diff --git a/api/sample.yaml b/api/sample.yaml
index e39a122..1359d23 100644
--- a/api/sample.yaml
+++ b/api/sample.yaml
@@ -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)
diff --git a/src/helpers/csv.ts b/src/helpers/csv.ts
index e6f07b2..d7774d7 100644
--- a/src/helpers/csv.ts
+++ b/src/helpers/csv.ts
@@ -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;
-}
\ No newline at end of file
diff --git a/src/helpers/flatten.ts b/src/helpers/flatten.ts
new file mode 100644
index 0000000..5c2d7d5
--- /dev/null
+++ b/src/helpers/flatten.ts
@@ -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;
+}
\ No newline at end of file
diff --git a/src/routes/sample.spec.ts b/src/routes/sample.spec.ts
index bd798a4..3d038c2 100644
--- a/src/routes/sample.spec.ts
+++ b/src/routes/sample.spec.ts
@@ -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',
diff --git a/src/routes/sample.ts b/src/routes/sample.ts
index dc29af9..8a82071 100644
--- a/src/routes/sample.ts
+++ b/src/routes/sample.ts
@@ -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'});
diff --git a/src/routes/user.ts b/src/routes/user.ts
index c8ebdc2..e90f1a0 100644
--- a/src/routes/user.ts
+++ b/src/routes/user.ts
@@ -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,
Your email address of your DeFinMa account was changed to ' + data.mail +
+ '
If you actually did this, just delete this email.' +
+ '
If you did not change your email, someone might be messing around with your account, ' +
+ 'so talk to the sysadmin quickly!
Have a nice day.' +
+ '
The DeFinMa team');
+ }
res.json(UserValidate.output(data));
}
else {
diff --git a/src/routes/validate/sample.ts b/src/routes/validate/sample.ts
index 96cbc9c..baabecb 100644
--- a/src/routes/validate/sample.ts
+++ b/src/routes/validate/sample.ts
@@ -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'])