RM-130: Update MME metrics to accommodate new gene statuses

core/metrics/pom.xml

@@ -62,6 +62,11 @@
       <artifactId>matching-notification-api</artifactId>
       <version>${patientNetwork.version}</version>
     </dependency>
+    <dependency>
+      <groupId>${project.groupId}</groupId>
+      <artifactId>patient-data-default-impl</artifactId>
+      <version>${phenotips.version}</version>
+    </dependency>
     <dependency>
       <groupId>javax.ws.rs</groupId>
       <artifactId>jsr311-api</artifactId>

core/metrics/src/main/java/org/phenotips/remote/metrics/internal/providers/NumberOfGenesProvider.java

@@ -49,14 +49,20 @@ public Object compute()
         Session session = null;
         try {
             session = this.sessionFactory.getSessionFactory().openSession();
+
+            String candidateStatuses = "";
+            GENE_STATUS_VALUES.stream()
+                .filter(status -> status.startsWith("candidate"))
+                .forEach(status -> candidateStatuses.concat("'" + status + "',"));
+
             Query q = session.createQuery("select count (geneObj.name) from "
                 + HQL_BASE_MME_PATIENT_FILTER_FROM
                 + ", BaseObject geneObj, StringProperty geneStatusProp"
                 + " where "
                 + HQL_BASE_MME_PATIENT_FILTER_WHERE
                 + " and geneObj.name = doc.fullName and geneObj.className = 'PhenoTips.GeneClass'"
                 + " and geneStatusProp.id.id = geneObj.id and geneStatusProp.id.name = 'status'"
-                + " and geneStatusProp.value in ('candidate', 'solved')");
+                + " and geneStatusProp.value in (" + candidateStatuses + " 'solved')");
             return q.uniqueResult();
         } finally {
             if (session != null) {

core/metrics/src/main/java/org/phenotips/remote/metrics/internal/providers/NumberOfUniqueGenesProvider.java

@@ -50,6 +50,11 @@ public Object compute()
         try {
             session = this.sessionFactory.getSessionFactory().openSession();
 
+            String candidateStatuses = "";
+            GENE_STATUS_VALUES.stream()
+                .filter(status -> status.startsWith("candidate"))
+                .forEach(status -> candidateStatuses.concat("'" + status + "',"));
+
             Query q = session.createQuery(
                 "select count (distinct geneIDProp.value) from "
                     + HQL_BASE_MME_PATIENT_FILTER_FROM
@@ -58,7 +63,7 @@ public Object compute()
                     + HQL_BASE_MME_PATIENT_FILTER_WHERE
                     + " and geneObj.name = doc.fullName and geneObj.className = 'PhenoTips.GeneClass'"
                     + " and geneStatusProp.id.id = geneObj.id and geneStatusProp.id.name = 'status'"
-                    + " and geneStatusProp.value in ('candidate', 'solved')"
+                    + " and geneStatusProp.value in (" + candidateStatuses + " 'solved')"
                     + " and geneIDProp.id.id = geneObj.id and geneIDProp.id.name = 'gene'");
             return q.uniqueResult();
         } finally {

core/metrics/src/main/java/org/phenotips/remote/metrics/internal/providers/NumberOfUniqueVariantsProvider.java

@@ -50,6 +50,12 @@ public Object compute()
         Session session = null;
         try {
             session = this.sessionFactory.getSessionFactory().openSession();
+
+            String candidateStatuses = "";
+            GENE_STATUS_VALUES.stream()
+                .filter(status -> status.startsWith("candidate"))
+                .forEach(status -> candidateStatuses.concat("'" + status + "',"));
+
             Query q = session.createQuery("select count (distinct variantIDProp.value) from "
                 + HQL_BASE_MME_PATIENT_FILTER_FROM
                 + ", BaseObject geneObj, BaseObject variantObj, StringProperty geneStatusProp"
@@ -58,7 +64,7 @@ public Object compute()
                 + " and geneObj.name = doc.fullName and geneObj.className = 'PhenoTips.GeneClass'"
                 + " and variantObj.name = doc.fullName and variantObj.className = 'PhenoTips.GeneVariantClass'"
                 + " and geneStatusProp.id.id = geneObj.id and geneStatusProp.id.name = 'status'"
-                + " and geneStatusProp.value in ('candidate', 'solved')"
+                + " and geneStatusProp.value in (" + candidateStatuses + " 'solved')"
                 + " and variantIDProp.id.id = variantObj.id and variantIDProp.id.name = 'cdna'"
                 + " and variantGeneProp.id.id = variantObj.id and variantGeneProp.id.name = 'gene'"
                 + " and geneIDProp.id.id = geneObj.id and geneIDProp.id.name = 'gene'"

core/metrics/src/main/java/org/phenotips/remote/metrics/internal/providers/NumberOfVariantsProvider.java

@@ -50,6 +50,12 @@ public Object compute()
         Session session = null;
         try {
             session = this.sessionFactory.getSessionFactory().openSession();
+
+            String candidateStatuses = "";
+            GENE_STATUS_VALUES.stream()
+                .filter(status -> status.startsWith("candidate"))
+                .forEach(status -> candidateStatuses.concat("'" + status + "',"));
+
             Query q = session.createQuery("select count (variantObj.name) from "
                 + HQL_BASE_MME_PATIENT_FILTER_FROM
                 + ", BaseObject geneObj, BaseObject variantObj, StringProperty geneStatusProp"
@@ -58,7 +64,7 @@ public Object compute()
                 + " and geneObj.name = doc.fullName and geneObj.className = 'PhenoTips.GeneClass'"
                 + " and variantObj.name = doc.fullName and variantObj.className = 'PhenoTips.GeneVariantClass'"
                 + " and geneStatusProp.id.id = geneObj.id and geneStatusProp.id.name = 'status'"
-                + " and geneStatusProp.value in ('candidate', 'solved')"
+                + " and geneStatusProp.value in (" + candidateStatuses + " 'solved')"
                 + " and variantGeneProp.id.id = variantObj.id and variantGeneProp.id.name = 'gene'"
                 + " and geneIDProp.id.id = geneObj.id and geneIDProp.id.name = 'gene'"
                 + " and geneIDProp.value = variantGeneProp.value");

core/metrics/src/main/java/org/phenotips/remote/metrics/spi/MetricProvider.java

@@ -17,10 +17,13 @@
  */
 package org.phenotips.remote.metrics.spi;
 
+import org.phenotips.data.internal.PhenoTipsGene;
 import org.phenotips.remote.metrics.MetricsRequestHandler;
 
 import org.xwiki.component.annotation.Role;
 
+import java.util.List;
+
 /**
  * Provides a specific metric to be included in a {@link MetricsRequestHandler#getMetrics() metrics response}. The
  * produced metric value will be included in the response JSON, inside the {@code metrics} map, under the same name as
@@ -50,6 +53,8 @@ public interface MetricProvider
             + " and visibilityProp.id.id = visibilityObj.id and visibilityProp.id.name = 'visibility'"
             + " and visibilityProp.value <> 'private'";
 
+    List<String> GENE_STATUS_VALUES = PhenoTipsGene.getStatusValues();
+
     /**
      * Compute and return a specific metric to be included in the response to a MME metrics query.
      *