From 13a2d43c04035e97ce94e380e9b0399ca2c70f06 Mon Sep 17 00:00:00 2001
From: Jim Balhoff <jim@balhoff.org>
Date: Fri, 20 Oct 2023 19:03:57 -0400
Subject: [PATCH] Ensure longest namespace match is used. Disallow prefixes
 that are substrings of OBO namespace.

---
 .../obo2owl/OBOFormatPrefixManager.java       | 175 ++++++++++++++++++
 .../org/obolibrary/obo2owl/OWLAPIOwl2Obo.java |   2 +-
 2 files changed, 176 insertions(+), 1 deletion(-)
 create mode 100644 oboformat/src/main/java/org/obolibrary/obo2owl/OBOFormatPrefixManager.java

diff --git a/oboformat/src/main/java/org/obolibrary/obo2owl/OBOFormatPrefixManager.java b/oboformat/src/main/java/org/obolibrary/obo2owl/OBOFormatPrefixManager.java
new file mode 100644
index 0000000000..fe1065e9e3
--- /dev/null
+++ b/oboformat/src/main/java/org/obolibrary/obo2owl/OBOFormatPrefixManager.java
@@ -0,0 +1,175 @@
+package org.obolibrary.obo2owl;
+
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLRuntimeException;
+import org.semanticweb.owlapi.model.PrefixManager;
+import org.semanticweb.owlapi.util.StringComparator;
+
+import javax.annotation.Nonnull;
+import javax.annotation.Nullable;
+import java.util.*;
+
+public class OBOFormatPrefixManager implements PrefixManager {
+
+    private final String OBO_NS = "http://purl.obolibrary.org/obo/";
+
+    @Nonnull
+    private StringComparator comparator = new StringComparator() {
+
+        final Comparator<String> comparer = Comparator.comparing(s -> -s.length());
+
+        @Override
+        public int compare(String o1, String o2) {
+            return comparer.compare(o1, o2);
+        }
+
+    };
+
+    @Nonnull
+    private final TreeMap<String, String> nsToPrefix;
+    @Nonnull
+    private final TreeMap<String, String> prefixToNS;
+
+    public OBOFormatPrefixManager(@Nullable PrefixManager pm) {
+        prefixToNS = new TreeMap<>(comparator);
+        nsToPrefix = new TreeMap<>(comparator);
+        if (pm != null) {
+            copyPrefixesFrom(pm);
+        }
+    }
+
+    @Nonnull
+    @Override
+    public StringComparator getPrefixComparator() {
+        return this.comparator;
+    }
+
+    @Override
+    public void setPrefixComparator(@Nonnull StringComparator comparator) {
+        this.comparator = comparator;
+    }
+
+    @Nullable
+    @Override
+    public String getDefaultPrefix() {
+        return null;
+    }
+
+    @Override
+    public boolean containsPrefixMapping(@Nonnull String prefixName) {
+        return prefixToNS.containsKey(prefixName);
+    }
+
+    @Nullable
+    @Override
+    public String getPrefix(@Nonnull String prefixName) {
+        return prefixToNS.get(prefixName);
+    }
+
+    @Nonnull
+    @Override
+    public Map<String, String> getPrefixName2PrefixMap() {
+        return Collections.unmodifiableMap(prefixToNS);
+    }
+
+    @Nonnull
+    @Override
+    public IRI getIRI(@Nonnull String prefixIRI) {
+        if (prefixIRI.startsWith("<")) {
+            return IRI.create(prefixIRI.substring(1, prefixIRI.length() - 1));
+        }
+        int sep = prefixIRI.indexOf(':');
+        if (sep == -1) {
+            if (getDefaultPrefix() != null) {
+                return IRI.create(getDefaultPrefix() + prefixIRI);
+            } else {
+                return IRI.create(prefixIRI);
+            }
+        } else {
+            String prefixName = prefixIRI.substring(0, sep + 1);
+            if (!containsPrefixMapping(prefixName)) {
+                throw new OWLRuntimeException(
+                        "Prefix not registered for prefix name: " + prefixName);
+            }
+            String prefix = getPrefix(prefixName);
+            String localName = prefixIRI.substring(sep + 1);
+            return IRI.create(prefix, localName);
+        }
+    }
+
+    @Nullable
+    @Override
+    public String getPrefixIRI(@Nonnull IRI iri) {
+        String iriString = iri.toString();
+        Optional<Map.Entry<String, String>> mappingOpt = nsToPrefix.entrySet().stream().filter(e -> iriString.startsWith(e.getKey())).findFirst();
+        if (mappingOpt.isPresent()) {
+            Map.Entry<String, String> mapping = mappingOpt.get();
+            String localId = iriString.substring(mapping.getKey().length());
+            return mapping.getValue() + ":" + localId;
+        } else return null;
+    }
+
+    @Nullable
+    @Override
+    public String getPrefixIRIIgnoreQName(@Nonnull IRI iri) {
+        return getPrefixIRI(iri);
+    }
+
+    @Nonnull
+    @Override
+    public Set<String> getPrefixNames() {
+        return prefixToNS.keySet();
+    }
+
+    @Override
+    public void setDefaultPrefix(@Nullable String defaultPrefix) {
+    }
+
+    @Override
+    public void setPrefix(@Nonnull String prefixName, @Nonnull String prefix) {
+        if (!prefixName.isEmpty() && !prefixName.equals(":") && !OBO_NS.startsWith(prefix)) {
+            System.out.println(prefixName + "  :::  " + prefix);
+            String cleanPrefixName = prefixName;
+            if (prefixName.endsWith(":")) {
+                cleanPrefixName = prefixName.substring(0, prefixName.length() - 1);
+            }
+            prefixToNS.put(cleanPrefixName, prefix);
+            nsToPrefix.put(prefix, cleanPrefixName);
+        }
+    }
+
+    @Override
+    public void copyPrefixesFrom(@Nonnull PrefixManager from) {
+        copyPrefixesFrom(from.getPrefixName2PrefixMap());
+    }
+
+    @Override
+    public void copyPrefixesFrom(@Nonnull Map<String, String> from) {
+        for (Map.Entry<String, String> e : from.entrySet()) {
+            String prefix = e.getKey();
+            if (!prefix.isEmpty()) {
+                setPrefix(e.getKey(), e.getValue());
+            }
+        }
+    }
+
+    @Override
+    public void unregisterNamespace(@Nonnull String namespace) {
+        List<String> toRemove = new ArrayList<>();
+        for (Map.Entry<String, String> e : prefixToNS.entrySet()) {
+            if (e.getValue().equals(namespace)) {
+                toRemove.add(e.getKey());
+            }
+        }
+        for (String s : toRemove) {
+            prefixToNS.remove(s);
+        }
+        nsToPrefix.remove(namespace);
+    }
+
+    @Override
+    public void clear() {
+        prefixToNS.clear();
+        nsToPrefix.clear();
+    }
+}
diff --git a/oboformat/src/main/java/org/obolibrary/obo2owl/OWLAPIOwl2Obo.java b/oboformat/src/main/java/org/obolibrary/obo2owl/OWLAPIOwl2Obo.java
index 2695b0805c..88cbcaa9a9 100644
--- a/oboformat/src/main/java/org/obolibrary/obo2owl/OWLAPIOwl2Obo.java
+++ b/oboformat/src/main/java/org/obolibrary/obo2owl/OWLAPIOwl2Obo.java
@@ -233,7 +233,7 @@ public void setObodoc(@Nonnull OBODoc obodoc) {
     }
 
     public void setPrefixManager(@Nonnull PrefixManager manager) {
-        this.prefixManager = manager;
+        this.prefixManager = new OBOFormatPrefixManager(manager);
     }
 
     /**