From 50afcb0641427a902ebb35bfe54d2f43d99c36e8 Mon Sep 17 00:00:00 2001 From: Soichi Hayashi Date: Thu, 7 Jul 2022 12:41:19 +0000 Subject: [PATCH] added taskevent api removed resource reporting moved package.json under /api --- Dockerfile | 27 - api/Dockerfile | 15 + api/build.sh | 1 + api/controllers/index.js | 1 + api/controllers/taskevent.js | 49 ++ api/events.js | 4 +- api/health.js | 2 +- api/models.js | 21 +- package-lock.json => api/package-lock.json | 796 ++++++++++++--------- package.json => api/package.json | 20 +- api/transfer.js | 3 + bin/task.js | 2 +- 12 files changed, 559 insertions(+), 382 deletions(-) delete mode 100644 Dockerfile create mode 100644 api/Dockerfile create mode 100755 api/build.sh create mode 100644 api/controllers/taskevent.js rename package-lock.json => api/package-lock.json (78%) rename package.json => api/package.json (84%) diff --git a/Dockerfile b/Dockerfile deleted file mode 100644 index 47beef5..0000000 --- a/Dockerfile +++ /dev/null @@ -1,27 +0,0 @@ -FROM node:10 - -MAINTAINER Soichi Hayashi - -#for occasional debugging -RUN apt-get update && apt install -y vim - -RUN npm install http-server -g - -# npm install pm2 -g && \ -# pm2 install pm2-slack && \ -# pm2 set pm2-slack:error false && \ -# pm2 set pm2-slack:exit true && \ -# pm2 install pm2-logrotate && \ -# pm2 set pm2-logrotate:retain 7 - -COPY . /app -RUN cd /app && npm install --production && cd ui && npm install --production - -#for webui -EXPOSE 80 - -#for api -EXPOSE 8080 - -#CMD [ "/app/docker/start.sh" ] - diff --git a/api/Dockerfile b/api/Dockerfile new file mode 100644 index 0000000..2844bdc --- /dev/null +++ b/api/Dockerfile @@ -0,0 +1,15 @@ +FROM node:16 + +MAINTAINER Soichi Hayashi + +WORKDIR /app + +COPY controllers . +COPY resource_test.sh . +COPY *.js ./ + +COPY package.json . +COPY package-lock.json . + +RUN npm install --production +CMD [ "node", "server.js" ] diff --git a/api/build.sh b/api/build.sh new file mode 100755 index 0000000..1a9b74e --- /dev/null +++ b/api/build.sh @@ -0,0 +1 @@ +docker build -t brainlife/amaretti-api:1.0 . diff --git a/api/controllers/index.js b/api/controllers/index.js index fd4481a..3c6ca60 100644 --- a/api/controllers/index.js +++ b/api/controllers/index.js @@ -55,6 +55,7 @@ router.use('/instance', require('./instance')); router.use('/resource', require('./resource')); router.use('/event', require('./event')); router.use('/admin', require('./admin')); +router.use('/taskevent', require('./taskevent')); //TODO DEPRECATED (currently used by th /wf/#!/resources UI) //use (get) /resource/type instead diff --git a/api/controllers/taskevent.js b/api/controllers/taskevent.js new file mode 100644 index 0000000..e06f6fd --- /dev/null +++ b/api/controllers/taskevent.js @@ -0,0 +1,49 @@ +'use strict'; + +const express = require('express'); +const router = express.Router(); +const async = require('async'); +const mongoose = require('mongoose'); +const path = require('path'); +const mime = require('mime'); +const multer = require('multer'); +const fs = require('fs'); + +const config = require('../../config'); +const db = require('../models'); +const events = require('../events'); +const common = require('../common'); + +/** + * @apiGroup Taskevent + * @api {get} /taskevent/:taskid + Query Task events + * @apiDescription Returns all task status update events for a given task id + * + * @apiHeader {String} authorization A valid JWT token "Bearer: xxxxx" + * + * @apiSuccess {Object} List of taskevents + */ +router.get('/:taskId', common.jwt(), function(req, res, next) { + let find = {task_id: req.params.taskId}; + + //access control + if(!req.user.scopes.amaretti || !~req.user.scopes.amaretti.indexOf("admin")) { + find['$or'] = [ + {user_id: req.user.sub}, + {_group_id: {$in: req.user.gids||[]}}, + ]; + } + + //if(req.query.select) console.log("select:"+req.query.select); + db.Taskevent.find(find) + .lean() + .sort('date') + .exec(function(err, taskevents) { + if(err) return next(err); + res.json({taskevents}); + }); +}); + +module.exports = router; + diff --git a/api/events.js b/api/events.js index 18024a3..bc984c2 100644 --- a/api/events.js +++ b/api/events.js @@ -90,7 +90,6 @@ function publish_or_log(ex, key, msg, cb) { } } -//deprecate this exports.task = function(task) { //get previous task status to see if status changed @@ -113,7 +112,7 @@ exports.task = function(task) { }); taskevent.save(); } - + //some fields are populated (foreign keys are de-referenced) //to normalize the field type, let's load the record from database //TODO - can't I just test to see if _id exists for those field and replace them with it? @@ -151,3 +150,4 @@ exports.publish = (key, message, cb)=>{ message.timestamp = (new Date().getTime())/1000; //it's crazy that amqp doesn't set this? publish_or_log(amaretti_ex, key, message, cb); } + diff --git a/api/health.js b/api/health.js index 5746f51..e4169df 100644 --- a/api/health.js +++ b/api/health.js @@ -7,7 +7,7 @@ const logger = winston.createLogger(config.logger.winston); const db = require('./models'); const common = require('./common'); -const pkg = require('../package.json'); +const pkg = require('./package.json'); var redis_client = redis.createClient(config.redis.port, config.redis.server); redis_client.on('error', err=>{throw err}); diff --git a/api/models.js b/api/models.js index db31ea7..155cb46 100644 --- a/api/models.js +++ b/api/models.js @@ -20,7 +20,7 @@ exports.init = async function(cb, connectEvent = true) { return cb(err); } } - + console.log("connecting to mongodb"); mongoose.connect(config.mongodb, { //writeConcern: majority slows down things.. let's just read/write @@ -33,9 +33,7 @@ exports.init = async function(cb, connectEvent = true) { //requires writeConcern to be set to "majority" also. level: 'majority', }, - writeConcern: { - w: 'majority', - }, + writeConcern: { w: 'majority', }, */ useNewUrlParser: true, useUnifiedTopology: true, @@ -258,8 +256,7 @@ var taskSchema = mongoose.Schema({ status_msg: String, - //resource where the task is currently running (or was). It gets cleared if rerun - //resource_id: {type: mongoose.Schema.Types.ObjectId, ref: 'Resource', index: true}, //accesses.ops is 0 + //resource where the task is last run (or attempted to run) resource_id: {type: mongoose.Schema.Types.ObjectId, ref: 'Resource' }, //resources where task dir exits (where it ran, or synced) @@ -323,6 +320,16 @@ taskSchema.index({service: 1, status: 1, "config._tid": 1, user_id: 1, _group_id //taskSchema.index({follow_task_id: 1 }); taskSchema.index({finish_date: 1, "config._app": 1, follow_task_id: 1 }); //sample tasks for an app +/////////////////////// +// +// for finding validator (can't merge these 2 as it will cause "CannotIndexParallelArrays" +// +taskSchema.index({"deps_config.task": 1}); +taskSchema.index({service: 1, instance_id: 1, "config._outputs.id": 1 }); //still testing to see if this helps +// +/////////////////////// + + exports.Task = mongoose.model('Task', taskSchema); /////////////////////////////////////////////////////////////////////////////////////////////////// @@ -402,6 +409,8 @@ var serviceinfoSchema = mongoose.Schema({ success_rate: Number, readme_status: String, //I think I am going to deprecate this (by status/status_msg) + + //monthlyCount: [Number], //dheeraj still working on this? }); exports.Serviceinfo = mongoose.model('Serviceinfo', serviceinfoSchema); diff --git a/package-lock.json b/api/package-lock.json similarity index 78% rename from package-lock.json rename to api/package-lock.json index 240375e..06faed6 100644 --- a/package-lock.json +++ b/api/package-lock.json @@ -3,10 +3,15 @@ "requires": true, "lockfileVersion": 1, "dependencies": { + "@colors/colors": { + "version": "1.5.0", + "resolved": "https://registry.npmjs.org/@colors/colors/-/colors-1.5.0.tgz", + "integrity": "sha512-ooWCrlZP11i8GImSjTHYHLkvFDP48nS4+204nGb1RiX/WXYHmJA2III9/e2DWVabCESdW7hBAEzHRqUn9OUVvQ==" + }, "@dabh/diagnostics": { - 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"integrity": "sha512-n/ShnvDi6FHbbVfviro+WojiFzv+s8MPMHBczVePfUpDJLwoLT0ht1l4YwBCbi8pJAveEEdnkHyPyTP/mzRfwg==", + "version": "1.3.0", + "resolved": "https://registry.npmjs.org/string_decoder/-/string_decoder-1.3.0.tgz", + "integrity": "sha512-hkRX8U1WjJFd8LsDJ2yQ/wWWxaopEsABU1XfkM8A+j0+85JAGppt16cr1Whg6KIbb4okU6Mql6BOj+uup/wKeA==", "requires": { - "safe-buffer": "~5.1.0" + "safe-buffer": "~5.2.0" } } } diff --git a/package.json b/api/package.json similarity index 84% rename from package.json rename to api/package.json index 10eeb1a..6c109d9 100644 --- a/package.json +++ b/api/package.json @@ -17,31 +17,31 @@ "author": "Soichi Hayashi ", "dependencies": { "amqp": "^0.2.7", - "async": "^3.2.2", + "async": "^3.2.3", "axios": "^0.24.0", - "body-parser": "^1.19.0", + "body-parser": "^1.20.0", "compression": "^1.7.4", "cors": "^2.8.5", "deepmerge": "^4.2.2", - "express": "^4.17.1", - "express-jwt": "^6.1.0", + "express": "^4.18.1", + "express-jwt": "^6.1.2", "hpss": "0.0.20", "jsonwebtoken": "^8.5.1", - "mime": "^2.5.2", - "mongoose": "^6", + "mime": "^2.6.0", + "mongoose": "^6.3.2", "morgan": "^1.10.0", - "multer": "^1.4.3", + "multer": "^1.4.4", "ps-node": "^0.1.6", "redis": "^3.1.2", "request": "^2.88.2", "request-promise-native": "^1.0.9", "simple-statistics": "^6.1.1", - "ssh2": "^1.5.0", + "ssh2": "^1.10.0", "ssh2-multiplexer": "github:soichih/ssh2-multiplexer", - "sshpk": "^1.16.1", + "sshpk": "^1.17.0", "sshpk-agent": "^1.8.1", "strip-ansi": "^6.0.1", - "winston": "^3.3.3", + "winston": "^3.7.2", "yargs": "^16.2.0" }, "devDependencies": { diff --git a/api/transfer.js b/api/transfer.js index 554b787..92fc1ea 100644 --- a/api/transfer.js +++ b/api/transfer.js @@ -93,6 +93,9 @@ exports.rsync_resource = function(source_resource, dest_resource, source_path, d if(err) return next(err); //https://unix.stackexchange.com/questions/34248/how-can-i-find-broken-symlinks + //If Osiris mount is temporarily down, this ends up removing the symlinks and when osiris + //comes back online, the staged path will remain removed. I wish there is a way to tell + //rsync to only copy things that it can copy.. conn.exec("timeout 30 find "+source_path+" -type l ! -exec test -e {} \\; -delete", (err, stream)=>{ if(err) return next(err); stream.on('close', (code, signal)=>{ diff --git a/bin/task.js b/bin/task.js index 17bc0fb..cb62734 100755 --- a/bin/task.js +++ b/bin/task.js @@ -24,7 +24,7 @@ const _resource_select = require('../api/resource').select; const _transfer = require('../api/transfer'); const _service = require('../api/service'); -const pkg = require('../package.json'); +const pkg = require('../api/package.json'); const argv = yargs .option('nonice', {