Automatically send gene sample results (#46)

db/data/gene-samples/README.md

@@ -0,0 +1,9 @@
+# Gene samples
+
+This directory contains a script to convert the gene sample PDF names to a hash of the person id. This is done so that the players can't guess the gene sample file names.
+
+1. Download the gene sample PDFs from Google Drive and place them in this directory
+2. Make sure that files.csv is up to date, as it maps the file names to person id's
+3. Make sure you are in this directory and run `./convert.sh`
+4. The script will create a new directory called `processed` that contains the PDFs where the file name is now the first 8 characters of the sha1 hash of the person id
+5. The contents of `processed` can be uploaded to the server to be served under `/gene-samples/`

db/data/gene-samples/convert.sh

@@ -0,0 +1,25 @@
+#!/usr/bin/env bash
+
+set -euo pipefail
+
+input="files.csv"
+
+# Function to generate a short hash from an ID
+generate_hash() {
+  echo -n "$1" | sha1sum | cut -c1-8
+}
+
+mkdir -p ./processed
+rm -f ./processed/*.pdf
+
+while IFS=',' read -r id file; do
+  # Skip the header line
+  if [ "$id" != "id" ]; then
+    # Remove leading ./ from the filename if present
+    filename="${file#./}"
+    hash=$(generate_hash "$id")
+    # hash="$id"
+    cp "$filename" "./processed/${hash}.pdf"
+  fi
+done < "$input"
+

db/data/gene-samples/files.csv

@@ -0,0 +1,105 @@
+id,file
+20077,./Gene test - Amir Bolton image.pdf
+20107,./Gene test - Jonah Malone image.pdf
+20011,./Gene test - Terran Wells image.pdf
+20022,./Gene test - Jardan image.pdf
+20066,./Gene test - Lane Hayakawa image.pdf
+20087,./Gene test - Beva Drugov image.pdf
+20040,./Gene test - Deron Richard image.pdf
+20026,./Gene test - Naethan image.pdf
+20073,./Gene test - Torrey Watson image.pdf
+20386,./Gene test - The Guardian image.pdf
+20130,./Gene test - Anix image.pdf
+20021,./Gene test - Alia Swanson image.pdf
+20096,./Gene test - Dayle Rogers image.pdf
+20085,./Gene test - Abe Arima image.pdf
+20004,./Gene test - Dallan Jordan image.pdf
+20025,./Gene test - Jaeco image.pdf
+20052,./Gene test - Glen Hollow image.pdf
+20012,./Gene test - Blake Ishimoto image.pdf
+20090,./Gene test - Harper Ellis image.pdf
+20005,./Gene test - Yera Romero image.pdf
+20060,./Gene test - Nicol Wells image.pdf
+20108,./Gene test - Malak Fukui image.pdf
+20094,./Gene test - Hayden Carson image.pdf
+20089,./Gene test - Fenix Ellis image.pdf
+20083,./Gene test - Tan Ellis image.pdf
+20124,./Gene test - Jovian Aurelios Cauruleos image.pdf
+20015,./Gene test - Gallan Reid image.pdf
+20086,./Gene test - Aeran Lester image.pdf
+20001,./Gene test - Vane Hodge image.pdf
+20039,./Gene test - Noe Walker image.pdf
+20121,./Gene test - Pax Houghton image.pdf
+20059,./Gene test - Ballard Case image.pdf
+20051,./Gene test - Roan Rowen image.pdf
+20006,./Gene test - Kai Rogers image.pdf
+20132,./Gene test - Nayel image.pdf
+20110,./Gene test - Jose Cain image.pdf
+20044,./Gene test - Jill Montoya image.pdf
+20007,./Gene test - Cal Allen image.pdf
+20131,./Gene test - Keana image.pdf
+20120,./Gene test - Remi Sharp image.pdf
+20023,./Gene test - Zaera image.pdf
+20104,./Gene test - Espen Nakahara image.pdf
+20043,./Gene test - Gail Wells image.pdf
+20058,./Gene test - Hali Okuma image.pdf
+20084,./Gene test - Arlyn Booth image.pdf
+20055,./Gene test - Julia Aurelios Cauruleos image.pdf
+20134,./Gene test - Tarai image.pdf
+20013,./Gene test - Devyn Pearson image.pdf
+20003,./Gene test - Jin Komatsu image.pdf
+20119,./Gene test - Yuri Mills image.pdf
+20126,./Gene test - Gene Hawkins image.pdf
+20123,./Gene test - Lee Savage image.pdf
+20014,./Gene test - Evin Reid image.pdf
+20082,./Gene test - Eva Ellis image.pdf
+20098,./Gene test - Briana Chambers image.pdf
+20103,./Gene test - Valerian Fukui image.pdf
+20101,./Gene test - Osha Green image.pdf
+20095,./Gene test - Han Barnes image.pdf
+20074,./Gene test - Nikita Watson image.pdf
+20106,./Gene test - Nico Lawrence image.pdf
+20088,./Gene test - Fran Abrankowich image.pdf
+20099,./Gene test - Heath Steele image.pdf
+20020,./Gene test - Xavier Blake image.pdf
+20133,./Gene test - Saria image.pdf
+20063,./Gene test - Eli Booth image.pdf
+20045,./Gene test - Isha Hayakawa image.pdf
+20097,./Gene test - Mel McBride image.pdf
+20019,./Gene test - Malak Kovalenko image.pdf
+20117,./Gene test - Leigh Kent image.pdf
+20017,./Gene test - Skye Duran image.pdf
+20116,./Gene test - Nolan Hunter image.pdf
+20061,./Gene test - Flann Hollow image.pdf
+20037,./Gene test - Hale Green image.pdf
+20018,./Gene test - Zyra Lee image.pdf
+20028,./Gene test - Briya image.pdf
+20100,./Gene test - Caden Andrews image.pdf
+20102,./Gene test - Lynn Ryan image.pdf
+20041,./Gene test - Nickie Ramirez image.pdf
+20125,./Gene test - Avery Higashi image.pdf
+20128,./Gene test - Aedan image.pdf
+20070,./Gene test - Jodey Agaki image.pdf
+20008,./Gene test - Idris McBride image.pdf
+20042,./Gene test - Lowan Romero image.pdf
+20024,./Gene test - Mael image.pdf
+20002,./Gene test - Lex Peters image.pdf
+20057,./Gene test - Eugenie Russell image.pdf
+20112,./Gene test - Zeya Cook image.pdf
+20127,./Gene test - Harley Carroll image.pdf
+20092,./Gene test - Hedly Walker image.pdf
+20062,./Gene test - Tristan Fukui image.pdf
+20016,./Gene test - Tyler Carrillo image.pdf
+20118,./Gene test - Lonnie Gordon image.pdf
+20081,./Gene test - Oriel Cook image.pdf
+20113,./Gene test - Karin Alexandrov image.pdf
+20111,./Gene test - Ziva Callahan image.pdf
+20114,./Gene test - Leone Mills image.pdf
+20064,./Gene test - Ismy Arima image.pdf
+20091,./Gene test - Gale Chapman image.pdf
+20038,./Gene test - Ashlin Hall image.pdf
+20129,./Gene test - Taelor image.pdf
+20010,./Gene test - Remy Hall image.pdf
+20093,./Gene test - Taren Yates image.pdf
+20115,./Gene test - Kerrie Ray image.pdf
+20050,./Gene test - Gaylen Russell image.pdf

src/routes/operation.ts

@@ -7,9 +7,9 @@ import { logger } from '@/logger';
 import { NotFound } from 'http-errors';
 import { get } from 'lodash';
 import Bookshelf from 'bookshelf';
-import { getBloodTestResultText } from '@/utils/blood-test-results';
+import { getBloodTestResultText, getGeneSampleResultText } from '@/utils/medical-test-results';
 import { getScienceAnalysisTime, addOperationResultsToArtifactEntry } from '@/utils/science';
-import { getPath } from "@/store/store";
+import { getPath } from '@/store/store';
 import moment from 'moment';
 import { Stores } from '@/store/types';
 import { saveBlob } from '@/rules/helpers';
@@ -57,6 +57,7 @@ async function processXrayOperation(operationResult: Bookshelf.Model<unknown>) {
 
 const addOperationResultToMedicalEntry = async (operationResult: Bookshelf.Model<unknown>) => {
 	const isBloodSample = operationResult.get('additional_type') === 'BLOOD_SAMPLE';
+	const isGeneSample = operationResult.get('additional_type') === 'GENE_SAMPLE';
 	const isAnalysed = operationResult.get('is_analysed');
 	const isComplete = operationResult.get('is_complete');
 	if (isBloodSample && isAnalysed && !isComplete) {
@@ -68,6 +69,15 @@ const addOperationResultToMedicalEntry = async (operationResult: Bookshelf.Model
 			`Added blood test results to ${person.get('full_name')} (${person.get('id')}), marking the operation as complete`
 		);
 		await operationResult.save({ is_complete: true }, { method: 'update', patch: true });
+	} else if (isGeneSample && isAnalysed && !isComplete) {
+		const person = await new Person().where({ bio_id: operationResult.get('bio_id') }).fetch();
+		const geneTestResult = getGeneSampleResultText(person.get('id'));
+		const entry = new Entry();
+		await entry.save({ added_by: EVA_ID, entry: geneTestResult, person_id: person.get('id'), type: 'MEDICAL' });
+		logger.success(
+			`Added gene test results to ${person.get('full_name')} (${person.get('id')}), marking the operation as complete`
+		);
+		await operationResult.save({ is_complete: true }, { method: 'update', patch: true });
 	}
 };
 
@@ -100,7 +110,7 @@ async function scheduleAddOperationResultToArtifactEntry(operationResult: Booksh
 				operation_result_id: operationResult.get('id'),
 				started_at: Date.now(),
 			},
-		]
+		],
 	});
 }
 
@@ -112,12 +122,15 @@ async function scheduleAddOperationResultToArtifactEntry(operationResult: Booksh
  * @param {boolean} include_complete.query - True if completed results should be included, defaults to false
  * @returns {Array.<OperationResult>} 200 - List of all OperationResult models
  */
-router.get('/', handleAsyncErrors(async (req: Request, res: Response) => {
-	const shouldContainRelations = get(req, 'query.relations') === 'true';
-	const include_complete = get(req, 'query.include_complete') === 'true';
-	const where = include_complete ? {} : { is_complete: false };
-	res.json(await OperationResult.forge().where(where)[shouldContainRelations ? 'fetchAllWithRelated' : 'fetchAll']());
-}));
+router.get(
+	'/',
+	handleAsyncErrors(async (req: Request, res: Response) => {
+		const shouldContainRelations = get(req, 'query.relations') === 'true';
+		const include_complete = get(req, 'query.include_complete') === 'true';
+		const where = include_complete ? {} : { is_complete: false };
+		res.json(await OperationResult.forge().where(where)[shouldContainRelations ? 'fetchAllWithRelated' : 'fetchAll']());
+	})
+);
 
 /**
  * Get a single operation by operation id
@@ -128,13 +141,17 @@ router.get('/', handleAsyncErrors(async (req: Request, res: Response) => {
  * @returns {Error} 404 - OperationResult not found
  * @returns {OperationResult.model} 200 - OperationResult model
  */
-router.get('/:id', handleAsyncErrors(async (req: Request, res: Response) => {
-	const shouldContainRelations = get(req, 'query.relations') === 'true';
-	const operationResult = await OperationResult
-		.forge({ id: req.params.id })[shouldContainRelations ? 'fetchWithRelated' : 'fetch']();
-	if (!operationResult) throw new NotFound('OperationResult not found');
-	res.json(operationResult);
-}));
+router.get(
+	'/:id',
+	handleAsyncErrors(async (req: Request, res: Response) => {
+		const shouldContainRelations = get(req, 'query.relations') === 'true';
+		const operationResult = await OperationResult.forge({ id: req.params.id })[
+			shouldContainRelations ? 'fetchWithRelated' : 'fetch'
+		]();
+		if (!operationResult) throw new NotFound('OperationResult not found');
+		res.json(operationResult);
+	})
+);
 
 /**
  * Insert a new operation result
@@ -144,27 +161,33 @@ router.get('/:id', handleAsyncErrors(async (req: Request, res: Response) => {
  * @param {OperationResult.model} operationresult.body.required - OperationResult model
  * @returns {OperationResult.model} 200 - Inserted OperationResult model
  */
-router.post('/', handleAsyncErrors(async (req: Request, res: Response) => {
-	const operationResult = await OperationResult.forge().save({
-		...req.body,
-		is_analysed: true, // All operations are now analysed by default and results get posted automatically
-	}, { method: 'insert' });
+router.post(
+	'/',
+	handleAsyncErrors(async (req: Request, res: Response) => {
+		const operationResult = await OperationResult.forge().save(
+			{
+				...req.body,
+				is_analysed: true, // All operations are now analysed by default and results get posted automatically
+			},
+			{ method: 'insert' }
+		);
 
-	const operationResultType = operationResult.get('type');
+		const operationResultType = operationResult.get('type');
 
-	if (operationResultType === 'MEDIC') {
-		// Automatically post blood test results, in case this is a blood sample
-		await addOperationResultToMedicalEntry(operationResult);
-	}
+		if (operationResultType === 'MEDIC') {
+			// Automatically post blood test results, in case this is a blood sample
+			await addOperationResultToMedicalEntry(operationResult);
+		}
 
-	if (operationResultType === 'SCIENCE') {
-		// Automatically post artifact test results if available
-		await scheduleAddOperationResultToArtifactEntry(operationResult);
-	}
+		if (operationResultType === 'SCIENCE') {
+			// Automatically post artifact test results if available
+			await scheduleAddOperationResultToArtifactEntry(operationResult);
+		}
 
-	await processXrayOperation(operationResult);
-	res.json(operationResult);
-}));
+		await processXrayOperation(operationResult);
+		res.json(operationResult);
+	})
+);
 
 /**
  * Update an operation result by id
@@ -175,13 +198,16 @@ router.post('/', handleAsyncErrors(async (req: Request, res: Response) => {
  * @param {OperationResult.model} operationresult.body.required - OperationResult model new values
  * @returns {OperationResult.model} 200 - Updated OperationResult model
  */
-router.put('/:id', handleAsyncErrors(async (req: Request, res: Response) => {
-	const operationResult = await OperationResult.forge({ id: req.params.id }).fetch();
-	if (!operationResult) throw new NotFound('OperationResult not found');
-	await operationResult.save(req.body, { method: 'update', patch: true });
-	await addOperationResultToMedicalEntry(operationResult);
-	await processXrayOperation(operationResult);
-	res.json(operationResult);
-}));
+router.put(
+	'/:id',
+	handleAsyncErrors(async (req: Request, res: Response) => {
+		const operationResult = await OperationResult.forge({ id: req.params.id }).fetch();
+		if (!operationResult) throw new NotFound('OperationResult not found');
+		await operationResult.save(req.body, { method: 'update', patch: true });
+		await addOperationResultToMedicalEntry(operationResult);
+		await processXrayOperation(operationResult);
+		res.json(operationResult);
+	})
+);
 
 export default router;

src/utils/blood-test-results.ts → src/utils/medical-test-results.ts

@@ -1,3 +1,13 @@
+import crypto from 'crypto';
+
+const GENE_SAMPLE_BASE_PATH = '/gene-samples';
+
+export function getGeneSampleFilename(personId: string) {
+	const hash = crypto.createHash('sha1').update(personId.toString()).digest('hex');
+	const shortHash = hash.substring(0, 8);
+	return `${GENE_SAMPLE_BASE_PATH}/${shortHash}.pdf`;
+}
+
 function getHemoglobinStatus(hemoglobinStr: string) {
 	const hemoglobin = parseFloat(hemoglobinStr);
 	if (isNaN(hemoglobin)) return null;
@@ -28,7 +38,8 @@ function getKaliumStatus(kaliumStr: string) {
 	const kalium = parseFloat(kaliumStr);
 	if (isNaN(kalium)) return null;
 
-	if (kalium < 3.5) return 'Hypokalemia (too little kalium in the system), feeling tired, leg cramps, weakness, and constipation. Risk of an abnormal heart rhythm. Can cause cardiac arrest.';
+	if (kalium < 3.5)
+		return 'Hypokalemia (too little kalium in the system), feeling tired, leg cramps, weakness, and constipation. Risk of an abnormal heart rhythm. Can cause cardiac arrest.';
 	if (kalium > 5.1) return 'Dehydrated';
 	return null;
 }
@@ -88,3 +99,8 @@ export function getBloodTestResultText(resultsModel: any) {
 
 	Details: ${resultsModel.get('details') || 'None'}`;
 }
+
+export function getGeneSampleResultText(personId: string) {
+	const filename = getGeneSampleFilename(personId);
+	return `**Gene sample results:** <a href="${filename}" target="_blank">Click here to view the results</a>`;
+}