Update code by clean up unused objects

.github/CONTRIBUTING.md

@@ -0,0 +1,3 @@
+# Example Contributing Guidelines
+
+This is an example of GitHub's contributing guidelines file. Check out GitHub's [CONTRIBUTING.md help center article](https://help.github.com/articles/setting-guidelines-for-repository-contributors/) for more information.

.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,9 @@
+- **I'm submitting a ...**
+  [ ] bug report
+  [ ] feature request
+  [ ] question about the decisions made in the repository
+  [ ] question about how to use this project
+
+- **Summary**
+
+- **Other information** (e.g. detailed explanation, stack traces, related issues, suggestions how to fix, links for us to have context, eg. StackOverflow, personal fork, etc.)

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,7 @@
+- **What kind of change does this PR introduce?** (Bug fix, feature, docs update, ...)
+
+- **What is the current behavior?** (You can also link to an open issue here)
+
+- **What is the new behavior (if this is a feature change)?**
+
+- **Other information**:

source/index.ts

@@ -2,3 +2,4 @@ export * from './lib/observation/observation';
 export * from './lib/authorize/authorize';
 export * from './lib/questionnaire/questionnaire';
 export * from './lib/careplan/careplan';
+export * from './query/json';

source/lib/careplan/careplan.ts

@@ -79,7 +79,7 @@ export const getCareplansByStatusAndCategory = async (
   ) as CarePlan[];
 
   log.info(
-    `getCareplansByStatusAndCategory - successful with pre-response ${filteredCareplans[0].toString()} - with status ${filteredCareplans[0]?.status}`
+    `getCareplansByStatusAndCategory - successful with pre-response ${filteredCareplans[0]?.toString()} - with status ${filteredCareplans[0]?.status}`
   );
   log.debug({ serviceName: 'getCareplansByStatusAndCategory', result: filteredCareplans });
   return filteredCareplans;

source/lib/observation/observation.ts

@@ -3,7 +3,7 @@ import FHIR from 'fhirclient';
 import { fhirclient } from 'fhirclient/lib/types';
 
 import { EccMode } from '../../constants/mode';
-import { getAllCodes } from '../../query/json';
+import { getAllCodes, getCodesFromValueSetCode } from '../../query/json';
 import type { ObservationMode } from '../../types';
 import log from '../../utils/loglevel';
 
@@ -65,9 +65,8 @@ export const getObservations = async (
   log.info(
     `getObservations - start with code - ${code} - ${mode} ${sort} ${max}`
   );
-  const queryPath = `Observation?${
-    EccMode[mode] ?? EccMode.code
-  }=http://loinc.org|${code}&_sort=${sortType}&_count=${max ?? 100}`;
+  const queryPath = `Observation?${EccMode[mode] ?? EccMode.code
+    }=http://loinc.org|${code}&_sort=${sortType}&_count=${max ?? 100}`;
   const observationRequest: fhirclient.JsonArray = await client.patient.request(
     queryPath,
     fhirOptions
@@ -199,3 +198,52 @@ export const getObservationsByCategory = async (
   });
   return filteredObservations;
 };
+
+export const getLatestObservation = async (code: string, translate: boolean, mode?: string): Promise<Observation> => {
+  if (!code) {
+    log.error('getLatestObservation - code not found');
+    return notFoundResponse() as unknown as Observation;
+  }
+
+  const client = await FHIR.oauth2.ready();
+  let codeValueSets = code;
+
+  if (translate) {
+    if (code.includes('|')) {
+      const codeArray = code.split('|')
+      codeValueSets = await getCodesFromValueSetCode(codeArray[0], codeArray[1]);
+    } else {
+      codeValueSets = await getCodesFromValueSetCode('http://loinc.org', code);
+    }
+  }
+
+  log.info(`getLatestObservation - start with code - ${code}`);
+  const queryPath = `Observation?${EccMode[mode] ?? EccMode.code}=http://loinc.org|${codeValueSets}&_sort=-date&_count=1`;
+  const observationRequest: fhirclient.JsonArray = await client.patient.request(
+    queryPath,
+    fhirOptions
+  );
+
+  const observationResource: Observation[] = resourcesFrom(
+    observationRequest
+  ) as Observation[];
+
+  const filteredObservations: Observation[] = observationResource.filter(
+    (v) => v !== undefined && v.resourceType === 'Observation'
+  );
+
+  if (!filteredObservations.length) {
+    log.error('getObservation - empty observation');
+    return notFoundResponse(code) as unknown as Observation;
+  }
+
+  log.info(
+    `getObservation - successful with code ${code} - with status ${filteredObservations[0].status}`
+  );
+  log.debug({ serviceName: 'getObservation', result: filteredObservations[0] });
+  return filteredObservations[0];
+};
+
+// TODO add query observation segmented
+
+// TODO add check for isBlackEgfr

source/query/convertCsvToJson.ts

@@ -1,5 +1,3 @@
-// README: This is only to convert CSV to JSON, to run this, change it to js and simply run node convertCsvToJson.js
-
 // const fs = require('fs')
 // const path = require('path')
 // let csvToJson = require('convert-csv-to-json');

source/query/json.ts

@@ -29,3 +29,21 @@ export const getAllCodes = async (valueName: string): Promise<string[]> => {
 
   return mappedCodes;
 };
+
+// check for getAllValueSet name from code
+export const getCodesFromValueSetCode = async (system: string, code: string) => {
+  const valueSetsList = await import(
+    `../resources/valueset_loadlist.json`
+  );
+
+
+  const valueSetsListParsed = await Promise.all(valueSetsList.map(async (v) => ({ fileName: v.Oid, valueSets: await import(`${v.Oid}.json`) })));
+
+  const foundValueSets = valueSetsListParsed.filter(v => v.valueSets.some(v => v['System'] === system && v['Code'] === code));
+
+  const valueSetCodes = getAllCodes(foundValueSets[0].fileName)
+
+  const joinedSetCodes = (await valueSetCodes).join(',');
+
+  return joinedSetCodes;
+}