Merge branch 'master' into POC-372

AMPATH · Aug 3, 2023 · 1fbd16f · 1fbd16f
2 parents e7745c7 + d227fe1
commit 1fbd16f
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Showing 49 changed files with 1,729 additions and 1,232 deletions.
diff --git a/app/reporting-framework/base-mysql.report.js b/app/reporting-framework/base-mysql.report.js
@@ -224,6 +224,10 @@ 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';
@@ -1271,6 +1275,14 @@ 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(

diff --git a/app/reporting-framework/json-reports/clinical-reminder-report.json b/app/reporting-framework/json-reports/clinical-reminder-report.json
@@ -71,6 +71,14 @@
         "joinCondition": "t3.person_uuid = t1.uuid"
       }
     },
+    {
+      "table": "predictions.ml_weekly_predictions",
+      "alias": "mwl",
+      "join": {
+        "type": "left",
+        "joinCondition": "mwl.person_id = t1.person_id"
+      }
+    },
     {
       "table": "amrs.relationship",
       "alias": "t6",
@@ -282,6 +290,21 @@
       "alias": "vl_error_date",
       "column": "t2.test_datetime"
     },
+    {
+      "type": "simple_column",
+      "alias": "predicted_risk",
+      "column": "mwl.predicted_risk"
+    },
+    {
+      "type": "simple_column",
+      "alias": "predicted_prob_disengage",
+      "column": "mwl.predicted_prob_disengage"
+    },
+    {
+      "type": "simple_column",
+      "alias": "prediction_generated_date",
+      "column": "mwl.prediction_generated_date"
+    },
     {
       "type": "simple_column",
       "alias": "test_date",
@@ -485,6 +508,10 @@
       {
         "column": "t1.encounter_datetime",
         "order": "desc"
+      },
+      {
+        "column": "mwl.prediction_generated_date",
+        "order": "desc"
       }
     ]
   },

diff --git a/app/reporting-framework/json-reports/differentiated-care-program-base.json b/app/reporting-framework/json-reports/differentiated-care-program-base.json
@@ -8,6 +8,22 @@
     {
       "table": "etl.dc_monthly_report_dataset",
       "alias": "dcr"
+    },
+    {
+      "table": "(SELECT fli.person_id, fli.hiv_viral_load as vl_1, fli.test_datetime as vl_1_date FROM etl.flat_labs_and_imaging fli INNER JOIN (SELECT person_id, MAX(test_datetime) AS max_vl_1_date FROM etl.flat_labs_and_imaging fli where fli.hiv_viral_load is not null GROUP BY person_id) max_dates ON fli.person_id = max_dates.person_id AND fli.test_datetime = max_dates.max_vl_1_date and fli.hiv_viral_load is not null)",
+      "alias": "fli_latest_vl",
+      "join": {
+        "type": "LEFT",
+        "joinCondition": "fli_latest_vl.person_id = dcr.person_id"
+      }
+    },
+    {
+      "table": "etl.flat_patient_identifiers_v1",
+      "alias": "flat_identifiers",
+      "join": {
+        "type": "LEFT",
+        "joinCondition": "dcr.person_id = flat_identifiers.patient_id"
+      }
     }
   ],
   "columns": [
@@ -16,6 +32,21 @@
       "alias": "persons_id",
       "column": "dcr.person_id"
     },
+    {
+      "type": "simple_column",
+      "alias": "ccc_number",
+      "column": "flat_identifiers.ccc"
+    },
+    {
+      "type": "simple_column",
+      "alias": "ovcid_id",
+      "column": "flat_identifiers.ovcid"
+    },
+    {
+      "type": "simple_column",
+      "alias": "upi_number",
+      "column": "flat_identifiers.nupi"
+    },
     {
       "type": "derived_column",
       "alias": "total_eligible_for_dc",
@@ -83,7 +114,7 @@
     {
       "type": "simple_column",
       "alias": "vl_1",
-      "column": "dcr.vl_1"
+      "column": "fli_latest_vl.vl_1"
     },
     {
       "type": "simple_column",
@@ -93,7 +124,7 @@
     {
       "type": "simple_column",
       "alias": "vl_1_date",
-      "column": "dcr.vl_1_date"
+      "column": "fli_latest_vl.vl_1_date"
     },
     {
       "type": "simple_column",

diff --git a/app/reporting-framework/json-reports/ml-predictions/ml-weekly-predictions-aggregate.json b/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"
+        }
+      }
+    }
+  }
+}