Add DASHBOARD_COLUMNS to config, with defaults to match current COSRI

patientsearch/config.py

@@ -26,6 +26,35 @@ def load_json_config(potential_json_string):
     "Your account is not authorized for access, please contact an administrator",
 )
 
+DASHBOARD_COLUMNS = json.loads(
+    os.getenv(
+        "DASHBOARD_COLUMNS",
+        json.dumps(
+            [
+                {
+                    "label": "First Name",
+                    "expr": "$.name[0].given[0]",
+                },
+                {
+                    "label": "Last Name",
+                    "expr": "$.name[0].family",
+                },
+                {
+                    "label": "Birth Date",
+                    "expr": "$.birthDate",
+                },
+                {
+                    "label": "Last Accessed",
+                    "defaultSort": "desc",
+                    "expr": "$.meta.lastUpdated",
+                    "dataType": "date",
+                },
+            ],
+        ),
+    )
+)
+
+FHIR_REST_EXTRA_PARAMS_LIST = json.loads(os.getenv("FHIR_REST_EXTRA_PARAMS_LIST", "[]"))
 LANDING_INTRO = os.getenv("LANDING_INTRO", "")
 LANDING_BUTTON_TEXT = os.getenv("LANDING_BUTTON_TEXT", "")
 LANDING_BODY = os.getenv("LANDING_BODY", "")

patientsearch/src/js/components/PatientListTable.js

@@ -27,6 +27,7 @@ import {
   getUrlParameter,
   getRolesFromToken,
   getClientsByRequiredRoles,
+  isEmptyArray,
   isString,
   validateToken,
 } from "../helpers/utility";
@@ -218,6 +219,7 @@ export default function PatientListTable() {
     last_name: "family",
     birth_date: "birthdate",
     last_accessed: "_lastUpdated",
+    mrn: "identifier"
   };
   const default_columns = [
     {
@@ -232,6 +234,12 @@ export default function PatientListTable() {
       label: "Birth Date",
       expr: "$.birthDate",
     },
+    {
+      label: "Last Accessed",
+      defaultSort: "desc",
+      expr: "$.meta.lastUpdated",
+      dataType: "date",
+    },
   ];
   const errorStyle = { display: errorMessage ? "block" : "none" };
   const toTop = () => {
@@ -245,7 +253,11 @@ export default function PatientListTable() {
   };
   const getColumns = () => {
     const configColumns = getAppSettingByKey("DASHBOARD_COLUMNS");
-    let cols = configColumns ? configColumns : default_columns;
+    const isValidConfig = configColumns && Array.isArray(configColumns);
+    let cols = isValidConfig ? configColumns : default_columns;
+    if (!isValidConfig) {
+      console.log("invalid columns via config. Null or not an array.");
+    }
     const hasIdField = cols.filter((col) => col.field === "id").length > 0;
     //columns must include an id field, add if not present
     if (!hasIdField)
@@ -634,6 +646,7 @@ export default function PatientListTable() {
       totalCount: 0,
     };
     let apiURL = `/fhir/Patient?_include=Patient:link&_total=accurate&_count=${pagination.pageSize}`;
+
     if (
       pagination.pageNumber > pagination.prevPageNumber &&
       pagination.nextPageURL
@@ -665,8 +678,7 @@ export default function PatientListTable() {
             resolve(defaults);
             return;
           }
-          let responseData = formatData(response.entry);
-          setData(responseData || []);
+
           if (needExternalAPILookup()) setNoPMPFlag(responseData);
           let responsePageoffset = 0;
           let responseSelfLink = response.link
@@ -711,11 +723,85 @@ export default function PatientListTable() {
               totalCount: response.total,
             },
           });
-          resolve({
+
+          let patientResources = response.entry.filter(
+            (item) => item.resource && item.resource.resourceType === "Patient"
+          );
+
+          let responseData = formatData(patientResources) || [];
+
+          const additionalParams = getAppSettingByKey(
+            "FHIR_REST_EXTRA_PARAMS_LIST"
+          );
+          const resolvedData = {
             data: responseData,
             page: currentPage,
             totalCount: response.total,
-          });
+          };
+          if (isEmptyArray(additionalParams)) {
+            setData(responseData);
+            resolve(resolvedData);
+            return;
+          }
+          // query for additional resources if specified via config
+          // gather patient id(s) from API returned result
+          const ids = patientResources
+            .map((item) => item.resource.id)
+            .join(",");
+          // FHIR resources request(s)
+          const requests = additionalParams.map((queryString) =>
+            fetchData(
+              `/fhir/${queryString}` +
+                (queryString.indexOf("?") !== -1 ? "&" : "?") +
+                `patient=${ids}&_count=1000`,
+              noCacheParam
+            )
+          );
+          const queryResults = (async () => {
+            const results = await Promise.all(requests).catch((e) => {
+              throw new Error(e);
+            });
+            if (isEmptyArray(results)) return patientResources;
+            return patientResources.map((item) => {
+              let subjectId = item.resource.id;
+              if (!item.resource["resources"]) item.resource["resources"] = [];
+              results.forEach((result) => {
+                if (isEmptyArray(result.entry)) return true;
+                item.resource["resources"] = [
+                  ...item.resource["resources"],
+                  ...result.entry
+                    .filter(
+                      (o) =>
+                        o.resource &&
+                        o.resource.subject &&
+                        o.resource.subject.reference &&
+                        o.resource.subject.reference.split("/")[1] === subjectId
+                    )
+                    .map((resourceItem) => resourceItem.resource),
+                ];
+              });
+              return item;
+            });
+          })();
+          queryResults
+            .then((data) => {
+              console.log("query result data ", data);
+              const resultData = formatData(data);
+              setData(resultData || []);
+              resolve({
+                data: resultData,
+                page: currentPage,
+                totalCount: response.total,
+              });
+            })
+            .catch((e) => {
+              setErrorMessage(
+                "Error retrieving additional FHIR resources.  See console for detail."
+              );
+              console.log(e);
+              setData(responseData);
+              resolve(resolvedData);
+            });
         })
         .catch((error) => {
           console.log("Failed to retrieve data", error);

patientsearch/src/js/helpers/utility.js

@@ -353,3 +353,7 @@ export function setFavicon(href) {
   if (!faviconEl) return;
   faviconEl.href = href;
 }
+
+export function isEmptyArray(arrObj) {
+  return !arrObj || !Array.isArray(arrObj) || arrObj.length === 0;
+}

tests/test_columnconfig.py

@@ -0,0 +1,55 @@
+from datetime import datetime
+import jmespath
+import json
+import os
+
+from pytest import fixture
+
+
+def load_json(datadir, filename):
+    with open(os.path.join(datadir, filename), "r") as json_file:
+        data = json.load(json_file)
+    return data
+
+
+@fixture
+def patient_bundle(datadir):
+    return load_json(datadir, "patient_bundle.json")
+
+
+def test_id_count(patient_bundle):
+    assert patient_bundle["total"] == 7
+    expr = jmespath.compile("entry[?resource.resourceType=='Patient'].resource.id")
+    results = expr.search(patient_bundle)
+    assert len(results) == 7
+
+
+def test_max_authored_by_patient(patient_bundle):
+    results = {}
+    date_format = "%Y-%m-%d"
+
+    expr = jmespath.compile("entry[?resource.resourceType=='Patient'].resource.id")
+    patient_ids = expr.search(patient_bundle)
+
+    for id in patient_ids:
+        # from each patient ID, obtain the list of QuestionnaireResponse.authored values
+        expr = jmespath.compile(
+            f"entry[?resource.subject.reference=='Patient/{id}'].resource.authored"
+        )
+
+        # create a list of sortable datetime objects from authored date strings
+        auth_dates = [
+            datetime.strptime(a, date_format) for a in expr.search(patient_bundle)
+        ]
+        auth_dates.sort()
+
+        # retain string form for max found for patient, or empty string
+        results[id] = (
+            datetime.strftime(auth_dates[-1], date_format) if auth_dates else ""
+        )
+
+    # Confirm a few known
+    assert len(results) == 7
+    assert results["53"] == "2022-11-02"
+    assert results["test-patient-1"] == ""
+    assert results["test-patient-2"] == "2022-11-02"