refactored user.ts

api/sample.yaml

@@ -2,7 +2,7 @@
   get:
     summary: all samples in overview
     description: 'Auth: all, levels: read, write, maintain, dev, admin'
-    x-doc: returns only samples with status 10  # TODO: methods /samples/new|deleted
+    x-doc: returns only samples with status 10
     tags:
       - /sample
     responses:
@@ -18,6 +18,30 @@
         $ref: 'api.yaml#/components/responses/401'
       500:
         $ref: 'api.yaml#/components/responses/500'
+
+/samples{group}:
+  parameters:
+    - $ref: 'api.yaml#/components/parameters/Group'
+  get:
+    summary: all new/deleted samples in overview
+    description: 'Auth: basic, levels: maintain, admin'
+    x-doc: returns only samples with status 0/-1
+    tags:
+      - /sample
+    responses:
+      200:
+        description: samples overview
+        content:
+          application/json:
+            schema:
+              type: array
+              items:
+                $ref: 'api.yaml#/components/schemas/SampleRefs'
+      401:
+        $ref: 'api.yaml#/components/responses/401'
+      500:
+        $ref: 'api.yaml#/components/responses/500'
+
 /sample/{id}:
   parameters:
     - $ref: 'api.yaml#/components/parameters/Id'
@@ -130,7 +154,7 @@
   get:
     summary: list all existing field names for custom notes fields
     description: 'Auth: all, levels: read, write, maintain, dev, admin'
-    x-doc: integrity has to be ensured  # TODO: implement mechanism to regularly check note_fields
+    x-doc: integrity has to be ensured
     tags:
       - /sample
     responses:

src/api.ts

@@ -20,7 +20,7 @@ export default class api {
       apiDoc = doc;
       apiDoc.paths = apiDoc.paths.allOf.reduce((s, e) => Object.assign(s, e));  // bundle routes
       apiDoc = this.resolveXDoc(apiDoc);
-      oasParser.validate(apiDoc, (err, api) => {
+      oasParser.validate(apiDoc, (err, api) => {  // validate oas schema
         if (err) {
           console.error(err);
         }
@@ -35,8 +35,8 @@ export default class api {
 
   private static resolveXDoc (doc) {  // resolve x-doc properties recursively
     Object.keys(doc).forEach(key => {
-      if (doc[key] !== null && doc[key].hasOwnProperty('x-doc')) {
-        doc[key].description += this.addHtml(doc[key]['x-doc']);
+      if (doc[key] !== null && doc[key].hasOwnProperty('x-doc')) {  // add x-doc to description, is styled via css
+        doc[key].description += '<details class="docs"><summary>docs</summary>' + doc[key]['x-doc'] + '</details>';
       }
       else if (typeof doc[key] === 'object' && doc[key] !== null) {  // go deeper into recursion
         doc[key] = this.resolveXDoc(doc[key]);
@@ -44,8 +44,4 @@ export default class api {
     });
     return doc;
   }
-
-  private static addHtml (text) {  // add docs HTML
-    return '<details class="docs"><summary>docs</summary>' + text + '</details>';
-  }
 }

src/db.ts

@@ -13,7 +13,7 @@ export default class db {
     mode: null,
   };
 
-  static connect (mode = '', done: Function = () => {}) {  // set mode to test for unit/integration tests, otherwise skip parameter. done is also only needed for testing
+  static connect (mode = '', done: Function = () => {}) {  // set mode to test for unit/integration tests, otherwise skip parameters. done is also only needed for testing
     if (this.state.db) return done();  // db is already connected
 
     // find right connection url
@@ -84,9 +84,9 @@ export default class db {
   }
 
   static loadJson (json, done: Function = () => {}) {  // insert given JSON data into db, uses core mongodb methods
-    if (!this.state.db || !json.hasOwnProperty('collections') || json.collections.length === 0) {
+    if (!this.state.db || !json.hasOwnProperty('collections') || json.collections.length === 0) {  // no db connection or nothing to load
       return done();
-    }  // no db connection or nothing to load
+    }
 
     let loadCounter = 0;  // count number of loaded collections to know when to return done()
     Object.keys(json.collections).forEach(collectionName => {  // create each collection
@@ -103,10 +103,10 @@ export default class db {
 
   private static oidResolve (object: any) {  // resolve $oid fields to actual ObjectIds recursively
     Object.keys(object).forEach(key => {
-      if (object[key] !== null && object[key].hasOwnProperty('$oid')) {
+      if (object[key] !== null && object[key].hasOwnProperty('$oid')) {  // found oid, replace
         object[key] = mongoose.Types.ObjectId(object[key].$oid);
       }
-      else if (typeof object[key] === 'object' && object[key] !== null) {
+      else if (typeof object[key] === 'object' && object[key] !== null) {  // deeper into recursion
         object[key] = this.oidResolve(object[key]);
       }
     });

src/helpers/authorize.ts

@@ -63,7 +63,7 @@ function basic (req, next): any {  // checks basic auth and returns changed user
         if (data.length === 1) {  // one user found
           bcrypt.compare(auth.pass, data[0].pass, (err, res) => {  // check password
             if (err) return next(err);
-            if (res === true) {
+            if (res === true) {  // password correct
               resolve({level: data[0].level, name: data[0].name, id: data[0]._id.toString(), location: data[0].location});
             }
             else {
@@ -84,7 +84,7 @@ function basic (req, next): any {  // checks basic auth and returns changed user
 
 function key (req, next): any {  // checks API key and returns changed user object
   return new Promise(resolve => {
-    if (req.query.key !== undefined) {
+    if (req.query.key !== undefined) {  // key available
       UserModel.find({key: req.query.key}).lean().exec( (err, data: any) => {  // find user
         if (err) return next(err);
         if (data.length === 1) {  // one user found

src/helpers/mail.ts

@@ -1,6 +1,6 @@
 import axios from 'axios';
 
-// sends an email
+// sends an email using the BIC service
 
 export default (mailAddress, subject, content, f) => {  // callback, executed empty or with error
   if (process.env.NODE_ENV === 'production') {

src/index.ts

@@ -5,7 +5,7 @@ import mongoSanitize from 'mongo-sanitize';
 import api from './api';
 import db from './db';
 
-// TODO: overall commenting/documentation review
+
 
 // tell if server is running in debug or production environment
 console.info(process.env.NODE_ENV === 'production' ? '===== PRODUCTION =====' : process.env.NODE_ENV === 'test' ? '' :'===== DEVELOPMENT =====');

src/routes/condition.ts

@@ -37,13 +37,14 @@ router.put('/condition/' + IdValidate.parameter(), async (req, res, next) => {
   if (!data) {
     res.status(404).json({status: 'Not found'});
   }
+
   // add properties needed for sampleIdCheck
   condition.treatment_template = data.treatment_template;
   condition.sample_id = data.sample_id;
   if (!await sampleIdCheck(condition, req, res, next)) return;
   if (condition.parameters) {
     condition.parameters = _.assign({}, data.parameters, condition.parameters);
-    if (!_.isEqual(condition.parameters, data.parameters)) {
+    if (!_.isEqual(condition.parameters, data.parameters)) {  // parameters did not change
       condition.status = 0;
     }
   }
@@ -83,7 +84,7 @@ router.post('/condition/new', async (req, res, next) => {
 
   condition.number = await numberGenerate(condition, treatmentData, next);
   if (!condition.number) return;
-  condition.status = 0;
+  condition.status = 0;  // set status to new
   await new ConditionModel(condition).save((err, data) => {
     if (err) return next(err);
     res.json(ConditionValidate.output(data.toObject()));
@@ -105,8 +106,8 @@ async function sampleIdCheck (condition, req, res, next) {  // validate sample_i
   return true;
 }
 
-async function numberGenerate (condition, treatmentData, next) {  // validate number, returns false if invalid
-  const conditionData = await ConditionModel
+async function numberGenerate (condition, treatmentData, next) {  // generate number, returns false on error
+  const conditionData = await ConditionModel  // find condition with highest number belonging to the same sample
     .find({sample_id: condition.sample_id, number: new RegExp('^' + treatmentData.number_prefix + '[0-9]+$', 'm')})
     .sort({number: -1})
     .limit(1)
@@ -114,7 +115,7 @@ async function numberGenerate (condition, treatmentData, next) {  // validate nu
     .exec()
     .catch(err => next(err)) as any;
   if (conditionData instanceof Error) return false;
-  return treatmentData.number_prefix + (conditionData.length > 0 ? Number(conditionData[0].number.replace(/[^0-9]+/g, '')) + 1 : 1);
+  return treatmentData.number_prefix + (conditionData.length > 0 ? Number(conditionData[0].number.replace(/[^0-9]+/g, '')) + 1 : 1);  // return new number
 }
 
 async function treatmentCheck (condition, param, res, next) {  // validate treatment template, returns false if invalid, otherwise template data

src/routes/material.ts

@@ -33,7 +33,6 @@ router.get('/materials/:group(new|deleted)', (req, res, next) => {
   }
   MaterialModel.find({status: status}).lean().exec((err, data) => {
     if (err) return next(err);
-    console.log(data);
     res.json(_.compact(data.map(e => MaterialValidate.output(e))));  // validate all and filter null values from validation errors
   });
 });
@@ -68,7 +67,7 @@ router.put('/material/' + IdValidate.parameter(), (req, res, next) => {
 
     // check for changes
     if (!_.isEqual(_.pick(IdValidate.stringify(materialData), _.keys(material)), material)) {
-      material.status = 0;
+      material.status = 0;  // set status to new
     }
 
     await MaterialModel.findByIdAndUpdate(req.params.id, material, {new: true}).lean().exec((err, data) => {
@@ -102,13 +101,12 @@ router.delete('/material/' + IdValidate.parameter(), (req, res, next) => {
 router.post('/material/new', async (req, res, next) => {
   if (!req.auth(res, ['write', 'maintain', 'dev', 'admin'], 'basic')) return;
 
-  // validate input
   const {error, value: material} = MaterialValidate.input(req.body, 'new');
   if (error) return res400(error, res);
 
   if (!await nameCheck(material, res, next)) return;
 
-  material.status = 0;
+  material.status = 0;  // set status to new
   await new MaterialModel(material).save((err, data) => {
     if (err) return next(err);
     res.json(MaterialValidate.output(data.toObject()));
@@ -120,7 +118,7 @@ module.exports = router;
 
 
 async function nameCheck (material, res, next) {  // check if name was already taken
-  const materialData = await MaterialModel.findOne({name: material.name}).lean().exec().catch(err => {next(err); return false;}) as any;
+  const materialData = await MaterialModel.findOne({name: material.name}).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 name already taken'});

src/routes/measurement.ts

@@ -36,16 +36,20 @@ router.put('/measurement/' + IdValidate.parameter(), async (req, res, next) => {
   if (!data) {
     res.status(404).json({status: 'Not found'});
   }
+
   // add properties needed for conditionIdCheck
   measurement.measurement_template = data.measurement_template;
   measurement.condition_id = data.condition_id;
   if (!await conditionIdCheck(measurement, req, res, next)) return;
+
+  // check for changes
   if (measurement.values) {
     measurement.values = _.assign({}, data.values, measurement.values);
     if (!_.isEqual(measurement.values, data.values)) {
-      measurement.status = 0;
+      measurement.status = 0;  // set status to new
     }
   }
+
   if (!await templateCheck(measurement, 'change', res, next)) return;
   await MeasurementModel.findByIdAndUpdate(req.params.id, measurement, {new: true}).lean().exec((err, data) => {
     if (err) return next(err);
@@ -99,7 +103,7 @@ async function conditionIdCheck (measurement, req, res, next) {  // validate con
   return true;
 }
 
-async function templateCheck (measurement, param, res, next) {  // validate measurement_template and values
+async function templateCheck (measurement, param, res, next) {  // validate measurement_template and values, param for new/change
   const templateData = await MeasurementTemplateModel.findById(measurement.measurement_template).lean().exec().catch(err => {next(err); return false;}) as any;
   if (!templateData) {  // template not found
     res.status(400).json({status: 'Measurement template not available'});
@@ -108,7 +112,6 @@ async function templateCheck (measurement, param, res, next) {  // validate meas
 
   // validate values
   const {error, value: ignore} = ParametersValidate.input(measurement.values, templateData.parameters, param);
-  console.log(error);
   if (error) {res400(error, res); return false;}
   return true;
 }

src/routes/sample.spec.ts

@@ -4,7 +4,6 @@ import NoteModel from '../models/note';
 import NoteFieldModel from '../models/note_field';
 import TestHelper from "../test/helper";
 
-// TODO: think again which parameters are required at POST
 
 describe('/sample', () => {
   let server;
@@ -23,16 +22,16 @@ describe('/sample', () => {
         if (err) return done(err);
         const json = require('../test/db.json');
         should(res.body).have.lengthOf(json.collections.samples.filter(e => e.status === 10).length);
-        should(res.body).matchEach(material => {
-          should(material).have.only.keys('_id', 'number', 'type', 'color', 'batch', 'material_id', 'note_id', 'user_id');
-          should(material).have.property('_id').be.type('string');
-          should(material).have.property('number').be.type('string');
-          should(material).have.property('type').be.type('string');
-          should(material).have.property('color').be.type('string');
-          should(material).have.property('batch').be.type('string');
-          should(material).have.property('material_id').be.type('string');
-          should(material).have.property('note_id');
-          should(material).have.property('user_id').be.type('string');
+        should(res.body).matchEach(sample => {
+          should(sample).have.only.keys('_id', 'number', 'type', 'color', 'batch', 'material_id', 'note_id', 'user_id');
+          should(sample).have.property('_id').be.type('string');
+          should(sample).have.property('number').be.type('string');
+          should(sample).have.property('type').be.type('string');
+          should(sample).have.property('color').be.type('string');
+          should(sample).have.property('batch').be.type('string');
+          should(sample).have.property('material_id').be.type('string');
+          should(sample).have.property('note_id');
+          should(sample).have.property('user_id').be.type('string');
         });
         done();
       });
@@ -70,6 +69,94 @@ describe('/sample', () => {
     });
   });
 
+  describe('GET /samples/{group}', () => {
+    it('returns all new samples', done => {
+      TestHelper.request(server, done, {
+        method: 'get',
+        url: '/samples/new',
+        auth: {basic: 'admin'},
+        httpStatus: 200
+      }).end((err, res) => {
+        if (err) return done(err);
+        const json = require('../test/db.json');
+        let asyncCounter = res.body.length;
+        should(res.body).have.lengthOf(json.collections.samples.filter(e => e.status === 0).length);
+        should(res.body).matchEach(sample => {
+          should(sample).have.only.keys('_id', 'number', 'type', 'color', 'batch', 'material_id', 'note_id', 'user_id');
+          should(sample).have.property('_id').be.type('string');
+          should(sample).have.property('number').be.type('string');
+          should(sample).have.property('type').be.type('string');
+          should(sample).have.property('color').be.type('string');
+          should(sample).have.property('batch').be.type('string');
+          should(sample).have.property('material_id').be.type('string');
+          should(sample).have.property('note_id');
+          should(sample).have.property('user_id').be.type('string');
+          SampleModel.findById(sample._id).lean().exec((err, data) => {
+            should(data).have.property('status', 0);
+            if (--asyncCounter === 0) {
+              done();
+            }
+          });
+        });
+        done();
+      });
+    });
+    it('returns all deleted samples', done => {
+      TestHelper.request(server, done, {
+        method: 'get',
+        url: '/samples/deleted',
+        auth: {basic: 'admin'},
+        httpStatus: 200
+      }).end((err, res) => {
+        if (err) return done(err);
+        const json = require('../test/db.json');
+        let asyncCounter = res.body.length;
+        should(res.body).have.lengthOf(json.collections.samples.filter(e => e.status === -1).length);
+        should(res.body).matchEach(sample => {
+          should(sample).have.only.keys('_id', 'number', 'type', 'color', 'batch', 'material_id', 'note_id', 'user_id');
+          should(sample).have.property('_id').be.type('string');
+          should(sample).have.property('number').be.type('string');
+          should(sample).have.property('type').be.type('string');
+          should(sample).have.property('color').be.type('string');
+          should(sample).have.property('batch').be.type('string');
+          should(sample).have.property('material_id').be.type('string');
+          should(sample).have.property('note_id');
+          should(sample).have.property('user_id').be.type('string');
+          SampleModel.findById(sample._id).lean().exec((err, data) => {
+            should(data).have.property('status', -1);
+            if (--asyncCounter === 0) {
+              done();
+            }
+          });
+        });
+        done();
+      });
+    });
+    it('rejects requests from a write user', done => {
+      TestHelper.request(server, done, {
+        method: 'get',
+        url: '/samples/new',
+        auth: {basic: 'janedoe'},
+        httpStatus: 403
+      });
+    });
+    it('rejects an API key', done => {
+      TestHelper.request(server, done, {
+        method: 'get',
+        url: '/samples/new',
+        auth: {key: 'admin'},
+        httpStatus: 401
+      });
+    });
+    it('rejects unauthorized requests', done => {
+      TestHelper.request(server, done, {
+        method: 'get',
+        url: '/samples/new',
+        httpStatus: 401
+      });
+    });
+  });
+
   describe('PUT /sample/{id}', () => {
     it('returns the right sample', done => {
       TestHelper.request(server, done, {
@@ -194,12 +281,10 @@ describe('/sample', () => {
       }).end(err => {
         if (err) return done(err);
         NoteFieldModel.findOne({name: 'not allowed for new applications'}).lean().exec((err, data) => {
-          console.log(data);
           if (err) return done(err);
           should(data).have.property('qty', 1);
           NoteFieldModel.findOne({name: 'field1'}).lean().exec((err, data) => {
             if (err) return done(err);
-            console.log(data);
             should(data).have.property('qty', 1);
             done();
           });
@@ -233,7 +318,6 @@ describe('/sample', () => {
         if (err) return done (err);
         NoteModel.findById(res.body.note_id).lean().exec((err, data) => {
           if (err) return done (err);
-          console.log(data);
           should(data).not.be.null();
           should(data).have.property('comment', 'Stoff gesperrt');
           should(data).have.property('sample_references').have.lengthOf(0);
@@ -448,7 +532,6 @@ describe('/sample', () => {
         setTimeout(() => {  // background action takes some time before we can check
           NoteModel.findById('500000000000000000000003').lean().exec((err, data: any) => {
             if (err) return done(err);
-            console.log(data);
             should(data).have.property('sample_references').with.lengthOf(1);
             should(data.sample_references[0].id.toString()).be.eql('400000000000000000000003');
             should(data.sample_references[0]).have.property('relation', 'part to sample');

src/routes/sample.ts

@@ -22,6 +22,22 @@ router.get('/samples', (req, res, next) => {
   })
 });
 
+router.get('/samples/:group(new|deleted)', (req, res, next) => {
+  if (!req.auth(res, ['maintain', 'admin'], 'basic')) return;
+
+  let status;
+  switch (req.params.group) {
+    case 'new': status = 0;
+      break;
+    case 'deleted': status = -1;
+      break;
+  }
+  SampleModel.find({status: status}).lean().exec((err, data) => {
+    if (err) return next(err);
+    res.json(_.compact(data.map(e => SampleValidate.output(e))));  // validate all and filter null values from validation errors
+  })
+});
+
 router.put('/sample/' + IdValidate.parameter(), (req, res, next) => {
   if (!req.auth(res, ['write', 'maintain', 'dev', 'admin'], 'basic')) return;
 
@@ -33,6 +49,7 @@ router.put('/sample/' + IdValidate.parameter(), (req, res, next) => {
     if (!sampleData) {
       return res.status(404).json({status: 'Not found'});
     }
+
     // only maintain and admin are allowed to edit other user's data
     if (sampleData.user_id.toString() !== req.authDetails.id && !req.auth(res, ['maintain', 'admin'], 'basic')) return;
 
@@ -48,12 +65,12 @@ router.put('/sample/' + IdValidate.parameter(), (req, res, next) => {
       if (sampleData.note_id !== null) {  // old notes data exists
         const data = await NoteModel.findById(sampleData.note_id).lean().exec().catch(err => {next(err);}) as any;
         if (data instanceof Error) return;
-        newNotes = !_.isEqual(_.pick(IdValidate.stringify(data), _.keys(sample.notes)), sample.notes);
+        newNotes = !_.isEqual(_.pick(IdValidate.stringify(data), _.keys(sample.notes)), sample.notes);  // check if notes were changed
         if (newNotes) {
           if (data.hasOwnProperty('custom_fields')) {  // update note_fields
             customFieldsChange(Object.keys(data.custom_fields), -1);
           }
-          NoteModel.findByIdAndDelete(sampleData.note_id).lean().exec(err => {  // delete old notes
+          await NoteModel.findByIdAndDelete(sampleData.note_id).lean().exec(err => {  // delete old notes
             if (err) return console.error(err);
           });
         }
@@ -74,7 +91,8 @@ router.put('/sample/' + IdValidate.parameter(), (req, res, next) => {
     if (!_.isEqual(_.pick(IdValidate.stringify(sampleData), _.keys(sample)), _.omit(sample, ['notes']))) {
       sample.status = 0;
     }
-    SampleModel.findByIdAndUpdate(req.params.id, sample, {new: true}).lean().exec((err, data) => {
+
+    await SampleModel.findByIdAndUpdate(req.params.id, sample, {new: true}).lean().exec((err, data) => {
       if (err) return next(err);
       res.json(SampleValidate.output(data));
     });
@@ -90,12 +108,13 @@ router.delete('/sample/' + IdValidate.parameter(), (req, res, next) => {
     if (!sampleData) {
       return res.status(404).json({status: 'Not found'});
     }
+
     // only maintain and admin are allowed to edit other user's data
     if (sampleData.user_id.toString() !== req.authDetails.id && !req.auth(res, ['maintain', 'admin'], 'basic')) return;
 
-    SampleModel.findByIdAndUpdate(req.params.id, {status: -1}).lean().exec(err => {  // set sample status
+    await SampleModel.findByIdAndUpdate(req.params.id, {status: -1}).lean().exec(err => {  // set sample status
       if (err) return next(err);
-      if (sampleData.note_id !== null) {
+      if (sampleData.note_id !== null) {  // handle notes
         NoteModel.findById(sampleData.note_id).lean().exec((err, data: any) => {  // find notes to update note_fields
           if (err) return next(err);
           if (data.hasOwnProperty('custom_fields')) {  // update note_fields
@@ -124,15 +143,15 @@ router.post('/sample/new', async (req, res, next) => {
     customFieldsChange(Object.keys(sample.notes.custom_fields), 1);
   }
 
-  sample.status = 0;
+  sample.status = 0;  // set status to new
   sample.number = await numberGenerate(sample, req, res, next);
   if (!sample.number) return;
-  new NoteModel(sample.notes).save((err, data) => {
+
+  await new NoteModel(sample.notes).save((err, data) => {  // save notes
     if (err) return next(err);
     delete sample.notes;
     sample.note_id = data._id;
     sample.user_id = req.authDetails.id;
-    console.log(sample);
     new SampleModel(sample).save((err, data) => {
       if (err) return next(err);
       res.json(SampleValidate.output(data.toObject()));
@@ -153,7 +172,7 @@ router.get('/sample/notes/fields', (req, res, next) => {
 module.exports = router;
 
 
-async function numberGenerate (sample, req, res, next) {  // validate number, returns false if invalid
+async function numberGenerate (sample, req, res, next) {  // generate number, returns false on error
   const sampleData = await SampleModel
     .find({number: new RegExp('^' + req.authDetails.location + '[0-9]+$', 'm')})
     .lean()
@@ -180,7 +199,8 @@ async function materialCheck (sample, res, next, id = sample.material_id) {  //
 function sampleRefCheck (sample, res, next) {  // validate sample_references, resolves false for invalid reference
   return new Promise(resolve => {
     if (sample.notes.sample_references.length > 0) {  // there are sample_references
-      let referencesCount = sample.notes.sample_references.length;
+      let referencesCount = sample.notes.sample_references.length;  // count to keep track of running async operations
+
       sample.notes.sample_references.forEach(reference => {
         SampleModel.findById(reference.id).lean().exec((err, data) => {
           if (err) {next(err); resolve(false)}
@@ -189,7 +209,7 @@ function sampleRefCheck (sample, res, next) {  // validate sample_references, re
             return resolve(false);
           }
           referencesCount --;
-          if (referencesCount <= 0) {
+          if (referencesCount <= 0) {  // all async requests done
             resolve(true);
           }
         });
@@ -201,7 +221,7 @@ function sampleRefCheck (sample, res, next) {  // validate sample_references, re
   });
 }
 
-function customFieldsChange (fields, amount) {
+function customFieldsChange (fields, amount) {  // update custom_fields and respective quantities
   fields.forEach(field => {
     NoteFieldModel.findOneAndUpdate({name: field}, {$inc: {qty: amount}}, {new: true}).lean().exec((err, data: any) => {  // check if field exists
       if (err) return console.error(err);

src/routes/template.spec.ts

@@ -200,7 +200,6 @@ describe('/template', () => {
           httpStatus: 200,
           req: {parameters: [{name: 'time', range: {type: 'array'}}]}
         }).end((err, res) => {
-          console.log(res.body);
           if (err) return done(err);
           should(_.omit(res.body, '_id')).be.eql({name: 'heat treatment', version: 2, number_prefix: 'A', parameters: [{name: 'time', range: {type: 'array'}}]});
           done();

src/routes/template.ts

@@ -14,7 +14,7 @@ const router = express.Router();
 router.get('/template/:collection(measurements|treatments)', (req, res, next) => {
   if (!req.auth(res, ['read', 'write', 'maintain', 'dev', 'admin'], 'basic')) return;
 
-  req.params.collection = req.params.collection.replace(/s$/g, '');
+  req.params.collection = req.params.collection.replace(/s$/g, '');  // remove trailing s
   model(req).find({}).lean().exec((err, data) => {
      if (err) next (err);
      res.json(_.compact(data.map(e => TemplateValidate.output(e, req.params.collection))));  // validate all and filter null values from validation errors
@@ -52,8 +52,8 @@ router.put('/template/:collection(measurement|treatment)/' + IdValidate.paramete
   }
 
   if (!_.isEqual(_.pick(templateData, _.keys(template)), template)) {  // data was changed
-    template.version = templateData.version + 1;
-    await new (model(req))(_.assign({}, _.omit(templateData, ['_id', '__v']), template)).save((err, data) => {
+    template.version = templateData.version + 1;  // increase version
+    await new (model(req))(_.assign({}, _.omit(templateData, ['_id', '__v']), template)).save((err, data) => {  // save new template, fill with old properties
       if (err) next (err);
       res.json(TemplateValidate.output(data.toObject(), req.params.collection));
     });
@@ -73,7 +73,7 @@ router.post('/template/:collection(measurement|treatment)/new', async (req, res,
     if (!await numberPrefixCheck(template, req, res, next)) return;
   }
 
-  template.version = 1;
+  template.version = 1;  // set template version
   await new (model(req))(template).save((err, data) => {
     if (err) next (err);
     res.json(TemplateValidate.output(data.toObject(), req.params.collection));
@@ -84,7 +84,7 @@ router.post('/template/:collection(measurement|treatment)/new', async (req, res,
 module.exports = router;
 
 
-async function numberPrefixCheck (template, req, res, next) {
+async function numberPrefixCheck (template, req, res, next) {  // check if number_prefix is available
   const data = await model(req).findOne({number_prefix: template.number_prefix}).lean().exec().catch(err => {next(err); return false;}) as any;
   if (data) {
     res.status(400).json({status: 'Number prefix already taken'});
@@ -93,6 +93,6 @@ async function numberPrefixCheck (template, req, res, next) {
   return true;
 }
 
-function model (req) {
+function model (req) {  // return right template model
   return req.params.collection === 'treatment' ? TemplateTreatmentModel : TemplateMeasurementModel;
 }

src/routes/user.ts

@@ -20,14 +20,10 @@ router.get('/users', (req, res) => {
 });
 
 router.get('/user:username([/](?!key|new).?*|/?)', (req, res, next) => {  // this path matches /user, /user/ and /user/xxx, but not /user/key or user/new. See https://forbeslindesay.github.io/express-route-tester/ for the generated regex
-  req.params.username = req.params[0];
   if (!req.auth(res, ['read', 'write', 'maintain', 'dev', 'admin'], 'basic')) return;
-  let username = req.authDetails.username;
-  if (req.params.username !== undefined) {
-    if (!req.auth(res, ['admin'], 'basic')) return;
-    username = req.params.username;
-  }
 
+  const username = getUsername(req, res);
+  if (!username) return;
   UserModel.findOne({name: username}).lean().exec(  (err, data:any) => {
     if (err) return next(err);
     if (data) {
@@ -39,14 +35,13 @@ router.get('/user:username([/](?!key|new).?*|/?)', (req, res, next) => {  // thi
   });
 });
 
-router.put('/user:username([/](?!key|new).?*|/?)', (req, res, next) => {  // this path matches /user, /user/ and /user/xxx, but not /user/key or user/new
-  req.params.username = req.params[0];
+router.put('/user:username([/](?!key|new).?*|/?)', async (req, res, next) => {  // this path matches /user, /user/ and /user/xxx, but not /user/key or user/new
   if (!req.auth(res, ['read', 'write', 'maintain', 'dev', 'admin'], 'basic')) return;
-  let username = req.authDetails.username;
-  if (req.params.username !== undefined) {
-    if (!req.auth(res, ['admin'], 'basic')) return;
-    username = req.params.username;
-  }
+
+  const username = getUsername(req, res);
+  if (!username) return;
+  console.log(username);
+
   const {error, value: user} = UserValidate.input(req.body, 'change' + (req.authDetails.level === 'admin'? 'admin' : ''));
   if (error) return res400(error, res);
 
@@ -56,45 +51,25 @@ router.put('/user:username([/](?!key|new).?*|/?)', (req, res, next) => {  // thi
 
   // check that user does not already exist if new name was specified
   if (user.hasOwnProperty('name') && user.name !== username) {
-    UserModel.find({name: user.name}).lean().exec(  (err, data:any) => {
-      if (err) return next(err);
-      if (data.length > 0 || UserValidate.isSpecialName(user.name)) {
-        res.status(400).json({status: 'Username already taken'});
-        return;
-      }
+    if (!await usernameCheck(user.name, res, next)) return;
+  }
 
-      UserModel.findOneAndUpdate({name: username}, user, {new: true}).lean().exec(  (err, data:any) => {
-        if (err) return next(err);
-        if (data) {
-          res.json(UserValidate.output(data));
-        }
-        else {
-          res.status(404).json({status: 'Not found'});
-        }
-      });
-    });
-  }
-  else {
-    UserModel.findOneAndUpdate({name: username}, user, {new: true}).lean().exec(  (err, data:any) => {
-      if (err) return next(err);
-      if (data) {
-        res.json(UserValidate.output(data));  // validate all and filter null values from validation errors
-      }
-      else {
-        res.status(404).json({status: 'Not found'});
-      }
-    });
-  }
+  await UserModel.findOneAndUpdate({name: username}, user, {new: true}).lean().exec(  (err, data:any) => {
+    if (err) return next(err);
+    if (data) {
+      res.json(UserValidate.output(data));
+    }
+    else {
+      res.status(404).json({status: 'Not found'});
+    }
+  });
 });
 
 router.delete('/user:username([/](?!key|new).?*|/?)', (req, res, next) => {  // this path matches /user, /user/ and /user/xxx, but not /user/key or user/new. See https://forbeslindesay.github.io/express-route-tester/ for the generated regex
-  req.params.username = req.params[0];
   if (!req.auth(res, ['read', 'write', 'maintain', 'dev', 'admin'], 'basic')) return;
-  let username = req.authDetails.username;
-  if (req.params.username !== undefined) {
-    if (!req.auth(res, ['admin'], 'basic')) return;
-    username = req.params.username;
-  }
+
+  const username = getUsername(req, res);
+  if (!username) return;
 
   UserModel.findOneAndDelete({name: username}).lean().exec(  (err, data:any) => {
     if (err) return next(err);
@@ -116,7 +91,7 @@ router.get('/user/key', (req, res, next) => {
   });
 });
 
-router.post('/user/new', (req, res, next) => {
+router.post('/user/new', async (req, res, next) => {
   if (!req.auth(res, ['admin'], 'basic')) return;
 
   // validate input
@@ -124,20 +99,14 @@ router.post('/user/new', (req, res, next) => {
   if (error) return res400(error, res);
 
   // check that user does not already exist
-  UserModel.find({name: user.name}).lean().exec(  (err, data:any) => {
-    if (err) return next(err);
-    if (data.length > 0  || UserValidate.isSpecialName(user.name)) {
-      res.status(400).json({status: 'Username already taken'});
-      return;
-    }
+  if (!await usernameCheck(user.name, res, next)) return;
 
-    user.key = mongoose.Types.ObjectId();  // use object id as unique API key
-    bcrypt.hash(user.pass, 10, (err, hash) => {  // password hashing
-      user.pass = hash;
-      new UserModel(user).save((err, data) => {  // store user
-        if (err) return next(err);
-        res.json(UserValidate.output(data.toObject()));
-      });
+  user.key = mongoose.Types.ObjectId();  // use object id as unique API key
+  bcrypt.hash(user.pass, 10, (err, hash) => {  // password hashing
+    user.pass = hash;
+    new UserModel(user).save((err, data) => {  // store user
+      if (err) return next(err);
+      res.json(UserValidate.output(data.toObject()));
     });
   });
 });
@@ -147,11 +116,14 @@ router.post('/user/passreset', (req, res, next) => {
   UserModel.find({name: req.body.name, email: req.body.email}).lean().exec( (err, data: any) => {
     if (err) return next(err);
     if (data.length === 1) {  // it exists
-      const newPass = Math.random().toString(36).substring(2);
+      const newPass = Math.random().toString(36).substring(2);  // generate temporary password
       bcrypt.hash(newPass, 10, (err, hash) => {  // password hashing
         if (err) return next(err);
+
         UserModel.findByIdAndUpdate(data[0]._id, {pass: hash}, err => {  // write new password
           if (err) return next(err);
+
+          // send email
           mail(data[0].email, 'Your new password for the DFOP database', 'Hi, <br><br> You requested to reset your password.<br>Your new password is:<br><br>' + newPass + '<br><br>If you did not request a password reset, talk to the sysadmin quickly!<br><br>Have a nice day.<br><br>The DFOP team', err => {
             if (err) return next(err);
             res.json({status: 'OK'});
@@ -166,4 +138,27 @@ router.post('/user/passreset', (req, res, next) => {
 });
 
 
-module.exports = router;
+module.exports = router;
+
+function getUsername (req, res) {  // returns username or false if action is not allowed
+  req.params.username = req.params[0];  // because of path regex
+  if (req.params.username !== undefined) {  // different username than request user
+    if (!req.auth(res, ['admin'], 'basic')) return false;
+    return req.params.username;
+  }
+  else {
+    return req.authDetails.username;
+  }
+}
+
+async function usernameCheck (name, res, next) {  // check if username is already taken
+  const userData = await UserModel.findOne({name: name}).lean().exec().catch(err => next(err)) as any;
+  if (userData instanceof Error) return false;
+  console.log(userData);
+  console.log(UserValidate.isSpecialName(name));
+  if (userData || UserValidate.isSpecialName(name)) {
+    res.status(400).json({status: 'Username already taken'});
+    return false;
+  }
+  return true;
+}

src/routes/validate/condition.ts

@@ -18,7 +18,7 @@ export default class ConditionValidate {
       )
   }
 
-  static input (data, param) {
+  static input (data, param) {  // validate input, set param to 'new' to make all attributes required
     if (param === 'new') {
       return Joi.object({
         sample_id: IdValidate.get().required(),
@@ -36,7 +36,7 @@ export default class ConditionValidate {
     }
   }
 
-  static output (data) {
+  static output (data) {  // validate output and strip unwanted properties, returns null if not valid
     data = IdValidate.stringify(data);
     const {value, error} = Joi.object({
       _id: IdValidate.get(),

src/routes/validate/id.ts

@@ -3,11 +3,11 @@ import Joi from '@hapi/joi';
 export default class IdValidate {
   private static id = Joi.string().pattern(new RegExp('[0-9a-f]{24}')).length(24);
 
-  static get () {
+  static get () {  // return joi validation
     return this.id;
   }
 
-  static valid (id) {
+  static valid (id) {  // validate id
     return this.id.validate(id).error === undefined;
   }
 
@@ -15,11 +15,14 @@ export default class IdValidate {
     return ':id([0-9a-f]{24})';
   }
 
-  static stringify (data) {
+  static stringify (data) {  // convert all ObjectID objects to plain strings
     Object.keys(data).forEach(key => {
-      if (data[key] !== null && data[key].hasOwnProperty('_bsontype') && data[key]._bsontype === 'ObjectID') {
+      if (data[key] !== null && data[key].hasOwnProperty('_bsontype') && data[key]._bsontype === 'ObjectID') {  // stringify id
         data[key] = data[key].toString();
       }
+      else if (typeof data[key] === 'object' && data[key] !== null) {  // deeper into recursion
+        data[key] = this.stringify(data[key]);
+      }
     });
     return data;
   }

src/routes/validate/material.ts

@@ -40,7 +40,7 @@ export default class MaterialValidate {  // validate input for material
       }))
   };
 
-  static input (data, param) {  // validate data, param: new(everything required)/change(available attributes are validated)
+  static input (data, param) {  // validate input, set param to 'new' to make all attributes required
     if (param === 'new') {
       return joi.object({
         name: this.material.name.required(),
@@ -68,7 +68,7 @@ export default class MaterialValidate {  // validate input for material
     }
   }
 
-  static output (data) {  // validate output from database for needed properties, strip everything else
+  static output (data) {  // validate output and strip unwanted properties, returns null if not valid
     data = IdValidate.stringify(data);
     const {value, error} = joi.object({
       _id: IdValidate.get(),

src/routes/validate/measurement.ts

@@ -15,7 +15,7 @@ export default class MeasurementValidate {
       )
   };
 
-  static input (data, param) {
+  static input (data, param) {  // validate input, set param to 'new' to make all attributes required
     if (param === 'new') {
       return Joi.object({
         condition_id: IdValidate.get().required(),
@@ -33,7 +33,7 @@ export default class MeasurementValidate {
     }
   }
 
-  static output (data) {
+  static output (data) {  // validate output and strip unwanted properties, returns null if not valid
     data = IdValidate.stringify(data);
     const {value, error} = Joi.object({
       _id: IdValidate.get(),

src/routes/validate/note_field.ts

@@ -8,7 +8,7 @@ export default class NoteFieldValidate {
     qty: Joi.number()
   };
 
-  static output (data) {
+  static output (data) {  // validate output and strip unwanted properties, returns null if not valid
     const {value, error} = Joi.object({
       name: this.note_field.name,
       qty: this.note_field.qty

src/routes/validate/parameters.ts

@@ -4,7 +4,7 @@ export default class ParametersValidate {
   static input (data, parameters, param) {  // data to validate, parameters from template, param: 'new', 'change'
     let joiObject = {};
     parameters.forEach(parameter => {
-      if (parameter.range.hasOwnProperty('values')) {
+      if (parameter.range.hasOwnProperty('values')) {  // append right validation method according to parameter
         joiObject[parameter.name] = Joi.alternatives()
           .try(Joi.string().max(128), Joi.number(), Joi.boolean())
           .valid(...parameter.range.values);

src/routes/validate/res400.ts

@@ -1,3 +1,5 @@
+// respond with 400 and include error details from the joi validation
+
 export default function res400 (error, res) {
   res.status(400).json({status: 'Invalid body format', details: error.details[0].message});
 }

src/routes/validate/sample.ts

@@ -41,7 +41,7 @@ export default class SampleValidate {
     })
   };
 
-  static input (data, param) {  // validate data, param: new(everything required)/change(available attributes are validated)
+  static input (data, param) {  // validate input, set param to 'new' to make all attributes required
     if (param === 'new') {
       return Joi.object({
         color: this.sample.color.required(),
@@ -65,7 +65,7 @@ export default class SampleValidate {
     }
   }
 
-  static output (data) {
+  static output (data) {  // validate output and strip unwanted properties, returns null if not valid
     data = IdValidate.stringify(data);
     const {value, error} = Joi.object({
       _id: IdValidate.get(),

src/routes/validate/template.ts

@@ -43,7 +43,7 @@ export default class TemplateValidate {
       )
   };
 
-  static input (data, param, template) {  // validate data, param: new(everything required)/change(available attributes are validated)
+  static input (data, param, template) {  // validate input, set param to 'new' to make all attributes required
     if (param === 'new') {
       if (template === 'treatment') {
         return Joi.object({
@@ -79,10 +79,10 @@ export default class TemplateValidate {
     }
   }
 
-  static output (data, template) {  // validate output from database for needed properties, strip everything else
+  static output (data, template) {  // validate output and strip unwanted properties, returns null if not valid
     data = IdValidate.stringify(data);
     let joiObject;
-    if (template === 'treatment') {
+    if (template === 'treatment') {  // differentiate between measurement and treatment (has number_prefix) template
       joiObject = {
         _id: IdValidate.get(),
         name: this.template.name,

src/routes/validate/user.ts

@@ -33,7 +33,7 @@ export default class UserValidate {  // validate input for user
 
   private static specialUsernames = ['admin', 'user', 'key', 'new', 'passreset'];  // names a user cannot take
 
-  static input (data, param) {
+  static input (data, param) {  // validate input, set param to 'new' to make all attributes required
     if (param === 'new') {
       return Joi.object({
         name: this.user.name.required(),
@@ -68,7 +68,7 @@ export default class UserValidate {  // validate input for user
     }
   }
 
-  static output (data) {  // validate output from database for needed properties, strip everything else
+  static output (data) {  // validate output and strip unwanted properties, returns null if not valid
     data = IdValidate.stringify(data);
     const {value, error} = Joi.object({
       _id: IdValidate.get(),

src/test/helper.ts

@@ -4,13 +4,13 @@ import db from "../db";
 
 
 export default class TestHelper {
-  public static auth = {
+  public static auth = {  // test user credentials
     admin: {pass: 'Abc123!#', key: '000000000000000000001003'},
     janedoe: {pass: 'Xyz890*)', key: '000000000000000000001002'},
     user: {pass: 'Xyz890*)', key: '000000000000000000001001'},
     johnnydoe: {pass: 'Xyz890*)', key: '000000000000000000001004'}
   }
-  public static res = {
+  public static res = {  // default responses
     400: {status: 'Bad request'},
     401: {status: 'Unauthorized'},
     403: {status: 'Forbidden'},
@@ -40,10 +40,10 @@ export default class TestHelper {
 
   static request (server, done, options) {  // options in form: {method, url, auth: {key/basic: 'name' or 'key'/{name, pass}}, httpStatus, req, res}
     let st = supertest(server);
-    if (options.hasOwnProperty('auth') && options.auth.hasOwnProperty('key')) {
+    if (options.hasOwnProperty('auth') && options.auth.hasOwnProperty('key')) {  // resolve API key
       options.url += '?key=' + (this.auth.hasOwnProperty(options.auth.key)? this.auth[options.auth.key].key : options.auth.key);
     }
-    switch (options.method) {
+    switch (options.method) {  // http method
       case 'get':
         st = st.get(options.url)
         break;
@@ -57,10 +57,10 @@ export default class TestHelper {
         st = st.delete(options.url)
         break;
     }
-    if (options.hasOwnProperty('req')) {
+    if (options.hasOwnProperty('req')) {  // request body
       st = st.send(options.req);
     }
-    if (options.hasOwnProperty('auth') && options.auth.hasOwnProperty('basic')) {
+    if (options.hasOwnProperty('auth') && options.auth.hasOwnProperty('basic')) {  // resolve basic auth
       if (this.auth.hasOwnProperty(options.auth.basic)) {
         st = st.auth(options.auth.basic, this.auth[options.auth.basic].pass)
       }
@@ -70,21 +70,21 @@ export default class TestHelper {
     }
     st = st.expect('Content-type', /json/)
       .expect(options.httpStatus);
-    if (options.hasOwnProperty('res')) {
+    if (options.hasOwnProperty('res')) {  // evaluate result
       return st.end((err, res) => {
         if (err) return done (err);
         should(res.body).be.eql(options.res);
         done();
       });
     }
-    else if (this.res.hasOwnProperty(options.httpStatus) && options.default !== false) {
+    else if (this.res.hasOwnProperty(options.httpStatus) && options.default !== false) {  // evaluate default results
       return st.end((err, res) => {
         if (err) return done (err);
         should(res.body).be.eql(this.res[options.httpStatus]);
         done();
       });
     }
-    else {
+    else {  // return object to do .end() manually
       return st;
     }
   }

src/test/loadDev.ts

@@ -1,5 +1,7 @@
 import db from '../db';
 
+// script to load test db into dev db for a clean start
+
 db.connect('dev', () => {
   console.info('dropping data...');
   db.drop(() => {  // reset database