Merge pull request #1281 from AMPATH/ml-weekly-predictions

ML weekly predictions API endpoint for patient list

app/reporting-framework/base-mysql.report.js

@@ -225,6 +225,10 @@ import * as hiv_cervical_cancer_monthly_summary_lesions_pcf_aggregate from './js
 import * as defaulter_list_aggregate from './json-reports/defaulter-list-aggregate.json';
 import * as defaulter_list_base from './json-reports/defaulter-list-base.json';
 
+// ML Weekly Predictions
+import * as ml_weekly_predictions_aggregate from './json-reports/ml-predictions/ml-weekly-predictions-aggregate.json';
+import * as ml_weekly_predictions_base from './json-reports/ml-predictions/ml-weekly-predictions-base.json';
+
 //clinic clow report
 import * as clinic_flow_provider_statistics_aggregate from './json-reports/clinic-flow-provider-statistics-aggregate.json';
 import * as clinic_flow_provider_statistics_base from './json-reports/clinic-flow-provider-statistics-base.json';
@@ -1272,6 +1276,14 @@ export class BaseMysqlReport {
             defaulterListBase: this.cloneJsonSchema(defaulter_list_base)
           });
           break;
+        case 'mlWeeklyPredictionsAggregate':
+          resolve({
+            main: this.cloneJsonSchema(ml_weekly_predictions_aggregate),
+            mlWeeklyPredictionsBase: this.cloneJsonSchema(
+              ml_weekly_predictions_base
+            )
+          });
+          break;
         case 'clinicFlowProviderStatisticsAggregate':
           resolve({
             main: this.cloneJsonSchema(

app/reporting-framework/json-reports/ml-predictions/ml-weekly-predictions-aggregate.json

@@ -0,0 +1,50 @@
+{
+  "name": "mlWeeklyPredictionsAggregate",
+  "version": "1.0",
+  "tag": "",
+  "description": "",
+  "uses": [
+    {
+      "name": "mlWeeklyPredictionsBase",
+      "version": "1.0",
+      "type": "dataset_def"
+    }
+  ],
+  "sources": [
+    {
+      "dataSet": "mlWeeklyPredictionsBase",
+      "alias": "t2"
+    }
+  ],
+  "columns": [
+    {
+      "type": "simple_column",
+      "alias": "person_id",
+      "column": "t2.person_id"
+    },
+    {
+      "type": "simple_column",
+      "alias": "total_predictions",
+      "column": "count(distinct t2.person_id)"
+    }
+  ],
+  "groupBy": {
+    "groupParam": "groupByParam",
+    "columns": ["person_id"],
+    "excludeParam": "excludeParam"
+  },
+  "dynamicJsonQueryGenerationDirectives": {
+    "patientListGenerator": {
+      "useTemplate": "patient-list-template",
+      "useTemplateVersion": "1.0",
+      "generatingDirectives": {
+        "joinDirectives": {
+          "joinType": "INNER",
+          "joinCondition": "<<base_column>> = <<template_column>>",
+          "baseColumn": "person_id",
+          "templateColumn": "person_id"
+        }
+      }
+    }
+  }
+}

app/reporting-framework/json-reports/ml-predictions/ml-weekly-predictions-base.json

@@ -0,0 +1,214 @@
+{
+  "name": "mlWeeklyPredictionsBase",
+  "version": "1.0",
+  "tag": "",
+  "description": "",
+  "uses": [],
+  "sources": [
+    {
+      "table": "predictions.ml_weekly_predictions",
+      "alias": "ml"
+    },
+    {
+      "table": "etl.flat_hiv_summary_v15b",
+      "alias": "de",
+      "join": {
+        "type": "LEFT",
+        "joinCondition": "de.encounter_id = ml.encounter_id"
+      }
+    },
+    {
+      "table": "etl.flat_patient_identifiers_v1",
+      "alias": "fi",
+      "join": {
+        "type": "LEFT",
+        "joinCondition": "de.person_id = fi.patient_id"
+      }
+    },
+    {
+      "table": "etl.program_visit_map",
+      "alias": "pm",
+      "join": {
+        "type": "LEFT",
+        "joinCondition": "de.visit_type = pm.visit_type_id"
+      }
+    },
+    {
+      "table": "amrs.program",
+      "alias": "p",
+      "join": {
+        "type": "LEFT",
+        "joinCondition": "p.program_id = pm.program_type_id"
+      }
+    },
+    {
+      "table": "etl.pre_appointment_summary",
+      "alias": "pre",
+      "join": {
+        "type": "LEFT",
+        "joinCondition": "pre.person_id = ml.person_id"
+      }
+    }
+  ],
+  "columns": [
+    {
+      "type": "simple_column",
+      "alias": "person_id",
+      "column": "ml.person_id"
+    },
+    {
+      "type": "simple_column",
+      "alias": "ccc_number",
+      "column": "fi.ccc"
+    },
+    {
+      "type": "simple_column",
+      "alias": "ovcid_id",
+      "column": "fi.ovcid"
+    },
+    {
+      "type": "simple_column",
+      "alias": "upi_number",
+      "column": "fi.nupi"
+    },
+    {
+      "type": "simple_column",
+      "alias": "program",
+      "column": "p.name"
+    },
+    {
+      "type": "simple_column",
+      "alias": "predicted_risk",
+      "column": "ml.predicted_risk"
+    },
+    {
+      "type": "simple_column",
+      "alias": "week",
+      "column": "ml.week"
+    },
+    {
+      "type": "simple_column",
+      "alias": "predicted_prob_disengage",
+      "column": "ml.predicted_prob_disengage"
+    },
+    {
+      "type": "simple_column",
+      "alias": "prediction_generated_date",
+      "column": "DATE_FORMAT(ml.prediction_generated_date,'%Y-%m-%d')"
+    },
+    {
+      "type": "simple_column",
+      "alias": "rtc_date",
+      "column": "DATE_FORMAT(ml.rtc_date,'%Y-%m-%d')"
+    },
+    {
+      "type": "simple_column",
+      "alias": "follow_up_type",
+      "column": "pre.follow_up_type"
+    },
+    {
+      "type": "simple_column",
+      "alias": "follow_up_reason",
+      "column": "pre.follow_up_reason"
+    },
+    {
+      "type": "simple_column",
+      "alias": "rescheduled_date",
+      "column": "pre.rescheduled_date"
+    },
+    {
+      "type": "simple_column",
+      "alias": "reschedule_appointment",
+      "column": "pre.reschedule_appointment"
+    },
+    {
+      "type": "simple_column",
+      "alias": "contact_reached",
+      "column": "pre.contact_reached_phone_follow_up"
+    },
+    {
+      "type": "simple_column",
+      "alias": "attempted_home_visit",
+      "column": "pre.attempted_home_visit"
+    },
+    {
+      "type": "simple_column",
+      "alias": "reason_not_attempted_home_visit",
+      "column": "pre.reason_not_attempted_home_visit"
+    },
+    {
+      "type": "simple_column",
+      "alias": "was_client_found",
+      "column": "pre.was_client_found"
+    },
+    {
+      "type": "simple_column",
+      "alias": "reason_client_not_found",
+      "column": "pre.reason_client_not_found"
+    },
+    {
+      "type": "simple_column",
+      "alias": "home_visit_personnel",
+      "column": "pre.home_visit_personnel"
+    },
+    {
+      "type": "derived_column",
+      "alias": "was_follow_up_successful",
+      "expressionType": "simple_expression",
+      "expressionOptions": {
+        "expression": "if((pre.is_successful_phone_follow_up = 'YES' OR (pre.attempted_home_visit = 'YES' AND pre.was_client_found = 'YES')), 1, 0)"
+      }
+    },
+    {
+      "type": "simple_column",
+      "alias": "comments",
+      "column": "pre.comments"
+    }
+  ],
+  "filters": {
+    "conditionJoinOperator": "and",
+    "conditions": [
+      {
+        "filterType": "tableColumns",
+        "conditionExpression": "ml.location_id in (?)",
+        "parameterName": "locations"
+      },
+      {
+        "filterType": "tableColumns",
+        "conditionExpression": "ml.week = ?",
+        "parameterName": "yearWeek"
+      },
+      {
+        "filterType": "tableColumns",
+        "conditionExpression": "(if((pre.is_successful_phone_follow_up = 'YES' OR (pre.attempted_home_visit = 'YES' AND pre.was_client_found = 'YES')), 1, 0)) = ?",
+        "parameterName": "successfulOutcome"
+      },
+      {
+        "filterType": "tableColumns",
+        "conditionExpression": "(if((pre.is_successful_phone_follow_up = 'NO' OR (pre.attempted_home_visit = 'YES' AND pre.was_client_found = 'NO')), 1, 0)) = ?",
+        "parameterName": "failedOutcome"
+      },
+      {
+        "filterType": "tableColumns",
+        "conditionExpression": "ml.predicted_risk is not null"
+      }
+    ]
+  },
+  "orderBy": {
+    "orderByParam": "orderByParam",
+    "columns": [
+      {
+        "column": "ml.predicted_prob_disengage",
+        "order": "desc"
+      },
+      {
+        "column": "ml.prediction_generated_date",
+        "order": "desc"
+      },
+      {
+        "column": "pre.encounter_datetime",
+        "order": "desc"
+      }
+    ]
+  }
+}

app/routes/ml-weekly-predictions.route.js

@@ -0,0 +1,11 @@
+const preRequest = require('../../pre-request-processing');
+const etlHelpers = require('../../etl-helpers');
+const Boom = require('boom');
+
+const {
+  MlWeeklyPredictionsService
+} = require('../../service/ml-weekly-predictions.service');
+
+const routes = [];
+
+exports.routes = (server) => server.route(routes);

etl-routes.js

@@ -79,6 +79,8 @@ import { DefaulterListService } from './service/defaulter-list-service';
 import { ClinicFlowService } from './service/clinic-flow-service';
 import { getPatientCovidVaccinationStatus } from './service/covid-19/covid-19-vaccination-summary';
 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';
 
 module.exports = (function () {
   var routes = [
@@ -6211,6 +6213,85 @@ module.exports = (function () {
           'Returns patient list of vaccinated i.e fully,partial and not vaccinated',
         tags: ['api']
       }
+    },
+    {
+      method: 'GET',
+      path: '/etl/ml-weekly-predictions',
+      config: {
+        auth: 'simple',
+        handler: function (request, reply) {
+          if (request.query.locationUuids) {
+            request.query.reportName = 'defaulter-list';
+            preRequest.resolveLocationIdsToLocationUuids(request, function () {
+              let requestParams = Object.assign(
+                {},
+                request.query,
+                request.params
+              );
+
+              const mlWeeklyPredictionsService = new MlWeeklyPredictionsService();
+
+              mlWeeklyPredictionsService
+                .getPatientListReport(requestParams)
+                .then((results) => {
+                  _.each(results.result, (item) => {
+                    item.cur_meds = etlHelpers.getARVNames(item.cur_meds);
+                  });
+                  reply(results);
+                })
+                .catch((err) => {
+                  reply(Boom.internal('An error occured', err));
+                });
+            });
+          }
+        },
+        plugins: {
+          hapiAuthorization: {
+            role: privileges.canViewClinicDashBoard
+          },
+          openmrsLocationAuthorizer: {
+            locationParameter: [
+              {
+                type: 'query',
+                name: 'locationUuids' //name of the location parameter
+              }
+            ]
+          }
+        },
+        description: "Get a location's ml weekly predictions list.",
+        notes: "Returns a location's ml weekly predictions list.",
+        tags: ['api'],
+        validate: {
+          options: {
+            allowUnknown: true
+          }
+        }
+      }
+    },
+    {
+      method: 'GET',
+      path: '/etl/predicted-score',
+      config: {
+        auth: 'simple',
+        plugins: {},
+        handler: function (request, reply) {
+          if (request.query.patientUuid) {
+            const patientUuid = request.query.patientUuid;
+            getPatientPredictedScore(patientUuid)
+              .then((results) => {
+                reply(results);
+              })
+              .catch((error) => {
+                reply(Boom.internal('An error occured', error));
+              });
+          } else {
+            reply(Boom.internal('Request misssing patient uuid'));
+          }
+        },
+        description: 'Patient predicted score of missing appointment.',
+        notes: 'Returns the patients predictions data.',
+        tags: ['api']
+      }
     }
   ];