Merge branch 'master' into POC-538

AMPATH · Oct 6, 2023 · dd3d516 · dd3d516
2 parents c634726 + 1ca7971
commit dd3d516
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Showing 90 changed files with 106,891 additions and 291 deletions.
diff --git a/.prettierrc b/.prettierrc
@@ -0,0 +1,6 @@
+{
+  "trailingComma": "none",
+  "tabWidth": 2,
+  "semi": true,
+  "singleQuote": true
+}
diff --git a/app/reporting-framework/base-mysql.report.js b/app/reporting-framework/base-mysql.report.js
diff --git a/app/reporting-framework/hiv/moh-731.report.js b/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.test_datetime = max_dates.max_vl_1_date)';
+      '(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);
   }

diff --git a/app/reporting-framework/json-reports/RRI/hei-infant-rri-testing-aggregate.json b/app/reporting-framework/json-reports/RRI/hei-infant-rri-testing-aggregate.json
@@ -0,0 +1,122 @@
+{
+  "name": "heiInfantRriTestingAggregate",
+  "version": "1.0",
+  "tag": "",
+  "description": "",
+  "uses": [
+    {
+      "name": "heiInfantRriTestingBase",
+      "version": "1.0",
+      "type": "dataset_def"
+    }
+  ],
+  "sources": [
+    {
+      "dataSet": "heiInfantRriTestingBase",
+      "alias": "hmds"
+    }
+  ],
+  "columns": [
+    {
+      "type": "simple_column",
+      "alias": "reporting_month",
+      "column": "hmds.reporting_month"
+    },
+    {
+      "type": "simple_column",
+      "alias": "location",
+      "column": "hmds.location"
+    },
+    {
+      "type": "simple_column",
+      "alias": "location_id",
+      "column": "hmds.location_id"
+    },
+    {
+      "type": "simple_column",
+      "alias": "location_uuid",
+      "column": "hmds.location_uuid"
+    },
+    {
+      "type": "derived_column",
+      "alias": "initial_pcr_less_than_8_wks",
+      "expressionType": "simple_expression",
+      "expressionOptions": {
+        "expression": "COUNT(hmds.initial_pcr_less_than_8_wks)"
+      }
+    },
+    {
+      "type": "derived_column",
+      "alias": "initial_pcr_8_wks_to_12_months",
+      "expressionType": "simple_expression",
+      "expressionOptions": {
+        "expression": "COUNT(hmds.initial_pcr_8_wks_to_12_months)"
+      }
+    },
+    {
+      "type": "derived_column",
+      "alias": "initial_pcr_less_than_12_months",
+      "expressionType": "simple_expression",
+      "expressionOptions": {
+        "expression": "COUNT(hmds.initial_pcr_less_than_12_months)"
+      }
+    },
+    {
+      "type": "derived_column",
+      "alias": "second_pcr_6_months",
+      "expressionType": "simple_expression",
+      "expressionOptions": {
+        "expression": "COUNT(hmds.second_pcr_6_months)"
+      }
+    },
+    {
+      "type": "derived_column",
+      "alias": "third_pcr_12_months",
+      "expressionType": "simple_expression",
+      "expressionOptions": {
+        "expression": "COUNT(hmds.third_pcr_12_months)"
+      }
+    },
+    {
+      "type": "derived_column",
+      "alias": "antibody_at_18_months",
+      "expressionType": "simple_expression",
+      "expressionOptions": {
+        "expression": "COUNT(hmds.antibody_at_18_months)"
+      }
+    },
+    {
+      "type": "derived_column",
+      "alias": "antibody_post_18_months",
+      "expressionType": "simple_expression",
+      "expressionOptions": {
+        "expression": "COUNT(hmds.antibody_post_18_months)"
+      }
+    }
+  ],
+  "groupBy": {
+    "groupParam": "groupByParam",
+    "columns": ["hmds.reporting_month", "hmds.location_id"],
+    "excludeParam": "excludeParam"
+  },
+  "transFormDirectives": {
+    "joinColumn": "location_id",
+    "skipColumns": [],
+    "disaggregationColumns": []
+  },
+  "dynamicJsonQueryGenerationDirectives": {
+    "patientListGenerator": {
+      "useTemplate": "hei-report-patient-list-template",
+      "useTemplateVersion": "1.0",
+      "generatingDirectives": {
+        "joinDirectives": {
+          "joinType": "INNER",
+          "joinCondition": "<<base_column>> = <<template_column>>",
+          "baseColumn": "person_id",
+          "templateColumn": "person_id"
+        }
+      },
+      "skipParams": []
+    }
+  }
+}
diff --git a/app/reporting-framework/json-reports/RRI/hei-infant-rri-testing-base.json b/app/reporting-framework/json-reports/RRI/hei-infant-rri-testing-base.json
@@ -0,0 +1,168 @@
+{
+  "name": "heiInfantRriTestingBase",
+  "version": "1.0",
+  "tag": "hei_infant_rri_testing_base",
+  "description": "",
+  "uses": [],
+  "sources": [
+    {
+      "table": "etl.pmtct_rri_dataset",
+      "alias": "prd"
+    },
+    {
+      "table": "etl.hei_monthly_report_dataset",
+      "alias": "hmd",
+      "join": {
+        "type": "inner",
+        "joinCondition": "prd.person_id = hmd.person_id"
+      }
+    },
+    {
+      "table": "amrs.location",
+      "alias": "l",
+      "join": {
+        "type": "inner",
+        "joinCondition": "hmd.location_id = l.location_id"
+      }
+    },
+    {
+      "table": "etl.flat_hei_summary",
+      "alias": "fhs",
+      "join": {
+        "type": "LEFT",
+        "joinCondition": "hmd.person_id = fhs.person_id AND fhs.next_clinical_datetime_hiv IS NULL"
+      }
+    }
+  ],
+  "columns": [
+    {
+      "type": "simple_column",
+      "alias": "person_id",
+      "column": "hmd.person_id"
+    },
+    {
+      "type": "simple_column",
+      "alias": "age",
+      "column": "prd.age"
+    },
+    {
+      "type": "simple_column",
+      "alias": "location",
+      "column": "hmd.clinic"
+    },
+    {
+      "type": "simple_column",
+      "alias": "location_uuid",
+      "column": "l.uuid"
+    },
+    {
+      "type": "simple_column",
+      "alias": "location_id",
+      "column": "hmd.location_id"
+    },
+    {
+      "type": "simple_column",
+      "alias": "reporting_month",
+      "column": "DATE_FORMAT(hmd.endDate,'%Y-%m')"
+    },
+    {
+      "type": "simple_column",
+      "alias": "month",
+      "column": "DATE_FORMAT(hmd.endDate,'%Y-%m')"
+    },
+    {
+      "type": "derived_column",
+      "alias": "initial_pcr_less_than_8_wks",
+      "expressionType": "simple_expression",
+      "expressionOptions": {
+        "expression": "IF(hmd.initial_pcr_this_month is null AND hmd.age_in_months < 2  ,NULL,1)"
+      }
+    },
+    {
+      "type": "derived_column",
+      "alias": "initial_pcr_8_wks_to_12_months",
+      "expressionType": "simple_expression",
+      "expressionOptions": {
+        "expression": "IF(hmd.initial_pcr_this_month is null AND hmd.age_in_months between 2 and 12,NULL,1)"
+      }
+    },
+    {
+      "type": "derived_column",
+      "alias": "initial_pcr_less_than_12_months",
+      "expressionType": "simple_expression",
+      "expressionOptions": {
+        "expression": "IF(hmd.initial_pcr_this_month is null AND hmd.age_in_months < 12,NULL,1)"
+      }
+    },
+    {
+      "type": "derived_column",
+      "alias": "second_pcr_6_months",
+      "expressionType": "simple_expression",
+      "expressionOptions": {
+        "expression": "IF(hmd.second_pcr_this_month is null AND hmd.age_in_months = 6,NULL,1)"
+      }
+    },
+    {
+      "type": "derived_column",
+      "alias": "third_pcr_12_months",
+      "expressionType": "simple_expression",
+      "expressionOptions": {
+        "expression": "IF(hmd.third_pcr_this_month is null AND hmd.age_in_months = 12,NULL,1)"
+      }
+    },
+    {
+      "type": "derived_column",
+      "alias": "antibody_at_18_months",
+      "expressionType": "simple_expression",
+      "expressionOptions": {
+        "expression": "IF(hmd.initial_antibody_screening_this_month is null AND hmd.age_in_months = 18,NULL,1)"
+      }
+    },
+    {
+      "type": "derived_column",
+      "alias": "antibody_post_18_months",
+      "expressionType": "simple_expression",
+      "expressionOptions": {
+        "expression": "IF(hmd.initial_antibody_screening_this_month is null AND hmd.age_in_months > 18,NULL,1)"
+      }
+    }
+  ],
+  "filters": {
+    "conditionJoinOperator": "and",
+    "conditions": [
+      {
+        "filterType": "tableColumns",
+        "conditionExpression": "prd.encounter_datetime >= ?",
+        "parameterName": "startDate"
+      },
+      {
+        "filterType": "tableColumns",
+        "conditionExpression": "prd.encounter_datetime <= ?",
+        "parameterName": "endDate"
+      },
+      {
+        "filterType": "tableColumns",
+        "conditionExpression": "prd.encounter_type in (115)"
+      },
+      {
+        "filterType": "tableColumns",
+        "conditionExpression": "hmd.endDate=?",
+        "parameterName": "endDate"
+      },
+      {
+        "filterType": "tableColumns",
+        "conditionExpression": "prd.age <=20"
+      },
+      {
+        "filterType": "tableColumns",
+        "conditionExpression": "hmd.location_id in (?)",
+        "parameterName": "locations"
+      }
+    ]
+  },
+  "groupBy": {
+    "groupParam": "groupByParam",
+    "columns": ["prd.person_id"],
+    "excludeParam": "excludeParam"
+  }
+}
diff --git a/app/reporting-framework/json-reports/RRI/pmtct-rri-cal-hiv-aggregate.json b/app/reporting-framework/json-reports/RRI/pmtct-rri-cal-hiv-aggregate.json
@@ -0,0 +1,84 @@
+{
+  "name": "pmtctRriCalhivAggregate",
+  "version": "1.0",
+  "tag": "pmtct_rri_cal_hiv_aggregate",
+  "uses": [
+    {
+      "name": "pmtctRriCalhivDataSetBase",
+      "version": "1.0",
+      "type": "dataset_def"
+    }
+  ],
+  "sources": [
+    {
+      "dataSet": "pmtctRriCalhivDataSetBase",
+      "alias": "prd_base"
+    }
+  ],
+  "columns": [
+    {
+      "type": "simple_column",
+      "alias": "Reporting_Month",
+      "column": "prd_base.reporting_month"
+    },
+    {
+      "type": "simple_column",
+      "alias": "location_id",
+      "column": "prd_base.location_id"
+    },
+    {
+      "type": "simple_column",
+      "alias": "location_Name",
+      "column": "prd_base.location"
+    },
+    {
+      "type": "derived_column",
+      "alias": "all_calhiv",
+      "expressionType": "simple_expression",
+      "expressionOptions": {
+        "expression": "COUNT(prd_base.person_id)"
+      }
+    },
+    {
+      "type": "derived_column",
+      "alias": "calhiv_vl_done_past_6_months",
+      "expressionType": "simple_expression",
+      "expressionOptions": {
+        "expression": "SUM(prd_base.calhiv_vl_done_past_6_months)"
+      }
+    },
+    {
+      "type": "derived_column",
+      "alias": "calhiv_virally_unsuppressed",
+      "expressionType": "simple_expression",
+      "expressionOptions": {
+        "expression": "SUM(prd_base.calhiv_virally_unsuppressed)"
+      }
+    }
+  ],
+  "groupBy": {
+    "groupParam": "groupByParam",
+    "columns": ["prd_base.location_id", "prd_base.reporting_month"],
+    "excludeParam": "excludeParam"
+  },
+  "transFormDirectives": {
+    "joinColumn": "location_id",
+    "joinColumnParam": "",
+    "skipColumns": [""],
+    "disaggregationColumns": []
+  },
+  "dynamicJsonQueryGenerationDirectives": {
+    "patientListGenerator": {
+      "useTemplate": "pmtct-rri-report-patient-list-template",
+      "useTemplateVersion": "1.0",
+      "generatingDirectives": {
+        "joinDirectives": {
+          "joinType": "INNER",
+          "joinCondition": "<<base_column>> = <<template_column>>",
+          "baseColumn": "person_id",
+          "templateColumn": "person_id"
+        }
+      }
+    }
+  }
+}