updated sample restore and validate
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8d894fa27e
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@ -271,7 +271,7 @@ describe('/sample', () => {
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it('adds the specified measurements', done => {
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TestHelper.request(server, done, {
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method: 'get',
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url: '/samples?status[]=new&status[]=validated&fields[]=number&fields[]=measurements.kf',
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url: '/samples?status[]=new&status[]=validated&fields[]=number&fields[]=measurements.kf.weight%20%25&fields[]=measurements.kf.standard%20deviation',
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auth: {basic: 'janedoe'},
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httpStatus: 200
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}).end((err, res) => {
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@ -1525,22 +1525,23 @@ describe('/sample', () => {
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});
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});
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});
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it('creates a changelog', done => {
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it('restores associated measurements', done => {
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TestHelper.request(server, done, {
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method: 'put',
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url: '/sample/restore/400000000000000000000005',
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auth: {basic: 'admin'},
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httpStatus: 200,
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req: {},
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log: {
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collection: 'samples',
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dataAdd: {
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group_id: '900000000000000000000002',
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supplier_id: '110000000000000000000002',
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status: 'new'
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},
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dataIgn: ['group_id', 'supplier_id']
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}
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req: {}
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}).end((err, res) => {
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if (err) return done (err);
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should(res.body).be.eql({status: 'OK'});
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MeasurementModel.find({sample_id: mongoose.Types.ObjectId('400000000000000000000005')}).lean().exec((err, data: any) => {
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if (err) return done(err);
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should(data).matchEach(measurement => {
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should(measurement).have.property('status', 'new')
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});
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done();
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});
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});
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});
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it('rejects an API key', done => {
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@ -1598,22 +1599,23 @@ describe('/sample', () => {
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});
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});
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});
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it('creates a changelog', done => {
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it('validates associated measurements', done => {
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TestHelper.request(server, done, {
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method: 'put',
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url: '/sample/validate/400000000000000000000003',
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auth: {basic: 'admin'},
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httpStatus: 200,
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req: {},
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log: {
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collection: 'samples',
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dataAdd: {
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group_id: '900000000000000000000002',
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supplier_id: '110000000000000000000002',
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status: 'validated'
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},
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dataIgn: ['group_id', 'supplier_id']
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}
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req: {}
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}).end((err, res) => {
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if (err) return done (err);
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should(res.body).be.eql({status: 'OK'});
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MeasurementModel.find({sample_id: mongoose.Types.ObjectId('400000000000000000000003')}).lean().exec((err, data: any) => {
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if (err) return done(err);
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should(data).matchEach(measurement => {
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should(measurement).have.property('status', 'validated')
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});
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done();
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});
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});
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});
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it('allows validating a sample without condition', done => {
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@ -29,6 +29,7 @@ router.get('/samples', async (req, res, next) => {
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if (!req.auth(res, ['read', 'write', 'dev', 'admin'], 'all')) return;
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const {error, value: filters} = SampleValidate.query(req.query, ['dev', 'admin'].indexOf(req.authDetails.level) >= 0);
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console.log(error);
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if (error) return res400(error, res);
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console.log(filters.filters);
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@ -221,7 +222,6 @@ router.get('/samples', async (req, res, next) => {
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const measurementFilterFields = _.uniq(sortFilterKeys.filter(e => /measurements\./.test(e))
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.map(e => e.split('.')[1])); // filter measurement names and remove duplicates from parameters
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if (sortFilterKeys.find(e => /measurements\./.test(e))) { // add measurement fields
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console.log(measurementFilterFields);
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const measurementTemplates = await MeasurementTemplateModel.find({name: {$in: measurementFilterFields}})
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.lean().exec().catch(err => {next(err);});
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if (measurementTemplates instanceof Error) return;
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@ -233,12 +233,7 @@ router.get('/samples', async (req, res, next) => {
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pipeline: [{$match: {$expr: {$and: [
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{$eq: ['$sample_id', '$$sId']},
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{$in: ['$measurement_template', measurementTemplates.map(e => mongoose.Types.ObjectId(e._id))]}
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]}}},
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{$project: _.merge(
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filters.fields.filter(e => /measurements\./.test(e))
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.map(e => 'values.' + e.split('.')[2]).reduce((s, e) => {s[e] = true; return s; }, {}),
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{measurement_template: true, status: true, sample_id: true}
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)}
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]}}}
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],
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as: 'measurements'
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}});
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@ -367,6 +362,7 @@ router.get('/samples', async (req, res, next) => {
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projection._id = false;
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}
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queryPtr.push({$project: projection});
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console.log(JSON.stringify(query));
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// use streaming when including spectrum files
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if (!fieldsToAdd.find(e => e.indexOf(globals.spectrum.spectrum + '.' + globals.spectrum.dpt) >= 0)) {
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collection.aggregate(query).allowDiskUse(true).exec((err, data) => {
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@ -904,6 +900,11 @@ function setStatus (status, req, res, next) {
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if (!data) {
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return res.status(404).json({status: 'Not found'});
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}
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res.json({status: 'OK'});
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MeasurementModel.updateMany({sample_id: mongoose.Types.ObjectId(req.params.id)}, {status})
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.log(req).lean().exec(err => {
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if (err) return next(err);
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res.json({status: 'OK'});
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});
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});
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}
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@ -11,6 +11,7 @@ export default class MeasurementValidate {
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Joi.string().max(128),
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Joi.number(),
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Joi.boolean(),
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Joi.array().items(Joi.array().items(Joi.number())), // for spectra
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Joi.array()
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)
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.allow(null)
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@ -192,9 +192,11 @@ export default class SampleValidate {
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if (filterValidation.error) return filterValidation;
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try {
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for (let i in data.filters) {
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// data.filters[i] = JSON.parse(decodeURIComponent(data.filters[i]));
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data.filters[i] = JSON.parse(decodeURIComponent(data.filters[i]));
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console.log(data.filters[i]);
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try {
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data.filters[i] = decodeURIComponent(data.filters[i]);
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}
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catch (ignore) {}
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data.filters[i] = JSON.parse(data.filters[i]);
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data.filters[i].values = data.filters[i].values.map(e => { // validate filter values
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if (e === null) { // null values are always allowed
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return null;
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@ -225,6 +227,7 @@ export default class SampleValidate {
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validator = Joi.object(this.sample);
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}
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const {value, error} = validator.validate({[field]: e});
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console.log(error);
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if (error) throw error; // reject invalid values
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return value[field];
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});
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@ -477,6 +477,21 @@
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"status": "validated",
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"measurement_template": {"$oid":"300000000000000000000001"},
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"__v": 0
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},
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{
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"_id": {"$oid":"800000000000000000000008"},
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"sample_id": {"$oid":"400000000000000000000005"},
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"values": {
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"dpt": [
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[3996.12558,98.00555],
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[3995.08519,98.03253],
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[3993.04480,98.02657]
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],
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"device": "Alpha II"
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},
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"status": "deleted",
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"measurement_template": {"$oid":"300000000000000000000001"},
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"__v": 0
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}
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],
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"condition_templates": [
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