LNK-2187 Refactor MVP tenant and report summaries (#723)

* * Facilities in UI only displays a single line per facility, not a separate line/row per report * Activities in UI only shows the number of patients (in-ip out of total). * Changed ApiConfig to capture short/long name for each measure def - the api config will need to be udpated when deployed * Removing run configuration from git * Updated Javadocs * Simplifying the process for getting a unique list of measures scheduled for a tenant * Simplfying reading get-reports.sql as a string * Using `StringUtils.containsIgnoreCase` instead of `property.toLowerCase().contains(value.toLowerCase())` * Correct SQL for getting reports including patient counts to not duplicate records Fixing bug in use of `IOUtils.resourceToString()` * De-duplicating logic that looks up a measure definition by id from the ApiConfig
lantanagroup · Mar 15, 2024 · 002681a · 002681a
1 parent ace3451
commit 002681a
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Showing 19 changed files with 238 additions and 182 deletions.
diff --git a/.idea/runConfigurations/API_DEV___No_Scheduling.xml b/.idea/runConfigurations/API_DEV___No_Scheduling.xml
diff --git a/api/src/main/java/com/lantanagroup/link/api/auth/PreAuthTokenHeaderFilter.java b/api/src/main/java/com/lantanagroup/link/api/auth/PreAuthTokenHeaderFilter.java
@@ -10,17 +10,17 @@
 import com.lantanagroup.link.config.api.ApiConfig;
 import com.lantanagroup.link.db.SharedService;
 import com.lantanagroup.link.db.model.User;
+import jakarta.servlet.FilterChain;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.ServletRequest;
+import jakarta.servlet.ServletResponse;
+import jakarta.servlet.http.HttpServletRequest;
 import org.apache.commons.lang3.StringUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.security.core.context.SecurityContextHolder;
 import org.springframework.security.web.authentication.preauth.AbstractPreAuthenticatedProcessingFilter;
 
-import jakarta.servlet.FilterChain;
-import jakarta.servlet.ServletException;
-import jakarta.servlet.ServletRequest;
-import jakarta.servlet.ServletResponse;
-import jakarta.servlet.http.HttpServletRequest;
 import java.io.IOException;
 import java.lang.reflect.Constructor;
 import java.lang.reflect.InvocationTargetException;
@@ -52,7 +52,7 @@ public void doFilter(ServletRequest request, ServletResponse response, FilterCha
       logger.debug("Validating the requesting IP address against the token IP address.");
       DecodedJWT jwt = JWT.decode(authHeader.substring(7));
 
-      if (!jwt.getClaim("ip").isNull() && !"0:0:0:0:0:0:0:1(0:0:0:0:0:0:0:1)".equals(ipAddress) && !jwt.getClaim("ip").asString().equals(ipAddress)) {
+      if (!jwt.getClaim("ip").isNull() && !"127.0.0.1(127.0.0.1)".equals(ipAddress) && !"0:0:0:0:0:0:0:1(0:0:0:0:0:0:0:1)".equals(ipAddress) && !jwt.getClaim("ip").asString().equals(ipAddress)) {
         throw new JWTVerificationException("IP Address does not match.");
       }
     }

diff --git a/api/src/main/java/com/lantanagroup/link/api/controller/GlobalReportController.java b/api/src/main/java/com/lantanagroup/link/api/controller/GlobalReportController.java
@@ -58,8 +58,7 @@ public List<GlobalReportResponse> getReports(
       reports = reports.stream().filter(x -> x.getStatus().equals(ReportStatuses.valueOf(status))).collect(Collectors.toList());
     }
 
-    if(measureIds.length() > 0)
-    {
+    if (!measureIds.isEmpty()) {
       String[] ids = measureIds.split(",");
       reports = reports.stream().filter(x -> {
         HashSet<String> measureIdsSet = new HashSet<>(x.getMeasureIds());
@@ -72,7 +71,11 @@ public List<GlobalReportResponse> getReports(
       }).collect(Collectors.toList());
     }
 
-    reports = reports.stream().skip((long) (page -1) * count).limit(count).collect(Collectors.toList());
+    reports = reports
+            .stream()
+            .skip((long) (page - 1) * count)
+            .limit(count)
+            .collect(Collectors.toList());
 
     return reports;
   }

diff --git a/api/src/main/java/com/lantanagroup/link/api/controller/MeasureDefController.java b/api/src/main/java/com/lantanagroup/link/api/controller/MeasureDefController.java
@@ -2,11 +2,11 @@
 
 import ca.uhn.fhir.rest.api.EncodingEnum;
 import com.lantanagroup.link.FhirContextProvider;
-import com.lantanagroup.link.FhirDataProvider;
 import com.lantanagroup.link.FhirHelper;
 import com.lantanagroup.link.Helper;
 import com.lantanagroup.link.api.MeasureServiceWrapper;
 import com.lantanagroup.link.config.api.ApiConfig;
+import com.lantanagroup.link.config.api.MeasureDefConfig;
 import com.lantanagroup.link.db.SharedService;
 import com.lantanagroup.link.db.model.MeasureDefinition;
 import com.lantanagroup.link.db.model.MeasurePackage;
@@ -86,11 +86,12 @@ public void createOrUpdateMeasureDef(@RequestBody(required = false) Bundle bundl
       throw new ResponseStatusException(HttpStatus.BAD_REQUEST, "Either a Bundle must be specified in a JSON body of the request, or a \"measureId\" query parameter must be specified");
     }
 
-    if (StringUtils.isNotEmpty(measureId) && this.apiConfig.getMeasureDefUrls().get(measureId) == null) {
+    MeasureDefConfig foundMeasureDef = this.apiConfig.getMeasureDefinition(measureId);
+    if (StringUtils.isNotEmpty(measureId) && foundMeasureDef == null) {
       throw new ResponseStatusException(HttpStatus.NOT_FOUND, "The specified measureId is not configured with a measure definition URL");
     }
 
-    String url = StringUtils.isNotEmpty(measureId) ? this.apiConfig.getMeasureDefUrls().get(measureId) : null;
+    String url = foundMeasureDef != null ? foundMeasureDef.getDefinitionUrl() : null;
     Bundle bundle = bundleBody == null ? this.getBundleFromUrl(url) : bundleBody;
 
     if (bundle == null) {

diff --git a/api/src/main/java/com/lantanagroup/link/api/controller/TenantController.java b/api/src/main/java/com/lantanagroup/link/api/controller/TenantController.java
@@ -4,6 +4,7 @@
 import com.lantanagroup.link.api.scheduling.Scheduler;
 import com.lantanagroup.link.db.SharedService;
 import com.lantanagroup.link.db.TenantService;
+import com.lantanagroup.link.db.model.Report;
 import com.lantanagroup.link.db.model.tenant.Tenant;
 import com.lantanagroup.link.db.model.tenant.TenantVendors;
 import com.lantanagroup.link.model.SearchTenantResponse;
@@ -49,7 +50,7 @@ public List<SearchTenantResponse> searchTenants() {
   }
 
   @GetMapping("summary")
-  public TenantSummaryResponse searchTenantSummaries(@RequestParam(required = false) String searchCriteria, @RequestParam(defaultValue = "NAME", required = false) String sort, @RequestParam(defaultValue = "1", required = false) int page, @RequestParam(defaultValue = "true", required = false) boolean sortAscend) {
+  public TenantSummaryResponse searchTenants(@RequestParam(required = false) String searchCriteria, @RequestParam(defaultValue = "NAME", required = false) String sort, @RequestParam(defaultValue = "1", required = false) int page, @RequestParam(defaultValue = "true", required = false) boolean sortAscend) {
     // validation
     int itemsPerPage = 5;
 
@@ -67,9 +68,22 @@ public TenantSummaryResponse searchTenantSummaries(@RequestParam(required = fals
         throw new ResponseStatusException(HttpStatus.BAD_REQUEST, "Invalid sort criteria. Valid values are NAME, NHSN_ORG_ID, SUBMISSION_DATE");
       }
     }
-    List<TenantSummary> tenants = this.sharedService.getTenantSummary(searchCriteria, TenantSummarySort.valueOf(sort.trim()), sortAscend).stream().collect(Collectors.toList());
 
-    List<TenantSummary> results = tenants.stream().skip(skip).limit(itemsPerPage).collect(Collectors.toList());
+    List<TenantSummary> tenants = this.sharedService.searchTenants(searchCriteria, TenantSummarySort.valueOf(sort.trim()), sortAscend);
+    List<TenantSummary> results = tenants.stream()
+            .skip(skip)
+            .limit(itemsPerPage)
+            .collect(Collectors.toList());
+
+    results.forEach(t -> {
+      TenantService tenantService = TenantService.create(this.sharedService.getTenantConfig(t.getId()));
+      Report lastReport = tenantService.findLastReport();
+
+      if (lastReport != null) {
+        t.setLastSubmissionId(lastReport.getId());
+        t.setLastSubmissionDate(String.valueOf(lastReport.getSubmittedTime()));
+      }
+    });
 
     TenantSummaryResponse response = new TenantSummaryResponse();
     response.setTotal(tenants.size());

diff --git a/core/src/main/java/com/lantanagroup/link/config/api/ApiConfig.java b/core/src/main/java/com/lantanagroup/link/config/api/ApiConfig.java
@@ -1,17 +1,16 @@
 package com.lantanagroup.link.config.api;
 
 import com.lantanagroup.link.config.YamlPropertySourceFactory;
+import jakarta.validation.constraints.NotNull;
+import jakarta.validation.constraints.PositiveOrZero;
 import lombok.Getter;
 import lombok.Setter;
 import org.springframework.boot.context.properties.ConfigurationProperties;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.PropertySource;
 import org.springframework.validation.annotation.Validated;
 
-import jakarta.validation.constraints.NotNull;
-import jakarta.validation.constraints.PositiveOrZero;
 import java.util.ArrayList;
-import java.util.HashMap;
 import java.util.List;
 
 @Getter
@@ -159,9 +158,9 @@ public class ApiConfig {
   private boolean noScheduling = false;
 
   /**
-   * <strong>api.measure-def-urls</strong><br>A set of URLs representing the latest measure definition, keyed by measure ID
+   * <strong>api.measure-definitions</strong><br>Each of the measure definitions supported by the installation, by identifier, short name, long name and the url for where the definition lives.
    */
-  private HashMap<String, String> measureDefUrls = new HashMap<>();
+  private List<MeasureDefConfig> measureDefinitions = new ArrayList<>();
 
   /**
    * Allows use of QA debugging endpoints. DO NOT ALLOW IN PRODUCTION!!!!
@@ -175,12 +174,24 @@ public class ApiConfig {
    */
   private String validationPackagesPath = "classpath:/packages/**";
 
-
   /**
    * Configuration for how to query the MRP (reporting plan) interface at CDC/NHSN to determine if a facility/tenant
    * is signed up to report during the calculated reporting period.
    */
   private ReportingPlan reportingPlan;
 
+  /**
+   * Finds a single measure definition by it's ID
+   * @param measureId The id of the measure to find
+   * @return MeasureDefConfig
+   */
+  public MeasureDefConfig getMeasureDefinition(String measureId) {
+    return measureDefinitions
+            .stream()
+            .filter(m -> m.getId().equals(measureId))
+            .findFirst()
+            .orElse(null);
+  }
+
 
 }
diff --git a/core/src/main/java/com/lantanagroup/link/config/api/MeasureDefConfig.java b/core/src/main/java/com/lantanagroup/link/config/api/MeasureDefConfig.java
@@ -0,0 +1,31 @@
+package com.lantanagroup.link.config.api;
+
+import lombok.Getter;
+import lombok.Setter;
+
+/**
+ * Configuration for a supported measure definition within the installation
+ */
+@Getter
+@Setter
+public class MeasureDefConfig {
+  /**
+   * The unique identifier for the measure definition
+   */
+  private String id;
+
+  /**
+   * The short name for the measure definition (i.e. "Hypo")
+   */
+  private String shortName;
+
+  /**
+   * The long name for the measure definition (i.e. "Hypoglycemia")
+   */
+  private String longName;
+
+  /**
+   * The URL where the latest version of the measure definition lives
+   */
+  private String definitionUrl;
+}