Improve naming

src/main/java/org/cbioportal/file/export/KeyValueMetadataWriter.java

@@ -0,0 +1,83 @@
+package org.cbioportal.file.export;
+
+import org.cbioportal.file.model.CancerStudyMetadata;
+import org.cbioportal.file.model.GenericDatatypeMetadata;
+import org.cbioportal.file.model.GenericProfileDatatypeMetadata;
+
+import java.io.IOException;
+import java.io.Writer;
+import java.util.LinkedHashMap;
+
+/**
+ * A serializer for file model records that serializes them the cBioPortal key-value metadata format.
+ * e.g. meta_study.txt
+ */
+public class KeyValueMetadataWriter {
+    private final Writer writer;
+
+    /**
+     * @param writer - the writer to write the key-value metadata to
+     *               e.g. StringWriter, FileWriter
+     */
+    public KeyValueMetadataWriter(Writer writer) {
+        this.writer = writer;
+    }
+
+    /**
+     * Write a cancer study metadata to the writer
+     */
+    public void write(CancerStudyMetadata cancerStudyMetadata) {
+        LinkedHashMap<String, String> metdata = new LinkedHashMap<>();
+        metdata.put("type_of_cancer", cancerStudyMetadata.typeOfCancer());
+        metdata.put("cancer_study_identifier", cancerStudyMetadata.cancerStudyIdentifier());
+        metdata.put("name", cancerStudyMetadata.name());
+        metdata.put("description", cancerStudyMetadata.description());
+        cancerStudyMetadata.citation().ifPresent(citation -> metdata.put("citation", citation));
+        cancerStudyMetadata.pmid().ifPresent(pmid -> metdata.put("pmid", pmid));
+        cancerStudyMetadata.groups().ifPresent(groups -> metdata.put("groups", groups));
+        cancerStudyMetadata.addGlobalCaseList().ifPresent(addGlobalCaseList -> metdata.put("add_global_case_list", addGlobalCaseList.toString()));
+        cancerStudyMetadata.tagsFile().ifPresent(tagsFile -> metdata.put("tags_file", tagsFile));
+        cancerStudyMetadata.referenceGenome().ifPresent(referenceGenome -> metdata.put("reference_genome", referenceGenome));
+        write(metdata);
+    }
+
+    /**
+     * Write a generic datatype metadata to the writer 
+     */
+    public void write(GenericDatatypeMetadata genericDatatypeMetadata) {
+        LinkedHashMap<String, String> metadata = new LinkedHashMap<>();
+        metadata.put("cancer_study_identifier", genericDatatypeMetadata.cancerStudyIdentifier());
+        metadata.put("generic_alteration_type", genericDatatypeMetadata.geneticAlterationType());
+        metadata.put("datatype", genericDatatypeMetadata.datatype());
+        metadata.put("data_filename", genericDatatypeMetadata.dataFilename());
+        write(metadata);
+    }
+
+    /**
+     * Write a generic profile datatype metadata to the writer 
+     */
+    public void write(GenericProfileDatatypeMetadata genericProfileDatatypeMetadata) {
+        write((GenericDatatypeMetadata) genericProfileDatatypeMetadata);
+        LinkedHashMap<String, String> metadata = new LinkedHashMap<>();
+        metadata.put("stable_id", genericProfileDatatypeMetadata.stableId());
+        metadata.put("show_profile_in_analysis_tab", genericProfileDatatypeMetadata.showProfileInAnalysisTab().toString().toLowerCase());
+        metadata.put("profile_name", genericProfileDatatypeMetadata.profileName());
+        metadata.put("profile_description", genericProfileDatatypeMetadata.profileDescription());
+        genericProfileDatatypeMetadata.genePanel().ifPresent(genePanel -> metadata.put("gene_panel", genePanel));
+        write(metadata);
+    }
+
+    private void write(LinkedHashMap<String, String> metadata) {
+        metadata.forEach((key, value) -> {
+            try {
+                writer.write(composeKeyValueLine(key, value));
+            } catch (IOException e) {
+                throw new RuntimeException(e);
+            }
+        });
+    }
+
+    private static String composeKeyValueLine(String key, String value) {
+        return key + ": " + value + "\n";
+    }
+}

src/main/java/org/cbioportal/file/model/CancerStudyMetadata.java

@@ -5,7 +5,7 @@
 /**
  * Represents metadata for a cancer study.
  */
-public record CancerStudyMetadata (
+public record CancerStudyMetadata(
     /**
      * The cancer type abbreviation, e.g., "brca". This should be the same cancer type as specified in the meta_cancer_type.txt file, if available. The type can be "mixed" for studies with multiple cancer types.
      */
@@ -55,4 +55,4 @@ public record CancerStudyMetadata (
      * The study reference genome (e.g. hg19, hg38). Without specifying this property, the study will be assigned to the reference genome specified in application.properties (property ucsc.build).
      */
     Optional<String> referenceGenome
-) implements StudyRelated {}
+) implements StudyRelatedMetadata {}

src/main/java/org/cbioportal/file/model/ClinicalSampleAttributesMetadata.java

@@ -3,7 +3,7 @@
 public record ClinicalSampleAttributesMetadata(
     String cancerStudyIdentifier,
     String dataFilename
-) implements GenericDatatypeFileMetadata {
+) implements GenericDatatypeMetadata {
     public String geneticAlterationType() {
         return "CLINICAL";
     }

src/main/java/org/cbioportal/file/model/GenericDatatypeFileMetadata.java → src/main/java/org/cbioportal/file/model/GenericDatatypeMetadata.java

@@ -1,6 +1,6 @@
 package org.cbioportal.file.model;
 
-public interface GenericDatatypeFileMetadata extends StudyRelated {
+public interface GenericDatatypeMetadata extends StudyRelatedMetadata {
     String geneticAlterationType();
     String datatype();
     String dataFilename();

src/main/java/org/cbioportal/file/model/GenericProfileDatatypeFileMetadata.java → src/main/java/org/cbioportal/file/model/GenericProfileDatatypeMetadata.java

@@ -2,7 +2,7 @@
 
 import java.util.Optional;
 
-public interface GenericProfileDatatypeFileMetadata extends GenericDatatypeFileMetadata {
+public interface GenericProfileDatatypeMetadata extends GenericDatatypeMetadata {
     String stableId();
     Boolean showProfileInAnalysisTab();
     String profileName();

src/main/java/org/cbioportal/file/model/MutationMetadata.java

@@ -8,7 +8,7 @@ public record MutationMetadata(
     String profileName,
     String profileDescription,
     Optional<String> genePanel
-) implements GenericProfileDatatypeFileMetadata {
+) implements GenericProfileDatatypeMetadata {
     public String geneticAlterationType() {
         return "MUTATION_EXTENDED";
     }

src/main/java/org/cbioportal/file/model/StudyRelated.java → src/main/java/org/cbioportal/file/model/StudyRelatedMetadata.java

@@ -1,5 +1,5 @@
 package org.cbioportal.file.model;
 
-public interface StudyRelated {
+public interface StudyRelatedMetadata {
     String cancerStudyIdentifier();
 }

src/test/java/org/cbioportal/file/export/MetadataWriterTest.java

@@ -13,7 +13,7 @@
 public class MetadataWriterTest {
 
     StringWriter output = new StringWriter();
-    KeyValueConfigurationWriter writer = new KeyValueConfigurationWriter(output);
+    KeyValueMetadataWriter writer = new KeyValueMetadataWriter(output);
 
     @Test
     public void testCancerStudyMetadataWriter() {