Merge branch '53-remove-isclosingafterparsing-from-de-unijena-bioinf-…

…babelms-parser-and-allow-for-multiple-calls' into 'master' Resolve "Remove `isClosingAfterParsing` from `de.unijena.bioinf.babelms.Parser` and allow for multiple calls to parse" Closes #53 See merge request bright-giant/sirius/sirius-libs!28
sirius-ms · Jan 11, 2024 · ef07ed0 · ef07ed0
2 parents b706b87 + 41e1b5d
commit ef07ed0
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Showing 6 changed files with 87 additions and 49 deletions.
diff --git a/io/src/main/java/de/unijena/bioinf/babelms/GenericParser.java b/io/src/main/java/de/unijena/bioinf/babelms/GenericParser.java
@@ -81,30 +81,25 @@ public void close() {
             }
 
             BufferedReader reader = r;
-            T elem = parse(reader, source);
+            T nextElement = parse(reader, source);
 
             @Override
             public boolean hasNext() {
-                if (elem == null) tryclose(); //for reader without any element
+                if (nextElement == null) tryclose(); //for reader without any element
                 return reader != null;
             }
 
             @Override
             public T next() {
-                T mem = elem;
+                T current = nextElement;
                 try {
-                    if (parser.isClosingAfterParsing()) {
-                        reader = null;
-                        elem = null;
-                        return mem;
-                    }
-                    elem = parse(reader, source);
+                    nextElement = parse(reader, source);
                 } catch (IOException e) {
                     tryclose();
                     throw new RuntimeException(e);
                 }
-                if (elem == null) tryclose();
-                return mem;
+                if (nextElement == null) tryclose();
+                return current;
             }
 
             private void tryclose() {
@@ -135,25 +130,13 @@ public CloseableIterator<T> parseFromPathIterator(Path file) throws IOException
 
 
     public List<T> parseFromFile(File file) throws IOException {
-        BufferedReader reader = null;
         final URI source = file.toURI();
-        try {
-            reader = FileUtils.ensureBuffering(new FileReader(file));
-            final ArrayList<T> list = new ArrayList<>();
-            T elem = parse(reader,source);
-            if (parser.isClosingAfterParsing()) {
-                list.add(elem);
-            } else {
-                while (elem != null) {
-                    list.add(elem);
-                    elem = parse(reader, source);
-                }
-            }
+        try (BufferedReader reader = FileUtils.ensureBuffering(new FileReader(file))) {
+            List<T> list = new ArrayList<>();
+            parseIterator(reader, source).forEachRemaining(list::add);
             return list;
         } catch (IOException e) {
             throw new IOException("Error while parsing " + file.getName(), e);
-        } finally {
-            if (reader != null) reader.close();
         }
     }
 

diff --git a/io/src/main/java/de/unijena/bioinf/babelms/Parser.java b/io/src/main/java/de/unijena/bioinf/babelms/Parser.java
@@ -41,9 +41,4 @@ public interface Parser<T> {
      * @throws IOException if an IO error happens
      */
     T parse(BufferedReader reader, URI source) throws IOException;
-
-    default boolean isClosingAfterParsing() {
-        return false;
-    }
-
 }
diff --git a/io/src/main/java/de/unijena/bioinf/babelms/json/FTJsonReader.java b/io/src/main/java/de/unijena/bioinf/babelms/json/FTJsonReader.java
@@ -57,6 +57,8 @@ public class FTJsonReader implements Parser<FTree> {
 
     protected final HashMap<String, MolecularFormula> formulaCache;
 
+    private Reader consumedReader = null;
+
     public FTJsonReader() {
         this.formulaCache = new HashMap<>();
     }
@@ -82,17 +84,16 @@ public FTree treeFromJsonString(String reader, URI source) throws IOException {
         return treeFromJson(new StringReader(reader), source);
     }
 
-    @Override
-    public boolean isClosingAfterParsing() {
-        return true;
-    }
-
     public FTree treeFromJson(Reader reader, URI source) throws IOException {
+        if (reader == consumedReader) {
+            return null;
+        }
         final JsonNode docRoot = new ObjectMapper().readTree(reader);
+        consumedReader = reader;
         return treeFromJson(docRoot, source);
     }
 
-    public FTree treeFromJson(@NotNull final JsonNode docRoot, @Nullable URI source) throws IOException {
+    public FTree treeFromJson(@NotNull final JsonNode docRoot, @Nullable URI source) {
         final DescriptorRegistry registry = DescriptorRegistry.getInstance();
         double score = 0d;
         double scoreBoost = 0d;
@@ -138,9 +139,7 @@ public FTree treeFromJson(@NotNull final JsonNode docRoot, @Nullable URI source)
                     incomingLossMap.put(bInfo, loss);
                     byId = true;
                 }
-            } catch (UnsupportedOperationException e) {
-
-            }
+            } catch (UnsupportedOperationException ignored) {}
 
             if (!byId) {
                 //this is for backwards compatibility, from now on we use ids to map
@@ -155,7 +154,7 @@ public FTree treeFromJson(@NotNull final JsonNode docRoot, @Nullable URI source)
         }
 
 
-        final ArrayDeque<Fragment> stack = new ArrayDeque<Fragment>();
+        final ArrayDeque<Fragment> stack = new ArrayDeque<>();
         stack.push(tree.getRoot());
         while (!stack.isEmpty()) {
             final Fragment u = stack.pollFirst();
@@ -260,9 +259,7 @@ private FragmentInfo getRootInfo(JsonNode
                 if (fragmentInfo == null) throw new RuntimeException("Cannot determine root fragment");
                 return fragmentInfo;
             }
-        } catch (UnsupportedOperationException e) {
-
-        }
+        } catch (UnsupportedOperationException ignored) {}
 
         //this is for backwards compatibility, from now on we use ids to map
         final MolecularFormula f = formula(rootElement.asText());

diff --git a/io/src/main/java/de/unijena/bioinf/babelms/json/JsonExperimentParserDispatcher.java b/io/src/main/java/de/unijena/bioinf/babelms/json/JsonExperimentParserDispatcher.java
@@ -20,6 +20,7 @@
 
 package de.unijena.bioinf.babelms.json;
 
+import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import de.unijena.bioinf.ChemistryBase.ms.Ms2Experiment;
@@ -33,12 +34,16 @@
 import java.io.BufferedReader;
 import java.io.IOException;
 import java.net.URI;
+import java.util.ArrayDeque;
 import java.util.List;
+import java.util.Queue;
 
 @Slf4j
 public class JsonExperimentParserDispatcher implements Parser<Ms2Experiment> {
 
     private final List<JsonExperimentParser> parsers;
+    private BufferedReader consumedReader;
+    private Queue<JsonNode> nextRoots;
 
     public JsonExperimentParserDispatcher() {
         this.parsers = List.of(
@@ -49,7 +54,31 @@ public JsonExperimentParserDispatcher() {
 
     @Override
     public Ms2Experiment parse(BufferedReader reader, URI source) throws IOException {
+        if (reader == consumedReader) {
+            if (nextRoots == null || nextRoots.isEmpty()) {
+                return null;
+            } else {
+                return parseNextRoot(source);
+            }
+        }
+
         JsonNode root = new ObjectMapper().readTree(reader);
+        consumedReader = reader;
+
+        if (root.isArray()) {
+            nextRoots = new ArrayDeque<>();
+            root.forEach(nextRoots::add);
+            return parseNextRoot(source);
+        }
+        return parseRoot(root, source);
+    }
+
+    private Ms2Experiment parseNextRoot(URI source) throws JsonProcessingException {
+        JsonNode root = nextRoots.remove();
+        return parseRoot(root, source);
+    }
+
+    public Ms2Experiment parseRoot(JsonNode root, URI source) throws JsonProcessingException {
         for (JsonExperimentParser parser : parsers) {
             if (parser.canParse(root)) {
                 Ms2Experiment experiment = parser.parse(root);
@@ -60,9 +89,4 @@ public Ms2Experiment parse(BufferedReader reader, URI source) throws IOException
         log.warn("Could not parse an experiment from json " + source);
         return null;
     }
-
-    @Override
-    public boolean isClosingAfterParsing() {
-        return true;
-    }
 }
diff --git a/io/src/test/java/de/unijena/bioinf/babelms/gnps/GnpsJsonParserTest.java b/io/src/test/java/de/unijena/bioinf/babelms/gnps/GnpsJsonParserTest.java
@@ -3,11 +3,16 @@
 import de.unijena.bioinf.ChemistryBase.chem.InChI;
 import de.unijena.bioinf.ChemistryBase.chem.Smiles;
 import de.unijena.bioinf.ChemistryBase.ms.*;
+import de.unijena.bioinf.babelms.MsExperimentParser;
+import de.unijena.bioinf.babelms.ParserTestUtils;
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.params.ParameterizedTest;
 import org.junit.jupiter.params.provider.ValueSource;
 
+import java.io.File;
 import java.io.IOException;
+import java.util.List;
+import java.util.Objects;
 
 import static de.unijena.bioinf.babelms.ParserTestUtils.loadExperiment;
 import static org.junit.jupiter.api.Assertions.assertEquals;
@@ -69,4 +74,15 @@ public void testParseSpectrum() throws IOException {
         assertEquals(940.25, experiment.getIonMass(), 1e-9);
         assertEquals("splash10-00dl-0000011189-7d4b9e412ca92d989b2d", experiment.getAnnotation(Splash.class).orElseThrow().getSplash());
     }
+
+    @Test
+    public void testRootArray() throws IOException {
+        File input = new File(Objects.requireNonNull(ParserTestUtils.class.getClassLoader().getResource("gnps/spectrum_array.json")).getFile());
+        List<Ms2Experiment> experiments = new MsExperimentParser().getParser(input).parseFromFile(input);
+
+        assertEquals(3, experiments.size());
+        assertEquals(1.0, experiments.get(0).getIonMass());
+        assertEquals(2.0, experiments.get(1).getIonMass());
+        assertEquals(3.0, experiments.get(2).getIonMass());
+    }
 }
diff --git a/io/src/test/resources/gnps/spectrum_array.json b/io/src/test/resources/gnps/spectrum_array.json
@@ -0,0 +1,23 @@
+[
+  {
+    "n_peaks": 1,
+    "peaks": [[1,1]],
+    "precursor_charge": 0,
+    "precursor_mz": 1,
+    "splash": ""
+  },
+  {
+    "n_peaks": 1,
+    "peaks": [[1,1]],
+    "precursor_charge": 0,
+    "precursor_mz": 2,
+    "splash": ""
+  },
+  {
+    "n_peaks": 1,
+    "peaks": [[1,1]],
+    "precursor_charge": 0,
+    "precursor_mz": 3,
+    "splash": ""
+  }
+]