json @@ -3,6 +3,8 @@ "target": "ES6", "alwaysStrict": true, "sourceMap": true, - "module": "CommonJS" + "module": "CommonJS", + "esModuleInterop": true, + "allowSyntheticDefaultImports": true } } diff --git a/dev.sh b/dev.sh index 75c15618..902ecb0f 100755 --- a/dev.sh +++ b/dev.sh @@ -4,11 +4,9 @@ set -ex git submodule update --init --recursive -(cd api && npm install) -(cd ui && npm install) - -mkdir -p /tmp/upload -mkdir -p /tmp/workdir +# export UID=$(id -u) +export UID +export GID=$(id -g) # ok docker compose is now included in docker as an option for docker if [[ $(command -v docker-compose) ]]; then diff --git a/docker-compose.yml b/docker-compose.yml index 2b596c59..8fea2f26 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -13,59 +13,58 @@ services: timeout: 10s retries: 5 ports: - - 27417:27017 #for local debugging + - 27417:27017 api: - build: . - platform: linux/amd64 + build: + context: ./ + dockerfile: ./api/Dockerfile + args: + UID: ${UID} + GID: ${GID} + user: $UID:$GID volumes: - ./api:/app/api - - /tmp:/tmp + - /app/api/node_modules + - .env.dev:/app/.env + - ./volumes:/app/volumes depends_on: mongodb: condition: service_healthy healthcheck: - test: ["CMD", "curl", "-f", "http://localhost:8082/health"] + test: ["CMD", "curl", "-f", "http://localhost:8082/health"] working_dir: /app/api - command: ./dev.sh ports: - - 8082:8082 #localhost runs on local browser to it needs to access api via host port + - 8082:8082 handler: - build: ./handler + build: + context: ./ + dockerfile: ./handler/Dockerfile + args: + UID: ${UID} + GID: ${GID} platform: linux/amd64 volumes: - - .:/app - - /tmp:/tmp + - ./handler:/app/handler + - /app/handler/node_modules + - .env.dev:/app/.env + - ./volumes:/app/volumes depends_on: mongodb: condition: service_healthy tty: - true #turn on color for bids-validator output - command: pm2 start handler.js --attach --watch --ignore-watch "ui **/node_modules" + true # for bids-validator color output ui: build: ./ui platform: linux/amd64 volumes: - - ./ui/src:/ui/src #don't copy node_modules which might be compiled for mac (vite won't work) + - ./ui:/ui + - /ui/node_modules environment: VITE_APIHOST: http://localhost:8082 healthcheck: test: ["CMD", "curl", "-f", "http://localhost:3000"] ports: - - 3000:3000 #vite wants to be exposed on the host for HMR? - -# nginx: -# image: nginx:1.18 -# depends_on: -# api: -# condition: service_healthy -# ui: -# condition: service_healthy -# volumes: -# - ./config/nginx/nginx.conf:/etc/nginx/nginx.conf -# ports: -# - 8082:80 - - + - 3000:3000 diff --git a/handler/.dockerignore b/handler/.dockerignore new file mode 100644 index 00000000..b512c09d --- /dev/null +++ b/handler/.dockerignore @@ -0,0 +1 @@ +node_modules \ No newline at end of file diff --git a/handler/Dockerfile b/handler/Dockerfile index 89f553f1..ba22f7ab 100755 --- a/handler/Dockerfile +++ b/handler/Dockerfile @@ -1,5 +1,9 @@ FROM neurodebian:nd20.04-non-free +ARG USER=docker +ARG UID +ARG GID + SHELL ["/bin/bash", "-c"] ENV DEBIAN_FRONTEND noninteractive @@ -35,25 +39,11 @@ ENV FSLOUTPUTTYPE=NIFTI_GZ # #make sure fslpython is properly installed # RUN which imcp -# # certs have expired for nodesource use the hack below to get around that for install -# #### HACK Warning #### -# # unfortuanetly this seems to work the most reliably -# # see https://github.com/nodesource/distributions/issues/1266#issuecomment-938408547 and -# RUN echo "insecure" > $HOME/.curlrc \ -# && echo "Acquire::https::Verify-Peer false;" >> /etc/apt/apt.conf.d/80ssl-exceptions \ -# && echo "Acquire::https::Verify-Host false;" >> /etc/apt/apt.conf.d/80ssl-exceptions \ -# && curl -fsSL https://deb.nodesource.com/setup_14.x | bash - \ -# && apt install -y nodejs \ -# && rm -f $HOME/.curlrc \ -# && rm -f /etc/apt/apt.conf.d/80ssl-exceptions \ -# && npm --version - +ARG NODE_MAJOR=16 RUN apt-get update \ && apt-get install -y ca-certificates curl gnupg \ && mkdir -p /etc/apt/keyrings \ && curl -fsSL https://deb.nodesource.com/gpgkey/nodesource-repo.gpg.key | gpg --dearmor -o /etc/apt/keyrings/nodesource.gpg - -ARG NODE_MAJOR=16 RUN echo "deb [signed-by=/etc/apt/keyrings/nodesource.gpg] https://deb.nodesource.com/node_$NODE_MAJOR.x nodistro main" | tee /etc/apt/sources.list.d/nodesource.list RUN apt-get update \ @@ -72,8 +62,9 @@ RUN git clone --branch development https://github.com/rordenlab/dcm2niix.git \ RUN cd && git clone https://github.com/bids-standard/bids-specification #install ROBEX -ADD https://www.nitrc.org/frs/download.php/5994/ROBEXv12.linux64.tar.gz//?i_agree=1&download_now=1 / -RUN tar -xzf /ROBEXv12.linux64.tar.gz +RUN mkdir /ROBEX && \ + curl -SL 'https://www.nitrc.org/frs/download.php/5994/ROBEXv12.linux64.tar.gz//?i_agree=1&download_now=1' | \ + tar -xvzC /ROBEX ENV PATH /ROBEX:$PATH ENV NODE_PATH $NVM_DIR/v$NODE_VERSION/lib/node_modules @@ -83,6 +74,18 @@ ENV PATH $NVM_DIR/v$NODE_VERSION/bin:$PATH RUN npm install -g bids-validator@1.11.0 RUN git clone https://github.com/bids-standard/bids-validator -# install source code from local +RUN groupadd -g "${GID}" ${USER} || true +RUN useradd --create-home --no-log-init -u "${UID}" -g "${GID}" ${USER} || true + +COPY . /app +RUN chown -R ${UID}:${GID} /app + +WORKDIR /app/api +RUN npm install + WORKDIR /app/handler -RUN npm -g install pm2 +RUN npm install + +USER ${UID}:${GID} + +CMD [ "npm", "run", "dev" ] diff --git a/handler/convert.js b/handler/convert.js deleted file mode 100755 index 0adaef48..00000000 --- a/handler/convert.js +++ /dev/null @@ -1,419 +0,0 @@ -#!/usr/bin/env node -"use strict"; -const fs = require('fs'); -const mkdirp = require('mkdirp'); -const async = require('async'); -const bidsEntitiesOrdered = require('../ui/src/assets/schema/rules/entities.json'); -//import { IObject, Subject, Session, OrganizedSession } from '../ui/src/store' -const root = process.argv[2]; -if (!root) - throw "please specify root directory"; -const info = JSON.parse(fs.readFileSync(root + "/finalized.json")); -//order the entityMappings correctly, as specified by the BIDS specification -let newEntityOrdering = {}; -Object.values(bidsEntitiesOrdered).forEach(order => { - Object.keys(info.entityMappings).forEach(key => { - if (order == key) { - newEntityOrdering[key] = info.entityMappings[key]; - } - }); -}); -info.entityMappings = newEntityOrdering; -const datasetName = info.datasetDescription.Name; -mkdirp.sync(root + "/bids/" + datasetName); -fs.writeFileSync(root + "/bids/" + datasetName + "/finalized.json", JSON.stringify(info, null, 4)); //copy the finalized.json -fs.writeFileSync(root + "/bids/" + datasetName + "/dataset_description.json", JSON.stringify(info.datasetDescription, null, 4)); -fs.writeFileSync(root + "/bids/" + datasetName + "/.bidsignore", ` -**/excluded -**/*_MP2RAGE.* -*finalized.json -`); -info.readme += ` - -## ezbids - -This dataset was converted to BIDS using ezBIDS (https://brainlife.io/ezbids) - -`; -fs.writeFileSync(root + "/bids/" + datasetName + "/README", info.readme); -fs.writeFileSync(root + "/bids/" + datasetName + "/participants.json", JSON.stringify(info.participantsColumn, null, 4)); -//convert participants.json to tsv -console.log("outputting participants.json/tsv"); -let keys = ["participant_id"]; -for (let key in info.participantsColumn) { - keys.push(key); -} -let tsv = []; -let tsvheader = []; -for (let key of keys) { - tsvheader.push(key); -} -tsv.push(tsvheader); -for (const subject_idx in info.participantInfo) { - const sub = info.subjects[subject_idx]; - let tsvrec = []; - tsvrec.push("sub-" + sub.subject); - for (let key in info.participantsColumn) { - tsvrec.push(info.participantInfo[subject_idx][key] || 'n/a'); - } - tsv.push(tsvrec); -} -let tsvf = fs.openSync(root + "/bids/" + datasetName + "/participants.tsv", "w"); -for (let rec of tsv) { - fs.writeSync(tsvf, rec.join("\t") + "\n"); -} -fs.closeSync(tsvf); -//handle each objects -async.forEachOf(info.objects, (o, idx, next_o) => { - if (o._type == "exclude" || o._exclude) { - o._type = "excluded/obj" + o.idx; - o._entities.description = o._SeriesDescription; //inject series desc to filename - } - let typeTokens = o._type.split("/"); - let modality = typeTokens[0]; //func, dwi, anat, etc.. (or exclude) - let suffix = typeTokens[1]; //t1w, bold, or "objN" for exclude) - //construct basename - let tokens = []; - //for(let k in o._entities) { - for (let k in info.entityMappings) { - const sk = info.entityMappings[k]; - if (o._entities[k]) { - tokens.push(sk + "-" + o._entities[k]); - } - } - if (o._exclude) { - //excluded object doesn't have to be validated, so some of the item might collide.. - //let's prevent it by setting some artificial tag - tokens.push("ezbids-" + idx); - } - const name = tokens.join("_"); - function composePath(derivatives) { - let path = "bids/" + datasetName; - if (derivatives) - path += "/derivatives/" + derivatives; - path += "/sub-" + o._entities.subject; - if (o._entities.session) - path += "/ses-" + o._entities.session; - path += "/" + modality; - return path; - } - function handleItem(item, filename, derivatives = null) { - const path = composePath(derivatives); - mkdirp.sync(root + "/" + path); - //setup directory - let fullpath = root + "/" + path + "/" + name + "_" + filename; - if (item.name == "json") { - //we create sidecar from sidecar object (edited by the user) - item.content = JSON.stringify(item.sidecar, null, 4); - } - if (item.content) { - //if item has content to write, then use it instead of normal file - fs.writeFileSync(fullpath, item.content); - } - else { - //otherwise, assume to be normal files (link from the source) - try { - fs.lstatSync(fullpath); - fs.unlinkSync(fullpath); - } - catch (err) { - //console.log("link doesn't exist yet"); - } - //I need to use hardlink so that when archiver tries to create .zip in download API - //the files will be found. As far as I know, archiver module can't de-reference - //symlinks - fs.linkSync(root + "/" + item.path, fullpath); - } - } - function handlePET() { - o.items.forEach(item => { - let derivatives = null; - switch (item.name) { - case "nii.gz": - handleItem(item, suffix + ".nii.gz", derivatives); - break; - case "json": - handleItem(item, suffix + ".json", derivatives); - break; - default: - console.error("unknown PET item name", item.name); - } - }); - } - function handleAnat() { - /* - - suffixes: - - T1w - - T2w - - T1rho - - T1map - - T2map - - T2star - - FLAIR - - FLASH - - PD - - PDmap - - PDT2 - - inplaneT1 - - inplaneT2 - - angio - */ - //find manufacturer (used by UNIT1 derivatives) - let manufacturer = "UnknownManufacturer"; - o.items.forEach(item => { - if (item.sidecar && item.sidecar.Manufacturer) - manufacturer = item.sidecar.Manufacturer; - }); - o.items.forEach(item => { - let derivatives = null; - if (suffix == "UNIT1") - derivatives = manufacturer; - switch (item.name) { - case "nii.gz": - if (o.defaced && o.defaceSelection == "defaced") { - item.path = item.path + ".defaced.nii.gz"; - console.log("using defaced version of t1w", item.path); - } - handleItem(item, suffix + ".nii.gz", derivatives); - break; - case "json": - //handle B0FieldIdentifier and B0FieldSource if present - if(o.B0FieldIdentifier.length) { - if(o.B0FieldIdentifier.length > 1) { - item.sidecar.B0FieldIdentifier = Object.values(o.B0FieldIdentifier) - }else{ - item.sidecar.B0FieldIdentifier = o.B0FieldIdentifier[0] - } - } - if(o.B0FieldSource.length) { - if(o.B0FieldSource.length > 1) { - item.sidecar.B0FieldSource = Object.values(o.B0FieldSource) - }else{ - item.sidecar.B0FieldSource = o.B0FieldSource[0] - } - } - handleItem(item, suffix + ".json", derivatives); - break; - default: - console.error("unknown anat item name", item.name); - } - }); - } - function handleFunc() { - /* - - suffixes: - - bold - - cbv - - sbref - - */ - if (suffix == "events") { - //we handle events a bit differently.. we need to generate events.tsv from items content - const events = o.items.find(o => !!o.eventsBIDS); - const headers = Object.keys(events.eventsBIDS[0]); //take first index value to see which columns user selected - events.content = headers.join("\t") + "\n"; - events.eventsBIDS.forEach(rec => { - if(rec.stim_file) { - if(!rec.stim_file.startsWith("/stimuli/")) { - rec.stim_file = "/stimuli/" + rec.stim_file - } - } - const row = []; - headers.forEach(key => { - row.push(rec[key]); - }); - events.content += row.join("\t") + "\n"; - }); - //add stuff to sidecar - const sidecar = o.items.find(o => o.name == "json"); - //sidecar.sidecar.TaskName = o._entities.task; - sidecar.sidecar.trial_type = { - LongName: info.events.trialTypes.longName, - Description: info.events.trialTypes.desc, - Levels: info.events.trialTypes.levels, - }; - //now save - handleItem(events, "events.tsv"); - handleItem(sidecar, "events.json"); - } - else { - //normal func stuff.. - o.items.forEach(item => { - switch (item.name) { - case "nii.gz": - handleItem(item, suffix + ".nii.gz"); - break; - case "json": - //handle B0FieldIdentifier and B0FieldSource if present - if(o.B0FieldIdentifier) { - if(o.B0FieldIdentifier.length > 1) { - item.sidecar.B0FieldIdentifier = Object.values(o.B0FieldIdentifier) - }else{ - item.sidecar.B0FieldIdentifier = o.B0FieldIdentifier[0] - } - } - if(o.B0FieldSource) { - if(o.B0FieldSource.length > 1) { - item.sidecar.B0FieldSource = Object.values(o.B0FieldSource) - }else{ - item.sidecar.B0FieldSource = o.B0FieldSource[0] - } - } - item.sidecar.TaskName = o._entities.task; - handleItem(item, suffix + ".json"); - break; - default: - console.error("unknown func item name", item.name); - } - }); - } - } - function handleFmap() { - /* - - suffixes: - - phasediff - - phase1 - - phase2 - - magnitude1 - - magnitude2 - - magnitude - - fieldmap - */ - o.items.forEach(item => { - switch (item.name) { - case "nii.gz": - handleItem(item, suffix + ".nii.gz"); - break; - case "json": - //handle B0FieldIdentifier and B0FieldSource if present - if(o.B0FieldIdentifier.length) { - if(o.B0FieldIdentifier.length > 1) { - item.sidecar.B0FieldIdentifier = Object.values(o.B0FieldIdentifier) - }else{ - item.sidecar.B0FieldIdentifier = o.B0FieldIdentifier[0] - } - } - if(o.B0FieldSource.length) { - if(o.B0FieldSource.length > 1) { - item.sidecar.B0FieldSource = Object.values(o.B0FieldSource) - }else{ - item.sidecar.B0FieldSource = o.B0FieldSource[0] - } - } - //handle IntendedFor - if (o.IntendedFor) { - item.sidecar.IntendedFor = []; - for (let idx of o.IntendedFor) { - const io = info.objects[idx]; - //this should not happen, but ezBIDS_core.json could be corrupted.. - if (!io) { - console.error("can't find object with ", idx); - continue; - } - //if intended object is excluded, skip it - if (io._type == "exclude") continue; - - const iomodality = io._type.split("/")[0]; - const suffix = io._type.split("/")[1]; - //construct a path relative to the subject - let path = ""; - if (io._entities.session) - path += "ses-" + io._entities.session + "/"; - path += iomodality + "/"; - let tokens = []; - //for(let k in io._entities) { - for (let k in info.entityMappings) { - const sk = info.entityMappings[k]; - if (io._entities[k]) - tokens.push(sk + "-" + io._entities[k]); - } - path += tokens.join("_"); - path += "_" + suffix + ".nii.gz"; //TODO - not sure if this is robust enough.. - item.sidecar.IntendedFor.push(path); - } - } - handleItem(item, suffix + ".json"); - break; - default: - console.error("unknown fmap item name", item.name); - } - }); - } - function handleDwi() { - o.items.forEach(item => { - switch (item.name) { - case "nii.gz": - handleItem(item, "dwi.nii.gz"); - break; - case "bvec": - handleItem(item, "dwi.bvec"); - break; - case "bval": - handleItem(item, "dwi.bval"); - break; - case "json": - //handle B0FieldIdentifier and B0FieldSource if present - if(o.B0FieldIdentifier.length) { - if(o.B0FieldIdentifier.length > 1) { - item.sidecar.B0FieldIdentifier = Object.values(o.B0FieldIdentifier) - }else{ - item.sidecar.B0FieldIdentifier = o.B0FieldIdentifier[0] - } - } - if(o.B0FieldSource.length) { - if(o.B0FieldSource.length > 1) { - item.sidecar.B0FieldSource = Object.values(o.B0FieldSource) - }else{ - item.sidecar.B0FieldSource = o.B0FieldSource[0] - } - } - handleItem(item, "dwi.json"); - break; - default: - console.error("unknown dwi item name", item.name); - } - }); - if (!o.items.find(item => item.name == "bvec")) { - console.log("bvec is missing.. assuming that this is b0, and setup empty bvec/bval"); - const path = composePath(false); - const zeros = []; - for (let j = 0; j < o.analysisResults.NumVolumes; ++j) { - zeros.push(0); - } - const bvec = `${zeros.join(" ")}\n${zeros.join(" ")}\n${zeros.join(" ")}\n`; - fs.writeFileSync(root + "/" + path + "/" + name + "_dwi.bvec", bvec); - const bval = zeros.join(" ") + "\n"; - fs.writeFileSync(root + "/" + path + "/" + name + "_dwi.bval", bval); - } - } - //now handle different modality - switch (modality) { - case "anat": - handleAnat(); - break; - case "func": - handleFunc(); - break; - case "fmap": - handleFmap(); - break; - case "dwi": - handleDwi(); - break; - case "pet": - handlePET(); - break; - case "excluded": - if (!info.includeExcluded) - break; - o.items.forEach((item, idx) => { - //sub-OpenSciJan22_desc-localizer_obj5-0.json - handleItem(item, "excluded." + item.name); - }); - break; - default: - console.error("unknown datatype:" + o._type); - } - next_o(); -}); -//# sourceMappingURL=convert.js.map \ No newline at end of file diff --git a/handler/convert.js.map b/handler/convert.js.map deleted file mode 100644 index 0c7a7d35..00000000 --- a/handler/convert.js.map +++ /dev/null @@ -1 +0,0 @@ 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\ No newline at end of file diff --git a/handler/convert.ts b/handler/convert.ts deleted file mode 100755 index 6b83d23a..00000000 --- a/handler/convert.ts +++ /dev/null @@ -1,449 +0,0 @@ -#!/usr/bin/env node - -const fs = require('fs'); -const mkdirp = require('mkdirp'); -const async = require('async'); -const bidsEntitiesOrdered = require('../ui/src/assets/schema/rules/entities.json') - -//import { IObject, Subject, Session, OrganizedSession } from '../ui/src/store' - -const root = process.argv[2]; -if(!root) throw "please specify root directory"; - -const info = JSON.parse(fs.readFileSync(root+"/finalized.json")); - -//order the entityMappings correctly, as specified by the BIDS specification -let newEntityOrdering = {}; -Object.values(bidsEntitiesOrdered).forEach(order=>{ - Object.keys(info.entityMappings).forEach(key=>{ - if(order == key) { - newEntityOrdering[key] = info.entityMappings[key] - } - }) -}) -info.entityMappings = newEntityOrdering - -const datasetName = info.datasetDescription.Name; - -mkdirp.sync(root+"/bids/"+datasetName); -fs.writeFileSync(root+"/bids/"+datasetName+"/finalized.json", JSON.stringify(info, null, 4)); //copy the finalized.json -fs.writeFileSync(root+"/bids/"+datasetName+"/dataset_description.json", JSON.stringify(info.datasetDescription, null, 4)); -fs.writeFileSync(root+"/bids/"+datasetName+"/.bidsignore", ` -**/excluded -**/*_MP2RAGE.* -*finalized.json -`); - -info.readme += ` - -## ezbids - -This dataset was converted from DICOM to BIDS using ezBIDS (https://brainlife.io/ezbids) - -`; -fs.writeFileSync(root+"/bids/"+datasetName+"/README", info.readme); -fs.writeFileSync(root+"/bids/"+datasetName+"/participants.json", JSON.stringify(info.participantsColumn, null, 4)); - -//convert participants.json to tsv -console.log("outputting participants.json/tsv"); -let keys = ["participant_id"]; -for(let key in info.participantsColumn) { - keys.push(key); -} -let tsv = []; -let tsvheader = []; -for(let key of keys) { - tsvheader.push(key); -} -tsv.push(tsvheader); - -for(const subject_idx in info.participantInfo) { - const sub = info.subjects[subject_idx]; - let tsvrec = []; - tsvrec.push("sub-"+sub.subject); - for(let key in info.participantsColumn) { - tsvrec.push(info.participantInfo[subject_idx][key]||'n/a'); - } - tsv.push(tsvrec); -} - -let tsvf = fs.openSync(root+"/bids/"+datasetName+"/participants.tsv", "w"); -for(let rec of tsv) { - fs.writeSync(tsvf, rec.join("\t")+"\n"); -} -fs.closeSync(tsvf); - -//handle each objects -async.forEachOf(info.objects, (o, idx, next_o)=>{ - - if(o._type == "exclude" || o._exclude) { - o._type = "excluded/obj"+o.idx; - o._entities.description = o._SeriesDescription; //inject series desc to filename - } - - let typeTokens = o._type.split("/"); - let modality = typeTokens[0]; //func, dwi, anat, etc.. (or exclude) - let suffix = typeTokens[1]; //t1w, bold, or "objN" for exclude) - - //construct basename - let tokens = []; - //for(let k in o._entities) { - for(let k in info.entityMappings) { - const sk = info.entityMappings[k]; - if(o._entities[k]) { - tokens.push(sk+"-"+o._entities[k]); - } - } - - if(o._exclude) { - //excluded object doesn't have to be validated, so some of the item might collide.. - //let's prevent it by setting some artificial tag - tokens.push("ezbids-"+idx); - } - - const name = tokens.join("_"); - - function composePath(derivatives) { - let path = "bids/"+datasetName; - if(derivatives) path += "/derivatives/"+derivatives; - path += "/sub-"+o._entities.subject; - if(o._entities.session) path += "/ses-"+o._entities.session; - path += "/"+modality; - - return path; - } - - function handleItem(item, filename, derivatives = null) { - const path = composePath(derivatives); - mkdirp.sync(root+"/"+path); - - //setup directory - let fullpath = root+"/"+path+"/"+name+"_"+filename; - - if(item.name == "json") { - //we create sidecar from sidecar object (edited by the user) - item.content = JSON.stringify(item.sidecar, null, 4); - } - - if(item.content) { - //if item has content to write, then use it instead of normal file - fs.writeFileSync(fullpath, item.content); - } else{ - //otherwise, assume to be normal files (link from the source) - try { - fs.lstatSync(fullpath); - fs.unlinkSync(fullpath); - } catch (err) { - //console.log("link doesn't exist yet"); - } - - //I need to use hardlink so that when archiver tries to create .zip in download API - //the files will be found. As far as I know, archiver module can't de-reference - //symlinks - fs.linkSync(root+"/"+item.path, fullpath); - } - } - function handlePET() { - o.items.forEach(item => { - let derivatives = null; - switch (item.name) { - case "nii.gz": - handleItem(item, suffix + ".nii.gz", derivatives); - break; - case "json": - handleItem(item, suffix + ".json", derivatives); - break; - default: - console.error("unknown PET item name", item.name); - } - }); - } - function handleAnat() { - /* - - suffixes: - - T1w - - T2w - - T1rho - - T1map - - T2map - - T2star - - FLAIR - - FLASH - - PD - - PDmap - - PDT2 - - inplaneT1 - - inplaneT2 - - angio - */ - - //find manufacturer (used by UNIT1 derivatives) - let manufacturer = "UnknownManufacturer"; - o.items.forEach(item=>{ - if(item.sidecar && item.sidecar.Manufacturer) manufacturer = item.sidecar.Manufacturer; - }); - - o.items.forEach(item=>{ - let derivatives = null; - if(suffix == "UNIT1") derivatives = manufacturer; - - switch(item.name) { - case "nii.gz": - if(o.defaced && o.defaceSelection == "defaced") { - item.path = item.path+".defaced.nii.gz"; - console.log("using defaced version of t1w", item.path); - } - handleItem(item, suffix+".nii.gz", derivatives); - break; - case "json": - //handle B0FieldIdentifier and B0FieldSource if present - if(o.B0FieldIdentifier) { - if(o.B0FieldIdentifier.length > 1) { - item.sidecar.B0FieldIdentifier = Object.values(o.B0FieldIdentifier) - }else{ - item.sidecar.B0FieldIdentifier = o.B0FieldIdentifier[0] - } - } - if(o.B0FieldSource) { - if(o.B0FieldSource.length > 1) { - item.sidecar.B0FieldSource = Object.values(o.B0FieldSource) - }else{ - item.sidecar.B0FieldSource = o.B0FieldSource[0] - } - } - handleItem(item, suffix+".json", derivatives); - break; - default: - console.error("unknown anat item name", item.name); - } - }); - } - - function handleFunc() { - /* - - suffixes: - - bold - - cbv - - sbref - - */ - if(suffix == "events") { - //we handle events a bit differently.. we need to generate events.tsv from items content - const events = o.items.find(o=>!!o.eventsBIDS); - const headers = Object.keys(events.eventsBIDS[0]) //take first index value to see which columns user selected - events.content = headers.join("\t")+"\n"; - events.eventsBIDS.forEach(rec=>{ - if(rec.stim_file) { - if(!rec.stim_file.startsWith("/stimuli/")) { - rec.stim_file = "/stimuli/" + rec.stim_file - } - } - const row = []; - headers.forEach(key=>{ - row.push(rec[key]); - }); - events.content += row.join("\t")+"\n"; - }); - - //add stuff to sidecar - const sidecar = o.items.find(o=>o.name == "json"); - //sidecar.sidecar.TaskName = o._entities.task; - sidecar.sidecar.trial_type = { - LongName: info.events.trialTypes.longName, - Description: info.events.trialTypes.desc, - Levels: info.events.trialTypes.levels, - } - - //now save - handleItem(events, "events.tsv"); - handleItem(sidecar, "events.json"); - } else { - - //normal func stuff.. - o.items.forEach(item=>{ - switch(item.name) { - case "nii.gz": - handleItem(item, suffix+".nii.gz"); - break; - case "json": - //handle B0FieldIdentifier and B0FieldSource if present - if(o.B0FieldIdentifier.length) { - if(o.B0FieldIdentifier.length > 1) { - item.sidecar.B0FieldIdentifier = Object.values(o.B0FieldIdentifier) - }else{ - item.sidecar.B0FieldIdentifier = o.B0FieldIdentifier[0] - } - } - if(o.B0FieldSource.length) { - if(o.B0FieldSource.length > 1) { - item.sidecar.B0FieldSource = Object.values(o.B0FieldSource) - }else{ - item.sidecar.B0FieldSource = o.B0FieldSource[0] - } - } - item.sidecar.TaskName = o._entities.task; - handleItem(item, suffix+".json"); - break; - default: - console.error("unknown func item name", item.name); - } - }); - } - } - - function handleFmap() { - /* - - suffixes: - - phasediff - - phase1 - - phase2 - - magnitude1 - - magnitude2 - - magnitude - - fieldmap - */ - o.items.forEach(item=>{ - switch(item.name) { - case "nii.gz": - handleItem(item, suffix+".nii.gz"); - break; - case "json": - //handle B0FieldIdentifier and B0FieldSource if present - if(o.B0FieldIdentifier.length) { - if(o.B0FieldIdentifier.length > 1) { - item.sidecar.B0FieldIdentifier = Object.values(o.B0FieldIdentifier) - }else{ - item.sidecar.B0FieldIdentifier = o.B0FieldIdentifier[0] - } - } - if(o.B0FieldSource.length) { - if(o.B0FieldSource.length > 1) { - item.sidecar.B0FieldSource = Object.values(o.B0FieldSource) - }else{ - item.sidecar.B0FieldSource = o.B0FieldSource[0] - } - } - //handle IntendedFor - if(o.IntendedFor) { - item.sidecar.IntendedFor = []; - for(let idx of o.IntendedFor) { - const io = info.objects[idx]; - - //this should not happen, but ezBIDS_core.json could be corrupted.. - if(!io) { - console.error("can't find object with ", idx); - continue; - } - - //if intended object is excluded, skip it - if(io._type == "exclude") continue; - - const iomodality = io._type.split("/")[0]; - const suffix = io._type.split("/")[1]; - - //construct a path relative to the subject - let path = ""; - if(io._entities.session) path += "ses-"+io._entities.session+"/"; - path += iomodality+"/"; - let tokens = []; - //for(let k in io._entities) { - for(let k in info.entityMappings) { - const sk = info.entityMappings[k]; - if(io._entities[k]) tokens.push(sk+"-"+io._entities[k]); - } - path += tokens.join("_"); - path += "_"+suffix+".nii.gz"; //TODO - not sure if this is robust enough.. - - item.sidecar.IntendedFor.push(path); - } - } - - handleItem(item, suffix+".json"); - break; - default: - console.error("unknown fmap item name", item.name); - } - }); - } - - function handleDwi() { - o.items.forEach(item=>{ - switch(item.name) { - case "nii.gz": - handleItem(item, "dwi.nii.gz"); - break; - case "bvec": - handleItem(item, "dwi.bvec"); - break; - case "bval": - handleItem(item, "dwi.bval"); - break; - case "json": - //handle B0FieldIdentifier and B0FieldSource if present - if(o.B0FieldIdentifier.length) { - if(o.B0FieldIdentifier.length > 1) { - item.sidecar.B0FieldIdentifier = Object.values(o.B0FieldIdentifier) - }else{ - item.sidecar.B0FieldIdentifier = o.B0FieldIdentifier[0] - } - } - if(o.B0FieldSource.length) { - if(o.B0FieldSource.length > 1) { - item.sidecar.B0FieldSource = Object.values(o.B0FieldSource) - }else{ - item.sidecar.B0FieldSource = o.B0FieldSource[0] - } - } - handleItem(item, "dwi.json"); - break; - default: - console.error("unknown dwi item name", item.name); - } - }); - - if(!o.items.find(item=>item.name == "bvec")) { - console.log("bvec is missing.. assuming that this is b0, and setup empty bvec/bval"); - const path = composePath(false); - const zeros = []; - for(let j = 0;j < o.analysisResults.NumVolumes; ++j) { - zeros.push(0); - } - const bvec = `${zeros.join(" ")}\n${zeros.join(" ")}\n${zeros.join(" ")}\n`; - fs.writeFileSync(root+"/"+path+"/"+name+"_dwi.bvec", bvec); - - const bval = zeros.join(" ")+"\n"; - fs.writeFileSync(root+"/"+path+"/"+name+"_dwi.bval", bval); - } - } - - //now handle different modality - switch(modality) { - case "anat": - handleAnat(); - break; - case "func": - handleFunc(); - break; - case "fmap": - handleFmap(); - break; - case "dwi": - handleDwi(); - break; - case "pet": - handlePET(); - break; - case "excluded": - if(!info.includeExcluded) break; - o.items.forEach((item, idx)=>{ - //sub-OpenSciJan22_desc-localizer_obj5-0.json - handleItem(item, "excluded."+item.name); - }); - break; - - default: - console.error("unknown datatype:"+o._type); - } - next_o(); -}); - diff --git a/handler/handler.js b/handler/handler.js deleted file mode 100644 index 4934d47b..00000000 --- a/handler/handler.js +++ /dev/null @@ -1,217 +0,0 @@ -"use strict"; -var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) { - return new (P || (P = Promise))(function (resolve, reject) { - function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } } - function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } } - function step(result) { result.done ? resolve(result.value) : new P(function (resolve) { resolve(result.value); }).then(fulfilled, rejected); } - step((generator = generator.apply(thisArg, _arguments || [])).next()); - }); -}; -Object.defineProperty(exports, "__esModule", { value: true }); -const { spawn } = require('child_process'); -const fs = require("fs"); -const config = require("../api/config"); -const models = require("../api/models"); -console.log("---------------------------------------"); -console.log(" starting ezbids-handler"); -console.log("---------------------------------------"); -models.connect(err => { - if (err) - throw err; - run(); -}); -function run() { - models.Session.find({ - //TODO- why don't we just look for "uploaded" session? - //upload_finish_date: {$exists: true}, - //pre_begin_date: {$exists: false}, - status: { $in: ["finalized", "uploaded", "deface"] }, - }).then((sessions) => __awaiter(this, void 0, void 0, function* () { - for (let session of sessions) { - try { - switch (session.status) { - case "uploaded": - yield handle_uploaded(session); - break; - case "finalized": - yield handle_finalized(session); - break; - case "deface": - yield handle_deface(session); - break; - } - } - catch (err) { - console.log("caught exception..."); - console.error(err); - } - } - console.log("waiting a bit before looking for more jobs"); - setTimeout(run, 1000 * 3); - })); -} -function handle_uploaded(session) { - return __awaiter(this, void 0, void 0, function* () { - let workdir = config.workdir + "/" + session._id; - session.pre_begin_date = new Date(); - session.pre_end_date = undefined; - session.status = "preprocessing"; - yield handle(session, "./preprocess.sh", "preprocess", cb => { - //monitoring callback - console.log("checking dcm2niix progress--------------------------"); - //load dcm2niix.list/done - let list = null; - if (fs.existsSync(workdir + "/dcm2niix.list")) { - list = fs.readFileSync(workdir + "/dcm2niix.list", "utf8").split("\n"); - session.dicomCount = list.length; - } - let done = null; - if (fs.existsSync(workdir + "/dcm2niix.done")) { - done = fs.readFileSync(workdir + "/dcm2niix.done", "utf8").split("\n"); - session.dicomDone = done.length; - } - cb(); - }, cb => { - //finish callback - fs.readFile(workdir + "/ezBIDS_core.json", "utf8", (err, data) => __awaiter(this, void 0, void 0, function* () { - if (err) - return cb(err); - try { - //try parsing the json! - const json = JSON.parse(data); - const ezbids = new models.ezBIDS({ - _session_id: session._id, - original: JSON.parse(data), - }); - yield ezbids.save(); - session.status = "analyzed"; - session.status_msg = "successfully run preprocess.sh"; - session.pre_finish_date = new Date(); - } - catch (err) { - return cb(err); - } - yield session.save(); - cb(); - })); - }); - }); -} -function handle_finalized(session) { - return __awaiter(this, void 0, void 0, function* () { - console.log("handling finalized request!-----------------------"); - session.finalize_begin_date = new Date(); - session.finalize_end_date = undefined; - session.status = "bidsing"; - yield handle(session, "./bids.sh", "bids", cb => { - //monitor cb - }, cb => { - //finish cb - session.finalize_finish_date = new Date(); - session.status = "finished"; - cb(); - }); - }); -} -function handle_deface(session) { - return __awaiter(this, void 0, void 0, function* () { - console.log("handling deface request!-----------------------"); - session.deface_begin_date = new Date(); - session.deface_end_date = undefined; - session.status = "defacing"; - yield handle(session, "./deface.sh", "deface", cb => { - //monitor cb - nothing special to do yet - cb(); - }, cb => { - //finish cb - session.deface_finish_date = new Date(); - session.status = "defaced"; - cb(); - }); - }); -} -function handle(session, script, name, cb_monitor, cb_finish) { - let workdir = config.workdir + "/" + session._id; - console.log("handling session " + session._id, name); - return new Promise((resolve, reject) => { - session.save().then(() => { - try { - let monitor; - let workdir = config.workdir + "/" + session._id; - const p = spawn(script, [workdir], { cwd: __dirname, detached: true }); - const logout = fs.openSync(workdir + "/" + name + ".log", "w"); - const errout = fs.openSync(workdir + "/" + name + ".err", "w"); - let lasterr = ""; - p.stdout.on('data', data => { - let out = data.toString("utf8").trim(); - console.log(out); - session.status_msg = out.substring(out.length - 1000); - fs.writeSync(logout, data); - }); - p.stderr.on('data', data => { - let out = data.toString("utf8").trim(); - console.log(out); - lasterr = out; - fs.writeSync(errout, data); - }); - p.on('close', code => { - clearInterval(monitor); - console.log("process closed"); - fs.closeSync(logout); - fs.closeSync(errout); - //check status - console.debug(name + " finished: " + code); - if (code != 0) { - session.status = "failed"; - session.status_msg = `failed to run ${name} -- code:${code}\n${lasterr}`; - session.save().then(resolve).catch(reject); - } - else { - session.status_msg = "successfully run " + name; - cb_finish(err => { - if (err) { - session.status = "failed"; - session.status_msg = err; - console.error(err); - } - session.save().then(resolve).catch(reject); - }); - } - }); - //update session periodically - monitor = setInterval(() => { - //handle cancel request - if (fs.existsSync(workdir + "/.cancel")) { - console.log("received .cancel request.. killing process group"); - //p.stdin.pause(); - process.kill(-p.pid); //, 'SIGKILL'); - setTimeout(() => { - //parallel will wait for child process to end unless we seng SIGTERM again - process.kill(-p.pid); //, 'SIGKILL'); - }, 1000); - fs.rename(workdir + "/" + name + ".log", workdir + "/" + name + ".log.canceled", err => { - if (err) - console.error(err); - }); - fs.rename(workdir + "/" + name + ".err", workdir + "/" + name + ".err.canceled", err => { - if (err) - console.error(err); - }); - fs.rename(workdir + "/.cancel", workdir + "/.cancel.ed", err => { - if (err) - console.error(err); - }); - } - cb_monitor(() => { - session.save(); //saves for stdout and any update made by monitor_cb - }); - }, 1000 * 5); - } - catch (err) { - //from spawn? - reject(err); - } - }); - }); -} -//# sourceMappingURL=handler.js.map \ No newline at end of file diff --git a/handler/handler.js.map b/handler/handler.js.map deleted file mode 100644 index 6b205aae..00000000 --- a/handler/handler.js.map +++ /dev/null @@ -1 +0,0 @@ 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\ No newline at end of file diff --git a/handler/handler.ts b/handler/handler.ts index 74475998..1b08d45b 100644 --- a/handler/handler.ts +++ b/handler/handler.ts @@ -1,3 +1,4 @@ +require('dotenv').config({ path:'../.env' }) const { spawn } = require('child_process'); import fs = require('fs'); @@ -45,7 +46,7 @@ function run() { } async function handle_uploaded(session) { - let workdir = config.workdir+"/"+session._id; + let workdir = process.env.WORK_DIR + "/"+session._id; session.pre_begin_date = new Date(); session.pre_end_date = undefined; @@ -127,13 +128,13 @@ async function handle_deface(session) { } function handle(session, script, name, cb_monitor, cb_finish) { - let workdir = config.workdir+"/"+session._id; + let workdir = process.env.WORK_DIR + "/"+session._id; console.log("handling session "+session._id, name); return new Promise((resolve, reject)=>{ session.save().then(()=>{ try { let monitor; - let workdir = config.workdir+"/"+session._id; + let workdir = process.env.WORK_DIR + "/"+session._id; const p = spawn(script, [workdir], {cwd: __dirname, detached: true}); const logout = fs.openSync(workdir+"/"+name+".log", "w"); const errout = fs.openSync(workdir+"/"+name+".err", "w"); diff --git a/api/models.js b/handler/models.ts similarity index 60% rename from api/models.js rename to handler/models.ts index e71bc2cb..69d91e6e 100644 --- a/api/models.js +++ b/handler/models.ts @@ -1,13 +1,11 @@ -"use strict"; -Object.defineProperty(exports, "__esModule", { value: true }); -exports.ezBIDS = exports.Session = exports.disconnect = exports.connect = void 0; -const mongoose = require("mongoose"); -const config = require("./config"); -if (config.mongoose_debug) - mongoose.set("debug", true); -function connect(cb) { +import mongoose from "mongoose"; + +if (process.env.MONGOOSE_DEBUG === 'true') mongoose.set("debug", true); + +export function connect(cb) { console.debug("connecting to mongo"); - mongoose.connect(config.mongodb, { + mongoose.connect(process.env.MONGO_URL, { + /* this really screwed up warehouse db.. readPreference: 'nearest', writeConcern: { @@ -15,72 +13,90 @@ function connect(cb) { }, readConcernLevel: 'majority',//prevents read to grab stale data from secondary */ + useNewUrlParser: true, useUnifiedTopology: true, //auto_reconnect: true, //isn't this the default? - }, err => { - if (err) - return cb(err); + }, err=>{ + if(err) return cb(err); console.log("connected to mongo"); cb(); }); } -exports.connect = connect; -function disconnect(cb) { + +export function disconnect(cb) { mongoose.disconnect(cb); } -exports.disconnect = disconnect; + /////////////////////////////////////////////////////////////////////////////////////////////////// // // upload sessions // -var sessionSchema = mongoose.Schema({ + +const sessionSchema = mongoose.Schema({ + create_date: { type: Date, default: Date.now }, update_date: { type: Date, default: Date.now }, + request_headers: mongoose.Schema.Types.Mixed, - upload_finish_date: Date, - pre_begin_date: Date, - pre_finish_date: Date, - deface_begin_date: Date, - deface_finish_date: Date, - finalize_begin_date: Date, + + upload_finish_date: Date, //when all files are uploaded + + pre_begin_date: Date, //when preprocessing is started + pre_finish_date: Date, //when preprocessing is finished + + deface_begin_date: Date, + deface_finish_date: Date, + + finalize_begin_date: Date, finalize_finish_date: Date, - status: String, + + status: String, //just message to show to the user //created //uploaded (waiting to be preprocessed) //preprocessing //analyzed //finalized //bidsing + //finished //failed + //dcm2niix status dicomCount: Number, dicomDone: Number, + status_msg: String, + /* files: [{ idx: Number, name: String, - size: Number, - path: String, + size: Number, + path: String, _upload: Object, //set when the file is uploaded.. just to store some extra information from multer }], */ + //workdir: String, //directory containing uploaded file structure + //removed: { type: Boolean, default: false }, }); -sessionSchema.pre('save', function (next) { +sessionSchema.pre('save', function(next) { this.update_date = Date.now(); next(); }); -exports.Session = mongoose.model("Session", sessionSchema); -var ezbidsSchema = mongoose.Schema({ - _session_id: mongoose.Schema.Types.ObjectId, +export const Session = mongoose.model("Session", sessionSchema); + +const ezbidsSchema = mongoose.Schema({ + _session_id: mongoose.Schema.Types.ObjectId, + original: mongoose.Schema.Types.Mixed, updated: mongoose.Schema.Types.Mixed, + create_date: { type: Date, default: Date.now }, update_date: { type: Date }, }); -exports.ezBIDS = mongoose.model("ezBIDS", ezbidsSchema); -//# sourceMappingURL=models.js.map \ No newline at end of file +export const ezBIDS = mongoose.model("ezBIDS", ezbidsSchema); + + diff --git a/handler/package-lock.json b/handler/package-lock.json new file mode 100644 index 00000000..823c7f69 --- /dev/null +++ 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b/ui/Dockerfile @@ -1,7 +1,7 @@ FROM node:16 -COPY . /ui -WORKDIR /ui +COPY . /home/node/ui +WORKDIR /home/node/ui RUN npm install diff --git a/ui/package-lock.json b/ui/package-lock.json index e9a503c0..2a896bf6 100644 --- a/ui/package-lock.json +++ b/ui/package-lock.json @@ -35,6 +35,7 @@ "sass": "^1.52.1", "typescript": "^4.7.2", "vite": "^2.9.9", + "vite-plugin-circular-dependency": "^0.2.1", "vue-tsc": "^0.34.17" } }, @@ -152,12 +153,15 @@ "node_modules/@niivue/niivue": { "version": "0.36.0", "resolved": "https://registry.npmjs.org/@niivue/niivue/-/niivue-0.36.0.tgz", - "integrity": "sha512-BhgliEQMR0eNeJvBMa4YM/3KY4ztTzsGbBr/koIfW6ePjNj90iqHcNMjGoiGvCAauN3IcOIXxE408/8s84wf7g==", + "integrity": "sha512-sTjXIThpIZh6+XngGjV6WgRl4FidhLlTya4twZNzChTvKY2GghWOxSja1nC1+5G6IMAQAzHMcFE331/xsRLy3Q==", "dependencies": { + "@ungap/structured-clone": "^1.0.2", + "daikon": "^1.2.43", + "fflate": "^0.7.4", "gl-matrix": "^3.4.3", - "nifti-reader-js": "^0.5.4", - "rxjs": "^7.4.0", - "uuid": 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"3.2.36", "resolved": "https://registry.npmjs.org/vue/-/vue-3.2.36.tgz", @@ -4946,6 +5218,11 @@ } } }, + "xss": { + "version": "0.0.9", + "resolved": "https://registry.npmjs.org/xss/-/xss-0.0.9.tgz", + "integrity": "sha512-jPFdM56EihzKcXeGjFy0kxYigtdB1CWCzS3FVp+HYv5a+BwSHpBe+FQOVgaVN1qQ81h8/W0ICj/4/sVRb8eZWQ==" + }, "y18n": { "version": "4.0.3", "resolved": "https://registry.npmjs.org/y18n/-/y18n-4.0.3.tgz", diff --git a/ui/package.json b/ui/package.json index 4c42e66c..a24352d6 100644 --- a/ui/package.json +++ b/ui/package.json @@ -2,38 +2,38 @@ "name": "ui", "version": "0.2.0", "scripts": { - "dev": "vite --host", - "build": "vite build --base=/ezbids/", - "serve": "vite preview" + "dev": "vite --host", + "build": "vite build --base=/ezbids/", + "serve": "vite preview" }, "dependencies": { - "@element-plus/icons": "0.0.11", - "@fortawesome/fontawesome-svg-core": "^1.3.0", - "@fortawesome/free-brands-svg-icons": "^6.1.1", - "@fortawesome/free-solid-svg-icons": "^6.1.1", - "@fortawesome/vue-fontawesome": "^3.0.0-5", - "@niivue/niivue": "^0.36.0", - "axios": "^0.24", - "element-plus": "^1.2.0-beta.6", - "lint": "^0.7.0", - "numeral": "^2.0.6", - "splitpanes": "^3.1.1", - "unplugin-vue-components": "^0.17.18", - "vue": "^3.2.36", - "vue-gtag-next": "^1.14.0", - "vue-router": "^4.0.14", - "vuex": "^4.0.2" + "@element-plus/icons": "0.0.11", + "@fortawesome/fontawesome-svg-core": "^1.3.0", + "@fortawesome/free-brands-svg-icons": "^6.1.1", + "@fortawesome/free-solid-svg-icons": "^6.1.1", + "@fortawesome/vue-fontawesome": "^3.0.0-5", + "@niivue/niivue": "^0.36.0", + "axios": "^0.24", + "element-plus": "^1.2.0-beta.6", + "lint": "^0.7.0", + "numeral": "^2.0.6", + "splitpanes": "^3.1.1", + "unplugin-vue-components": "^0.17.18", + "vue": "^3.2.36", + "vue-gtag-next": "^1.14.0", + "vue-router": "^4.0.14", + "vuex": "^4.0.2" }, "devDependencies": { - "@types/node": "^16.11.38", - "@types/vue-router": "^2.0.0", - "@vitejs/plugin-vue": "^2.3.3", - "@vue/compiler-sfc": "^3.2.36", - "@vue/shared": "^3.2.36", - "ansi-to-html": "^0.7.2", - "sass": "^1.52.1", - "typescript": "^4.7.2", - "vite": "^2.9.9", - "vue-tsc": "^0.34.17" + "@types/node": "^16.11.38", + "@types/vue-router": "^2.0.0", + "@vitejs/plugin-vue": "^2.3.3", + "@vue/compiler-sfc": "^3.2.36", + "@vue/shared": "^3.2.36", + "ansi-to-html": "^0.7.2", + "sass": "^1.52.1", + "typescript": "^4.7.2", + "vite": "^2.9.9", + "vue-tsc": "^0.34.17" } } From 26bc56dc6105759b81e1908bdc478ae5ecbcc814 Mon Sep 17 00:00:00 2001 From: Anibal Date: Thu, 28 Sep 2023 14:37:03 -0500 Subject: [PATCH 02/10] eh: add proxy to docker compose command --- dev.sh | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/dev.sh b/dev.sh index 902ecb0f..2ec024fe 100755 --- a/dev.sh +++ b/dev.sh @@ -4,6 +4,12 @@ set -ex git submodule update --init --recursive +CMD=$@ +if [ -z "$CMD" ]; +then + CMD="up"; +fi + # export UID=$(id -u) export UID export GID=$(id -g) @@ -11,8 +17,8 @@ export GID=$(id -g) # ok docker compose is now included in docker as an option for docker if [[ $(command -v docker-compose) ]]; then # if the older version is installed use the dash - docker-compose up + docker-compose $CMD else # if the newer version is installed don't use the dash - docker compose up + docker compose $CMD fi From 9c0688e3293f59a782f97b19d218ef3008c28cda Mon Sep 17 00:00:00 2001 From: Anibal Date: Thu, 28 Sep 2023 15:26:16 -0500 Subject: [PATCH 03/10] fix: keep folder before docker generates it --- .gitignore | 3 ++- volumes/.gitkeep | 0 2 files changed, 2 insertions(+), 1 deletion(-) create mode 100644 volumes/.gitkeep diff --git a/.gitignore b/.gitignore index 89a5570b..ca5941c6 100644 --- a/.gitignore +++ b/.gitignore @@ -1,6 +1,7 @@ .DS_Store node_modules -volumes +volumes/* +!volumes/.gitkeep # local env files .env.local diff --git a/volumes/.gitkeep b/volumes/.gitkeep new file mode 100644 index 00000000..e69de29b From 64d546698b0fc2f35ee5c6a23827d3c4cdb4d2d6 Mon Sep 17 00:00:00 2001 From: Anibal Date: Mon, 2 Oct 2023 16:00:28 -0500 Subject: [PATCH 04/10] fix: robex folder path --- handler/Dockerfile | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/handler/Dockerfile b/handler/Dockerfile index ba22f7ab..fad380e5 100755 --- a/handler/Dockerfile +++ b/handler/Dockerfile @@ -62,10 +62,9 @@ RUN git clone --branch development https://github.com/rordenlab/dcm2niix.git \ RUN cd && git clone https://github.com/bids-standard/bids-specification #install ROBEX -RUN mkdir /ROBEX && \ - curl -SL 'https://www.nitrc.org/frs/download.php/5994/ROBEXv12.linux64.tar.gz//?i_agree=1&download_now=1' | \ - tar -xvzC /ROBEX -ENV PATH /ROBEX:$PATH +RUN curl -SL 'https://www.nitrc.org/frs/download.php/5994/ROBEXv12.linux64.tar.gz//?i_agree=1&download_now=1' | \ + tar -xvzC /opt ROBEX +ENV PATH /opt/ROBEX:$PATH ENV NODE_PATH $NVM_DIR/v$NODE_VERSION/lib/node_modules ENV PATH $NVM_DIR/v$NODE_VERSION/bin:$PATH From 7465bf0198d739bee089d89e0c08f24eb41f9900 Mon Sep 17 00:00:00 2001 From: Anibal Date: Tue, 3 Oct 2023 18:50:59 -0500 Subject: [PATCH 05/10] enh: package lock --- api/package-lock.json | 414 +++++++++++++++++++++++++++++++++++++++++- 1 file changed, 413 insertions(+), 1 deletion(-) diff --git a/api/package-lock.json b/api/package-lock.json index 1c22e189..3eb04116 100644 --- a/api/package-lock.json +++ b/api/package-lock.json @@ -25,7 +25,9 @@ "nocache": "^2.1.0", "node-pty": "^0.10.1", "range-stream": "^1.1.0", - "send-seekable": "^1.0.4" + "send-seekable": "^1.0.4", + "swagger-jsdoc": "^6.2.8", + "swagger-ui-express": "^5.0.0" }, "devDependencies": { "@types/async": "^3.2.12", @@ -36,6 +38,46 @@ "typescript": "^4.7.2" } }, + "node_modules/@apidevtools/json-schema-ref-parser": { + "version": "9.1.2", + "resolved": "https://registry.npmjs.org/@apidevtools/json-schema-ref-parser/-/json-schema-ref-parser-9.1.2.tgz", + "integrity": "sha512-r1w81DpR+KyRWd3f+rk6TNqMgedmAxZP5v5KWlXQWlgMUUtyEJch0DKEci1SorPMiSeM8XPl7MZ3miJ60JIpQg==", + "dependencies": { + "@jsdevtools/ono": "^7.1.3", + "@types/json-schema": "^7.0.6", + "call-me-maybe": "^1.0.1", + "js-yaml": "^4.1.0" + } + }, + "node_modules/@apidevtools/openapi-schemas": { + "version": "2.1.0", + "resolved": "https://registry.npmjs.org/@apidevtools/openapi-schemas/-/openapi-schemas-2.1.0.tgz", + "integrity": "sha512-Zc1AlqrJlX3SlpupFGpiLi2EbteyP7fXmUOGup6/DnkRgjP9bgMM/ag+n91rsv0U1Gpz0H3VILA/o3bW7Ua6BQ==", + "engines": { + "node": ">=10" + } + }, + "node_modules/@apidevtools/swagger-methods": { + "version": "3.0.2", + "resolved": "https://registry.npmjs.org/@apidevtools/swagger-methods/-/swagger-methods-3.0.2.tgz", + "integrity": "sha512-QAkD5kK2b1WfjDS/UQn/qQkbwF31uqRjPTrsCs5ZG9BQGAkjwvqGFjjPqAuzac/IYzpPtRzjCP1WrTuAIjMrXg==" + }, + "node_modules/@apidevtools/swagger-parser": { + "version": "10.0.3", + "resolved": "https://registry.npmjs.org/@apidevtools/swagger-parser/-/swagger-parser-10.0.3.tgz", + "integrity": "sha512-sNiLY51vZOmSPFZA5TF35KZ2HbgYklQnTSDnkghamzLb3EkNtcQnrBQEj5AOCxHpTtXpqMCRM1CrmV2rG6nw4g==", + "dependencies": { + "@apidevtools/json-schema-ref-parser": "^9.0.6", + "@apidevtools/openapi-schemas": "^2.0.4", + "@apidevtools/swagger-methods": "^3.0.2", + "@jsdevtools/ono": "^7.1.3", + "call-me-maybe": "^1.0.1", + "z-schema": "^5.0.1" + }, + "peerDependencies": { + "openapi-types": ">=7" + } + }, "node_modules/@aws-crypto/crc32": { "version": "3.0.0", "resolved": "https://registry.npmjs.org/@aws-crypto/crc32/-/crc32-3.0.0.tgz", @@ -704,6 +746,11 @@ "@jridgewell/sourcemap-codec": "^1.4.10" } }, + "node_modules/@jsdevtools/ono": { + "version": "7.1.3", + "resolved": "https://registry.npmjs.org/@jsdevtools/ono/-/ono-7.1.3.tgz", + "integrity": "sha512-4JQNk+3mVzK3xh2rqd6RB4J46qUR19azEHBneZyTZM+c456qOrbbM/5xcR8huNCCcbVt7+UmizG6GuUvPvKUYg==" + }, "node_modules/@mongodb-js/saslprep": { "version": "1.1.0", "resolved": "https://registry.npmjs.org/@mongodb-js/saslprep/-/saslprep-1.1.0.tgz", 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}, "node_modules/array-flatten": { "version": "1.1.1", "resolved": "https://registry.npmjs.org/array-flatten/-/array-flatten-1.1.1.tgz", @@ -1682,6 +1739,11 @@ "url": "https://github.com/sponsors/ljharb" } }, + "node_modules/call-me-maybe": { + "version": "1.0.2", + "resolved": "https://registry.npmjs.org/call-me-maybe/-/call-me-maybe-1.0.2.tgz", + "integrity": "sha512-HpX65o1Hnr9HH25ojC1YGs7HCQLq0GCOibSaWER0eNpgJ/Z1MZv2mTc7+xh6WOPxbRVcmgbv4hGU+uSQ/2xFZQ==" + }, "node_modules/chokidar": { "version": "3.5.3", "resolved": "https://registry.npmjs.org/chokidar/-/chokidar-3.5.3.tgz", @@ -1709,6 +1771,14 @@ "fsevents": "~2.3.2" } }, + "node_modules/commander": { + "version": "6.2.0", + "resolved": "https://registry.npmjs.org/commander/-/commander-6.2.0.tgz", + "integrity": "sha512-zP4jEKbe8SHzKJYQmq8Y9gYjtO/POJLgIdKgV7B9qNmABVFVc+ctqSX6iXh4mCpJfRBOabiZ2YKPg8ciDw6C+Q==", + "engines": { + "node": ">= 6" + } + }, "node_modules/compress-commons": { "version": "4.1.2", "resolved": "https://registry.npmjs.org/compress-commons/-/compress-commons-4.1.2.tgz", @@ -1972,6 +2042,17 @@ "node": ">=0.3.1" } }, + "node_modules/doctrine": { + "version": "3.0.0", + "resolved": "https://registry.npmjs.org/doctrine/-/doctrine-3.0.0.tgz", + "integrity": "sha512-yS+Q5i3hBf7GBkd4KG8a7eBNNWNGLTaEwwYWUijIYM7zrlYDM0BFXHjjPWlWZ1Rg7UaddZeIDmi9jF3HmqiQ2w==", + "dependencies": { + "esutils": "^2.0.2" + }, + "engines": { + "node": ">=6.0.0" + } + }, "node_modules/dotenv": { "version": "16.3.1", "resolved": "https://registry.npmjs.org/dotenv/-/dotenv-16.3.1.tgz", @@ -2018,6 +2099,14 @@ "resolved": "https://registry.npmjs.org/escape-html/-/escape-html-1.0.3.tgz", "integrity": "sha512-NiSupZ4OeuGwr68lGIeym/ksIZMJodUGOSCZ/FSnTxcrekbvqrgdUxlJOMpijaKZVjAJrWrGs/6Jy8OMuyj9ow==" }, + "node_modules/esutils": { + "version": "2.0.3", + "resolved": "https://registry.npmjs.org/esutils/-/esutils-2.0.3.tgz", + "integrity": 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"sha512-wa7YjyUGfNZngI/vtK0UHAN+lgDCxBPCylVXGp0zu59Fz5aiGtNXaq3DhIov063MorB+VfufLh3JlF2KdTK3xg==", "dev": true }, + "validator": { + "version": "13.11.0", + "resolved": "https://registry.npmjs.org/validator/-/validator-13.11.0.tgz", + "integrity": "sha512-Ii+sehpSfZy+At5nPdnyMhx78fEoPDkR2XW/zimHEL3MyGJQOCQ7WeP20jPYRz7ZCpcKLB21NxuXHF3bxjStBQ==" + }, "vary": { "version": "1.1.2", "resolved": "https://registry.npmjs.org/vary/-/vary-1.1.2.tgz", @@ -6383,12 +6771,36 @@ "resolved": "https://registry.npmjs.org/xtend/-/xtend-4.0.2.tgz", "integrity": "sha512-LKYU1iAXJXUgAXn9URjiu+MWhyUXHsvfp7mcuYm9dSUKK0/CjtrUwFAxD82/mCWbtLsGjFIad0wIsod4zrTAEQ==" }, + "yaml": { + "version": "2.0.0-1", + "resolved": "https://registry.npmjs.org/yaml/-/yaml-2.0.0-1.tgz", + "integrity": "sha512-W7h5dEhywMKenDJh2iX/LABkbFnBxasD27oyXWDS/feDsxiw0dD5ncXdYXgkvAsXIY2MpW/ZKkr9IU30DBdMNQ==" + }, "yn": { "version": "3.1.1", "resolved": "https://registry.npmjs.org/yn/-/yn-3.1.1.tgz", "integrity": "sha512-Ux4ygGWsu2c7isFWe8Yu1YluJmqVhxqK2cLXNQA5AcC3QfbGNpM7fu0Y8b/z16pXLnFxZYvWhd3fhBY9DLmC6Q==", "dev": true }, + "z-schema": { + "version": "5.0.5", + "resolved": "https://registry.npmjs.org/z-schema/-/z-schema-5.0.5.tgz", + "integrity": "sha512-D7eujBWkLa3p2sIpJA0d1pr7es+a7m0vFAnZLlCEKq/Ij2k0MLi9Br2UPxoxdYystm5K1yeBGzub0FlYUEWj2Q==", + "requires": { + "commander": "^9.4.1", + "lodash.get": "^4.4.2", + "lodash.isequal": "^4.5.0", + "validator": "^13.7.0" + }, + "dependencies": { + "commander": { + "version": "9.5.0", + "resolved": "https://registry.npmjs.org/commander/-/commander-9.5.0.tgz", + "integrity": "sha512-KRs7WVDKg86PWiuAqhDrAQnTXZKraVcCc6vFdL14qrZ/DcWwuRo7VoiYXalXO7S5GKpqYiVEwCbgFDfxNHKJBQ==", + "optional": true + } + } + }, "zip-stream": { "version": "4.1.1", "resolved": "https://registry.npmjs.org/zip-stream/-/zip-stream-4.1.1.tgz", From fd499fc6b77f71a95a6aedef3917d09e2df8e7dd Mon Sep 17 00:00:00 2001 From: Anibal Date: Tue, 3 Oct 2023 18:52:21 -0500 Subject: [PATCH 06/10] fix: typo --- handler/ezBIDS_core/ezBIDS_core.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/handler/ezBIDS_core/ezBIDS_core.py b/handler/ezBIDS_core/ezBIDS_core.py index 064c8105..853d4851 100755 --- a/handler/ezBIDS_core/ezBIDS_core.py +++ b/handler/ezBIDS_core/ezBIDS_core.py @@ -839,7 +839,7 @@ def generate_dataset_list(uploaded_files_list, exclude_data): def organize_dataset(dataset_list): """ - Organize data files into pseudo subject (and session, if appplicable) groups. + Organize data files into pseudo subject (and session, if applicable) groups. This is particularly necessary when anaonymized data is provided, since crucial metadata including AcquisitionDateTime, PatientName, PatientID, etc are removed. Typically, these fields assist ezBIDS in determining subject (and session) mapping, From 03c8a894058f599f2f1dfc5530cfe042d9cd1691 Mon Sep 17 00:00:00 2001 From: Anibal Date: Tue, 3 Oct 2023 18:53:54 -0500 Subject: [PATCH 07/10] enh: cleanup --- .gitignore | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/.gitignore b/.gitignore index ca5941c6..08f15906 100644 --- a/.gitignore +++ b/.gitignore @@ -6,6 +6,7 @@ volumes/* # local env files .env.local .env.*.local +.env # Log files npm-debug.log* @@ -27,7 +28,3 @@ testdata barn nohup.out tsc.log - -api/config.json - -handler/container/ROBEXv12.linux64.tar.gz From dddabbb2533e8ba1b59637e07ee166fdae3c185c Mon Sep 17 00:00:00 2001 From: Anibal Date: Tue, 3 Oct 2023 20:14:44 -0500 Subject: [PATCH 08/10] fix: enforce home to be from user (?) --- handler/Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/handler/Dockerfile b/handler/Dockerfile index fad380e5..5c68052d 100755 --- a/handler/Dockerfile +++ b/handler/Dockerfile @@ -78,6 +78,7 @@ RUN useradd --create-home --no-log-init -u "${UID}" -g "${GID}" ${USER} || true COPY . /app RUN chown -R ${UID}:${GID} /app +RUN chown -R ${UID}:${GID} ~ WORKDIR /app/api RUN npm install From acb80d535eef3f3ec98f6f8098d6c04e0569d9bf Mon Sep 17 00:00:00 2001 From: Dheeraj Bhatia Date: Wed, 4 Oct 2023 16:36:55 -0500 Subject: [PATCH 09/10] adds types for swagger, points to swagger.ts --- api/ezbids.ts | 6 +++--- api/package-lock.json | 34 ++++++++++++++++++++++++++++++++++ api/package.json | 2 ++ 3 files changed, 39 insertions(+), 3 deletions(-) diff --git a/api/ezbids.ts b/api/ezbids.ts index 3ac861cf..cb5687cc 100644 --- a/api/ezbids.ts +++ b/api/ezbids.ts @@ -10,8 +10,8 @@ import * as models from "./models"; import controllers from "./controllers"; // setup swagger -import swaggerUi = require('swagger-ui-express'); -import swaggerJsdoc = require('swagger-jsdoc'); +import swaggerUi from 'swagger-ui-express'; +import swaggerJsdoc from 'swagger-jsdoc' ; const options = { definition: { @@ -21,7 +21,7 @@ const options = { version: '1.0.0', }, }, - apis: ['./controllers.js'], // files containing annotations as above + apis: ['./controllers.ts'], // files containing annotations as above }; const swaggerSpec = swaggerJsdoc(options); diff --git a/api/package-lock.json b/api/package-lock.json index 3eb04116..f071a790 100644 --- a/api/package-lock.json +++ b/api/package-lock.json @@ -33,6 +33,8 @@ "@types/async": "^3.2.12", "@types/cors": "^2.8.12", "@types/node": "^16.11.26", + "@types/swagger-jsdoc": "^6.0.1", + "@types/swagger-ui-express": "^4.1.4", "ts-node": "^10.9.1", "ts-node-dev": "^2.0.0", "typescript": "^4.7.2" @@ -1423,6 +1425,22 @@ "integrity": "sha512-7NQmHra/JILCd1QqpSzl8+mJRc8ZHz3uDm8YV1Ks9IhK0epEiTw8aIErbvH9PI+6XbqhyIQy3462nEsn7UVzjQ==", "dev": true }, + "node_modules/@types/swagger-jsdoc": { + "version": "6.0.1", + "resolved": "https://registry.npmjs.org/@types/swagger-jsdoc/-/swagger-jsdoc-6.0.1.tgz", + "integrity": "sha512-+MUpcbyxD528dECUBCEVm6abNuORdbuGjbrUdHDeAQ+rkPuo2a+L4N02WJHF3bonSSE6SJ3dUJwF2V6+cHnf0w==", + "dev": true + }, + "node_modules/@types/swagger-ui-express": { + "version": "4.1.4", + "resolved": "https://registry.npmjs.org/@types/swagger-ui-express/-/swagger-ui-express-4.1.4.tgz", + "integrity": "sha512-h6dfIPFveCJKpStDtjrB+4pig4DAf9Uu2Z51RB7Fj3s6AifexmqhZxBoG50K/k3Afz7wyXsIAY5ZIDTlC2VjrQ==", + "dev": true, + "dependencies": { + "@types/express": "*", + "@types/serve-static": "*" + } + }, "node_modules/@types/webidl-conversions": { "version": "7.0.0", "resolved": "https://registry.npmjs.org/@types/webidl-conversions/-/webidl-conversions-7.0.0.tgz", @@ -5029,6 +5047,22 @@ "integrity": "sha512-7NQmHra/JILCd1QqpSzl8+mJRc8ZHz3uDm8YV1Ks9IhK0epEiTw8aIErbvH9PI+6XbqhyIQy3462nEsn7UVzjQ==", "dev": true }, + "@types/swagger-jsdoc": { + "version": "6.0.1", + "resolved": "https://registry.npmjs.org/@types/swagger-jsdoc/-/swagger-jsdoc-6.0.1.tgz", + "integrity": "sha512-+MUpcbyxD528dECUBCEVm6abNuORdbuGjbrUdHDeAQ+rkPuo2a+L4N02WJHF3bonSSE6SJ3dUJwF2V6+cHnf0w==", + "dev": true + }, + "@types/swagger-ui-express": { + "version": "4.1.4", + "resolved": "https://registry.npmjs.org/@types/swagger-ui-express/-/swagger-ui-express-4.1.4.tgz", + "integrity": "sha512-h6dfIPFveCJKpStDtjrB+4pig4DAf9Uu2Z51RB7Fj3s6AifexmqhZxBoG50K/k3Afz7wyXsIAY5ZIDTlC2VjrQ==", + "dev": true, + "requires": { + "@types/express": "*", + "@types/serve-static": "*" + } + }, "@types/webidl-conversions": { "version": "7.0.0", "resolved": "https://registry.npmjs.org/@types/webidl-conversions/-/webidl-conversions-7.0.0.tgz", diff --git a/api/package.json b/api/package.json index 059b922f..aef51b88 100644 --- a/api/package.json +++ b/api/package.json @@ -33,6 +33,8 @@ "@types/async": "^3.2.12", "@types/cors": "^2.8.12", "@types/node": "^16.11.26", + "@types/swagger-jsdoc": "^6.0.1", + "@types/swagger-ui-express": "^4.1.4", "ts-node": "^10.9.1", "ts-node-dev": "^2.0.0", "typescript": "^4.7.2" From 0a40fed637678b3d1adb55309c94e432483a4c4b Mon Sep 17 00:00:00 2001 From: Anibal Date: Mon, 30 Oct 2023 15:47:32 -0500 Subject: [PATCH 10/10] chaos: will prob revert some of these --- .gitignore | 149 +- api/.gitignore | 3 +- api/Dockerfile | 13 +- api/controllers.ts | 12 +- api/ezbids.ts | 13 +- api/package-lock.json | 87 +- api/package.json | 7 +- api/tsconfig.json | 3 +- docker-compose.yml | 5 + handler/.gitignore | 2 + handler/Dockerfile | 12 +- handler/bids.sh | 2 +- handler/convert.js | 446 ++ handler/convert.js.map | 1 + handler/convert.ts | 14 +- handler/handler.js | 218 + handler/handler.js.map | 1 + handler/handler.ts | 7 +- handler/models.ts | 102 - handler/package-lock.json | 73 + handler/package.json | 7 +- handler/tsconfig.json | 20 +- shared/index.ts | 2 + {api => shared}/models.ts | 21 +- shared/schema/index.ts | 1 + shared/schema/objects/entities.json | 210 + shared/schema/objects/entities.json.js | 1 + shared/schema/rules/datatypes/anat.json | 239 ++ shared/schema/rules/datatypes/beh.json | 43 + shared/schema/rules/datatypes/dwi.json | 71 + shared/schema/rules/datatypes/eeg.json | 139 + shared/schema/rules/datatypes/fmap.json | 173 + shared/schema/rules/datatypes/func.json | 99 + shared/schema/rules/datatypes/ieeg.json | 137 + shared/schema/rules/datatypes/meg.json | 209 + shared/schema/rules/datatypes/micr.json | 61 + shared/schema/rules/datatypes/perf.json | 84 + shared/schema/rules/datatypes/pet.json | 86 + shared/schema/rules/entities.js | 1 + shared/schema/rules/entities.json | 30 + shared/schema/rules/entities.json.js | 1 + shared/schema/rules/index.ts | 1 + shared/schema/rules/sidecars/asl.yaml | 201 + .../schema/rules/sidecars/metadata_types.yaml | 3686 +++++++++++++++++ shared/schema/rules/sidecars/pet.yaml | 267 ++ ui/.dockerignore | 2 + ui/.gitignore | 5 +- ui/Dockerfile | 5 +- ui/components.d.ts | 2 + ui/package-lock.json | 35 +- ui/package.json | 3 +- ui/src/store/index.js.map | 1 - ui/src/store/index.ts | 2 - ui/vite.config.ts | 2 +- 54 files changed, 6807 insertions(+), 210 deletions(-) create mode 100644 handler/.gitignore create mode 100644 handler/convert.js create mode 100644 handler/convert.js.map create mode 100644 handler/handler.js create mode 100644 handler/handler.js.map delete mode 100644 handler/models.ts create mode 100644 shared/index.ts rename {api => shared}/models.ts (77%) create mode 100644 shared/schema/index.ts create mode 100644 shared/schema/objects/entities.json create mode 100644 shared/schema/objects/entities.json.js create mode 100644 shared/schema/rules/datatypes/anat.json create mode 100644 shared/schema/rules/datatypes/beh.json create mode 100644 shared/schema/rules/datatypes/dwi.json create mode 100644 shared/schema/rules/datatypes/eeg.json create mode 100644 shared/schema/rules/datatypes/fmap.json create mode 100644 shared/schema/rules/datatypes/func.json create mode 100644 shared/schema/rules/datatypes/ieeg.json create mode 100644 shared/schema/rules/datatypes/meg.json create mode 100644 shared/schema/rules/datatypes/micr.json create mode 100644 shared/schema/rules/datatypes/perf.json create mode 100644 shared/schema/rules/datatypes/pet.json create mode 100644 shared/schema/rules/entities.js create mode 100644 shared/schema/rules/entities.json create mode 100644 shared/schema/rules/entities.json.js create mode 100644 shared/schema/rules/index.ts create mode 100644 shared/schema/rules/sidecars/asl.yaml create mode 100644 shared/schema/rules/sidecars/metadata_types.yaml create mode 100644 shared/schema/rules/sidecars/pet.yaml create mode 100644 ui/.dockerignore delete mode 100644 ui/src/store/index.js.map diff --git a/.gitignore b/.gitignore index 08f15906..ff962215 100644 --- a/.gitignore +++ b/.gitignore @@ -1,30 +1,135 @@ .DS_Store -node_modules + volumes/* !volumes/.gitkeep -# local env files -.env.local -.env.*.local -.env - -# Log files +# Logs +logs +*.log npm-debug.log* yarn-debug.log* yarn-error.log* +lerna-debug.log* +.pnpm-debug.log* + +# Diagnostic reports (https://nodejs.org/api/report.html) +report.[0-9]*.[0-9]*.[0-9]*.[0-9]*.json + +# Runtime data +pids +*.pid +*.seed +*.pid.lock + +# Directory for instrumented libs generated by jscoverage/JSCover +lib-cov + +# Coverage directory used by tools like istanbul +coverage +*.lcov + +# nyc test coverage +.nyc_output + +# Grunt intermediate storage (https://gruntjs.com/creating-plugins#storing-task-files) +.grunt + +# Bower dependency directory (https://bower.io/) +bower_components + +# node-waf configuration +.lock-wscript + +# Compiled binary addons (https://nodejs.org/api/addons.html) +build/Release + +# Dependency directories +node_modules/ +jspm_packages/ + +# Snowpack dependency directory (https://snowpack.dev/) +web_modules/ + +# TypeScript cache +*.tsbuildinfo + +# Optional npm cache directory +.npm + +# Optional eslint cache +.eslintcache + +# Optional stylelint cache +.stylelintcache + +# Microbundle cache +.rpt2_cache/ +.rts2_cache_cjs/ +.rts2_cache_es/ +.rts2_cache_umd/ + +# Optional REPL history +.node_repl_history + +# Output of 'npm pack' +*.tgz + +# Yarn Integrity file +.yarn-integrity + +# dotenv environment variable files +.env +.env.development.local +.env.test.local +.env.production.local +.env.local + +# parcel-bundler cache (https://parceljs.org/) +.cache +.parcel-cache + +# Next.js build output +.next +out + +# Nuxt.js build / generate output +.nuxt +dist + +# Gatsby files +.cache/ +# Comment in the public line in if your project uses Gatsby and not Next.js +# https://nextjs.org/blog/next-9-1#public-directory-support +# public + +# vuepress build output +.vuepress/dist + +# vuepress v2.x temp and cache directory +.temp +.cache + +# Docusaurus cache and generated files +.docusaurus + +# Serverless directories +.serverless/ + +# FuseBox cache +.fusebox/ + +# DynamoDB Local files +.dynamodb/ + +# TernJS port file +.tern-port + +# Stores VSCode versions used for testing VSCode extensions +.vscode-test -# Editor directories and files -.idea -.vscode -*.suo -*.ntvs* -*.njsproj -*.sln -*.sw? -*code-workspace* - -testdata - -barn -nohup.out -tsc.log +# yarn v2 +.yarn/cache +.yarn/unplugged +.yarn/build-state.yml +.yarn/install-state.gz +.pnp.* \ No newline at end of file diff --git a/api/.gitignore b/api/.gitignore index 1bf4259a..b7dab5e9 100644 --- a/api/.gitignore +++ b/api/.gitignore @@ -1 +1,2 @@ -config.js +node_modules +build \ No newline at end of file diff --git a/api/Dockerfile b/api/Dockerfile index 3b4c355f..f875f70d 100644 --- a/api/Dockerfile +++ b/api/Dockerfile @@ -1,4 +1,4 @@ -FROM node:16 +FROM node:16 as base ARG USER=docker ARG UID @@ -8,10 +8,19 @@ RUN groupadd -g "${GID}" ${USER} || true RUN useradd --create-home --no-log-init -u "${UID}" -g "${GID}" ${USER} || true COPY . /app -RUN chown -R ${UID}:${GID} /app + +WORKDIR /app/shared +RUN npm install + WORKDIR /app/api RUN npm install USER ${UID}:${GID} CMD [ "npm", "run", "dev" ] + +FROM base as production + +RUN npm run build + +CMD [ "node", "./build/api/ezbids.js" ] \ No newline at end of file diff --git a/api/controllers.ts b/api/controllers.ts index 455f094a..37bd00e4 100644 --- a/api/controllers.ts +++ b/api/controllers.ts @@ -6,7 +6,7 @@ import mkdirp from 'mkdirp'; import archiver from 'archiver'; import async from 'async'; -import * as models from './models'; +import { models } from 'ezbids-shared'; const upload = multer({ dest: process.env.UPLOAD_DIR, @@ -384,7 +384,7 @@ router.get('/download/:session_id/*', (req, res, next)=>{ }); }); -router.post('/upload-multi/:session_id', upload.any(), (req:any, res, next)=>{ +router.post('/upload-multi/:session_id', upload.any(), (req, res, next)=>{ //when a single file is uploaded paths becomes just a string. convert it to an array of 1 let paths = req.body["paths"]; @@ -395,7 +395,7 @@ router.post('/upload-multi/:session_id', upload.any(), (req:any, res, next)=>{ models.Session.findById(req.params.session_id).then(async session=>{ let idx = -1; - async.eachSeries(req.files, (file, next_file)=>{ + async.eachSeries(req.files as Express.Multer.File[], (file, next_file)=>{ idx++; const src_path = file.path; /* //file @@ -414,7 +414,9 @@ router.post('/upload-multi/:session_id', upload.any(), (req:any, res, next)=>{ const dest_path = path.resolve(dirty_path); const mtime = mtimes[idx]/1000; //browser uses msec.. filesystem uses sec since epoch - if(!dest_path.startsWith(process.env.WORK_DIR ) ) return next_file("invalid path:", dest_path); + if (!dest_path.startsWith(process.env.WORK_DIR)) + return next_file(new Error("invalid path: " + dest_path)); + const destdir = path.dirname(dest_path); //move the file over to workdir @@ -448,4 +450,4 @@ router.patch('/session/uploaded/:session_id', (req, res, next)=>{ }); }); -module.exports = router; \ No newline at end of file +export default router; \ No newline at end of file diff --git a/api/ezbids.ts b/api/ezbids.ts index 3ac861cf..9cf1952a 100644 --- a/api/ezbids.ts +++ b/api/ezbids.ts @@ -6,7 +6,8 @@ import compression from 'compression'; import cors from 'cors'; import nocache from 'nocache'; -import * as models from "./models"; +import { models } from 'ezbids-shared'; + import controllers from "./controllers"; // setup swagger @@ -49,11 +50,11 @@ app.use('/api/docs', swaggerUi.serve, swaggerUi.setup(swaggerSpec)); //error handling //app.use(expressWinston.errorLogger(config.logger.winston)); app.use(function(err, req, res, next) { - if(typeof err == "string") err = { message: err }; - if(!err.name || err.name != "UnauthorizedError") { + if (typeof err === "string") err = { message: err }; + if (!err.name || err.name != "UnauthorizedError") { console.error(err); } - if(err.stack) err.stack = "hidden"; //don't sent call stack to UI - for security reason + if (err.stack) err.stack = "hidden"; //don't sent call stack to UI - for security reason res.status(err.status || 500); res.json(err); }); @@ -64,8 +65,8 @@ process.on('uncaughtException', err=>{ }); models.connect(err=>{ - if(err) throw err; - const port = process.env.PORT || '8081'; + if (err) throw err; + const port = +(process.env.PORT || '8082'); const host = process.env.HOST || 'localhost'; app.listen(port, host, function() { console.log("ezbids api service running on %s:%d in %s mode", host, port, app.settings.env); diff --git a/api/package-lock.json b/api/package-lock.json index 3eb04116..667f18f4 100644 --- a/api/package-lock.json +++ b/api/package-lock.json @@ -9,7 +9,6 @@ "version": "1.0.0", "license": "MIT", "dependencies": { - "@types/express": "^4.17.13", "archiver": "^5.3.0", "async": "^3.2.3", "body-parser": "^1.19.2", @@ -18,6 +17,7 @@ "dotenv": "^16.3.1", "express": "^4.17.3", "express-fileupload": "^1.3.1", + "ezbids-shared": "file:../shared", "mkdirp": "^1.0.4", "mongoose": "^6.2.7", "multer": "^1.4.4", @@ -32,12 +32,21 @@ "devDependencies": { "@types/async": "^3.2.12", "@types/cors": "^2.8.12", + "@types/express": "^4.17.18", + "@types/multer": "^1.4.8", "@types/node": "^16.11.26", "ts-node": "^10.9.1", "ts-node-dev": "^2.0.0", "typescript": "^4.7.2" } }, + "../shared": { + "version": "1.0.0", + "license": "MIT", + "dependencies": { + "yaml": "^2.3.2" + } + }, "node_modules/@apidevtools/json-schema-ref-parser": { "version": "9.1.2", "resolved": "https://registry.npmjs.org/@apidevtools/json-schema-ref-parser/-/json-schema-ref-parser-9.1.2.tgz", @@ -1318,6 +1327,7 @@ "version": "1.19.3", "resolved": "https://registry.npmjs.org/@types/body-parser/-/body-parser-1.19.3.tgz", "integrity": "sha512-oyl4jvAfTGX9Bt6Or4H9ni1Z447/tQuxnZsytsCaExKlmJiU8sFgnIBRzJUpKwB5eWn9HuBYlUlVA74q/yN0eQ==", + "dev": true, "dependencies": { "@types/connect": "*", "@types/node": "*" @@ -1327,6 +1337,7 @@ "version": "3.4.36", "resolved": "https://registry.npmjs.org/@types/connect/-/connect-3.4.36.tgz", "integrity": "sha512-P63Zd/JUGq+PdrM1lv0Wv5SBYeA2+CORvbrXbngriYY0jzLUWfQMQQxOhjONEz/wlHOAxOdY7CY65rgQdTjq2w==", + "dev": true, "dependencies": { "@types/node": "*" } @@ -1341,9 +1352,10 @@ } }, "node_modules/@types/express": { - 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"integrity": "sha512-lPG6KlZs88gef6aD85z3HNkztpj7w2R7HmR3gygjfXCQmsLloWNARFkMuzKiiY8FGdh1XDpgBdrSf4aKDiA7Kg==" + "integrity": "sha512-lPG6KlZs88gef6aD85z3HNkztpj7w2R7HmR3gygjfXCQmsLloWNARFkMuzKiiY8FGdh1XDpgBdrSf4aKDiA7Kg==", + "dev": true }, "@types/json-schema": { "version": "7.0.13", @@ -4981,7 +5018,17 @@ "@types/mime": { "version": "1.3.2", "resolved": "https://registry.npmjs.org/@types/mime/-/mime-1.3.2.tgz", - "integrity": "sha512-YATxVxgRqNH6nHEIsvg6k2Boc1JHI9ZbH5iWFFv/MTkchz3b1ieGDa5T0a9RznNdI0KhVbdbWSN+KWWrQZRxTw==" + "integrity": "sha512-YATxVxgRqNH6nHEIsvg6k2Boc1JHI9ZbH5iWFFv/MTkchz3b1ieGDa5T0a9RznNdI0KhVbdbWSN+KWWrQZRxTw==", + "dev": true + }, + "@types/multer": { + "version": "1.4.8", + "resolved": "https://registry.npmjs.org/@types/multer/-/multer-1.4.8.tgz", + "integrity": "sha512-VMZOW6mnmMMhA5m3fsCdXBwFwC+a+27/8gctNMuQC4f7UtWcF79KAFGoIfKZ4iqrElgWIa3j5vhMJDp0iikQ1g==", + "dev": true, + "requires": { + "@types/express": "*" + } }, "@types/node": { "version": "16.18.53", @@ -4991,17 +5038,20 @@ "@types/qs": { "version": "6.9.8", "resolved": "https://registry.npmjs.org/@types/qs/-/qs-6.9.8.tgz", - "integrity": "sha512-u95svzDlTysU5xecFNTgfFG5RUWu1A9P0VzgpcIiGZA9iraHOdSzcxMxQ55DyeRaGCSxQi7LxXDI4rzq/MYfdg==" + "integrity": "sha512-u95svzDlTysU5xecFNTgfFG5RUWu1A9P0VzgpcIiGZA9iraHOdSzcxMxQ55DyeRaGCSxQi7LxXDI4rzq/MYfdg==", + "dev": true }, "@types/range-parser": { "version": "1.2.4", "resolved": "https://registry.npmjs.org/@types/range-parser/-/range-parser-1.2.4.tgz", - "integrity": "sha512-EEhsLsD6UsDM1yFhAvy0Cjr6VwmpMWqFBCb9w07wVugF7w9nfajxLuVmngTIpgS6svCnm6Vaw+MZhoDCKnOfsw==" + "integrity": "sha512-EEhsLsD6UsDM1yFhAvy0Cjr6VwmpMWqFBCb9w07wVugF7w9nfajxLuVmngTIpgS6svCnm6Vaw+MZhoDCKnOfsw==", + "dev": true }, "@types/send": { "version": "0.17.1", "resolved": "https://registry.npmjs.org/@types/send/-/send-0.17.1.tgz", "integrity": "sha512-Cwo8LE/0rnvX7kIIa3QHCkcuF21c05Ayb0ZfxPiv0W8VRiZiNW/WuRupHKpqqGVGf7SUA44QSOUKaEd9lIrd/Q==", + "dev": true, "requires": { "@types/mime": "^1", "@types/node": "*" @@ -5011,6 +5061,7 @@ "version": "1.15.2", "resolved": "https://registry.npmjs.org/@types/serve-static/-/serve-static-1.15.2.tgz", "integrity": "sha512-J2LqtvFYCzaj8pVYKw8klQXrLLk7TBZmQ4ShlcdkELFKGwGMfevMLneMMRkMgZxotOD9wg497LpC7O8PcvAmfw==", + "dev": true, "requires": { "@types/http-errors": "*", "@types/mime": "*", @@ -5642,6 +5693,12 @@ "busboy": "^1.6.0" } }, + "ezbids-shared": { + "version": "file:../shared", + "requires": { + "yaml": "^2.3.2" + } + }, "fast-xml-parser": { "version": "4.2.5", "resolved": "https://registry.npmjs.org/fast-xml-parser/-/fast-xml-parser-4.2.5.tgz", diff --git a/api/package.json b/api/package.json index 059b922f..9b2cd4ba 100644 --- a/api/package.json +++ b/api/package.json @@ -4,12 +4,12 @@ "description": "", "scripts": { "dev": "ts-node-dev --respawn --transpile-only ezbids.ts", - "prod": "tsc && node ./build/ezbids.js" + "build": "tsc", + "prod": "node ./build/ezbids.js" }, "author": "", "license": "MIT", "dependencies": { - "@types/express": "^4.17.13", "archiver": "^5.3.0", "async": "^3.2.3", "body-parser": "^1.19.2", @@ -18,6 +18,7 @@ "dotenv": "^16.3.1", "express": "^4.17.3", "express-fileupload": "^1.3.1", + "ezbids-shared": "file:../shared", "mkdirp": "^1.0.4", "mongoose": "^6.2.7", "multer": "^1.4.4", @@ -32,6 +33,8 @@ "devDependencies": { "@types/async": "^3.2.12", "@types/cors": "^2.8.12", + "@types/express": "^4.17.18", + "@types/multer": "^1.4.8", "@types/node": "^16.11.26", "ts-node": "^10.9.1", "ts-node-dev": "^2.0.0", diff --git a/api/tsconfig.json b/api/tsconfig.json index a634c35f..08cf5783 100644 --- a/api/tsconfig.json +++ b/api/tsconfig.json @@ -1,10 +1,11 @@ { "compilerOptions": { + "outDir": "build", "target": "ES6", "alwaysStrict": true, "sourceMap": true, "module": "CommonJS", "esModuleInterop": true, - "allowSyntheticDefaultImports": true + "resolveJsonModule": true } } diff --git a/docker-compose.yml b/docker-compose.yml index 8fea2f26..412d79a2 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -19,6 +19,7 @@ services: build: context: ./ dockerfile: ./api/Dockerfile + target: base args: UID: ${UID} GID: ${GID} @@ -26,6 +27,7 @@ services: volumes: - ./api:/app/api - /app/api/node_modules + - ./shared:/app/api/shared - .env.dev:/app/.env - ./volumes:/app/volumes depends_on: @@ -41,6 +43,7 @@ services: build: context: ./ dockerfile: ./handler/Dockerfile + target: base args: UID: ${UID} GID: ${GID} @@ -48,6 +51,7 @@ services: volumes: - ./handler:/app/handler - /app/handler/node_modules + - ./shared:/app/handler/shared - .env.dev:/app/.env - ./volumes:/app/volumes depends_on: @@ -61,6 +65,7 @@ services: platform: linux/amd64 volumes: - ./ui:/ui + - ./shared:/app/ui/shared - /ui/node_modules environment: VITE_APIHOST: http://localhost:8082 diff --git a/handler/.gitignore b/handler/.gitignore new file mode 100644 index 00000000..b7dab5e9 --- /dev/null +++ b/handler/.gitignore @@ -0,0 +1,2 @@ +node_modules +build \ No newline at end of file diff --git a/handler/Dockerfile b/handler/Dockerfile index 5c68052d..71fd8cd9 100755 --- a/handler/Dockerfile +++ b/handler/Dockerfile @@ -1,4 +1,4 @@ -FROM neurodebian:nd20.04-non-free +FROM neurodebian:nd20.04-non-free as base ARG USER=docker ARG UID @@ -80,6 +80,9 @@ COPY . /app RUN chown -R ${UID}:${GID} /app RUN chown -R ${UID}:${GID} ~ +WORKDIR /app/shared +RUN npm install + WORKDIR /app/api RUN npm install @@ -89,3 +92,10 @@ RUN npm install USER ${UID}:${GID} CMD [ "npm", "run", "dev" ] + + +FROM base as production + +RUN npm run build + +CMD [ "node", "./build/handler/handler.js" ] \ No newline at end of file diff --git a/handler/bids.sh b/handler/bids.sh index 189219fc..75add6f2 100755 --- a/handler/bids.sh +++ b/handler/bids.sh @@ -17,7 +17,7 @@ rootDir="$root/bids/$datasetName" rm -rf $root/bids echo "converting output to bids" -./convert.js $root +npm run convert $root echo "output bids directory structure" tree "$rootDir" > $root/tree.log diff --git a/handler/convert.js b/handler/convert.js new file mode 100644 index 00000000..8dc061e3 --- /dev/null +++ b/handler/convert.js @@ -0,0 +1,446 @@ +"use strict"; +Object.defineProperty(exports, "__esModule", { value: true }); +const fs = require("fs"); +const mkdirp_1 = require("mkdirp"); +const async = require("async"); +const ezbids_shared_1 = require("ezbids-shared"); +const { rules: { entities: bidsEntitiesOrdered } } = ezbids_shared_1.schema; +//import { IObject, Subject, Session, OrganizedSession } from '../ui/src/store' +const root = process.argv[2]; +if (!root) + throw "please specify root directory"; +const info = JSON.parse(fs.readFileSync(root + "/finalized.json", "utf8")); +//order the entityMappings correctly, as specified by the BIDS specification +let newEntityOrdering = {}; +Object.values(bidsEntitiesOrdered).forEach(order => { + Object.keys(info.entityMappings).forEach(key => { + if (order == key) { + newEntityOrdering[key] = info.entityMappings[key]; + } + }); +}); +info.entityMappings = newEntityOrdering; +const datasetName = info.datasetDescription.Name; +mkdirp_1.default.sync(root + "/bids/" + datasetName); +fs.writeFileSync(root + "/bids/" + datasetName + "/finalized.json", JSON.stringify(info, null, 4)); //copy the finalized.json +fs.writeFileSync(root + "/bids/" + datasetName + "/dataset_description.json", JSON.stringify(info.datasetDescription, null, 4)); +fs.writeFileSync(root + "/bids/" + datasetName + "/.bidsignore", ` +**/excluded +**/*_MP2RAGE.* +*finalized.json +`); +info.readme += ` + +## ezbids + +This dataset was converted from DICOM to BIDS using ezBIDS (https://brainlife.io/ezbids) + +`; +fs.writeFileSync(root + "/bids/" + datasetName + "/README", info.readme); +fs.writeFileSync(root + "/bids/" + datasetName + "/participants.json", JSON.stringify(info.participantsColumn, null, 4)); +//convert participants.json to tsv +console.log("outputting participants.json/tsv"); +let keys = ["participant_id"]; +for (let key in info.participantsColumn) { + keys.push(key); +} +let tsv = []; +let tsvheader = []; +for (let key of keys) { + tsvheader.push(key); +} +tsv.push(tsvheader); +for (const subject_idx in info.participantInfo) { + const sub = info.subjects[subject_idx]; + let tsvrec = []; + tsvrec.push("sub-" + sub.subject); + for (let key in info.participantsColumn) { + tsvrec.push(info.participantInfo[subject_idx][key] || 'n/a'); + } + tsv.push(tsvrec); +} +let tsvf = fs.openSync(root + "/bids/" + datasetName + "/participants.tsv", "w"); +for (let rec of tsv) { + fs.writeSync(tsvf, rec.join("\t") + "\n"); +} +fs.closeSync(tsvf); +//handle each objects +async.forEachOf(info.objects, (o, idx, next_o) => { + if (o._type == "exclude" || o._exclude) { + o._type = "excluded/obj" + o.idx; + o._entities.description = o._SeriesDescription; //inject series desc to filename + } + let typeTokens = o._type.split("/"); + let modality = typeTokens[0]; //func, dwi, anat, etc.. (or exclude) + let suffix = typeTokens[1]; //t1w, bold, or "objN" for exclude) + //construct basename + let tokens = []; + //for(let k in o._entities) { + for (let k in info.entityMappings) { + const sk = info.entityMappings[k]; + if (o._entities[k]) { + tokens.push(sk + "-" + o._entities[k]); + } + } + if (o._exclude) { + //excluded object doesn't have to be validated, so some of the item might collide.. + //let's prevent it by setting some artificial tag + tokens.push("ezbids-" + idx); + } + const name = tokens.join("_"); + function composePath(derivatives) { + let path = "bids/" + datasetName; + if (derivatives) + path += "/derivatives/" + derivatives; + path += "/sub-" + o._entities.subject; + if (o._entities.session) + path += "/ses-" + o._entities.session; + path += "/" + modality; + return path; + } + function handleItem(item, filename, derivatives = null) { + const path = composePath(derivatives); + mkdirp_1.default.sync(root + "/" + path); + //setup directory + let fullpath = root + "/" + path + "/" + name + "_" + filename; + if (item.name == "json") { + //we create sidecar from sidecar object (edited by the user) + item.content = JSON.stringify(item.sidecar, null, 4); + } + if (item.content) { + //if item has content to write, then use it instead of normal file + fs.writeFileSync(fullpath, item.content); + } + else { + //otherwise, assume to be normal files (link from the source) + try { + fs.lstatSync(fullpath); + fs.unlinkSync(fullpath); + } + catch (err) { + //console.log("link doesn't exist yet"); + } + //I need to use hardlink so that when archiver tries to create .zip in download API + //the files will be found. As far as I know, archiver module can't de-reference + //symlinks + fs.linkSync(root + "/" + item.path, fullpath); + } + } + function handlePET() { + o.items.forEach(item => { + let derivatives = null; + switch (item.name) { + case "nii.gz": + handleItem(item, suffix + ".nii.gz", derivatives); + break; + case "json": + handleItem(item, suffix + ".json", derivatives); + break; + default: + console.error("unknown PET item name", item.name); + } + }); + } + function handlePerf() { + o.items.forEach(item => { + let derivatives = null; + switch (item.name) { + case "nii.gz": + handleItem(item, suffix + ".nii.gz", derivatives); + break; + case "json": + handleItem(item, suffix + ".json", derivatives); + break; + default: + console.error("unknown Perfusion item name", item.name); + } + }); + } + function handleAnat() { + /* + - suffixes: + - T1w + - T2w + - T1rho + - T1map + - T2map + - T2star + - FLAIR + - FLASH + - PD + - PDmap + - PDT2 + - inplaneT1 + - inplaneT2 + - angio + */ + //find manufacturer (used by UNIT1 derivatives) + let manufacturer = "UnknownManufacturer"; + o.items.forEach(item => { + if (item.sidecar && item.sidecar.Manufacturer) + manufacturer = item.sidecar.Manufacturer; + }); + o.items.forEach(item => { + let derivatives = null; + if (suffix == "UNIT1") + derivatives = manufacturer; + switch (item.name) { + case "nii.gz": + if (o.defaced && o.defaceSelection == "defaced") { + item.path = item.path + ".defaced.nii.gz"; + console.log("using defaced version of t1w", item.path); + } + handleItem(item, suffix + ".nii.gz", derivatives); + break; + case "json": + //handle B0FieldIdentifier and B0FieldSource if present + if (o.B0FieldIdentifier) { + if (o.B0FieldIdentifier.length > 1) { + item.sidecar.B0FieldIdentifier = Object.values(o.B0FieldIdentifier); + } + else { + item.sidecar.B0FieldIdentifier = o.B0FieldIdentifier[0]; + } + } + if (o.B0FieldSource) { + if (o.B0FieldSource.length > 1) { + item.sidecar.B0FieldSource = Object.values(o.B0FieldSource); + } + else { + item.sidecar.B0FieldSource = o.B0FieldSource[0]; + } + } + handleItem(item, suffix + ".json", derivatives); + break; + default: + console.error("unknown anat item name", item.name); + } + }); + } + function handleFunc() { + /* + - suffixes: + - bold + - cbv + - sbref + + */ + if (suffix == "events") { + //we handle events a bit differently.. we need to generate events.tsv from items content + const events = o.items.find(o => !!o.eventsBIDS); + const headers = Object.keys(events.eventsBIDS[0]); //take first index value to see which columns user selected + events.content = headers.join("\t") + "\n"; + events.eventsBIDS.forEach(rec => { + if (rec.stim_file) { + if (!rec.stim_file.startsWith("/stimuli/")) { + rec.stim_file = "/stimuli/" + rec.stim_file; + } + } + const row = []; + headers.forEach(key => { + row.push(rec[key]); + }); + events.content += row.join("\t") + "\n"; + }); + //add stuff to sidecar + const sidecar = o.items.find(o => o.name == "json"); + //sidecar.sidecar.TaskName = o._entities.task; + sidecar.sidecar.trial_type = { + LongName: info.events.trialTypes.longName, + Description: info.events.trialTypes.desc, + Levels: info.events.trialTypes.levels, + }; + //now save + handleItem(events, "events.tsv"); + handleItem(sidecar, "events.json"); + } + else { + //normal func stuff.. + o.items.forEach(item => { + switch (item.name) { + case "nii.gz": + handleItem(item, suffix + ".nii.gz"); + break; + case "json": + //handle B0FieldIdentifier and B0FieldSource if present + if (o.B0FieldIdentifier.length) { + if (o.B0FieldIdentifier.length > 1) { + item.sidecar.B0FieldIdentifier = Object.values(o.B0FieldIdentifier); + } + else { + item.sidecar.B0FieldIdentifier = o.B0FieldIdentifier[0]; + } + } + if (o.B0FieldSource.length) { + if (o.B0FieldSource.length > 1) { + item.sidecar.B0FieldSource = Object.values(o.B0FieldSource); + } + else { + item.sidecar.B0FieldSource = o.B0FieldSource[0]; + } + } + item.sidecar.TaskName = o._entities.task; + handleItem(item, suffix + ".json"); + break; + default: + console.error("unknown func item name", item.name); + } + }); + } + } + function handleFmap() { + /* + - suffixes: + - phasediff + - phase1 + - phase2 + - magnitude1 + - magnitude2 + - magnitude + - fieldmap + */ + o.items.forEach(item => { + switch (item.name) { + case "nii.gz": + handleItem(item, suffix + ".nii.gz"); + break; + case "json": + //handle B0FieldIdentifier and B0FieldSource if present + if (o.B0FieldIdentifier.length) { + if (o.B0FieldIdentifier.length > 1) { + item.sidecar.B0FieldIdentifier = Object.values(o.B0FieldIdentifier); + } + else { + item.sidecar.B0FieldIdentifier = o.B0FieldIdentifier[0]; + } + } + if (o.B0FieldSource.length) { + if (o.B0FieldSource.length > 1) { + item.sidecar.B0FieldSource = Object.values(o.B0FieldSource); + } + else { + item.sidecar.B0FieldSource = o.B0FieldSource[0]; + } + } + //handle IntendedFor + if (o.IntendedFor) { + item.sidecar.IntendedFor = []; + for (let idx of o.IntendedFor) { + const io = info.objects[idx]; + //this should not happen, but ezBIDS_core.json could be corrupted.. + if (!io) { + console.error("can't find object with ", idx); + continue; + } + //if intended object is excluded, skip it + if (io._type == "exclude") + continue; + const iomodality = io._type.split("/")[0]; + const suffix = io._type.split("/")[1]; + //construct a path relative to the subject + let path = ""; + if (io._entities.session) + path += "ses-" + io._entities.session + "/"; + path += iomodality + "/"; + let tokens = []; + //for(let k in io._entities) { + for (let k in info.entityMappings) { + const sk = info.entityMappings[k]; + if (io._entities[k]) + tokens.push(sk + "-" + io._entities[k]); + } + path += tokens.join("_"); + path += "_" + suffix + ".nii.gz"; //TODO - not sure if this is robust enough.. + item.sidecar.IntendedFor.push(path); + } + } + handleItem(item, suffix + ".json"); + break; + default: + console.error("unknown fmap item name", item.name); + } + }); + } + function handleDwi() { + o.items.forEach(item => { + switch (item.name) { + case "nii.gz": + handleItem(item, "dwi.nii.gz"); + break; + case "bvec": + handleItem(item, "dwi.bvec"); + break; + case "bval": + handleItem(item, "dwi.bval"); + break; + case "json": + //handle B0FieldIdentifier and B0FieldSource if present + if (o.B0FieldIdentifier.length) { + if (o.B0FieldIdentifier.length > 1) { + item.sidecar.B0FieldIdentifier = Object.values(o.B0FieldIdentifier); + } + else { + item.sidecar.B0FieldIdentifier = o.B0FieldIdentifier[0]; + } + } + if (o.B0FieldSource.length) { + if (o.B0FieldSource.length > 1) { + item.sidecar.B0FieldSource = Object.values(o.B0FieldSource); + } + else { + item.sidecar.B0FieldSource = o.B0FieldSource[0]; + } + } + handleItem(item, "dwi.json"); + break; + default: + console.error("unknown dwi item name", item.name); + } + }); + if (!o.items.find(item => item.name == "bvec")) { + console.log("bvec is missing.. assuming that this is b0, and setup empty bvec/bval"); + const path = composePath(false); + const zeros = []; + for (let j = 0; j < o.analysisResults.NumVolumes; ++j) { + zeros.push(0); + } + const bvec = `${zeros.join(" ")}\n${zeros.join(" ")}\n${zeros.join(" ")}\n`; + fs.writeFileSync(root + "/" + path + "/" + name + "_dwi.bvec", bvec); + const bval = zeros.join(" ") + "\n"; + fs.writeFileSync(root + "/" + path + "/" + name + "_dwi.bval", bval); + } + } + //now handle different modality + switch (modality) { + case "anat": + handleAnat(); + break; + case "func": + handleFunc(); + break; + case "fmap": + handleFmap(); + break; + case "dwi": + handleDwi(); + break; + case "perf": + handlePerf(); + break; + case "pet": + handlePET(); + break; + case "excluded": + if (!info.includeExcluded) + break; + o.items.forEach((item, idx) => { + //sub-OpenSciJan22_desc-localizer_obj5-0.json + handleItem(item, "excluded." + item.name); + }); + break; + default: + console.error("unknown datatype:" + o._type); + } + next_o(); +}); +//# sourceMappingURL=convert.js.map \ No newline at end of file diff --git a/handler/convert.js.map b/handler/convert.js.map new file mode 100644 index 00000000..5f5eb3b5 --- /dev/null +++ b/handler/convert.js.map @@ -0,0 +1 @@ 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\ No newline at end of file diff --git a/handler/convert.ts b/handler/convert.ts index 3895f358..2d4f3454 100755 --- a/handler/convert.ts +++ b/handler/convert.ts @@ -1,16 +1,16 @@ -#!/usr/bin/env node +import * as fs from 'fs'; +import mkdirp from 'mkdirp'; +import * as async from 'async'; +import { schema } from './shared'; -const fs = require('fs'); -const mkdirp = require('mkdirp'); -const async = require('async'); -const bidsEntitiesOrdered = require('../ui/src/assets/schema/rules/entities.json') +const { rules: { entities: bidsEntitiesOrdered } } = schema; //import { IObject, Subject, Session, OrganizedSession } from '../ui/src/store' const root = process.argv[2]; if(!root) throw "please specify root directory"; -const info = JSON.parse(fs.readFileSync(root+"/finalized.json")); +const info = JSON.parse(fs.readFileSync(root + "/finalized.json", "utf8")); //order the entityMappings correctly, as specified by the BIDS specification let newEntityOrdering = {}; @@ -74,7 +74,7 @@ for(let rec of tsv) { fs.closeSync(tsvf); //handle each objects -async.forEachOf(info.objects, (o, idx, next_o)=>{ +async.forEachOf(info.objects, (o: any, idx, next_o)=>{ if(o._type == "exclude" || o._exclude) { o._type = "excluded/obj"+o.idx; diff --git a/handler/handler.js b/handler/handler.js new file mode 100644 index 00000000..7cdaefbe --- /dev/null +++ b/handler/handler.js @@ -0,0 +1,218 @@ +"use strict"; +var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) { + function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); } + return new (P || (P = Promise))(function (resolve, reject) { + function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } } + function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } } + function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); } + step((generator = generator.apply(thisArg, _arguments || [])).next()); + }); +}; +Object.defineProperty(exports, "__esModule", { value: true }); +require('dotenv').config({ path: '../.env' }); +const child_process_1 = require("child_process"); +const fs = require("fs"); +const ezbids_shared_1 = require("ezbids-shared"); +console.log("---------------------------------------"); +console.log(" starting ezbids-handler"); +console.log("---------------------------------------"); +ezbids_shared_1.models.connect(err => { + if (err) + throw err; + run(); +}); +function run() { + ezbids_shared_1.models.Session.find({ + //TODO- why don't we just look for "uploaded" session? + //upload_finish_date: {$exists: true}, + //pre_begin_date: {$exists: false}, + status: { $in: ["finalized", "uploaded", "deface"] }, + }).then((sessions) => __awaiter(this, void 0, void 0, function* () { + for (let session of sessions) { + try { + switch (session.status) { + case "uploaded": + yield handle_uploaded(session); + break; + case "finalized": + yield handle_finalized(session); + break; + case "deface": + yield handle_deface(session); + break; + } + } + catch (err) { + console.log("caught exception..."); + console.error(err); + } + } + console.log("waiting a bit before looking for more jobs"); + setTimeout(run, 1000 * 3); + })); +} +function handle_uploaded(session) { + return __awaiter(this, void 0, void 0, function* () { + let workdir = process.env.WORK_DIR + "/" + session._id; + session.pre_begin_date = new Date(); + session.pre_end_date = undefined; + session.status = "preprocessing"; + yield handle(session, "./preprocess.sh", "preprocess", cb => { + //monitoring callback + console.log("checking dcm2niix progress--------------------------"); + //load dcm2niix.list/done + let list = null; + if (fs.existsSync(workdir + "/dcm2niix.list")) { + list = fs.readFileSync(workdir + "/dcm2niix.list", "utf8").split("\n"); + session.dicomCount = list.length; + } + let done = null; + if (fs.existsSync(workdir + "/dcm2niix.done")) { + done = fs.readFileSync(workdir + "/dcm2niix.done", "utf8").split("\n"); + session.dicomDone = done.length; + } + cb(); + }, cb => { + //finish callback + fs.readFile(workdir + "/ezBIDS_core.json", "utf8", (err, data) => __awaiter(this, void 0, void 0, function* () { + if (err) + return cb(err); + try { + //try parsing the json! + const json = JSON.parse(data); + const ezbids = new ezbids_shared_1.models.ezBIDS({ + _session_id: session._id, + original: JSON.parse(data), + }); + yield ezbids.save(); + session.status = "analyzed"; + session.status_msg = "successfully run preprocess.sh"; + session.pre_finish_date = new Date(); + } + catch (err) { + return cb(err); + } + yield session.save(); + cb(); + })); + }); + }); +} +function handle_finalized(session) { + return __awaiter(this, void 0, void 0, function* () { + console.log("handling finalized request!-----------------------"); + session.finalize_begin_date = new Date(); + session.finalize_end_date = undefined; + session.status = "bidsing"; + yield handle(session, "./bids.sh", "bids", cb => { + //monitor cb + }, cb => { + //finish cb + session.finalize_finish_date = new Date(); + session.status = "finished"; + cb(); + }); + }); +} +function handle_deface(session) { + return __awaiter(this, void 0, void 0, function* () { + console.log("handling deface request!-----------------------"); + session.deface_begin_date = new Date(); + session.deface_end_date = undefined; + session.status = "defacing"; + yield handle(session, "./deface.sh", "deface", cb => { + //monitor cb - nothing special to do yet + cb(); + }, cb => { + //finish cb + session.deface_finish_date = new Date(); + session.status = "defaced"; + cb(); + }); + }); +} +function handle(session, script, name, cb_monitor, cb_finish) { + let workdir = process.env.WORK_DIR + "/" + session._id; + console.log("handling session " + session._id, name); + return new Promise((resolve, reject) => { + session.save().then(() => { + try { + let monitor; + let workdir = process.env.WORK_DIR + "/" + session._id; + const p = (0, child_process_1.spawn)(script, [workdir], { cwd: __dirname, detached: true }); + const logout = fs.openSync(workdir + "/" + name + ".log", "w"); + const errout = fs.openSync(workdir + "/" + name + ".err", "w"); + let lasterr = ""; + p.stdout.on('data', data => { + let out = data.toString("utf8").trim(); + console.log(out); + session.status_msg = out.substring(out.length - 1000); + fs.writeSync(logout, data); + }); + p.stderr.on('data', data => { + let out = data.toString("utf8").trim(); + console.log(out); + lasterr = out; + fs.writeSync(errout, data); + }); + p.on('close', code => { + clearInterval(monitor); + console.log("process closed"); + fs.closeSync(logout); + fs.closeSync(errout); + //check status + console.debug(name + " finished: " + code); + if (code != 0) { + session.status = "failed"; + session.status_msg = `failed to run ${name} -- code:${code}\n${lasterr}`; + session.save().then(resolve).catch(reject); + } + else { + session.status_msg = "successfully run " + name; + cb_finish(err => { + if (err) { + session.status = "failed"; + session.status_msg = err; + console.error(err); + } + session.save().then(resolve).catch(reject); + }); + } + }); + //update session periodically + monitor = setInterval(() => { + //handle cancel request + if (fs.existsSync(workdir + "/.cancel")) { + console.log("received .cancel request.. killing process group"); + //p.stdin.pause(); + process.kill(-p.pid); //, 'SIGKILL'); + setTimeout(() => { + //parallel will wait for child process to end unless we seng SIGTERM again + process.kill(-p.pid); //, 'SIGKILL'); + }, 1000); + fs.rename(workdir + "/" + name + ".log", workdir + "/" + name + ".log.canceled", err => { + if (err) + console.error(err); + }); + fs.rename(workdir + "/" + name + ".err", workdir + "/" + name + ".err.canceled", err => { + if (err) + console.error(err); + }); + fs.rename(workdir + "/.cancel", workdir + "/.cancel.ed", err => { + if (err) + console.error(err); + }); + } + cb_monitor(() => { + session.save(); //saves for stdout and any update made by monitor_cb + }); + }, 1000 * 5); + } + catch (err) { + //from spawn? + reject(err); + } + }); + }); +} +//# sourceMappingURL=handler.js.map \ No newline at end of file diff --git a/handler/handler.js.map b/handler/handler.js.map new file mode 100644 index 00000000..86fc3993 --- /dev/null +++ b/handler/handler.js.map @@ -0,0 +1 @@ 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\ No newline at end of file diff --git a/handler/handler.ts b/handler/handler.ts index 1b08d45b..a9309fb2 100644 --- a/handler/handler.ts +++ b/handler/handler.ts @@ -1,10 +1,9 @@ require('dotenv').config({ path:'../.env' }) -const { spawn } = require('child_process'); -import fs = require('fs'); +import { spawn } from 'child_process'; +import * as fs from 'fs'; -import config = require('../api/config'); -import models = require('../api/models'); +import { models } from 'ezbids-shared'; console.log("---------------------------------------") console.log(" starting ezbids-handler"); diff --git a/handler/models.ts b/handler/models.ts deleted file mode 100644 index 69d91e6e..00000000 --- a/handler/models.ts +++ /dev/null @@ -1,102 +0,0 @@ -import mongoose from "mongoose"; - -if (process.env.MONGOOSE_DEBUG === 'true') mongoose.set("debug", true); - -export function connect(cb) { - console.debug("connecting to mongo"); - mongoose.connect(process.env.MONGO_URL, { - - /* this really screwed up warehouse db.. - readPreference: 'nearest', - writeConcern: { - w: 'majority', //isn't this the default? - }, - readConcernLevel: 'majority',//prevents read to grab stale data from secondary - */ - - useNewUrlParser: true, - useUnifiedTopology: true, - //auto_reconnect: true, //isn't this the default? - }, err=>{ - if(err) return cb(err); - console.log("connected to mongo"); - cb(); - }); -} - -export function disconnect(cb) { - mongoose.disconnect(cb); -} - -/////////////////////////////////////////////////////////////////////////////////////////////////// -// -// upload sessions -// - -const sessionSchema = mongoose.Schema({ - - create_date: { type: Date, default: Date.now }, - update_date: { type: Date, default: Date.now }, - - request_headers: mongoose.Schema.Types.Mixed, - - upload_finish_date: Date, //when all files are uploaded - - pre_begin_date: Date, //when preprocessing is started - pre_finish_date: Date, //when preprocessing is finished - - deface_begin_date: Date, - deface_finish_date: Date, - - finalize_begin_date: Date, - finalize_finish_date: Date, - - status: String, //just message to show to the user - //created - //uploaded (waiting to be preprocessed) - //preprocessing - //analyzed - //finalized - //bidsing - - //finished - //failed - - //dcm2niix status - dicomCount: Number, - dicomDone: Number, - - status_msg: String, - - /* - files: [{ - idx: Number, - name: String, - size: Number, - path: String, - _upload: Object, //set when the file is uploaded.. just to store some extra information from multer - }], - */ - - //workdir: String, //directory containing uploaded file structure - - //removed: { type: Boolean, default: false }, -}); -sessionSchema.pre('save', function(next) { - this.update_date = Date.now(); - next(); -}); -export const Session = mongoose.model("Session", sessionSchema); - -const ezbidsSchema = mongoose.Schema({ - _session_id: mongoose.Schema.Types.ObjectId, - - original: mongoose.Schema.Types.Mixed, - updated: mongoose.Schema.Types.Mixed, - - create_date: { type: Date, default: Date.now }, - update_date: { type: Date }, -}); -export const ezBIDS = mongoose.model("ezBIDS", ezbidsSchema); - - diff --git a/handler/package-lock.json b/handler/package-lock.json index 823c7f69..40107116 100644 --- a/handler/package-lock.json +++ b/handler/package-lock.json @@ -9,7 +9,9 @@ "version": "1.0.0", "license": "MIT", "dependencies": { + "async": "^3.2.3", "dotenv": "^16.3.1", + "ezbids-shared": "file:../shared", "mongoose": "^6.2.7" }, "devDependencies": { @@ -17,9 +19,19 @@ "@types/node": "^16.11.26", "ts-node": "^10.9.1", "ts-node-dev": "^2.0.0", + "tsc-hooks": "^1.1.2", "typescript": "^4.7.2" } }, + "../shared": { + "name": "ezbids-shared", + "version": "1.0.0", + "license": "MIT", + "dependencies": { + "mongoose": "^6.2.7", + "yaml": "^2.3.2" + } + }, "node_modules/@aws-crypto/crc32": { "version": "3.0.0", "resolved": "https://registry.npmjs.org/@aws-crypto/crc32/-/crc32-3.0.0.tgz", @@ -1322,6 +1334,11 @@ "integrity": "sha512-58S9QDqG0Xx27YwPSt9fJxivjYl432YCwfDMfZ+71RAqUrZef7LrKQZ3LHLOwCS4FLNBplP533Zx895SeOCHvA==", "dev": true }, + "node_modules/async": { + "version": "3.2.4", + "resolved": "https://registry.npmjs.org/async/-/async-3.2.4.tgz", + "integrity": "sha512-iAB+JbDEGXhyIUavoDl9WP/Jj106Kz9DEn1DPgYw5ruDn0e3Wgi3sKFm55sASdGBNOQB8F59d9qQ7deqrHA8wQ==" + }, "node_modules/balanced-match": { "version": "1.0.2", "resolved": "https://registry.npmjs.org/balanced-match/-/balanced-match-1.0.2.tgz", @@ -1492,6 +1509,10 @@ "xtend": "^4.0.0" } }, + "node_modules/ezbids-shared": { + "resolved": "../shared", + "link": true + }, "node_modules/fast-xml-parser": { "version": "4.2.5", "resolved": "https://registry.npmjs.org/fast-xml-parser/-/fast-xml-parser-4.2.5.tgz", @@ -1690,6 +1711,18 @@ "node": ">=0.12.0" } }, + "node_modules/json5": { + "version": "2.2.3", + "resolved": "https://registry.npmjs.org/json5/-/json5-2.2.3.tgz", + "integrity": "sha512-XmOWe7eyHYH14cLdVPoyg+GOH3rYX++KpzrylJwSW98t3Nk+U8XOl8FWKOgwtzdb8lXGf6zYwDUzeHMWfxasyg==", + "dev": true, + "bin": { + "json5": "lib/cli.js" + }, + "engines": { + "node": ">=6" + } + }, "node_modules/kareem": { "version": "2.5.1", "resolved": "https://registry.npmjs.org/kareem/-/kareem-2.5.1.tgz", @@ -2129,6 +2162,19 @@ } } }, + "node_modules/tsc-hooks": { + "version": "1.1.2", + "resolved": "https://registry.npmjs.org/tsc-hooks/-/tsc-hooks-1.1.2.tgz", + "integrity": "sha512-U3RvEYOZAdCWKT3apcV3UOgsIUMXUzKntqX/jiE3/w3MPuvwk9Yjl5i1Z9rxLBht4LI6x6xkUJpQ5kHKidBjtw==", + "dev": true, + "hasInstallScript": true, + "dependencies": { + "json5": "^2.2.0" + }, + "peerDependencies": { + "typescript": "^4.3.2 || ^5.0.2 " + } + }, "node_modules/tsconfig": { "version": "7.0.0", "resolved": "https://registry.npmjs.org/tsconfig/-/tsconfig-7.0.0.tgz", @@ -3341,6 +3387,11 @@ "integrity": "sha512-58S9QDqG0Xx27YwPSt9fJxivjYl432YCwfDMfZ+71RAqUrZef7LrKQZ3LHLOwCS4FLNBplP533Zx895SeOCHvA==", "dev": true }, + "async": { + "version": "3.2.4", + "resolved": "https://registry.npmjs.org/async/-/async-3.2.4.tgz", + "integrity": "sha512-iAB+JbDEGXhyIUavoDl9WP/Jj106Kz9DEn1DPgYw5ruDn0e3Wgi3sKFm55sASdGBNOQB8F59d9qQ7deqrHA8wQ==" + }, "balanced-match": { "version": "1.0.2", "resolved": "https://registry.npmjs.org/balanced-match/-/balanced-match-1.0.2.tgz", @@ -3454,6 +3505,13 @@ "xtend": "^4.0.0" } }, + "ezbids-shared": { + "version": "file:../shared", + "requires": { + "mongoose": "^6.2.7", + "yaml": "^2.3.2" + } + }, "fast-xml-parser": { "version": "4.2.5", "resolved": "https://registry.npmjs.org/fast-xml-parser/-/fast-xml-parser-4.2.5.tgz", @@ -3588,6 +3646,12 @@ "integrity": "sha512-41Cifkg6e8TylSpdtTpeLVMqvSBEVzTttHvERD741+pnZ8ANv0004MRL43QKPDlK9cGvNp6NZWZUBlbGXYxxng==", "dev": true }, + "json5": { + "version": "2.2.3", + "resolved": "https://registry.npmjs.org/json5/-/json5-2.2.3.tgz", + "integrity": "sha512-XmOWe7eyHYH14cLdVPoyg+GOH3rYX++KpzrylJwSW98t3Nk+U8XOl8FWKOgwtzdb8lXGf6zYwDUzeHMWfxasyg==", + "dev": true + }, "kareem": { "version": "2.5.1", "resolved": "https://registry.npmjs.org/kareem/-/kareem-2.5.1.tgz", @@ -3893,6 +3957,15 @@ "tsconfig": "^7.0.0" } }, + "tsc-hooks": { + "version": "1.1.2", + "resolved": "https://registry.npmjs.org/tsc-hooks/-/tsc-hooks-1.1.2.tgz", + "integrity": "sha512-U3RvEYOZAdCWKT3apcV3UOgsIUMXUzKntqX/jiE3/w3MPuvwk9Yjl5i1Z9rxLBht4LI6x6xkUJpQ5kHKidBjtw==", + "dev": true, + "requires": { + "json5": "^2.2.0" + } + }, "tsconfig": { "version": "7.0.0", "resolved": "https://registry.npmjs.org/tsconfig/-/tsconfig-7.0.0.tgz", diff --git a/handler/package.json b/handler/package.json index 8990218e..c216234f 100644 --- a/handler/package.json +++ b/handler/package.json @@ -4,12 +4,16 @@ "description": "", "scripts": { "dev": "ts-node-dev --respawn --transpile-only handler.ts", - "prod": "tsc && node ./build/handler.js" + "build": "tsc", + "prod": "node ./build/handler.js", + "convert": "tsc --build && node ./build/convert.js" }, "author": "", "license": "MIT", "dependencies": { + "async": "^3.2.3", "dotenv": "^16.3.1", + "ezbids-shared": "file:../shared", "mongoose": "^6.2.7" }, "devDependencies": { @@ -17,6 +21,7 @@ "@types/node": "^16.11.26", "ts-node": "^10.9.1", "ts-node-dev": "^2.0.0", + "tsc-hooks": "^1.1.2", "typescript": "^4.7.2" } } diff --git a/handler/tsconfig.json b/handler/tsconfig.json index ed52f29a..14c24303 100644 --- a/handler/tsconfig.json +++ b/handler/tsconfig.json @@ -1,9 +1,19 @@ { "compilerOptions": { - "target": "ES6", + "composite": true, + "outDir": "build", + "target": "es5", "alwaysStrict": true, + "allowJs": true, "sourceMap": true, - "module": "CommonJS", - "esModuleInterop": true - } -} + "esModuleInterop": true, + "module": "commonjs", + "moduleResolution": "node", + }, + "hooks": [ + // "../shared/ts-hooks/schema.js" + ], + "references": [ + { "path": "../shared", "composite": true } + ] +} \ No newline at end of file diff --git a/shared/index.ts b/shared/index.ts new file mode 100644 index 00000000..562023ec --- /dev/null +++ b/shared/index.ts @@ -0,0 +1,2 @@ +export * as models from './models'; +export * as schema from './schema'; diff --git a/api/models.ts b/shared/models.ts similarity index 77% rename from api/models.ts rename to shared/models.ts index 69d91e6e..eca7f28c 100644 --- a/api/models.ts +++ b/shared/models.ts @@ -4,20 +4,7 @@ if (process.env.MONGOOSE_DEBUG === 'true') mongoose.set("debug", true); export function connect(cb) { console.debug("connecting to mongo"); - mongoose.connect(process.env.MONGO_URL, { - - /* this really screwed up warehouse db.. - readPreference: 'nearest', - writeConcern: { - w: 'majority', //isn't this the default? - }, - readConcernLevel: 'majority',//prevents read to grab stale data from secondary - */ - - useNewUrlParser: true, - useUnifiedTopology: true, - //auto_reconnect: true, //isn't this the default? - }, err=>{ + mongoose.connect(process.env.MONGO_URL, {}, err=>{ if(err) return cb(err); console.log("connected to mongo"); cb(); @@ -33,7 +20,7 @@ export function disconnect(cb) { // upload sessions // -const sessionSchema = mongoose.Schema({ +const sessionSchema = new mongoose.Schema({ create_date: { type: Date, default: Date.now }, update_date: { type: Date, default: Date.now }, @@ -83,12 +70,12 @@ const sessionSchema = mongoose.Schema({ //removed: { type: Boolean, default: false }, }); sessionSchema.pre('save', function(next) { - this.update_date = Date.now(); + this.update_date = new Date(Date.now()); next(); }); export const Session = mongoose.model("Session", sessionSchema); -const ezbidsSchema = mongoose.Schema({ +const ezbidsSchema = new mongoose.Schema({ _session_id: mongoose.Schema.Types.ObjectId, original: mongoose.Schema.Types.Mixed, diff --git a/shared/schema/index.ts b/shared/schema/index.ts new file mode 100644 index 00000000..6f1612ff --- /dev/null +++ b/shared/schema/index.ts @@ -0,0 +1 @@ +export * as rules from './rules'; diff --git a/shared/schema/objects/entities.json b/shared/schema/objects/entities.json new file mode 100644 index 00000000..c43c5e0c --- /dev/null +++ b/shared/schema/objects/entities.json @@ -0,0 +1,210 @@ +{ + "acquisition": { + "name": "Acquisition", + "entity": "acq", + "description": "The `acq-