Merge pull request #27 in ~VLE2FE/definma-api from develop to master

* commit 'ed8b549752cbfbeba497adda8427f34c8b8497a4':
  flattened samples result
  csv only for dev/admin, mail change notice

api/sample.yaml

@@ -40,12 +40,6 @@
         schema:
           type: string
         example: color-asc
-      - name: csv
-        description: output as csv
-        in: query
-        schema:
-          type: boolean
-        example: false
       - name: fields[]
         description: "the fields to include in the output as array, defaults to ['_id', 'number', 'type',
         'batch', 'material_id', 'color', 'condition', 'note_id', 'user_id', 'added']"
@@ -57,7 +51,8 @@
         example: ['number', 'batch']
       - name: filters[]
         description: "the filters to apply as an array of URIComponent encoded objects in the form {mode:
-        'eq/ne/lt/lte/gt/gte/in/nin/stringin', field: 'material.m', values: ['15']} using encodeURIComponent(JSON.stringify({}))"
+        'eq/ne/lt/lte/gt/gte/in/nin/stringin', field: 'material.m', values: ['15']} using
+        encodeURIComponent(JSON.stringify({}))"
         in: query
         schema:
          type: array
@@ -66,6 +61,13 @@
         example: '["%7B%22mode%22%3A%22eq%22%2C%22field%22%3A%22material.m%22%2C%22values%22%3A%5B%2215%22%5D%7D",
         "%7B%22mode%22%3A%22isin%22%2C%22field%22%3A%22material.supplier%22%2C%22values%22%3A%5B%22BASF%22%2C%22DSM%22
         %5D%7D"]'
+      - name: output
+        description: 'output format, available values are csv, json, flatten (converts material: {number: x} to
+        material.number: x), defaults to json'
+        in: query
+        schema:
+          type: boolean
+        example: csv
     responses:
       200:
         description: samples overview (output depends on the fields specified)<br>

src/helpers/csv.ts

@@ -1,4 +1,5 @@
 import {parseAsync} from 'json2csv';
+import flatten from './flatten';
 
 export default function csv(input: any[], f: (err, data) => void) {
   parseAsync(input.map(e => flatten(e)), {includeEmptyRows: true})
@@ -6,34 +7,3 @@ export default function csv(input: any[], f: (err, data) => void) {
     .catch(err => f(err, null));
 }
 
-function flatten (data) {  // flatten object: {a: {b: true}} -> {a.b: true}
-  const result = {};
-  function recurse (cur, prop) {
-    if (Object(cur) !== cur || Object.keys(cur).length === 0) {
-      result[prop] = cur;
-    }
-    else if (Array.isArray(cur)) {
-      if (cur.length && (Object(cur[0]) !== cur || Object.keys(cur[0]).length === 0)) {  // array of non-objects
-        result[prop] = '[' + cur.join(', ') + ']';
-      }
-      else {
-        let l = 0;
-        for(let i = 0, l = cur.length; i < l; i++)
-          recurse(cur[i], prop + "[" + i + "]");
-        if (l == 0)
-          result[prop] = [];
-      }
-    }
-    else {
-      let isEmpty = true;
-      for (let p in cur) {
-        isEmpty = false;
-        recurse(cur[p], prop ? prop+"."+p : p);
-      }
-      if (isEmpty && prop)
-        result[prop] = {};
-    }
-  }
-  recurse(data, '');
-  return result;
-}

src/helpers/flatten.ts

@@ -0,0 +1,41 @@
+export default function flatten (data, keepArray = false) {  // flatten object: {a: {b: true}} -> {a.b: true}
+  const result = {};
+  function recurse (cur, prop) {
+    if (Object(cur) !== cur || Object.keys(cur).length === 0) {
+      result[prop] = cur;
+    }
+    else if (prop === 'spectrum.dpt') {
+      console.log('dpt');
+      result[prop + '.labels'] = cur.map(e => e[0]);
+      result[prop + '.values'] = cur.map(e => e[1]);
+    }
+    else if (Array.isArray(cur)) {
+      if (keepArray) {
+        result[prop] = cur;
+      }
+      else {  // array to string
+        if (cur.length && (Object(cur[0]) !== cur || Object.keys(cur[0]).length === 0)) {  // array of non-objects
+          result[prop] = '[' + cur.join(', ') + ']';
+        }
+        else {
+          let l = 0;
+          for(let i = 0, l = cur.length; i < l; i++)
+            recurse(cur[i], prop + "[" + i + "]");
+          if (l == 0)
+            result[prop] = [];
+        }
+      }
+    }
+    else {
+      let isEmpty = true;
+      for (let p in cur) {
+        isEmpty = false;
+        recurse(cur[p], prop ? prop+"."+p : p);
+      }
+      if (isEmpty && prop)
+        result[prop] = {};
+    }
+  }
+  recurse(data, '');
+  return result;
+}

src/routes/sample.spec.ts

@@ -7,8 +7,6 @@ import TestHelper from "../test/helper";
 import mongoose from 'mongoose';
 
 
-// TODO: allowed types: tension rod, part, granulate, other
-// TODO: filter by conditions and material properties
 
 describe('/sample', () => {
   let server;
@@ -451,12 +449,12 @@ describe('/sample', () => {
         res: {status: 'Invalid body format', details: 'Measurement key not found'}
       });
     });
-    it('returns a correct csv file if specified', done => {
+    it('returns a correct csv file for admins if specified', done => {
       TestHelper.request(server, done, {
         method: 'get',
-        url: '/samples?status[]=new&status[]=validated&page-size=2&csv=true',
+        url: '/samples?status[]=new&status[]=validated&page-size=2&output=csv',
         contentType: /text\/csv/,
-        auth: {basic: 'janedoe'},
+        auth: {basic: 'admin'},
         httpStatus: 200
       }).end((err, res) => {
         if (err) return done(err);
@@ -466,6 +464,30 @@ describe('/sample', () => {
         done();
       });
     });
+    it('rejects returning a csv file for a write user', done => {
+      TestHelper.request(server, done, {
+        method: 'get',
+        url: '/samples?status[]=new&status[]=validated&page-size=2&output=csv',
+        auth: {basic: 'janedoe'},
+        httpStatus: 403
+      });
+    });
+    it('returns the object flattened if specified', done => {
+      TestHelper.request(server, done, {
+        method: 'get',
+        url: '/samples?status[]=new&status[]=validated&fields[]=number&fields[]=measurements.spectrum.device&fields[]=measurements.spectrum.dpt&page-size=1&output=flatten',
+        auth: {basic: 'admin'},
+        httpStatus: 200
+      }).end((err, res) => {
+        if (err) return done(err);
+        should(res.body[0]).have.only.keys('number', 'spectrum.device', 'spectrum.dpt.labels', 'spectrum.dpt.values');
+        should(res.body[0]).have.property('number', '1');
+        should(res.body[0]).have.property('spectrum.device', 'Alpha I');
+        should(res.body[0]).have.property('spectrum.dpt.labels', [3997.12558, 3995.08519, 3993.0448]);
+        should(res.body[0]).have.property('spectrum.dpt.values', [98.00555, 98.03253, 98.02657]);
+        done();
+      });
+    });
     it('returns only the fields specified', done => {
       TestHelper.request(server, done, {
         method: 'get',

src/routes/sample.ts

@@ -16,6 +16,7 @@ import ConditionTemplateModel from '../models/condition_template';
 import ParametersValidate from './validate/parameters';
 import db from '../db';
 import csv from '../helpers/csv';
+import flatten from '../helpers/flatten';
 
 
 const router = express.Router();
@@ -34,8 +35,9 @@ router.get('/samples', async (req, res, next) => {
   const {error, value: filters} = SampleValidate.query(req.query, ['dev', 'admin'].indexOf(req.authDetails.level) >= 0);
   if (error) return res400(error, res);
 
-  // spectral data not allowed for read/write users
+  // spectral data and csv not allowed for read/write users
-  if (filters.fields.find(e => /\.dpt$/.test(e)) && !req.auth(res, ['dev', 'admin'], 'all')) return;
+  if ((filters.fields.find(e => /\.dpt$/.test(e)) || filters.output !== 'json') &&
+    !req.auth(res, ['dev', 'admin'], 'all')) return;
 
   // TODO: find a better place for these
   const sampleKeys = ['_id', 'color', 'number', 'type', 'batch', 'added', 'condition', 'material_id', 'note_id',
@@ -195,7 +197,8 @@ router.get('/samples', async (req, res, next) => {
         {$addFields: {'material.group': { $arrayElemAt: ['$material.group.name', 0]}}}
       );
     }
-    // if (sortFilterKeys.find(e => e === 'material.number')) {  // add material number if needed  // TODO: adapt code to new numbers format
+    // TODO: adapt code to new numbers format
+    // if (sortFilterKeys.find(e => e === 'material.number')) {  // add material number if needed
     //   materialQuery.push(
     //     {$addFields: {'material.number': { $arrayElemAt: [
     //       '$material.numbers.number', {$indexOfArray: ['$material.numbers.color', '$color']}
@@ -393,13 +396,16 @@ router.get('/samples', async (req, res, next) => {
         [filters.sort[0].split('.')[1],
         ...measurementFilterFields, ...measurementFieldsFields]
       );
-      if (filters.csv) {  // output as csv
+      if (filters.output === 'csv') {  // output as csv
         csv(_.compact(data.map(e => SampleValidate.output(e, 'refs', measurementFields))), (err, data) => {
           if (err) return next(err);
           res.set('Content-Type', 'text/csv');
           res.send(data);
         });
       }
+      else if (filters.output === 'flatten') {
+        res.json(_.compact(data.map(e => flatten(SampleValidate.output(e, 'refs', measurementFields), true))));
+      }
       else {  // validate all and filter null values from validation errors
         res.json(_.compact(data.map(e => SampleValidate.output(e, 'refs', measurementFields))));
       }
@@ -417,6 +423,9 @@ router.get('/samples', async (req, res, next) => {
           delete data._id;
         }
       }
+      if (filters.output === 'flatten') {
+        data = flatten(data, true);
+      }
       res.write((count === 0 ? '' : ',\n') + JSON.stringify(data)); count ++;
     });
     stream.on('error', err => {
@@ -478,9 +487,6 @@ router.put('/sample/' + IdValidate.parameter(), (req, res, next) => {
     if (sample.hasOwnProperty('material_id')) {
       if (!await materialCheck(sample, res, next)) return;
     }
-    else if (sample.hasOwnProperty('color')) {
-      if (!await materialCheck(sample, res, next, sampleData.material_id)) return;
-    }
     // do not execute check if condition is and was empty
     if (sample.hasOwnProperty('condition') && !(_.isEmpty(sample.condition) && _.isEmpty(sampleData.condition))) {
       if (!await conditionCheck(sample.condition, 'change', res, next,
@@ -706,8 +712,8 @@ async function numberCheck(sample, res, next) {
 }
 
 // validate material_id and color, returns false if invalid
-async function materialCheck (sample, res, next, id = sample.material_id) {
+async function materialCheck (sample, res, next) {
-  const materialData = await MaterialModel.findById(id).lean().exec().catch(err => next(err)) as any;
+  const materialData = await MaterialModel.findById(sample.material_id).lean().exec().catch(err => next(err)) as any;
   if (materialData instanceof Error) return false;
   if (!materialData) {  // could not find material_id
     res.status(400).json({status: 'Material not available'});

src/routes/user.ts

@@ -59,9 +59,20 @@ router.put('/user:username([/](?!key|new).?*|/?)', async (req, res, next) => {
     if (!await usernameCheck(user.name, res, next)) return;
   }
 
+  // get current mail address to compare to given address
+  const {email: oldMail} = await UserModel.findOne({name: username}).lean().exec().catch(err => next(err));
+
   await UserModel.findOneAndUpdate({name: username}, user, {new: true}).log(req).lean().exec(  (err, data:any) => {
     if (err) return next(err);
     if (data) {
+      if (data.mail !== oldMail) {  // mail address was changed, send notice to old address
+        Mail.send(oldMail, 'Email change in your DeFinMa database account',
+          'Hi, <br><br> Your email address of your DeFinMa account was changed to ' + data.mail +
+          '<br><br>If you actually did this, just delete this email.' +
+          '<br><br>If you did not change your email, someone might be messing around with your account, ' +
+          'so talk to the sysadmin quickly!<br><br>Have a nice day.' +
+          '<br><br>The DeFinMa team');
+      }
       res.json(UserValidate.output(data));
     }
     else {

src/routes/validate/sample.ts

@@ -227,7 +227,7 @@ export default class SampleValidate {
       sort: Joi.string().pattern(
         new RegExp('^(' + this.sortKeys.join('|').replace(/\./g, '\\.').replace(/\*/g, '.+') + ')-(asc|desc)$', 'm')
       ).default('_id-asc'),
-      csv: Joi.boolean().default(false),
+      output: Joi.string().valid('json', 'flatten', 'csv').default('json'),
       fields: Joi.array().items(Joi.string().pattern(
         new RegExp('^(' + this.fieldKeys.join('|').replace(/\./g, '\\.').replace(/\*/g, '.+') + ')$', 'm')
       )).default(['_id','number','type','batch','material_id','color','condition','note_id','user_id','added'])