Query struct (#2301)

* Save draft

* Refactor single generalized query

containers/tefca-viewer/src/app/CustomQuery.ts

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+/**
+ * A Data Class designed to store and manipulate various code values used
+ * to create a fully customized FHIR query. The class holds instance variables
+ * for each of four types of input codes (lab LOINCs, SNOMED/conditions, RXNorm,
+ * and Class/System-Type); the class uses these to automatically compile query
+ * strings for each subtype of eCR query that can be built using those codes'
+ * information.
+ */
+export class CustomQuery {
+  // Store four types of input codes
+  labCodes: string[] = [];
+  snomedCodes: string[] = [];
+  rxnormCodes: string[] = [];
+  classTypeCodes: string[] = [];
+
+  // Need default initialization of query strings outstide constructor,
+  // since the `try` means we might not find the JSON spec
+  observationQuery: string = "";
+  diagnosticReportQuery: string = "";
+  conditionQuery: string = "";
+  medicationRequestQuery: string = "";
+  socialHistoryQuery: string = "";
+  encounterQuery: string = "";
+  encounterClassTypeQuery: string = "";
+
+  // Some queries need to be batched in waves because their encounter references
+  // might depend on demographic information
+  hasSecondEncounterQuery: boolean = false;
+
+  /**
+   * Creates a CustomQuery Object. The constructor accepts a JSONspec, a
+   * DIBBs-defined JSON structure consisting of four keys corresponding to
+   * the four types of codes this data class encompasses. These Specs are
+   * currently located in the `customQueries` directory of the app.
+   * @param jsonSpec A JSON Object containing four code fields to load.
+   * @param patientId The ID of the patient to build into query strings.
+   */
+  constructor(jsonSpec: any, patientId: string) {
+    try {
+      this.labCodes = jsonSpec?.labCodes || [];
+      this.snomedCodes = jsonSpec?.snomedCodes || [];
+      this.rxnormCodes = jsonSpec?.rxnormCodes || [];
+      this.classTypeCodes = jsonSpec?.classTypeCodes || [];
+      this.hasSecondEncounterQuery = jsonSpec?.hasSecondEncounterQuery || false;
+      this.compileQueries(patientId);
+    } catch (error) {
+      console.error("Could not create CustomQuery Object: ", error);
+    }
+  }
+
+  /**
+   * Compile the stored code information and given patientID into all applicable
+   * query strings for later use. If a particular code category has no values in
+   * the provided spec (e.g. a Newborn Screening case will have no rxnorm codes),
+   * any query built using those codes' filter will be left as the empty string.
+   * @param patientId The ID of the patient to query for.
+   */
+  compileQueries(patientId: string): void {
+    const labsFilter = this.labCodes.join(",");
+    const snomedFilter = this.snomedCodes.join(",");
+    const rxnormFilter = this.rxnormCodes.join(",");
+    const classTypeFilter = this.classTypeCodes.join(",");
+
+    this.observationQuery =
+      labsFilter !== ""
+        ? `/Observation?subject=Patient/${patientId}&code=${labsFilter}`
+        : "";
+    this.diagnosticReportQuery =
+      labsFilter !== ""
+        ? `/DiagnosticReport?subject=${patientId}&code=${labsFilter}`
+        : "";
+    this.conditionQuery =
+      snomedFilter !== ""
+        ? `/Condition?subject=${patientId}&code=${snomedFilter}`
+        : "";
+    this.medicationRequestQuery =
+      rxnormFilter !== ""
+        ? `/MedicationRequest?subject=${patientId}&code=${rxnormFilter}&_include=MedicationRequest:medication&_include=MedicationRequest:medication.administration`
+        : "";
+    this.socialHistoryQuery = `/Observation?subject=${patientId}&category=social-history`;
+    this.encounterQuery =
+      snomedFilter !== ""
+        ? `/Encounter?subject=${patientId}&reason-code=${snomedFilter}`
+        : "";
+    this.encounterClassTypeQuery =
+      classTypeFilter !== ""
+        ? `/Encounter?subject=${patientId}&class=${classTypeFilter}`
+        : "";
+  }
+
+  /**
+   * Yields all non-empty-string queries compiled using the stored codes.
+   * @returns A list of queries.
+   */
+  getAllQueries(): string[] {
+    const queryRequests: string[] = [
+      this.observationQuery,
+      this.diagnosticReportQuery,
+      this.conditionQuery,
+      this.medicationRequestQuery,
+      this.socialHistoryQuery,
+      this.encounterQuery,
+      this.encounterClassTypeQuery,
+    ];
+    const filteredRequests = queryRequests.filter((q) => q !== "");
+    return filteredRequests;
+  }
+
+  /**
+   * Sometimes, only a single query is desired rather than a full list. In
+   * those cases, this function returns a single specified query string.
+   * @param desiredQuery The type of query the user wants.
+   * @returns The compiled query string for that type.
+   */
+  getQuery(desiredQuery: string): string {
+    switch (desiredQuery) {
+      case "observation":
+        return this.observationQuery;
+      case "diagnostic":
+        return this.diagnosticReportQuery;
+      case "condition":
+        return this.conditionQuery;
+      case "medication":
+        return this.medicationRequestQuery;
+      case "social":
+        return this.socialHistoryQuery;
+      case "encounter":
+        return this.encounterQuery;
+      case "encounterClass":
+        return this.encounterClassTypeQuery;
+      default:
+        return "";
+    }
+  }
+}

containers/tefca-viewer/src/app/demoQueries.ts

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+export type QueryStruct = {
+  labCodes: string[];
+  snomedCodes: string[];
+  rxnormCodes: string[];
+  classTypeCodes: string[];
+  hasSecondEncounterQuery: boolean;
+};
+
+export const SOCIAL_DETERMINANTS_QUERY: QueryStruct = {
+  labCodes: [],
+  snomedCodes: [],
+  rxnormCodes: [],
+  classTypeCodes: [],
+  hasSecondEncounterQuery: false,
+};
+
+export const CANCER_QUERY: QueryStruct = {
+  labCodes: [],
+  snomedCodes: ["92814006"],
+  rxnormCodes: ["828265"],
+  classTypeCodes: [],
+  hasSecondEncounterQuery: true,
+};
+
+export const CHLAMYDIA_QUERY: QueryStruct = {
+  labCodes: ["24111-7", "72828-7", "21613-5", "82810-3", "11350-6", "83317-8"],
+  snomedCodes: ["2339001", "72531000052105", "102874004", "A74.9"],
+  rxnormCodes: ["434692", "82122", "1649987", "1665005"],
+  classTypeCodes: ["54", "441"],
+  hasSecondEncounterQuery: true,
+};
+
+export const GONORRHEA_QUERY: QueryStruct = {
+  labCodes: ["24111-7", "11350-6", "21613-5", "82810-3", "83317-8"],
+  snomedCodes: ["15628003", "2339001", "72531000052105", "102874004"],
+  rxnormCodes: ["1665005", "434692"],
+  classTypeCodes: ["54", "441"],
+  hasSecondEncounterQuery: true,
+};
+
+export const NEWBORN_SCREENING_QUERY: QueryStruct = {
+  labCodes: [
+    "73700-7",
+    "73698-3",
+    "54108-6",
+    "54109-4",
+    "58232-0",
+    "57700-7",
+    "73739-5",
+    "73742-9",
+    "2708-6",
+    "8336-0",
+  ],
+  snomedCodes: [],
+  rxnormCodes: [],
+  classTypeCodes: [],
+  hasSecondEncounterQuery: false,
+};
+
+export const SYPHILIS_QUERY: QueryStruct = {
+  labCodes: ["LP70657-9", "53605-2"],
+  snomedCodes: ["76272004", "186847001"],
+  rxnormCodes: ["2671695"],
+  classTypeCodes: ["54", "441"],
+  hasSecondEncounterQuery: true,
+};