cleanup

DataBiosphere · Aug 11, 2023 · 55dde04 · 55dde04
1 parent 347fc42
commit 55dde04
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Showing 4 changed files with 20 additions and 35 deletions.
diff --git a/library/build.gradle b/library/build.gradle
@@ -44,4 +44,8 @@ apply from: "publishing.gradle"
 
 srcclr {
     scope = "runtimeClasspath"
+}
+
+sourcesJar {
+    duplicatesStrategy = DuplicatesStrategy.EXCLUDE
 }
diff --git a/library/src/main/avro/sample.avdl b/library/src/main/avro/sample.avdl
@@ -74,8 +74,4 @@ protocol SimplePFB {
         union{Metadata,string} object;
         union{null,array<Relation>} relations;
     }
-
-    record PFB {
-        array<Entity> entities;
-    }
 }
diff --git a/library/src/main/java/bio/terra/pfb/PfbReader.java b/library/src/main/java/bio/terra/pfb/PfbReader.java
@@ -4,17 +4,13 @@
 import java.io.*;
 import java.net.URL;
 import java.net.URLConnection;
-import java.nio.charset.StandardCharsets;
 import java.util.HashMap;
 import java.util.List;
 import java.util.stream.Collectors;
 import org.apache.avro.Schema;
 import org.apache.avro.file.DataFileReader;
 import org.apache.avro.file.DataFileStream;
 import org.apache.avro.io.DatumReader;
-import org.apache.avro.io.Decoder;
-import org.apache.avro.io.DecoderFactory;
-import org.apache.avro.specific.SpecificData;
 import org.apache.avro.specific.SpecificDatumReader;
 
 public class PfbReader {
@@ -36,21 +32,16 @@ public String showNodes(String fileLocation) throws IOException {
   }
 
   public String show(String fileLocation) throws IOException {
-    // "object" is ia union between metadata and demographic. So, it's possible this parsing will
-    // fail
-    // I think the generated files are not handling this quite right.
-    SpecificData data = deserializeAvroFile(fileLocation).getSpecificData();
-    return data.toString();
+    // TODO - figure out how to read the rest of the Entity objects into a list of single json
+    // objects
+    return "NOT IMPLEMENTED";
   }
 
   public String showMetadata(String fileLocation) throws IOException {
     Metadata metadata = deserializeAvroFile(fileLocation);
     return metadata.toString();
   }
 
-  // List particular enum symbols
-  // schema.getField("object").schema().getTypes().get(3).getFields().get(1).schema().getTypes().stream().filter(s -> s.getType().equals(Schema.Type.ENUM)).findFirst().get().getEnumSymbols()
-
   public Schema getSchema(String fileLocation) throws IOException {
     boolean isUrl = isValidUrl(fileLocation);
     if (isUrl) {
@@ -93,25 +84,6 @@ public Metadata deserializeAvroFile(String fileLocation) throws IOException {
     throw new InvalidPfbException("No metadata object found in PFB file");
   }
 
-  Entity decodeStream(String fileLocation) throws FileNotFoundException {
-    Entity result = null;
-    Decoder decoder = null;
-    DatumReader<Entity> datumReader = new SpecificDatumReader<>(Entity.class);
-    try {
-      File initialFile = new File(fileLocation);
-      InputStream inputStream = new FileInputStream(initialFile);
-      String text =
-          new BufferedReader(new InputStreamReader(inputStream, StandardCharsets.UTF_8))
-              .lines()
-              .collect(Collectors.joining("\n"));
-      decoder = DecoderFactory.get().jsonDecoder(Entity.getClassSchema(), text);
-      return datumReader.read(null, decoder);
-    } catch (IOException e) {
-      System.err.println("Deserialization error:" + e.getMessage());
-    }
-    return result;
-  }
-
   Schema readUrlPFBSchema(String signedUrl) throws IOException {
     Schema schema;
     DatumReader<Entity> datumReader = new SpecificDatumReader<>(Entity.class);
@@ -126,6 +98,9 @@ Schema readUrlPFBSchema(String signedUrl) throws IOException {
 
   // Helper methods
 
+  // List particular enum symbols
+  // schema.getField("object").schema().getTypes().get(3).getFields().get(1).schema().getTypes().stream().filter(s -> s.getType().equals(Schema.Type.ENUM)).findFirst().get().getEnumSymbols()
+
   boolean isValidUrl(String fileLocation) {
     try {
       new URL(fileLocation);

diff --git a/library/src/test/java/bio/terra/pfb/PfbReaderTest.java b/library/src/test/java/bio/terra/pfb/PfbReaderTest.java
@@ -35,6 +35,16 @@ void showMetadata() throws IOException {
     }
   }
 
+  // TODO: Show is not yet working
+  //  @Test
+  //  void showTest() throws IOException {
+  //    var listOfTestFiles = List.of("minimal_data");
+  //    for (String fileName : listOfTestFiles) {
+  //      CompareOutputUtils.compareJsonOutputWithPyPFB(
+  //          fileName, CompareOutputUtils.PfbCommandType.show, "");
+  //    }
+  //  }
+
   @Disabled("Disabled because we don't have a way to generate a signed URL for testing")
   @Test
   void testSignedURL() throws IOException {