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Clinical id service integration #1176

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Clinical id service integration #1176

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dddca11
added id generation logic
Apr 9, 2024
c4b472d
added id generation logic
Apr 11, 2024
1ae27f8
updated donor-repo calls
Apr 11, 2024
ec4a991
added config values for token and id-service url
Apr 11, 2024
f893255
made changes to incorporate review feedback
Apr 29, 2024
5bcf37b
Merge branch 'develop' into clinical_id_service_integration
Jun 11, 2024
1a7ff29
pkg json update
Jun 11, 2024
7221bbc
missing return statement
Jun 23, 2024
cb48085
changed some error handling during id generation
Jun 24, 2024
79d9f6b
review updates
Aug 12, 2024
40e926e
Update src/clinical/id-generator.ts
UmmulkiramR Aug 12, 2024
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94 changes: 31 additions & 63 deletions src/clinical/donor-repo.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,7 @@ import mongoose, { PaginateModel } from 'mongoose';
import mongoosePaginate from 'mongoose-paginate-v2';
import { DeepReadonly } from 'deep-freeze';
import { F, MongooseUtils, notEmpty } from '../utils';
import { setEntityIds, setEntityIdsForDonors } from './id-generator';

export const SUBMITTER_ID = 'submitterId';
export const SPECIMEN_SUBMITTER_ID = 'specimen.submitterId';
Expand Down Expand Up @@ -109,20 +110,22 @@ export interface DonorRepository {
): Promise<DeepReadonly<Donor> | undefined>;
iterateAllByProgramId(programId: string): AsyncIterable<DeepReadonly<Donor>>;
create(donor: DeepReadonly<Partial<Donor>>): Promise<DeepReadonly<Donor>>;
update(donor: DeepReadonly<Donor>): Promise<DeepReadonly<Donor>>;
updateAll(donors: DeepReadonly<Donor>[]): Promise<DeepReadonly<Donor>[]>;
update(donor: Donor): Promise<DeepReadonly<Donor>>;
updateAll(donors: Donor[]): Promise<DeepReadonly<Donor>[]>;
countBy(filter: any): Promise<number>;
}

// Mongoose implementation of the DonorRepository
export const donorDao: DonorRepository = {
async insertDonors(donors: Donor[]) {
await mongoose.connection.db.collection('donors').insertMany(donors);
const donorsWithIds = await setEntityIdsForDonors(donors);
await mongoose.connection.db.collection('donors').insertMany(donorsWithIds);
},
async updateDonor(donor: Donor) {
const donorsWithIds = await setEntityIds(donor);
Comment on lines 119 to +125
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Both setEntityIds functions throw errors when network errors occur, should there be some sort of error handling here to handle failures or is this now expected to be handled by the caller of updateDonor and insertDonors?

await mongoose.connection.db
.collection('donors')
.findOneAndUpdate({ donorId: donor.donorId }, { $set: donor });
.findOneAndUpdate({ donorId: donor.donorId }, { $set: donorsWithIds });
},
async countBy(filter: any) {
return await DonorModel.count(filter).exec();
Expand Down Expand Up @@ -413,27 +416,41 @@ export const donorDao: DonorRepository = {
return iterateAllByProgramId(programId);
},

async update(donor: DeepReadonly<Donor>) {
const newDonor = new DonorModel(donor);
async update(donor: Donor) {
const dnr = await setEntityIds(donor);
const newDonor = new DonorModel(await setEntityIds(donor));
unsetIsNewFlagForUpdate(newDonor);

await newDonor.save();
return F(MongooseUtils.toPojo(newDonor) as Donor);
},

async updateAll(donors: DeepReadonly<Donor>[]) {
const newDonors = donors.map((donor) => {
const newDonor = new DonorModel(donor);
async updateAll(donors: Donor[]) {
const newDonors = donors.map(async (donor) => {
const newDonor = new DonorModel(await setEntityIds(donor));
unsetIsNewFlagForUpdate(newDonor);
return newDonor;
});

const results = await Promise.all(newDonors.map((donor) => donor.save()));
return newDonors.map((donor) => F(MongooseUtils.toPojo(donor) as Donor));
await Promise.all(
newDonors.map((donor) => {
donor.then(async (d) => {
await d.save();
});
}),
);
const result = await Promise.all(
newDonors.map((donor) =>
donor.then((d) => {
return F(MongooseUtils.toPojo(d) as Donor);
}),
),
);

return result;
},

async create(donor: DeepReadonly<Donor>) {
const newDonor = new DonorModel(donor);
async create(donor: Partial<Donor>) {
const newDonor = new DonorModel(await setEntityIds(donor));
const doc = await newDonor.save();
return F(MongooseUtils.toPojo(newDonor) as Donor);
},
Expand Down Expand Up @@ -656,58 +673,9 @@ DonorSchema.index({ 'specimens.samples.submitterId': 1, programId: 1 }, { unique
* multiple times, and that makes them hard to test because tests depend
* on resetting the config and bootstraping but global variables keep their state.
*/
DonorSchema.plugin(AutoIncrement, {
inc_field: 'donorId',
start_seq: process.env.DONOR_ID_SEED || 250000,
});

DonorSchema.plugin(mongoosePaginate);

SpecimenSchema.plugin(AutoIncrement, {
inc_field: 'specimenId',
start_seq: process.env.SPECIMEN_ID_SEED || 210000,
});

SampleSchema.plugin(AutoIncrement, {
inc_field: 'sampleId',
start_seq: process.env.SAMPLE_ID_SEED || 610000,
});

FollowUpSchema.plugin(AutoIncrement, {
inc_field: 'followUpId',
start_seq: 1,
});

PrimaryDiagnosisSchema.plugin(AutoIncrement, {
inc_field: 'primaryDiagnosisId',
start_seq: 1,
});

FamilyHistorySchema.plugin(AutoIncrement, {
inc_field: 'familyHistoryId',
start_seq: 1,
});

ExposureSchema.plugin(AutoIncrement, {
inc_field: 'exposureId',
start_seq: 1,
});

BiomarkerSchema.plugin(AutoIncrement, {
inc_field: 'biomarkerId',
start_seq: 1,
});

ComorbiditySchema.plugin(AutoIncrement, {
inc_field: 'comorbidityId',
start_seq: 1,
});

TreatmentSchema.plugin(AutoIncrement, {
inc_field: 'treatmentId',
start_seq: 1,
});

export let DonorModel = mongoose.model<DonorDocument>('Donor', DonorSchema) as PaginateModel<
DonorDocument
>;
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