Merge pull request #6 from monarch-initiative/develop

Develop
monarch-initiative · Jul 13, 2024 · 1754fb2 · 1754fb2
2 parents 4fd643b + 642a047
commit 1754fb2
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Showing 15 changed files with 443 additions and 295 deletions.
diff --git a/pom.xml b/pom.xml
@@ -4,7 +4,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>org.monarchinitiative.hpotools</groupId>
     <artifactId>hpotools</artifactId>
-    <version>0.0.3</version>
+    <version>0.0.7</version>
     <packaging>jar</packaging>
     <name>hpotools</name>
 
@@ -156,7 +156,12 @@
             <groupId>org.apache.logging.log4j</groupId>
             <artifactId>log4j-api</artifactId>
         </dependency>
-
+        <dependency>
+            <groupId>org.junit.jupiter</groupId>
+            <artifactId>junit-jupiter</artifactId>
+            <version>5.9.0</version> <!-- Use the latest version available -->
+            <scope>test</scope>
+        </dependency>
     </dependencies>
 
     <build>
@@ -178,11 +183,6 @@
                     <!--  <release>1.8</release> -->
                 </configuration>
             </plugin>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-surefire-plugin</artifactId>
-                <version>3.0.0-M5</version>
-            </plugin>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-jar-plugin</artifactId>
@@ -215,7 +215,11 @@
                 <artifactId>maven-site-plugin</artifactId>
                 <version>3.7.1</version>
             </plugin>
-
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-surefire-plugin</artifactId>
+                <version>3.0.0-M5</version> <!-- Use the latest version -->
+            </plugin>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-shade-plugin</artifactId>

diff --git a/src/main/java/org/monarchinitiative/hpotools/analysis/EncodingCheck.java b/src/main/java/org/monarchinitiative/hpotools/analysis/EncodingCheck.java
@@ -42,7 +42,7 @@ public void checkEncoding() {
         }
     }
 
-    public static void checkLine(String line, int lineno, String previous) throws UnsupportedEncodingException {
+    public static void checkLine(String line, int lineno, String previous) {
         byte[] bytes = line.getBytes(StandardCharsets.ISO_8859_1);
         String decodedLine = new String(bytes);
         if (! line.equals(decodedLine)) {

diff --git a/src/main/java/org/monarchinitiative/hpotools/analysis/OntologyTerm.java b/src/main/java/org/monarchinitiative/hpotools/analysis/OntologyTerm.java
@@ -2,6 +2,11 @@
 
 import org.monarchinitiative.phenol.ontology.data.TermId;
 
+/**
+ * POJO for dealing with HPO and MONDO terms
+ * @param id
+ * @param label
+ */
 public record OntologyTerm(
         TermId id,
         String label) {

diff --git a/src/main/java/org/monarchinitiative/hpotools/analysis/mondo/ClintLrItem.java b/src/main/java/org/monarchinitiative/hpotools/analysis/mondo/ClintLrItem.java
diff --git a/src/main/java/org/monarchinitiative/hpotools/analysis/mondo/MondoClintlrItem.java b/src/main/java/org/monarchinitiative/hpotools/analysis/mondo/MondoClintlrItem.java
@@ -5,15 +5,28 @@
 import java.io.File;
 import java.util.List;
 
+/**
+ * An item that represents a Mondo disease together with its narrow and broad parents
+ * This is intended for use to similate data for ClintLR.
+ * @param omimId
+ * @param mondoId
+ * @param mondoLabel
+ * @param narrowId
+ * @param narrowLabel
+ * @param broadId
+ * @param broadLabel
+ * @param cohort
+ * @param ppktFile
+ */
 public record MondoClintlrItem(TermId omimId,
                                TermId mondoId,
-                                String mondoLabel,
+                               String mondoLabel,
                                TermId narrowId,
                                String narrowLabel,
                                TermId broadId,
-                               String   broadLabel,
-                                String cohort,
-                                File ppktFile) {
+                               String broadLabel,
+                               String cohort,
+                               File ppktFile) {
 
     public String getTsvLine() {
         List<String> fields = List.of(omimId.getValue(),