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GET and POST method for measurement

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This commit is contained in:
VLE2FE 2020-05-12 12:15:36 +02:00
parent c9be3f4eb7
commit a516062822
11 changed files with 434 additions and 17 deletions
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1
src/index.ts
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@ -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'));

12
src/models/measurement.ts Normal file
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@ -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);

2
src/routes/condition.spec.ts
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@ -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;

8
src/routes/condition.ts
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@ -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
}

2
src/routes/material.spec.ts
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@ -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;

260
src/routes/measurement.spec.ts Normal file
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@ -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'}
});
});
});
});

68
src/routes/measurement.ts Normal file
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@ -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;
}

2
src/routes/sample.spec.ts
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@ -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;

17
src/routes/validate/condition.ts
View File

@ -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;
}

46
src/routes/validate/measurement.ts Normal file
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@ -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;
}
}

33
src/test/db.json
View File

@ -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": [