Merge branch 'AMPATH:master' into POC-341

.prettierrc

@@ -0,0 +1,6 @@
+{
+  "trailingComma": "none",
+  "tabWidth": 2,
+  "semi": true,
+  "singleQuote": true
+}

app/otz/cohort-module.service.js

@@ -0,0 +1,54 @@
+var db = require('../../etl-db');
+
+export class CohortModuleService {
+  getCohortSummary = (cohortUuids) => {
+    const uuids = cohortUuids
+      .split(',')
+      .map((s) => {
+        return `"${s}"`;
+      })
+      .join(',');
+    return new Promise((resolve, reject) => {
+      let queryParts = {};
+      const sql = `SELECT 
+        c.uuid,
+        COUNT(DISTINCT cm.patient_id) AS total_patients,
+        IFNULL(SUM(CASE
+                    WHEN fl.hiv_viral_load < 200 THEN 1
+                    ELSE 0
+                END) / NULLIF(COUNT(DISTINCT cm.patient_id), 0) * 100,
+                0) AS suppression_rate_percentage
+    FROM
+        amrs.cohort c
+            LEFT JOIN
+        amrs.location l ON l.location_id = c.location_id
+            INNER JOIN
+        amrs.cohort_member cm ON c.cohort_id = cm.cohort_id
+            LEFT JOIN
+        (SELECT 
+            person_id, MAX(test_datetime) AS latest_test_datetime
+        FROM
+            etl.flat_labs_and_imaging
+        WHERE
+            hiv_viral_load IS NOT NULL
+        GROUP BY person_id) AS latest_tests ON cm.patient_id = latest_tests.person_id
+            LEFT JOIN
+        etl.flat_labs_and_imaging fl ON latest_tests.person_id = fl.person_id
+            AND latest_tests.latest_test_datetime = fl.test_datetime
+    WHERE
+        l.uuid = '${cohortUuids}'
+    GROUP BY c.cohort_id;
+    
+    `;
+
+      queryParts = {
+        sql: sql
+      };
+
+      return db.queryServer(queryParts, function (result) {
+        result.sql = sql;
+        resolve(result);
+      });
+    });
+  };
+}

app/reporting-framework/hiv/moh-731.report.js

@@ -15,7 +15,7 @@ export class Moh731Report extends MultiDatasetPatientlistReport {
     }
     params.hivMonthlyDatasetSource = 'etl.hiv_monthly_report_dataset_frozen'; // defaults to frozen
     params.hivVlDataSource =
-      '(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,max(encounter_id) as encounter_id 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.encounter_id = max_dates.encounter_id)';
+      '(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,max(encounter_id) as encounter_id 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.encounter_id = max_dates.encounter_id)';
     console.log('creating new moh 731 report service');
     super(reportName, params);
   }

app/reporting-framework/json-reports/clinical-reminder-report.json

@@ -16,7 +16,7 @@
       "alias": "t1"
     },
     {
-      "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,max(encounter_id) as encounter_id 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.encounter_id = max_dates.encounter_id)",
+      "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,max(encounter_id) as encounter_id 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.encounter_id = max_dates.encounter_id)",
       "alias": "fli",
       "join": {
         "type": "LEFT",
@@ -79,6 +79,14 @@
         "joinCondition": "mwl.person_id = t1.person_id"
       }
     },
+    {
+      "table": "etl.pre_appointment_summary",
+      "alias": "pre_s",
+      "join": {
+        "type": "left",
+        "joinCondition": "mwl.person_id = pre_s.person_id "
+      }
+    },
     {
       "table": "amrs.relationship",
       "alias": "t6",
@@ -222,13 +230,43 @@
     {
       "type": "simple_column",
       "alias": "last_encounter_date",
-      "column": "ls.encounter_datetime"
+      "column": "t1.encounter_datetime"
     },
     {
       "type": "simple_column",
       "alias": "latest_CD4_Date",
       "column": "ls.cd4_1_date"
     },
+    {
+      "type": "simple_column",
+      "alias": "ipt_start_date",
+      "column": "ls.ipt_start_date"
+    },
+    {
+      "type": "simple_column",
+      "alias": "ipt_stop_date",
+      "column": "ls.ipt_stop_date"
+    },
+    {
+      "type": "simple_column",
+      "alias": "on_ipt",
+      "column": "ls.on_ipt"
+    },
+    {
+      "type": "simple_column",
+      "alias": "ipt_completion_date",
+      "column": "ls.ipt_completion_date"
+    },
+    {
+      "type": "simple_column",
+      "alias": "tb_tx_start_date",
+      "column": "ls.tb_tx_start_date"
+    },
+    {
+      "type": "simple_column",
+      "alias": "tb_tx_end_date",
+      "column": "ls.tb_tx_end_date"
+    },
     {
       "type": "simple_column",
       "alias": "on_tb_tx",
@@ -305,6 +343,16 @@
       "alias": "prediction_generated_date",
       "column": "mwl.prediction_generated_date"
     },
+    {
+      "type": "simple_column",
+      "alias": "reschedule_appointment",
+      "column": "pre_s.reschedule_appointment"
+    },
+    {
+      "type": "simple_column",
+      "alias": "rescheduled_date",
+      "column": "pre_s.rescheduled_date"
+    },
     {
       "type": "simple_column",
       "alias": "test_date",

app/reporting-framework/json-reports/defaulter-list-base.json

@@ -14,7 +14,15 @@
       "alias": "de",
       "join": {
         "type": "LEFT",
-        "joinCondition": "de.encounter_id = fd.encounter_id"
+        "joinCondition": "de.encounter_id = fd.encounter_id "
+      }
+    },
+    {
+      "table": "(SELECT MAX(am.encounter_datetime) AS max_encounter_datetime, am.encounter_datetime, am.encounter_type, am.patient_id, fd.person_id , fd.rtc_date FROM etl.flat_defaulters fd INNER JOIN amrs.encounter am on (am.patient_id = fd.person_id) group by am.patient_id)",
+      "alias": "am",
+      "join": {
+        "type": "INNER",
+        "joinCondition": "am.patient_id = fd.person_id"
       }
     },
     {
@@ -82,6 +90,14 @@
       "type": "simple_column",
       "alias": "rtc_date",
       "column": "DATE_FORMAT(fd.rtc_date,'%Y-%m-%d')"
+    },
+    {
+      "type": "derived_column",
+      "alias": "outreach_follow_up",
+      "expressionType": "simple_expression",
+      "expressionOptions": {
+        "expression": "case when max_encounter_datetime >= fd.rtc_date  then 'Yes' else 'No' end"
+      }
     }
   ],
   "filters": {

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

@@ -46,7 +46,23 @@
       "alias": "pre",
       "join": {
         "type": "LEFT",
-        "joinCondition": "pre.person_id = ml.person_id"
+        "joinCondition": "pre.person_id = ml.person_id and(DATEDIFF(ml.start_date, pre.encounter_datetime) <= 7)"
+      }
+    },
+    {
+      "table": "( select max(is_successful_phone_follow_up) as latest_phone_follow_up, person_id, follow_up_type from  etl.pre_appointment_summary group by person_id )",
+      "alias": "s",
+      "join": {
+        "type": "LEFT",
+        "joinCondition": "pre.person_id = s.person_id"
+      }
+    },
+    {
+      "table": "(SELECT et.person_id, SUM(CASE WHEN et.is_successful_phone_follow_up = 'YES' THEN 0 WHEN et.is_successful_phone_follow_up = 'NO' THEN 1 ELSE 0 END) AS counter FROM etl.pre_appointment_summary et left join predictions.ml_weekly_predictions mwl on et.person_id = mwl.person_id WHERE et.encounter_datetime BETWEEN mwl.prediction_generated_date AND DATE_ADD(mwl.prediction_generated_date, INTERVAL 14 DAY) GROUP BY et.person_id)",
+      "alias": "etc",
+      "join": {
+        "type": "LEFT",
+        "joinCondition": "ml.person_id = etc.person_id"
       }
     }
   ],
@@ -156,9 +172,14 @@
       "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)"
+        "expression": "if((latest_phone_follow_up = 'YES' OR (pre.attempted_home_visit = 'YES' AND pre.was_client_found = 'YES')), 1, 0)"
       }
     },
+    {
+      "type": "simple_column",
+      "alias": "number_of_failed_phone_attempts",
+      "column": "etc.counter"
+    },
     {
       "type": "simple_column",
       "alias": "comments",
@@ -180,14 +201,19 @@
       },
       {
         "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)) = ?",
+        "conditionExpression": "(if((latest_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)) = ?",
+        "conditionExpression": "(if((latest_phone_follow_up = 'NO' OR (pre.attempted_home_visit = 'YES' AND pre.was_client_found = 'NO')), 1, 0)) = ?",
         "parameterName": "failedOutcome"
       },
+      {
+        "filterType": "tableColumns",
+        "conditionExpression": "(if((pre.is_successful_phone_follow_up IS NULL AND pre.attempted_home_visit IS NULL AND pre.was_client_found IS NULL), 0, 1)) = ?",
+        "parameterName": "unknownOutcome"
+      },
       {
         "filterType": "tableColumns",
         "conditionExpression": "ml.predicted_risk is not null"

app/reporting-framework/json-reports/patient-list-template.json

@@ -9,7 +9,7 @@
       "alias": "t1"
     },
     {
-      "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,max(encounter_id) as encounter_id 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.encounter_id = max_dates.encounter_id)",
+      "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,max(encounter_id) as encounter_id 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.encounter_id = max_dates.encounter_id)",
       "alias": "fli",
       "join": {
         "type": "LEFT",

app/reporting-framework/json-reports/patient-list-with-contacts-template.json

@@ -9,7 +9,7 @@
       "alias": "t1"
     },
     {
-      "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,max(encounter_id) as encounter_id 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.encounter_id = max_dates.encounter_id)",
+      "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,max(encounter_id) as encounter_id 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.encounter_id = max_dates.encounter_id)",
       "alias": "fli",
       "join": {
         "type": "LEFT",
@@ -103,6 +103,14 @@
         "type": "LEFT",
         "joinCondition": "delivery_report.person_id = t1.person_id and DATE_FORMAT(delivery_report.date_created, '%Y-%m-%d')='{startDate}'"
       }
+    },
+    {
+      "table": "etl.flat_prep_summary_v1_1",
+      "alias": "fps",
+      "join": {
+        "type": "LEFT",
+        "joinCondition": "t1.person_id = fps.person_id AND fps.next_encounter_datetime IS NULL AND fps.encounter_type NOT IN (99999)"
+      }
     }
   ],
   "columns": [
@@ -142,6 +150,112 @@
         "expression": "extract(year from (from_days(datediff(now(),t1.birthdate))))"
       }
     },
+    {
+      "type": "simple_column",
+      "alias": "prev_rtc_date",
+      "column": "date_format(fps.prev_rtc_date, '%Y-%m-%d')"
+    },
+    {
+      "type": "simple_column",
+      "alias": "cur_prep_meds_names",
+      "column": "fps.cur_prep_meds_names"
+    },
+    {
+      "type": "simple_column",
+      "alias": "rapid_test_date",
+      "column": "date_format(fps.hiv_rapid_test_date, '%Y-%m-%d')"
+    },
+    {
+      "type": "derived_column",
+      "alias": "hiv_rapid_test",
+      "expressionType": "case_statement",
+      "expressionOptions": {
+        "caseOptions": [
+          {
+            "condition": "fps.hiv_rapid_test_result = 703",
+            "value": "Positive"
+          },
+          {
+            "condition": "fps.hiv_rapid_test_result = 664",
+            "value": "Negative"
+          },
+          {
+            "condition": "fps.hiv_rapid_test_result = 1138",
+            "value": "Indeterminate"
+          },
+          {
+            "condition": "fps.hiv_rapid_test_result = 1304",
+            "value": "Poor sample quality"
+          },
+          {
+            "condition": "fps.hiv_rapid_test_result = 1067",
+            "value": "Unknown"
+          }
+        ]
+      }
+    },
+    {
+      "type": "derived_column",
+      "alias": "population_type_category",
+      "expressionType": "case_statement",
+      "expressionOptions": {
+        "caseOptions": [
+          {
+            "condition": "fps.sub_population_type = 1",
+            "value": "MSM"
+          },
+          {
+            "condition": "fps.sub_population_type = 2",
+            "value": "MSW"
+          },
+          {
+            "condition": "fps.sub_population_type = 3",
+            "value": "FSW"
+          },
+          {
+            "condition": "fps.sub_population_type = 4",
+            "value": "IDU"
+          },
+          {
+            "condition": "fps.sub_population_type = 5",
+            "value": "TRANS WOMAN"
+          },
+          {
+            "condition": "fps.sub_population_type = 6",
+            "value": "TRANS MAN"
+          },
+          {
+            "condition": "fps.sub_population_type = 7",
+            "value": "FISHER FOLK"
+          },
+          {
+            "condition": "fps.sub_population_type = 8",
+            "value": "CSW"
+          },
+          {
+            "condition": "fps.sub_population_type = 9",
+            "value": "DISPLACED PERSONS"
+          },
+          {
+            "condition": "fps.sub_population_type = 10",
+            "value": "Military and other"
+          },
+          {
+            "condition": "fps.sub_population_type = 12",
+            "value": "TRUCK/LORRY DRIVER"
+          },
+          {
+            "condition": "fps.sub_population_type = 13",
+            "value": "NIDU"
+          }
+        ]
+      }
+    },
+    {
+      "type": "simple_column",
+      "alias": "enrollment_date",
+      "column": "date_format(fps.enrollment_date, '%Y-%m-%d')"
+    },
     {
       "type": "derived_column",
       "alias": "person_name",