GET and POST method for measurement

src/index.ts

@@ -50,6 +50,7 @@ app.use('/', require('./routes/material'));
 app.use('/', require('./routes/template'));
 app.use('/', require('./routes/user'));
 app.use('/', require('./routes/condition'));
+app.use('/', require('./routes/measurement'));
 
 // static files
 app.use('/static', express.static('static'));

src/models/measurement.ts

@@ -0,0 +1,12 @@
+import mongoose from 'mongoose';
+import ConditionModel from './condition';
+import MeasurementTemplateModel from './measurement_template';
+
+const MeasurementSchema = new mongoose.Schema({
+  condition_id: {type: mongoose.Schema.Types.ObjectId, ref: ConditionModel},
+  values: mongoose.Schema.Types.Mixed,
+  status: Number,
+  measurement_template: {type: mongoose.Schema.Types.ObjectId, ref: MeasurementTemplateModel}
+});
+
+export default mongoose.model('measurement', MeasurementSchema);

src/routes/condition.spec.ts

@@ -1,7 +1,7 @@
 import should from 'should/as-function';
 import ConditionModel from '../models/condition';
 import TestHelper from "../test/helper";
-
+// TODO: status
 
 describe('/condition', () => {
   let server;

src/routes/condition.ts

@@ -49,7 +49,7 @@ router.put('/condition/' + IdValidate.parameter(), async (req, res, next) => {
   if (!await treatmentCheck(condition, 'change', res, next)) return;
 
   console.log(condition);
-  ConditionModel.findByIdAndUpdate(req.params.id, condition, {new: true}).lean().exec((err, data) => {
+  await ConditionModel.findByIdAndUpdate(req.params.id, condition, {new: true}).lean().exec((err, data) => {
     if (err) return next(err);
     res.json(ConditionValidate.output(data));
   });
@@ -64,7 +64,7 @@ router.delete('/condition/' + IdValidate.parameter(), (req, res, next) => {
       res.status(404).json({status: 'Not found'});
     }
     if (!await sampleIdCheck(data, req, res, next)) return;
-    ConditionModel.findByIdAndDelete(req.params.id).lean().exec(async err => {
+    await ConditionModel.findByIdAndDelete(req.params.id).lean().exec(async err => {
       if (err) return next(err);
       res.json({status: 'OK'});
     });
@@ -81,7 +81,7 @@ router.post('/condition/new', async (req, res, next) => {
   if (!await numberCheck(condition, res, next)) return;
   if (!await treatmentCheck(condition, 'new', res, next)) return;
 
-  new ConditionModel(condition).save((err, data) => {
+  await new ConditionModel(condition).save((err, data) => {
     if (err) return next(err);
     res.json(ConditionValidate.output(data.toObject()));
   });
@@ -113,7 +113,7 @@ async function numberCheck (condition, res, next) {  // validate number, returns
 
 async function treatmentCheck (condition, param, res, next) {
   const treatmentData = await TreatmentTemplateModel.findById(condition.treatment_template).lean().exec().catch(err => {next(err); return false;}) as any;
-  if (!treatmentData) {  // sample_id not found
+  if (!treatmentData) {  // template not found
     res.status(400).json({status: 'Treatment template not available'});
     return false
   }

src/routes/material.spec.ts

@@ -1,7 +1,7 @@
 import should from 'should/as-function';
 import MaterialModel from '../models/material';
 import TestHelper from "../test/helper";
-
+// TODO: status
 
 describe('/material', () => {
   let server;

src/routes/measurement.spec.ts

@@ -0,0 +1,260 @@
+import should from 'should/as-function';
+import MeasurementModel from '../models/measurement';
+import TestHelper from "../test/helper";
+
+describe('/measurement', () => {
+  let server;
+  before(done => TestHelper.before(done));
+  beforeEach(done => server = TestHelper.beforeEach(server, done));
+  afterEach(done => TestHelper.afterEach(server, done));
+
+  describe('GET /mesurement/{id}', () => {
+    it('returns the right measurement', done => {
+      TestHelper.request(server, done, {
+        method: 'get',
+        url: '/measurement/800000000000000000000001',
+        auth: {basic: 'janedoe'},
+        httpStatus: 200,
+        res: {_id: '800000000000000000000001', condition_id: '700000000000000000000001', values: {dpt: [[3997.12558,98.00555],[3995.08519,98.03253],[3993.04480,98.02657]]}, measurement_template: '300000000000000000000001'}
+      });
+    });
+    it('returns the measurement for an API key', done => {
+      TestHelper.request(server, done, {
+        method: 'get',
+        url: '/measurement/800000000000000000000001',
+        auth: {key: 'janedoe'},
+        httpStatus: 200,
+        res: {_id: '800000000000000000000001', condition_id: '700000000000000000000001', values: {dpt: [[3997.12558,98.00555],[3995.08519,98.03253],[3993.04480,98.02657]]}, measurement_template: '300000000000000000000001'}
+      });
+    });
+    it('rejects an invalid id', done => {
+      TestHelper.request(server, done, {
+        method: 'get',
+        url: '/measurement/8000000000h0000000000001',
+        auth: {basic: 'janedoe'},
+        httpStatus: 404
+      });
+    });
+    it('rejects an unknown id', done => {
+      TestHelper.request(server, done, {
+        method: 'get',
+        url: '/measurement/000000000000000000000001',
+        auth: {basic: 'janedoe'},
+        httpStatus: 404
+      });
+    });
+    it('rejects unauthorized requests', done => {
+      TestHelper.request(server, done, {
+        method: 'get',
+        url: '/measurement/800000000000000000000001',
+        httpStatus: 401
+      });
+    });
+  });
+
+  describe('POST /measurement/new', () => {
+    it('returns the right measurement', done => {
+      TestHelper.request(server, done, {
+        method: 'post',
+        url: '/measurement/new',
+        auth: {basic: 'janedoe'},
+        httpStatus: 200,
+        req: {condition_id: '700000000000000000000001', values: {'weight %': 0.8, 'standard deviation': 0.1}, measurement_template: '300000000000000000000002'}
+      }).end((err, res) => {
+        if (err) return done(err);
+        should(res.body).have.only.keys('_id', 'condition_id', 'values', 'measurement_template');
+        should(res.body).have.property('_id').be.type('string');
+        should(res.body).have.property('condition_id', '700000000000000000000001');
+        should(res.body).have.property('measurement_template', '300000000000000000000002');
+        should(res.body).have.property('values');
+        should(res.body.values).have.property('weight %', 0.8);
+        should(res.body.values).have.property('standard deviation', 0.1);
+        done();
+      });
+    });
+    it('stores the measurement', done => {
+      TestHelper.request(server, done, {
+        method: 'post',
+        url: '/measurement/new',
+        auth: {basic: 'janedoe'},
+        httpStatus: 200,
+        req: {condition_id: '700000000000000000000001', values: {'weight %': 0.8, 'standard deviation': 0.1}, measurement_template: '300000000000000000000002'}
+      }).end((err, res) => {
+        if (err) return done(err);
+        MeasurementModel.findById(res.body._id).lean().exec((err, data: any) => {
+          should(data).have.only.keys('_id', 'condition_id', 'values', 'measurement_template', '__v');
+          should(data.condition_id.toString()).be.eql('700000000000000000000001');
+          should(data.measurement_template.toString()).be.eql('300000000000000000000002');
+          should(data).have.property('values');
+          should(data.values).have.property('weight %', 0.8);
+          should(data.values).have.property('standard deviation', 0.1);
+          done();
+        });
+      });
+    });
+    it('rejects an invalid condition id', done => {
+      TestHelper.request(server, done, {
+        method: 'post',
+        url: '/measurement/new',
+        auth: {basic: 'janedoe'},
+        httpStatus: 400,
+        req: {condition_id: '700000000000h00000000001', values: {'weight %': 0.8, 'standard deviation': 0.1}, measurement_template: '300000000000000000000002'},
+        res: {status: 'Invalid body format', details: '"condition_id" with value "700000000000h00000000001" fails to match the required pattern: /[0-9a-f]{24}/'}
+      });
+    });
+    it('rejects a condition id not available', done => {
+      TestHelper.request(server, done, {
+        method: 'post',
+        url: '/measurement/new',
+        auth: {basic: 'janedoe'},
+        httpStatus: 400,
+        req: {condition_id: '000000000000000000000001', values: {'weight %': 0.8, 'standard deviation': 0.1}, measurement_template: '300000000000000000000002'},
+        res: {status: 'Condition id not available'}
+      });
+    });
+    it('rejects an invalid measurement_template id', done => {
+      TestHelper.request(server, done, {
+        method: 'post',
+        url: '/measurement/new',
+        auth: {basic: 'janedoe'},
+        httpStatus: 400,
+        req: {condition_id: '700000000000000000000001', values: {'weight %': 0.8, 'standard deviation': 0.1}, measurement_template: '30000000000h000000000002'},
+        res: {status: 'Invalid body format', details: '"measurement_template" with value "30000000000h000000000002" fails to match the required pattern: /[0-9a-f]{24}/'}
+      });
+    });
+    it('rejects a measurement_template not available', done => {
+      TestHelper.request(server, done, {
+        method: 'post',
+        url: '/measurement/new',
+        auth: {basic: 'janedoe'},
+        httpStatus: 400,
+        req: {condition_id: '700000000000000000000001', values: {'weight %': 0.8, 'standard deviation': 0.1}, measurement_template: '000000000000000000000002'},
+        res: {status: 'Measurement template not available'}
+      });
+    });
+    it('rejects not specified values', done => {
+      TestHelper.request(server, done, {
+        method: 'post',
+        url: '/measurement/new',
+        auth: {basic: 'janedoe'},
+        httpStatus: 400,
+        req: {condition_id: '700000000000000000000001', values: {'weight %': 0.8, 'standard deviation': 0.1, xx: 44}, measurement_template: '300000000000000000000002'},
+        res: {status: 'Invalid body format', details: '"xx" is not allowed'}
+      });
+    });
+    it('rejects missing values', done => {
+      TestHelper.request(server, done, {
+        method: 'post',
+        url: '/measurement/new',
+        auth: {basic: 'janedoe'},
+        httpStatus: 400,
+        req: {condition_id: '700000000000000000000001', values: {'weight %': 0.8}, measurement_template: '300000000000000000000002'},
+        res: {status: 'Invalid body format', details: '"standard deviation" is required'}
+      });
+    });
+    it('rejects a value not in the value range', done => {
+      TestHelper.request(server, done, {
+        method: 'post',
+        url: '/measurement/new',
+        auth: {basic: 'janedoe'},
+        httpStatus: 400,
+        req: {condition_id: '700000000000000000000001', values: {val1: 4}, measurement_template: '300000000000000000000003'},
+        res: {status: 'Invalid body format', details: '"val1" must be one of [1, 2, 3]'}
+      });
+    });
+    it('rejects a value below minimum range', done => {
+      TestHelper.request(server, done, {
+        method: 'post',
+        url: '/measurement/new',
+        auth: {basic: 'janedoe'},
+        httpStatus: 400,
+        req: {condition_id: '700000000000000000000001', values: {'weight %': -1, 'standard deviation': 0.1}, measurement_template: '300000000000000000000002'},
+        res: {status: 'Invalid body format', details: '"weight %" must be larger than or equal to 0'}
+      });
+    });
+    it('rejects a value above maximum range', done => {
+      TestHelper.request(server, done, {
+        method: 'post',
+        url: '/measurement/new',
+        auth: {basic: 'janedoe'},
+        httpStatus: 400,
+        req: {condition_id: '700000000000000000000001', values: {'weight %': 0.8, 'standard deviation': 2}, measurement_template: '300000000000000000000002'},
+        res: {status: 'Invalid body format', details: '"standard deviation" must be less than or equal to 0.5'}
+      });
+    });
+    it('rejects a missing condition id', done => {
+      TestHelper.request(server, done, {
+        method: 'post',
+        url: '/measurement/new',
+        auth: {basic: 'janedoe'},
+        httpStatus: 400,
+        req: {values: {'weight %': 0.8, 'standard deviation': 0.1}, measurement_template: '300000000000000000000002'},
+        res: {status: 'Invalid body format', details: '"condition_id" is required'}
+      });
+    });
+    it('rejects a missing measurement_template', done => {
+      TestHelper.request(server, done, {
+        method: 'post',
+        url: '/measurement/new',
+        auth: {basic: 'janedoe'},
+        httpStatus: 400,
+        req: {condition_id: '700000000000000000000001', values: {'weight %': 0.8, 'standard deviation': 0.1}},
+        res: {status: 'Invalid body format', details: '"measurement_template" is required'}
+      });
+    });
+    it('rejects adding a measurement to the sample of another user for a write user', done => {
+      TestHelper.request(server, done, {
+        method: 'post',
+        url: '/measurement/new',
+        auth: {basic: 'janedoe'},
+        httpStatus: 403,
+        req: {condition_id: '700000000000000000000003', values: {'weight %': 0.8, 'standard deviation': 0.1}, measurement_template: '300000000000000000000002'}
+      });
+    });
+    it('accepts adding a measurement to the sample of another user for a maintain/admin user', done => {
+      TestHelper.request(server, done, {
+        method: 'post',
+        url: '/measurement/new',
+        auth: {basic: 'admin'},
+        httpStatus: 200,
+        req: {condition_id: '700000000000000000000001', values: {'weight %': 0.8, 'standard deviation': 0.1}, measurement_template: '300000000000000000000002'}
+      }).end((err, res) => {
+        if (err) return done(err);
+        should(res.body).have.only.keys('_id', 'condition_id', 'values', 'measurement_template');
+        should(res.body).have.property('_id').be.type('string');
+        should(res.body).have.property('condition_id', '700000000000000000000001');
+        should(res.body).have.property('measurement_template', '300000000000000000000002');
+        should(res.body).have.property('values');
+        should(res.body.values).have.property('weight %', 0.8);
+        should(res.body.values).have.property('standard deviation', 0.1);
+        done();
+      });
+    });
+    it('rejects an API key', done => {
+      TestHelper.request(server, done, {
+        method: 'post',
+        url: '/measurement/new',
+        auth: {key: 'janedoe'},
+        httpStatus: 401,
+        req: {condition_id: '700000000000000000000001', values: {'weight %': 0.8, 'standard deviation': 0.1}, measurement_template: '300000000000000000000002'}
+      });
+    });
+    it('rejects requests from a read user', done => {
+      TestHelper.request(server, done, {
+        method: 'post',
+        url: '/measurement/new',
+        auth: {basic: 'user'},
+        httpStatus: 403,
+        req: {condition_id: '700000000000000000000001', values: {'weight %': 0.8, 'standard deviation': 0.1}, measurement_template: '300000000000000000000002'}
+      });
+    });
+    it('rejects unauthorized requests', done => {
+      TestHelper.request(server, done, {
+        method: 'post',
+        url: '/measurement/new',
+        httpStatus: 401,
+        req: {condition_id: '700000000000000000000001', values: {'weight %': 0.8, 'standard deviation': 0.1}, measurement_template: '300000000000000000000002'}
+      });
+    });
+  });
+});

src/routes/measurement.ts

@@ -0,0 +1,68 @@
+import express from 'express';
+
+import MeasurementModel from '../models/measurement';
+import ConditionModel from '../models/condition';
+import MeasurementTemplateModel from '../models/measurement_template';
+import MeasurementValidate from './validate/measurement';
+import IdValidate from './validate/id';
+import res400 from './validate/res400';
+import ParametersValidate from './validate/parameters';
+
+
+const router = express.Router();
+
+router.get('/measurement/' + IdValidate.parameter(), (req, res, next) => {
+  if (!req.auth(res, ['read', 'write', 'maintain', 'dev', 'admin'], 'all')) return;
+
+  MeasurementModel.findById(req.params.id).lean().exec((err, data) => {
+    if (err) return next(err);
+    if (!data) {
+      return res.status(404).json({status: 'Not found'});
+    }
+
+    res.json(MeasurementValidate.output(data));
+  });
+});
+
+router.post('/measurement/new', async (req, res, next) => {
+  if (!req.auth(res, ['write', 'maintain', 'dev', 'admin'], 'basic')) return;
+
+  const {error, value: measurement} = MeasurementValidate.input(req.body, 'new');
+  if (error) return res400(error, res);
+
+  if (!await conditionIdCheck(measurement, req, res, next)) return;
+  if (!await templateCheck(measurement, 'new', res, next)) return;
+
+  await new MeasurementModel(measurement).save((err, data) => {
+    if (err) return next(err);
+    res.json(MeasurementValidate.output(data.toObject()));
+  });
+});
+
+
+module.exports = router;
+
+
+async function conditionIdCheck (measurement, req, res, next) {  // validate condition_id, returns false if invalid
+  const sampleData = await ConditionModel.findById(measurement.condition_id).populate('sample_id').lean().exec().catch(err => {next(err); return false;}) as any;
+  if (!sampleData) {  // sample_id not found
+    res.status(400).json({status: 'Condition id not available'});
+    return false
+  }
+  if (sampleData.sample_id.user_id.toString() !== req.authDetails.id && !req.auth(res, ['maintain', 'admin'], 'basic')) return false;  // sample does not belong to user
+  return true;
+}
+
+async function templateCheck (measurement, param, res, next) {  // validate measurement_template and values
+  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'});
+    return false
+  }
+
+  // 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

@@ -4,6 +4,8 @@ import NoteModel from '../models/note';
 import NoteFieldModel from '../models/note_field';
 import TestHelper from "../test/helper";
 // TODO: generate sample number
+// TODO: think again which parameters are required at POST
+// TODO: status
 
 describe('/sample', () => {
   let server;

src/routes/validate/condition.ts

@@ -4,8 +4,6 @@ import IdValidate from './id';
 
 export default class ConditionValidate {
   private static condition = {
-    sample_id: IdValidate.get(),
-
     number: Joi.string()
       .max(128),
 
@@ -14,20 +12,19 @@ export default class ConditionValidate {
         .try(
           Joi.string().max(128),
           Joi.number(),
-          Joi.boolean()
+          Joi.boolean(),
+          Joi.array()
         )
-      ),
+      )
-
-    treatment_template: IdValidate.get()
   }
 
   static input (data, param) {
     if (param === 'new') {
       return Joi.object({
-        sample_id: this.condition.sample_id.required(),
+        sample_id: IdValidate.get().required(),
         number: this.condition.number.required(),
         parameters: this.condition.parameters.required(),
-        treatment_template: this.condition.treatment_template.required()
+        treatment_template: IdValidate.get().required()
       }).validate(data);
     }
     else if (param === 'change') {
@@ -45,10 +42,10 @@ export default class ConditionValidate {
     data = IdValidate.stringify(data);
     const {value, error} = Joi.object({
       _id: IdValidate.get(),
-      sample_id: this.condition.sample_id,
+      sample_id: IdValidate.get(),
       number: this.condition.number,
       parameters: this.condition.parameters,
-      treatment_template: this.condition.treatment_template
+      treatment_template: IdValidate.get()
     }).validate(data, {stripUnknown: true});
     return error !== undefined? null : value;
   }

src/routes/validate/measurement.ts

@@ -0,0 +1,46 @@
+import Joi from '@hapi/joi';
+
+import IdValidate from './id';
+
+export default class MeasurementValidate {
+  private static measurement = {
+    values: Joi.object()
+      .pattern(/.*/, Joi.alternatives()
+        .try(
+          Joi.string().max(128),
+          Joi.number(),
+          Joi.boolean(),
+          Joi.array()
+        )
+      )
+  };
+
+  static input (data, param) {
+    if (param === 'new') {
+      return Joi.object({
+        condition_id: IdValidate.get().required(),
+        values: this.measurement.values.required(),
+        measurement_template: IdValidate.get().required()
+      }).validate(data);
+    }
+    else if (param === 'change') {
+      return Joi.object({
+        values: this.measurement.values
+      }).validate(data);
+    }
+    else {
+      return{error: 'No parameter specified!', value: {}};
+    }
+  }
+
+  static output (data) {
+    data = IdValidate.stringify(data);
+    const {value, error} = Joi.object({
+      _id: IdValidate.get(),
+      condition_id: IdValidate.get(),
+      values: this.measurement.values,
+      measurement_template: IdValidate.get()
+    }).validate(data, {stripUnknown: true});
+    return error !== undefined? null : value;
+  }
+}

src/test/db.json

@@ -229,6 +229,22 @@
         "__v": 0
       }
     ],
+    "measurements": [
+      {
+        "_id": {"$oid":"800000000000000000000001"},
+        "condition_id": {"$oid":"700000000000000000000001"},
+        "values": {
+          "dpt": [
+            [3997.12558,98.00555],
+            [3995.08519,98.03253],
+            [3993.04480,98.02657]
+          ]
+        },
+        "status": 10,
+        "measurement_template": {"$oid":"300000000000000000000001"},
+        "__v": 0
+      }
+    ],
     "treatment_templates": [
       {
         "_id": {"$oid":"200000000000000000000001"},
@@ -272,7 +288,9 @@
         "parameters": [
           {
             "name": "dpt",
-            "range": {}
+            "range": {
+              "type": "array"
+            }
           }
         ],
         "__v": 0
@@ -297,6 +315,19 @@
           }
         ],
         "__v": 0
+      },
+      {
+        "_id": {"$oid":"300000000000000000000003"},
+        "name": "mt 3",
+        "parameters": [
+          {
+            "name": "val1",
+            "range": {
+              "values": [1,2,3]
+            }
+          }
+        ],
+        "__v": 0
       }
     ],
     "users": [