Support escaping of pipe characters within multi-valued slots.

core/src/main/java/org/incenp/obofoundry/sssom/TSVWriter.java

@@ -32,7 +32,6 @@
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
-import java.util.regex.Pattern;
 
 import org.incenp.obofoundry.sssom.model.ExtensionDefinition;
 import org.incenp.obofoundry.sssom.model.ExtensionValue;
@@ -72,9 +71,6 @@
  */
 public class TSVWriter extends SSSOMWriter {
 
-    private static final Pattern tsvSpecialChars = Pattern.compile("[\t\n\r\"]");
-    private static final Pattern csvSpecialChars = Pattern.compile("[,\n\r\"]");
-
     private BufferedWriter tsvWriter, metaWriter;
     private Set<String> usedPrefixes = new HashSet<String>();
     private boolean isCSV = false;
@@ -630,16 +626,7 @@ public void visit(StringSlot<Mapping> slot, Mapping object, List<String> values)
                 results.add("");
                 return;
             }
-
-            StringBuilder sb = new StringBuilder();
-            for ( int i = 0, n = values.size(); i < n; i++ ) {
-                String value = values.get(i);
-                sb.append(escapeTSV(value));
-                if ( i < n - 1 ) {
-                    sb.append('|');
-                }
-            }
-            results.add(sb.toString());
+            results.add(escapeTSV(values));
         }
 
         @Override
@@ -649,15 +636,7 @@ public void visit(EntityReferenceSlot<Mapping> slot, Mapping object, List<String
                 return;
             }
 
-            StringBuilder sb = new StringBuilder();
-            for ( int i = 0, n = values.size(); i < n; i++ ) {
-                String value = values.get(i);
-                sb.append(escapeTSV(prefixManager.shortenIdentifier(value)));
-                if ( i < n - 1 ) {
-                    sb.append('|');
-                }
-            }
-            results.add(sb.toString());
+            results.add(escapeTSV(prefixManager.shortenIdentifiers(values)));
         }
 
         @Override
@@ -691,12 +670,117 @@ public void visit(ExtensionSlot<Mapping> slot, Mapping object, Map<String, Exten
          * https://datatracker.ietf.org/doc/html/rfc4180#section-2
          */
         private String escapeTSV(String value) {
-            Pattern specialChars = isCSV ? csvSpecialChars : tsvSpecialChars;
-            if ( specialChars.matcher(value).find() ) {
-                return "\"" + value.replace("\"", "\"\"") + "\"";
-            } else {
-                return value;
+            StringBuilder sb = new StringBuilder();
+            int len = value.length();
+            boolean quotesNeeded = false;
+            for ( int i = 0; i < len; i++ ) {
+                char c = value.charAt(i);
+                switch ( c ) {
+                case ',':
+                    if ( isCSV ) {
+                        quotesNeeded = true;
+                    }
+                    break;
+
+                case '\t':
+                    if ( !isCSV ) {
+                        quotesNeeded = true;
+                    }
+                    break;
+
+                case '\n':
+                case '\r':
+                    quotesNeeded = true;
+                    break;
+
+                case '"':
+                    quotesNeeded = true;
+                    sb.append('"');
+                    break;
+                }
+                sb.append(c);
             }
+
+            if ( quotesNeeded ) {
+                sb.insert(0, '"');
+                sb.append('"');
+            }
+
+            return sb.toString();
+        }
+
+        /*
+         * Likewise, but for multi-valued slots, where in addition we need to escape
+         * pipe characters. The duplicated code from the previous method is unfortunate,
+         * but we can't simply call that method because we don't want to quote
+         * <em>individual</em> values here, it is the entire |-separated multivalue that
+         * must be quoted if any single value within it contains quote-triggering
+         * characters.
+         */
+        private String escapeTSV(List<String> values) {
+            StringBuilder sb = new StringBuilder();
+            boolean quotesNeeded = false;
+            int nValues = values.size();
+            for ( int i = 0; i < nValues; i++ ) {
+                String value = values.get(i);
+                if ( i > 0 ) {
+                    sb.append('|');
+                }
+
+                int len = value.length();
+                for ( int j = 0; j < len; j++ ) {
+                    char c = value.charAt(j);
+                    switch ( c ) {
+                    case ',':
+                        if ( isCSV ) {
+                            quotesNeeded = true;
+                        }
+                        break;
+
+                    case '\t':
+                        if ( !isCSV ) {
+                            quotesNeeded = true;
+                        }
+                        break;
+
+                    case '\r':
+                    case '\n':
+                        quotesNeeded = true;
+                        break;
+
+                    case '"':
+                        quotesNeeded = true;
+                        sb.append('"');
+                        break;
+
+                    case '\\':
+                        // The backslash needs escaping only if (1) it is followed by another backslash
+                        // or a pipe, or (2) it is the last character of the current value and there are
+                        // more values to follow.
+                        if ( j < len - 1 ) {
+                            char next = value.charAt(j + 1);
+                            if ( next == '\\' || next == '|' ) {
+                                sb.append('\\');
+                            }
+                        } else if ( i < nValues - 1 ) {
+                            sb.append('\\');
+                        }
+                        break;
+
+                    case '|':
+                        sb.append('\\');
+                        break;
+                    }
+                    sb.append(c);
+                }
+            }
+
+            if ( quotesNeeded ) {
+                sb.insert(0, '"');
+                sb.append('"');
+            }
+
+            return sb.toString();
         }
     }
 }

core/src/main/java/org/incenp/obofoundry/sssom/YAMLConverter.java

@@ -56,6 +56,7 @@ public class YAMLConverter {
     private ExtensionSlotManager extensionManager;
     private ExtraMetadataPolicy extraPolicy = ExtraMetadataPolicy.NONE;
     private Version assumedVersion = Version.SSSOM_1_0;
+    private boolean supportEscapedPipes = false;
 
     /**
      * Creates a new YAML converter.
@@ -184,6 +185,7 @@ public MappingSet convertMappingSet(Map<String, Object> rawMap) throws SSSOMForm
         if ( version == Version.UNKNOWN ) {
             version = Version.LATEST;
         }
+        supportEscapedPipes = version != Version.SSSOM_1_0;
 
         // Process the CURIE map, so that we can expand CURIEs as soon as possible
         Object rawCurieMap = rawMap.getOrDefault("curie_map", new HashMap<String, String>());
@@ -400,7 +402,7 @@ private List<String> getListOfStrings(String slotName, Object rawValue) throws S
              * they were single-valued, which is strictly speaking but happens in the wild
              * (including in the examples shown in the SSSOM documentation!).
              */
-            for ( String item : rawValue.toString().split("\\|") ) {
+            for ( String item : splitString(rawValue.toString()) ) {
                 value.add(item);
             }
         } else {
@@ -409,6 +411,49 @@ private List<String> getListOfStrings(String slotName, Object rawValue) throws S
         return value;
     }
 
+    /*
+     * Splits a string along pipe (`|`) characters, with support for backslash
+     * escaping.
+     */
+    private List<String> splitString(String value) {
+        ArrayList<String> list = new ArrayList<>();
+        StringBuilder sb = new StringBuilder();
+        int len = value.length();
+        boolean escaped = false;
+        for ( int i = 0; i < len; i++ ) {
+            char c = value.charAt(i);
+            if ( escaped ) {
+                sb.append(c);
+                escaped = false;
+            } else if ( c == '\\' && supportEscapedPipes ) {
+                // The backslash is treated as an escape character only if it is followed by
+                // another backslash or a pipe.
+                if ( i < len - 1 ) {
+                    char next = value.charAt(i + 1);
+                    if ( next == '\\' || next == '|' ) {
+                        escaped = true;
+                    }
+                }
+                // Otherwise it is a normal character.
+                if ( !escaped ) {
+                    sb.append(c);
+                }
+            } else if ( c == '|' ) {
+                if ( sb.length() > 0 ) {
+                    list.add(sb.toString());
+                    sb.delete(0, sb.length());
+                }
+            } else {
+                sb.append(c);
+            }
+        }
+        if ( sb.length() > 0 ) {
+            list.add(sb.toString());
+        }
+
+        return list;
+    }
+
     /*
      * Parses the "extension_definitions" key.
      */

core/src/test/java/org/incenp/obofoundry/sssom/TSVReaderTest.java

@@ -493,6 +493,38 @@ void testEscapedTSV() throws IOException, SSSOMFormatException {
         Assertions.assertEquals("Value\u0009with\u0009tab\u0009characters", m.getComment());
         Assertions.assertEquals("Value with \"quote\" characters", m.getObjectLabel());
         Assertions.assertEquals("Value with\nnew line character", m.getIssueTrackerItem());
+        Assertions.assertEquals("Alice", m.getAuthorLabel().get(0));
+        Assertions.assertEquals("Bob\tand\tCharlie", m.getAuthorLabel().get(1));
+    }
+
+    /*
+     * Test that the parser can handle escaped pipe characters in multi-valued
+     * slots.
+     */
+    @Test
+    void testEscapedPipe() throws IOException, SSSOMFormatException {
+        TSVReader reader = new TSVReader("src/test/resources/sets/test-escaping-pipe.sssom.tsv");
+        reader.setAssumedVersion(Version.SSSOM_1_1);
+        MappingSet ms = reader.read();
+        Mapping m = ms.getMappings().get(0);
+
+        Assertions.assertEquals("Alice|Bob", m.getAuthorLabel().get(0));
+        Assertions.assertEquals("Charlie", m.getAuthorLabel().get(1));
+
+        m = ms.getMappings().get(1);
+        Assertions.assertEquals(3, m.getAuthorLabel().size());
+        Assertions.assertEquals("Alice\\Bob", m.getAuthorLabel().get(0));
+        Assertions.assertEquals("Charlie\\", m.getAuthorLabel().get(1));
+        Assertions.assertEquals("David\\|Eve\\", m.getAuthorLabel().get(2));
+
+        // Try again in SSSOM 1.0 compliance mode; there should be no escaping
+        reader = new TSVReader("src/test/resources/sets/test-escaping-pipe.sssom.tsv");
+        reader.setAssumedVersion(Version.SSSOM_1_0);
+        m = reader.read().getMappings().get(0);
+
+        Assertions.assertEquals("Alice\\", m.getAuthorLabel().get(0));
+        Assertions.assertEquals("Bob", m.getAuthorLabel().get(1));
+        Assertions.assertEquals("Charlie", m.getAuthorLabel().get(2));
     }
 
     /*

core/src/test/java/org/incenp/obofoundry/sssom/TSVWriterTest.java

@@ -333,10 +333,29 @@ void testEscapingTSV() throws IOException, SSSOMFormatException {
         ms.getMappings().get(0).setComment("Value\twith\ttab\tcharacters");
         ms.getMappings().get(0).setObjectLabel("Value with \"quote\" characters");
         ms.getMappings().get(0).setIssueTrackerItem("Value with\nnew line character");
+        ms.getMappings().get(0).getAuthorLabel(true).add("Alice");
+        ms.getMappings().get(0).getAuthorLabel().add("Bob\tand\tCharlie");
 
         assertWrittenAsExpected(ms, "test-escaping-tsv", null, null, null);
     }
 
+    @Test
+    void testEscapingPipeCharacter() throws IOException, SSSOMFormatException {
+        MappingSet ms = getTestSet();
+        ms.setMappingSetId("https://example.org/sets/test-escaping-pipe");
+        ms.getMappings().get(0).getAuthorLabel(true).add("Alice|Bob");
+        ms.getMappings().get(0).getAuthorLabel().add("Charlie");
+
+        Mapping m2 = ms.getMappings().get(0).toBuilder().subjectId("https://example.org/entities/0002")
+                .authorLabel(new ArrayList<>()).build();
+        m2.getAuthorLabel().add("Alice\\Bob");
+        m2.getAuthorLabel().add("Charlie\\");
+        m2.getAuthorLabel().add("David\\|Eve\\");
+        ms.getMappings().add(m2);
+
+        assertWrittenAsExpected(ms, "test-escaping-pipe", null, null, null);
+    }
+
     @Test
     void testWritingEnumValuesInYAML() throws IOException, SSSOMFormatException {
         MappingSet ms = getTestSet();

core/src/test/resources/sets/test-escaping-pipe.sssom.tsv

@@ -0,0 +1,8 @@
+#curie_map:
+#  COMENT: https://example.com/entities/
+#  ORGENT: https://example.org/entities/
+#mapping_set_id: https://example.org/sets/test-escaping-pipe
+#license: https://creativecommons.org/licenses/by/4.0/
+subject_id	subject_label	predicate_id	object_id	object_label	mapping_justification	author_label
+ORGENT:0001	alice	skos:closeMatch	COMENT:0011	alpha	semapv:ManualMappingCuration	Alice\|Bob|Charlie
+ORGENT:0002	alice	skos:closeMatch	COMENT:0011	alpha	semapv:ManualMappingCuration	Alice\Bob|Charlie\\|David\\\|Eve\

core/src/test/resources/sets/test-escaping-tsv.sssom.tsv

@@ -3,6 +3,6 @@
 #  ORGENT: https://example.org/entities/
 #mapping_set_id: https://example.org/sets/test-escaping-tsv
 #license: https://creativecommons.org/licenses/by/4.0/
-subject_id	subject_label	predicate_id	object_id	object_label	mapping_justification	issue_tracker_item	comment
-ORGENT:0001	Value with , characters	skos:closeMatch	COMENT:0011	"Value with ""quote"" characters"	semapv:ManualMappingCuration	"Value with
+subject_id	subject_label	predicate_id	object_id	object_label	mapping_justification	author_label	issue_tracker_item	comment
+ORGENT:0001	Value with , characters	skos:closeMatch	COMENT:0011	"Value with ""quote"" characters"	semapv:ManualMappingCuration	"Alice|Bob	and	Charlie"	"Value with
 new line character"	"Value	with	tab	characters"