banana/definma-api
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improved globals and added status and spectrum

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This commit is contained in:
VLE2FE
2020-08-11 16:06:51 +02:00
parent 2c57d2045c
commit f94653f389
19 changed files with 101 additions and 88 deletions
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20
src/routes/material.ts
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@ -9,10 +9,10 @@ import MaterialSupplierModel from '../models/material_suppliers';
import IdValidate from './validate/id';
import res400 from './validate/res400';
import mongoose from 'mongoose';
import globals from '../globals';
import db from '../db';
import MaterialTemplateModel from '../models/material_template';
import ParametersValidate from './validate/parameters';
import globals from '../globals';
@ -28,14 +28,14 @@ router.get('/materials', (req, res, next) => {
if (filters.hasOwnProperty('status')) {
if(filters.status === 'all') {
conditions = {$or: [{status: 'validated'}, {status: 'new'}]}
conditions = {$or: [{status: globals.status.val}, {status: globals.status.new}]}
}
else {
conditions = {status: filters.status};
}
}
else { // default
conditions = {status: 'validated'};
conditions = {status: globals.status.val};
}
MaterialModel.find(conditions).populate('group_id').populate('supplier_id').lean().exec((err, data) => {
@ -46,7 +46,7 @@ router.get('/materials', (req, res, next) => {
});
});
router.get('/materials/:state(new|deleted)', (req, res, next) => {
router.get(`/materials/:state(${globals.status.new}|${globals.status.del})`, (req, res, next) => {
if (!req.auth(res, ['dev', 'admin'], 'basic')) return;
MaterialModel.find({status: req.params.state}).populate('group_id').populate('supplier_id')
@ -69,7 +69,7 @@ router.get('/material/' + IdValidate.parameter(), (req, res, next) => {
}
// deleted materials only available for dev/admin
if (data.status === 'deleted' && !req.auth(res, ['dev', 'admin'], 'all')) return;
if (data.status === globals.status.del && !req.auth(res, ['dev', 'admin'], 'all')) return;
res.json(MaterialValidate.output(data));
});
});
@ -105,7 +105,7 @@ router.put('/material/' + IdValidate.parameter(), (req, res, next) => {
// check for changes
if (!_.isEqual(_.pick(IdValidate.stringify(materialData), _.keys(material)), IdValidate.stringify(material))) {
material.status = 'new'; // set status to new
material.status = globals.status.new; // set status to new
}
await MaterialModel.findByIdAndUpdate(req.params.id, material, {new: true})
@ -125,7 +125,7 @@ router.delete('/material/' + IdValidate.parameter(), (req, res, next) => {
if (data.length) {
return res.status(400).json({status: 'Material still in use'});
}
MaterialModel.findByIdAndUpdate(req.params.id, {status:'deleted'})
MaterialModel.findByIdAndUpdate(req.params.id, {status: globals.status.del})
.log(req).populate('group_id').populate('supplier_id').lean().exec((err, data) => {
if (err) return next(err);
if (data) {
@ -141,13 +141,13 @@ router.delete('/material/' + IdValidate.parameter(), (req, res, next) => {
router.put('/material/restore/' + IdValidate.parameter(), (req, res, next) => {
if (!req.auth(res, ['dev', 'admin'], 'basic')) return;
setStatus('new', req, res, next);
setStatus(globals.status.new, req, res, next);
});
router.put('/material/validate/' + IdValidate.parameter(), (req, res, next) => {
if (!req.auth(res, ['dev', 'admin'], 'basic')) return;
setStatus('validated', req, res, next);
setStatus(globals.status.val, req, res, next);
});
router.post('/material/new', async (req, res, next) => {
@ -163,7 +163,7 @@ router.post('/material/new', async (req, res, next) => {
if (!material) return;
if (!await propertiesCheck(material.properties, 'new', res, next)) return;
material.status = 'new'; // set status to new
material.status = globals.status.new; // set status to new
await new MaterialModel(material).save(async (err, data) => {
if (err) return next(err);
db.log(req, 'materials', {_id: data._id}, data.toObject());

1
src/routes/measurement.spec.ts
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@ -1,7 +1,6 @@
import should from 'should/as-function';
import MeasurementModel from '../models/measurement';
import TestHelper from "../test/helper";
import globals from '../globals';
describe('/measurement', () => {

14
src/routes/measurement.ts
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@ -8,8 +8,8 @@ import MeasurementValidate from './validate/measurement';
import IdValidate from './validate/id';
import res400 from './validate/res400';
import ParametersValidate from './validate/parameters';
import globals from '../globals';
import db from '../db';
import globals from '../globals';
const router = express.Router();
@ -23,7 +23,7 @@ router.get('/measurement/' + IdValidate.parameter(), (req, res, next) => {
return res.status(404).json({status: 'Not found'});
}
// deleted measurements only available for dev/admin
if (data.status === 'deleted' && !req.auth(res, ['dev', 'admin'], 'all')) return;
if (data.status === globals.status.del && !req.auth(res, ['dev', 'admin'], 'all')) return;
res.json(MeasurementValidate.output(data, req));
});
@ -53,7 +53,7 @@ router.put('/measurement/' + IdValidate.parameter(), async (req, res, next) => {
if (measurement.values) { // fill not changed values from database
measurement.values = _.assign({}, data.values, measurement.values);
if (!_.isEqual(measurement.values, data.values)) {
measurement.status = 'new'; // set status to new
measurement.status = globals.status.new; // set status to new
}
}
@ -74,7 +74,7 @@ router.delete('/measurement/' + IdValidate.parameter(), (req, res, next) => {
return res.status(404).json({status: 'Not found'});
}
if (!await sampleIdCheck(data, req, res, next)) return;
await MeasurementModel.findByIdAndUpdate(req.params.id, {status:'deleted'})
await MeasurementModel.findByIdAndUpdate(req.params.id, {status: globals.status.del})
.log(req).lean().exec(err => {
if (err) return next(err);
return res.json({status: 'OK'});
@ -85,13 +85,13 @@ router.delete('/measurement/' + IdValidate.parameter(), (req, res, next) => {
router.put('/measurement/restore/' + IdValidate.parameter(), (req, res, next) => {
if (!req.auth(res, ['dev', 'admin'], 'basic')) return;
setStatus('new', req, res, next);
setStatus(globals.status.new, req, res, next);
});
router.put('/measurement/validate/' + IdValidate.parameter(), (req, res, next) => {
if (!req.auth(res, ['dev', 'admin'], 'basic')) return;
setStatus('validated', req, res, next);
setStatus(globals.status.val, req, res, next);
});
router.post('/measurement/new', async (req, res, next) => {
@ -104,7 +104,7 @@ router.post('/measurement/new', async (req, res, next) => {
measurement.values = await templateCheck(measurement, 'new', res, next);
if (!measurement.values) return;
measurement.status = 'new';
measurement.status = globals.status.new;
await new MeasurementModel(measurement).save((err, data) => {
if (err) return next(err);
db.log(req, 'measurements', {_id: data._id}, data.toObject());

2
src/routes/root.ts
View File

@ -13,7 +13,7 @@ router.get('/', (req, res) => {
});
router.get('/authorized', (req, res) => {
if (!req.auth(res, globals.levels)) return;
if (!req.auth(res, Object.values(globals.levels))) return;
res.json({
status: 'Authorization successful',
method: req.authDetails.method,

46
src/routes/sample.ts
View File

@ -17,6 +17,7 @@ import ParametersValidate from './validate/parameters';
import db from '../db';
import csv from '../helpers/csv';
import flatten from '../helpers/flatten';
import globals from '../globals';
const router = express.Router();
@ -36,7 +37,7 @@ router.get('/samples', async (req, res, next) => {
if (error) return res400(error, res);
// spectral data and csv not allowed for read/write users
if ((filters.fields.find(e => /\.dpt$/.test(e)) || filters.output !== 'json') &&
if ((filters.fields.find(e => e.indexOf('.' + globals.spectrum.dpt) >= 0) || filters.output !== 'json') &&
!req.auth(res, ['dev', 'admin'], 'all')) return;
// TODO: find a better place for these
@ -260,7 +261,7 @@ router.get('/samples', async (req, res, next) => {
// count total number of items before $skip and $limit, only works when from-id is not specified and spectra are not
// included
if (!filters.fields.find(e => /spectrum\./.test(e)) && !filters['from-id']) {
if (!filters.fields.find(e => e.indexOf(globals.spectrum.spectrum + '.') >= 0) && !filters['from-id']) {
queryPtr.push({$facet: {count: [{$count: 'count'}], samples: []}});
queryPtr = queryPtr[queryPtr.length - 1].$facet.samples; // add rest of aggregation pipeline into $facet
}
@ -328,7 +329,7 @@ router.get('/samples', async (req, res, next) => {
return res.status(400).json({status: 'Invalid body format', details: 'Measurement key not found'});
}
// use different lookup methods with and without spectrum for the best performance
if (fieldsToAdd.find(e => /spectrum\./.test(e))) {
if (fieldsToAdd.find(e => e.indexOf(globals.spectrum.spectrum + '.') >= 0)) {
queryPtr.push(
{$lookup: {from: 'measurements', localField: '_id', foreignField: 'sample_id', as: 'measurements'}}
);
@ -343,22 +344,12 @@ router.get('/samples', async (req, res, next) => {
as: 'measurements'
}});
}
measurementTemplates.forEach(template => { // TODO: hard coded dpt for special treatment, change later
measurementTemplates.forEach(template => {
addMeasurements(queryPtr, template);
if (measurementFieldsFields.find(e => e === 'spectrum')) {
queryPtr.push({$unwind: '$spectrum'});
if (measurementFieldsFields.find(e => e === globals.spectrum.spectrum)) {
queryPtr.push({$unwind: '$' + globals.spectrum.spectrum});
}
});
// if (measurementFieldsFields.find(e => e === 'spectrum')) { // TODO: remove hardcoded as well
// queryPtr.push(
// {$addFields: {spectrum: {$filter: {input: '$measurements', cond: {
// $eq: ['$$this.measurement_template', measurementTemplates.filter(e => e.name === 'spectrum')[0]._id]
// }}}}},
// {$addFields: {spectrum: '$spectrum.values'}},
// {$unwind: '$spectrum'}
// );
// }
// queryPtr.push({$unset: 'measurements'});
queryPtr.push({$project: {measurements: 0}});
}
@ -372,7 +363,8 @@ router.get('/samples', async (req, res, next) => {
projection._id = false;
}
queryPtr.push({$project: projection});
if (!fieldsToAdd.find(e => /spectrum\./.test(e))) { // use streaming when including spectrum files
// use streaming when including spectrum files
if (!fieldsToAdd.find(e => e.indexOf(globals.spectrum.spectrum + '.') >= 0)) {
collection.aggregate(query).allowDiskUse(true).exec((err, data) => {
if (err) return next(err);
if (data[0] && data[0].count) {
@ -439,7 +431,7 @@ router.get('/samples', async (req, res, next) => {
}
});
router.get('/samples/:state(new|deleted)', (req, res, next) => {
router.get(`/samples/:state(${globals.status.new}|${globals.status.del})`, (req, res, next) => {
if (!req.auth(res, ['dev', 'admin'], 'basic')) return;
SampleModel.find({status: req.params.state}).lean().exec((err, data) => {
@ -479,7 +471,7 @@ router.put('/sample/' + IdValidate.parameter(), (req, res, next) => {
if (!sampleData) {
return res.status(404).json({status: 'Not found'});
}
if (sampleData.status === 'deleted') {
if (sampleData.status === globals.status.del) {
return res.status(403).json({status: 'Forbidden'});
}
@ -527,7 +519,7 @@ router.put('/sample/' + IdValidate.parameter(), (req, res, next) => {
// check for changes
if (!_.isEqual(_.pick(IdValidate.stringify(sampleData), _.keys(sample)), _.omit(sample, ['notes']))) {
sample.status = 'new';
sample.status = globals.status.new;
}
await SampleModel.findByIdAndUpdate(req.params.id, sample, {new: true}).log(req).lean().exec((err, data: any) => {
@ -555,7 +547,7 @@ router.delete('/sample/' + IdValidate.parameter(), (req, res, next) => {
if (err) return next(err);
// set status of associated measurements also to deleted
MeasurementModel.updateMany({sample_id: mongoose.Types.ObjectId(req.params.id)}, {status: 'deleted'})
MeasurementModel.updateMany({sample_id: mongoose.Types.ObjectId(req.params.id)}, {status: globals.status.del})
.log(req).lean().exec(err => {
if (err) return next(err);
@ -589,7 +581,7 @@ router.get('/sample/number/:number', (req, res, next) => {
router.put('/sample/restore/' + IdValidate.parameter(), (req, res, next) => {
if (!req.auth(res, ['dev', 'admin'], 'basic')) return;
SampleModel.findByIdAndUpdate(req.params.id, {status: 'new'}).log(req).lean().exec((err, data) => {
SampleModel.findByIdAndUpdate(req.params.id, {status: globals.status.new}).log(req).lean().exec((err, data) => {
if (err) return next(err);
if (!data) {
@ -602,7 +594,7 @@ router.put('/sample/restore/' + IdValidate.parameter(), (req, res, next) => {
router.put('/sample/validate/' + IdValidate.parameter(), (req, res, next) => {
if (!req.auth(res, ['dev', 'admin'], 'basic')) return;
SampleModel.findByIdAndUpdate(req.params.id, {status: 'validated'}).log(req).lean().exec((err, data) => {
SampleModel.findByIdAndUpdate(req.params.id, {status: globals.status.val}).log(req).lean().exec((err, data) => {
if (err) return next(err);
if (!data) {
return res.status(404).json({status: 'Not found'});
@ -635,7 +627,7 @@ router.post('/sample/new', async (req, res, next) => {
if (!await conditionCheck(sample.condition, 'change', res, next)) return;
}
sample.status = 'new'; // set status to new
sample.status = globals.status.new; // set status to new
if (sample.hasOwnProperty('number')) {
if (!await numberCheck(sample, res, next)) return;
}
@ -885,7 +877,7 @@ async function sampleReturn (sampleData, req, res, next) {
sampleData = sampleData.toObject();
// deleted samples only available for dev/admin
if (sampleData.status === 'deleted' && !req.auth(res, ['dev', 'admin'], 'all')) return;
if (sampleData.status === globals.status.del && !req.auth(res, ['dev', 'admin'], 'all')) return;
sampleData.material = sampleData.material_id; // map data to right keys
sampleData.material.group = sampleData.material.group_id.name;
sampleData.material.supplier = sampleData.material.supplier_id.name;
@ -896,8 +888,8 @@ async function sampleReturn (sampleData, req, res, next) {
sampleData.measurements = data;
if (['dev', 'admin'].indexOf(req.authDetails.level) < 0) { // strip dpt values if not dev or admin
sampleData.measurements.forEach(measurement => {
if (measurement.values.dpt) {
delete measurement.values.dpt;
if (measurement.values[globals.spectrum.dpt]) {
delete measurement.values[globals.spectrum.dpt];
}
});
}

6
src/routes/user.ts
View File

@ -60,13 +60,13 @@ router.put('/user:username([/](?!key|new).?*|/?)', async (req, res, next) => {
}
// get current mail address to compare to given address
const {email: oldMail} = await UserModel.findOne({name: username}).lean().exec().catch(err => next(err));
const oldUserData = 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',
if (data.mail !== oldUserData.email) { // mail address was changed, send notice to old address
Mail.send(oldUserData.email, '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, ' +

3
src/routes/validate/material.ts
View File

@ -1,6 +1,7 @@
import Joi from 'joi';
import IdValidate from './id';
import globals from '../../globals';
export default class MaterialValidate { // validate input for material
private static material = {
@ -84,7 +85,7 @@ export default class MaterialValidate { // validate input for material
static query (data) {
return Joi.object({
status: Joi.string().valid('validated', 'new', 'all')
status: Joi.string().valid(globals.status.val, globals.status.new, 'all')
}).validate(data);
}
}

5
src/routes/validate/measurement.ts
View File

@ -1,6 +1,7 @@
import Joi from 'joi';
import IdValidate from './id';
import globals from '../../globals';
export default class MeasurementValidate {
private static measurement = {
@ -37,8 +38,8 @@ export default class MeasurementValidate {
static output (data, req) { // validate output and strip unwanted properties, returns null if not valid
data = IdValidate.stringify(data);
// spectral data not allowed for read/write users
if (['dev', 'admin'].indexOf(req.authDetails.level) < 0 && data.values.dpt) {
delete data.values.dpt;
if (['dev', 'admin'].indexOf(req.authDetails.level) < 0 && data.values[globals.spectrum.dpt]) {
delete data.values[globals.spectrum.dpt];
}
const {value, error} = Joi.object({
_id: IdValidate.get(),

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

@ -36,7 +36,7 @@ export default class RootValidate { // validate input for root methods
static changelogOutput (data) {
data.date = data._id.getTimestamp();
data.collection = data.collectionName;
data.collection = data.collection_name;
data = IdValidate.stringify(data);
const {value, error} = Joi.object({
date: this.changelog.timestamp,

12
src/routes/validate/sample.ts
View File

@ -53,7 +53,7 @@ export default class SampleValidate {
.min('1970-01-01T00:00:00.000Z'),
status: Joi.string()
.valid(...globals.status)
.valid(...Object.values(globals.status))
};
private static sortKeys = [
@ -68,7 +68,7 @@ export default class SampleValidate {
'material.supplier',
'material.group',
'material.properties.*',
'measurements.(?!spectrum\.dpt)*'
`measurements.(?!${globals.spectrum.spectrum}.${globals.spectrum.dpt})*`
];
private static fieldKeys = [
@ -81,7 +81,7 @@ export default class SampleValidate {
'user_id',
'material._id',
'material.numbers',
'measurements.spectrum.dpt',
`measurements.${globals.spectrum.spectrum}.${globals.spectrum.dpt}`,
];
static input (data, param) { // validate input, set param to 'new' to make all attributes required
@ -215,12 +215,12 @@ export default class SampleValidate {
return {error: {details: [{message: 'Invalid JSON string for filter parameter'}]}, value: null}
}
}
const acceptedStatuses = ['validated', 'new'];
const acceptedStatuses = [globals.status.val, globals.status.new];
if (dev) { // dev and admin can also access deleted samples
acceptedStatuses.push('deleted')
acceptedStatuses.push(globals.status.del)
}
return Joi.object({
status: Joi.array().items(Joi.string().valid(...acceptedStatuses)).default(['validated']),
status: Joi.array().items(Joi.string().valid(...acceptedStatuses)).default([globals.status.val]),
'from-id': IdValidate.get(),
'to-page': Joi.number().integer(),
'page-size': Joi.number().integer().min(1),

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

@ -21,7 +21,7 @@ export default class UserValidate { // validate input for user
.max(128),
level: Joi.string()
.valid(...globals.levels),
.valid(...Object.values(globals.levels)),
location: Joi.string()
.alphanum()