Merge pull request #1348 from sainingo/POC-571

POC-571

app/otz/cohort-module.service.js

@@ -0,0 +1,52 @@
+var db = require('../../etl-db');
+
+export class CohortModuleService {
+  getCohortSummary = (cohortUuids) => {
+    const uuids = cohortUuids
+      .split(',')
+      .map((s) => {
+        return `"${s}"`;
+      })
+      .join(',');
+    return new Promise((resolve, reject) => {
+      let queryParts = {};
+      const sql = `SELECT 
+        c.uuid,
+        COUNT(DISTINCT cm.patient_id) AS total_patients,
+        IFNULL(SUM(CASE
+                    WHEN fl.hiv_viral_load < 200 THEN 1
+                    ELSE 0
+                END) / NULLIF(COUNT(DISTINCT cm.patient_id), 0) * 100,
+                0) AS suppression_rate_percentage
+    FROM
+        amrs.cohort c
+            INNER JOIN
+        amrs.cohort_member cm ON c.cohort_id = cm.cohort_id
+            LEFT JOIN
+        (SELECT 
+            person_id, MAX(test_datetime) AS latest_test_datetime
+        FROM
+            etl.flat_labs_and_imaging
+        WHERE
+            hiv_viral_load IS NOT NULL
+        GROUP BY person_id) AS latest_tests ON cm.patient_id = latest_tests.person_id
+            LEFT JOIN
+        etl.flat_labs_and_imaging fl ON latest_tests.person_id = fl.person_id
+            AND latest_tests.latest_test_datetime = fl.test_datetime
+    WHERE
+        c.uuid in (${uuids})
+    GROUP BY c.cohort_id;
+    
+    `;
+
+      queryParts = {
+        sql: sql
+      };
+
+      return db.queryServer(queryParts, function (result) {
+        result.sql = sql;
+        resolve(result);
+      });
+    });
+  };
+}

dao/patient/etl-patient-dao.js

@@ -718,6 +718,39 @@ module.exports = (function () {
     });
   }
 
+  function getPatientsLatestHivSummmary(request, callback) {
+    return new Promise(function (resolve, reject) {
+      const uuid = request.query.uuid ? request.query.uuid.split(',') : [];
+
+      const whereClause = [
+        't1.uuid  in ? and t1.next_encounter_datetime_hiv is null',
+        uuid
+      ];
+      const queryParts = {
+        columns:
+          request.query.fields ||
+          ' t1.vl_1 as latest_vl, t1.vl_1_date as latest_vl_date, t2.rtc_date, t1.cur_arv_adherence as adherence, t1.encounter_datetime as latest_appointment, t1.uuid',
+        table: 'etl.flat_hiv_summary_v15b',
+        where: whereClause,
+        leftOuterJoins: [
+          [
+            'etl.flat_hiv_summary_v15b',
+            't2',
+            't1.person_id = t2.person_id  and t2.next_clinical_datetime_hiv is null and t2.is_clinical_encounter = 1'
+          ]
+        ]
+      };
+
+      db.queryDb(queryParts)
+        .then(function (data) {
+          resolve(data.result);
+        })
+        .catch((error) => {
+          reject(error);
+        });
+    });
+  }
+
   return {
     getPatientHivSummary: getPatientHivSummary,
     getPatientOncologySummary: getPatientOncologySummary,
@@ -728,6 +761,7 @@ module.exports = (function () {
     getHivPatientClinicalSummary: getHivPatientClinicalSummary,
     getPatientCountGroupedByLocation: getPatientCountGroupedByLocation,
     getPatientDetailsGroupedByLocation: getPatientDetailsGroupedByLocation,
-    getHivNegativesPatientSummary: getHivNegativesPatientSummary
+    getHivNegativesPatientSummary: getHivNegativesPatientSummary,
+    getPatientsLatestHivSummmary: getPatientsLatestHivSummmary
   };
 })();

departments/department-programs-config.json

@@ -69,6 +69,10 @@
       {
         "uuid": "03552f68-8233-4793-8353-3db1847bb617",
         "name": "NUTRITION PROGRAM"
+      },
+      {
+        "uuid": "203571d6-a4f2-4953-9e8b-e1105e2340f5",
+        "name": "OTZ PROGRAM"
       }
     ]
   },

etl-routes.js

@@ -81,6 +81,7 @@ import { getPatientCovidVaccinationStatus } from './service/covid-19/covid-19-va
 import { Covid19MonthlyReport } from './service/covid-19/covid-19-monthly-report';
 import { MlWeeklyPredictionsService } from './service/ml-weekly-predictions.service';
 import { getPatientPredictedScore } from './service/predictions/ml-prediction-service';
+import { CohortModuleService } from './app/otz/cohort-module.service';
 
 module.exports = (function () {
   var routes = [
@@ -6291,6 +6292,45 @@ module.exports = (function () {
         notes: 'Returns the patients predictions data.',
         tags: ['api']
       }
+    },
+    {
+      method: 'GET',
+      path: '/etl/hiv-latest-summaries',
+      config: {
+        auth: 'simple',
+        plugins: {},
+        handler: function (request, reply) {
+          dao.getPatientsLatestHivSummmary(request).then((summary) => {
+            reply(summary);
+          });
+        },
+        description: 'Get cohort hiv summaries',
+        notes: 'Api endpoint that returns cohort hiv summaries',
+        tags: ['api']
+      }
+    },
+    {
+      method: 'GET',
+      path: '/etl/viral-load-suppression-rate',
+      config: {
+        auth: 'simple',
+        plugins: {},
+        handler: function (request, reply) {
+          const { uuid } = request.query;
+          const cohortService = new CohortModuleService();
+          cohortService
+            .getCohortSummary(uuid)
+            .then(function (cohortUsers) {
+              reply(cohortUsers);
+            })
+            .catch(function (error) {
+              reply(new Boom(500, 'Internal server error.', '', '', error));
+            });
+        },
+        description: 'Get cohort viral load suppression rate',
+        notes: 'Api endpoint that returns cohort viral load suppression rate',
+        tags: ['api']
+      }
     }
   ];
 

programs/patient-program-config.json

@@ -2090,6 +2090,51 @@
       }
     ]
   },
+  "203571d6-a4f2-4953-9e8b-e1105e2340f5": {
+    "name": "OTZ PROGRAM",
+    "enrollmentOptions": {
+      "requiredProgramQuestions": [],
+      "allowMultipleEnrollment": false,
+      "stateChangeEncounterTypes": {
+        "enrollment": [],
+        "transfer": [
+          {
+            "uuid": "cbe2d31d-2201-44ce-b52e-fbd5dc7cff33",
+            "name": "AMPATH POC Transfer Out Form v0.01",
+            "required": true
+          }
+        ],
+        "discharge": [
+          {
+            "uuid": "c2380050-5e55-4d93-9f4f-cc4cd9d59dc0",
+            "name": "AMPATH POC OTZ Exit Form V1.0",
+            "required": true
+          }
+        ]
+      }
+    },
+    "dataDependencies": [
+      "patient",
+      "enrollment",
+      "hivLastTenClinicalEncounters"
+    ],
+    "incompatibleWith": [],
+    "visitTypes": [
+      {
+        "uuid": "d3d5fd4a-508c-4610-97b7-5197a0bdb88d",
+        "name": "OTZ Visit ",
+        "groupVisit": true,
+        "allowedIf": "age > 9 && age <= 24",
+        "message": "Patient has to be between the age of 10 and 24",
+        "encounterTypes": [
+          {
+            "uuid": "76680613-2974-4d89-9b85-6b0a4bf56267",
+            "display": "OTZACTIVITY"
+          }
+        ]
+      }
+    ]
+  },
   "781d8768-1359-11df-a1f1-0026b9348837": {
     "name": "DERMATOLOGY PROGRAM",
     "enrollmentOptions": {