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

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* commit 'ed8b549752cbfbeba497adda8427f34c8b8497a4':
  flattened samples result
  csv only for dev/admin, mail change notice
This commit is contained in:
Veit Lukas (PEA4-Fe) 2020-08-10 12:36:44 +02:00
commit 917b9044c7
7 changed files with 105 additions and 53 deletions
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16
api/sample.yaml
View File

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

32
src/helpers/csv.ts
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@ -1,4 +1,5 @@
import {parseAsync} from 'json2csv';
import flatten from './flatten';
export default function csv(input: any[], f: (err, data) => void) {
parseAsync(input.map(e => flatten(e)), {includeEmptyRows: true})
@ -6,34 +7,3 @@ export default function csv(input: any[], f: (err, data) => void) {
.catch(err => f(err, null));
}
function flatten (data) { // flatten object: {a: {b: true}} -> {a.b: true}
const result = {};
function recurse (cur, prop) {
if (Object(cur) !== cur || Object.keys(cur).length === 0) {
result[prop] = cur;
}
else if (Array.isArray(cur)) {
if (cur.length && (Object(cur[0]) !== cur || Object.keys(cur[0]).length === 0)) { // array of non-objects
result[prop] = '[' + cur.join(', ') + ']';
}
else {
let l = 0;
for(let i = 0, l = cur.length; i < l; i++)
recurse(cur[i], prop + "[" + i + "]");
if (l == 0)
result[prop] = [];
}
}
else {
let isEmpty = true;
for (let p in cur) {
isEmpty = false;
recurse(cur[p], prop ? prop+"."+p : p);
}
if (isEmpty && prop)
result[prop] = {};
}
}
recurse(data, '');
return result;
}

41
src/helpers/flatten.ts Normal file
View File

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

32
src/routes/sample.spec.ts
View File

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

24
src/routes/sample.ts
View File

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

11
src/routes/user.ts
View File

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

2
src/routes/validate/sample.ts
View File

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