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definma-api
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Merge pull request #36 in ~VLE2FE/definma-api from develop to master 

* commit '3fbd6ccec37bb7844578a8611c8ee3a3e5523589':
  updated sample restore and validate
  added /measurement/sample/{id} route
This commit is contained in:
Veit Lukas (PEA4-Fe) 2020-08-21 16:14:29 +02:00
parent 0c4f99117d 3fbd6ccec3
commit e5abb4ae69
8 changed files with 165 additions and 37 deletions
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34
api/measurement.yaml
View File

@ -77,6 +77,40 @@
500:
$ref: 'api.yaml#/components/responses/500'
/measurement/sample/{id}:
parameters:
- $ref: 'api.yaml#/components/parameters/Id'
get:
summary: all measurements of the given sample
description: 'Auth: basic, levels: dev, admin'
tags:
- /measurement
security:
- BasicAuth: []
responses:
200:
description: measurement details
content:
application/json:
schema:
type: array
items:
allOf:
- $ref: 'api.yaml#/components/schemas/Measurement'
properties:
status:
type: string
description: can be deleted/new/validated
example: new
401:
$ref: 'api.yaml#/components/responses/401'
403:
$ref: 'api.yaml#/components/responses/403'
404:
$ref: 'api.yaml#/components/responses/404'
500:
$ref: 'api.yaml#/components/responses/500'
/measurement/restore/{id}:
parameters:
- $ref: 'api.yaml#/components/parameters/Id'

54
src/routes/measurement.spec.ts
View File

@ -404,6 +404,60 @@ describe('/measurement', () => {
});
});
describe('GET /measurement/sample/{id}', () => {
it('returns the right measurements', done => {
TestHelper.request(server, done, {
method: 'get',
url: '/measurement/sample/400000000000000000000003',
auth: {basic: 'admin'},
httpStatus: 200,
res: [
{_id: '800000000000000000000003', sample_id: '400000000000000000000003', values: {val1: 1}, measurement_template: '300000000000000000000003', status: 'new'},
{_id: '800000000000000000000004', sample_id: '400000000000000000000003', values: {val1: 1}, measurement_template: '300000000000000000000003', status: 'deleted'}
]
});
});
it('rejects an API key', done => {
TestHelper.request(server, done, {
method: 'get',
url: '/measurement/sample/400000000000000000000003',
auth: {key: 'admin'},
httpStatus: 401
});
});
it('rejects a write user', done => {
TestHelper.request(server, done, {
method: 'get',
url: '/measurement/sample/400000000000000000000003',
auth: {basic: 'janedoe'},
httpStatus: 403
});
});
it('rejects an invalid id', done => {
TestHelper.request(server, done, {
method: 'get',
url: '/measurement/sample/4000000000h0000000000003',
auth: {basic: 'admin'},
httpStatus: 404
});
});
it('rejects an unknown id', done => {
TestHelper.request(server, done, {
method: 'get',
url: '/measurement/sample/000000000000000000000003',
auth: {basic: 'admin'},
httpStatus: 404
});
});
it('rejects unauthorized requests', done => {
TestHelper.request(server, done, {
method: 'get',
url: '/measurement/sample/400000000000000000000003',
httpStatus: 401
});
});
});
describe('PUT /measurement/restore/{id}', () => {
it('sets the status', done => {
TestHelper.request(server, done, {

14
src/routes/measurement.ts
View File

@ -10,6 +10,7 @@ import res400 from './validate/res400';
import ParametersValidate from './validate/parameters';
import db from '../db';
import globals from '../globals';
import mongoose from "mongoose";
const router = express.Router();
@ -82,6 +83,19 @@ router.delete('/measurement/' + IdValidate.parameter(), (req, res, next) => {
});
});
router.get('/measurement/sample/' + IdValidate.parameter(), (req, res, next) => {
if (!req.auth(res, ['dev', 'admin'], 'basic')) return;
MeasurementModel.find({sample_id: mongoose.Types.ObjectId(req.params.id)}).lean().exec((err, data: any) => {
if (err) return next(err);
if (!data.length) {
return res.status(404).json({status: 'Not found'});
}
res.json(_.compact(data.map(e => MeasurementValidate.output(e, req, true))));
});
});
router.put('/measurement/restore/' + IdValidate.parameter(), (req, res, next) => {
if (!req.auth(res, ['dev', 'admin'], 'basic')) return;

48
src/routes/sample.spec.ts
View File

@ -271,7 +271,7 @@ describe('/sample', () => {
it('adds the specified measurements', done => {
TestHelper.request(server, done, {
method: 'get',
url: '/samples?status[]=new&status[]=validated&fields[]=number&fields[]=measurements.kf',
url: '/samples?status[]=new&status[]=validated&fields[]=number&fields[]=measurements.kf.weight%20%25&fields[]=measurements.kf.standard%20deviation',
auth: {basic: 'janedoe'},
httpStatus: 200
}).end((err, res) => {
@ -1525,22 +1525,23 @@ describe('/sample', () => {
});
});
});
it('creates a changelog', done => {
it('restores associated measurements', done => {
TestHelper.request(server, done, {
method: 'put',
url: '/sample/restore/400000000000000000000005',
auth: {basic: 'admin'},
httpStatus: 200,
req: {},
log: {
collection: 'samples',
dataAdd: {
group_id: '900000000000000000000002',
supplier_id: '110000000000000000000002',
status: 'new'
},
dataIgn: ['group_id', 'supplier_id']
}
req: {}
}).end((err, res) => {
if (err) return done (err);
should(res.body).be.eql({status: 'OK'});
MeasurementModel.find({sample_id: mongoose.Types.ObjectId('400000000000000000000005')}).lean().exec((err, data: any) => {
if (err) return done(err);
should(data).matchEach(measurement => {
should(measurement).have.property('status', 'new')
});
done();
});
});
});
it('rejects an API key', done => {
@ -1598,22 +1599,23 @@ describe('/sample', () => {
});
});
});
it('creates a changelog', done => {
it('validates associated measurements', done => {
TestHelper.request(server, done, {
method: 'put',
url: '/sample/validate/400000000000000000000003',
auth: {basic: 'admin'},
httpStatus: 200,
req: {},
log: {
collection: 'samples',
dataAdd: {
group_id: '900000000000000000000002',
supplier_id: '110000000000000000000002',
status: 'validated'
},
dataIgn: ['group_id', 'supplier_id']
}
req: {}
}).end((err, res) => {
if (err) return done (err);
should(res.body).be.eql({status: 'OK'});
MeasurementModel.find({sample_id: mongoose.Types.ObjectId('400000000000000000000003')}).lean().exec((err, data: any) => {
if (err) return done(err);
should(data).matchEach(measurement => {
should(measurement).have.property('status', 'validated')
});
done();
});
});
});
it('allows validating a sample without condition', done => {

17
src/routes/sample.ts
View File

@ -29,6 +29,7 @@ router.get('/samples', async (req, res, next) => {
if (!req.auth(res, ['read', 'write', 'dev', 'admin'], 'all')) return;
const {error, value: filters} = SampleValidate.query(req.query, ['dev', 'admin'].indexOf(req.authDetails.level) >= 0);
console.log(error);
if (error) return res400(error, res);
console.log(filters.filters);
@ -221,7 +222,6 @@ router.get('/samples', async (req, res, next) => {
const measurementFilterFields = _.uniq(sortFilterKeys.filter(e => /measurements\./.test(e))
.map(e => e.split('.')[1])); // filter measurement names and remove duplicates from parameters
if (sortFilterKeys.find(e => /measurements\./.test(e))) { // add measurement fields
console.log(measurementFilterFields);
const measurementTemplates = await MeasurementTemplateModel.find({name: {$in: measurementFilterFields}})
.lean().exec().catch(err => {next(err);});
if (measurementTemplates instanceof Error) return;
@ -233,12 +233,7 @@ router.get('/samples', async (req, res, next) => {
pipeline: [{$match: {$expr: {$and: [
{$eq: ['$sample_id', '$$sId']},
{$in: ['$measurement_template', measurementTemplates.map(e => mongoose.Types.ObjectId(e._id))]}
]}}},
{$project: _.merge(
filters.fields.filter(e => /measurements\./.test(e))
.map(e => 'values.' + e.split('.')[2]).reduce((s, e) => {s[e] = true; return s; }, {}),
{measurement_template: true, status: true, sample_id: true}
)}
]}}}
],
as: 'measurements'
}});
@ -367,6 +362,7 @@ router.get('/samples', async (req, res, next) => {
projection._id = false;
}
queryPtr.push({$project: projection});
console.log(JSON.stringify(query));
// use streaming when including spectrum files
if (!fieldsToAdd.find(e => e.indexOf(globals.spectrum.spectrum + '.' + globals.spectrum.dpt) >= 0)) {
collection.aggregate(query).allowDiskUse(true).exec((err, data) => {
@ -904,6 +900,11 @@ function setStatus (status, req, res, next) {
if (!data) {
return res.status(404).json({status: 'Not found'});
}
res.json({status: 'OK'});
MeasurementModel.updateMany({sample_id: mongoose.Types.ObjectId(req.params.id)}, {status})
.log(req).lean().exec(err => {
if (err) return next(err);
res.json({status: 'OK'});
});
});
}

11
src/routes/validate/measurement.ts
View File

@ -36,18 +36,23 @@ export default class MeasurementValidate {
}
}
static output (data, req) { // validate output and strip unwanted properties, returns null if not valid
// validate output and strip unwanted properties, returns null if not valid
static output (data, req, status = false) {
data = IdValidate.stringify(data);
// spectral data not allowed for read/write users
if (['dev', 'admin'].indexOf(req.authDetails.level) < 0 && data.values[globals.spectrum.dpt]) {
delete data.values[globals.spectrum.dpt];
}
const {value, error} = Joi.object({
const validation: any = {
_id: IdValidate.get(),
sample_id: IdValidate.get(),
values: this.measurement.values,
measurement_template: IdValidate.get()
}).validate(data, {stripUnknown: true});
};
if (status) {
validation.status = Joi.string().valid(...Object.values(globals.status));
}
const {value, error} = Joi.object(validation).validate(data, {stripUnknown: true});
return error !== undefined? null : value;
}

9
src/routes/validate/sample.ts
View File

@ -192,9 +192,11 @@ export default class SampleValidate {
if (filterValidation.error) return filterValidation;
try {
for (let i in data.filters) {
// data.filters[i] = JSON.parse(decodeURIComponent(data.filters[i]));
data.filters[i] = JSON.parse(decodeURIComponent(data.filters[i]));
console.log(data.filters[i]);
try {
data.filters[i] = decodeURIComponent(data.filters[i]);
}
catch (ignore) {}
data.filters[i] = JSON.parse(data.filters[i]);
data.filters[i].values = data.filters[i].values.map(e => { // validate filter values
if (e === null) { // null values are always allowed
return null;
@ -225,6 +227,7 @@ export default class SampleValidate {
validator = Joi.object(this.sample);
}
const {value, error} = validator.validate({[field]: e});
console.log(error);
if (error) throw error; // reject invalid values
return value[field];
});

15
src/test/db.json
View File

@ -477,6 +477,21 @@
"status": "validated",
"measurement_template": {"$oid":"300000000000000000000001"},
"__v": 0
},
{
"_id": {"$oid":"800000000000000000000008"},
"sample_id": {"$oid":"400000000000000000000005"},
"values": {
"dpt": [
[3996.12558,98.00555],
[3995.08519,98.03253],
[3993.04480,98.02657]
],
"device": "Alpha II"
},
"status": "deleted",
"measurement_template": {"$oid":"300000000000000000000001"},
"__v": 0
}
],
"condition_templates": [