Java: resolve some more -1 to this conflicts

Author: Jami Cogswell

java/ql/lib/ext/java.awt.model.yml

@@ -5,3 +5,11 @@ extensions:
     data:
       - ["java.awt", "Container", True, "add", "(Component)", "", "Argument[0]", "Argument[-1].Element", "value", "manual"] # ! signature as "" instead?
       - ["java.awt", "Container", True, "add", "(Component,Object)", "", "Argument[0]", "Argument[-1].Element", "value", "manual"]
+
+  - addsTo:
+      pack: codeql/java-all
+      extensible: neutralModel
+    data:
+      # The below APIs have numeric flow and are currently being stored as neutral models.
+      # These may be changed to summary models with kinds "value-numeric" and "taint-numeric" (or similar) in the future.
+      - ["java.awt", "Insets", "Insets", "(int,int,int,int)", "manual"] # value-numeric

java/ql/lib/ext/java.io.model.yml

@@ -59,11 +59,9 @@ extensions:
       - ["java.io", "CharArrayReader", False, "CharArrayReader", "", "", "Argument[0]", "Argument[this]", "taint", "manual"]
       - ["java.io", "CharArrayWriter", True, "toCharArray", "", "", "Argument[this]", "ReturnValue", "taint", "manual"]
       - ["java.io", "DataInput", True, "readFully", "", "", "Argument[this]", "Argument[0]", "taint", "manual"]
-      - ["java.io", "DataInput", True, "readInt", "()", "", "Argument[-1]", "ReturnValue", "taint", "manual"]
       - ["java.io", "DataInput", True, "readLine", "()", "", "Argument[this]", "ReturnValue", "taint", "manual"]
       - ["java.io", "DataInput", True, "readUTF", "()", "", "Argument[this]", "ReturnValue", "taint", "manual"]
       - ["java.io", "DataInputStream", False, "DataInputStream", "", "", "Argument[0]", "Argument[this]", "taint", "manual"]
-      - ["java.io", "DataOutput", True, "writeInt", "(int)", "", "Argument[0]", "Argument[-1]", "taint", "manual"]
       - ["java.io", "File", False, "File", "", "", "Argument[0]", "Argument[this]", "taint", "manual"]
       - ["java.io", "File", False, "File", "", "", "Argument[1]", "Argument[this]", "taint", "manual"]
       - ["java.io", "File", True, "getAbsoluteFile", "", "", "Argument[this]", "ReturnValue", "taint", "manual"]
@@ -99,7 +97,21 @@ extensions:
       pack: codeql/java-all
       extensible: neutralModel
     data:
+      - ["java.io", "Closeable", "close", "()", "manual"]
       - ["java.io", "File", "delete", "()", "manual"]
       - ["java.io", "File", "exists", "()", "manual"]
+      - ["java.io", "File", "getParentFile", "()", "manual"] # ! little unsure about this as a neutral
+      - ["java.io", "File", "isFile", "()", "manual"]
+      - ["java.io", "File", "length", "()", "manual"]
+      - ["java.io", "File", "listFiles", "()", "manual"] # ! little unsure about this as a neutral
       - ["java.io", "File", "isDirectory", "()", "manual"]
       - ["java.io", "File", "mkdirs", "()", "manual"]
+      - ["java.io", "InputStream", "close", "()", "manual"]
+      - ["java.io", "OutputStream", "flush", "()", "manual"] # ! little unsure about this as a neutral, but not sure how to represent output if summary model...
+
+      # The below APIs have numeric flow and are currently being stored as neutral models.
+      # These may be changed to summary models with kinds "value-numeric" and "taint-numeric" (or similar) in the future.
+      - ["java.io", "DataInput", "readInt", "()", "manual"]         # taint-numeric
+      - ["java.io", "DataInput", "readLong", "()", "manual"]        # taint-numeric
+      - ["java.io", "DataOutput", "writeInt", "(int)", "manual"]    # taint-numeric
+      - ["java.io", "DataOutput", "writeLong", "(long)", "manual"]  # taint-numeric

java/ql/lib/ext/java.lang.invoke.model.yml

@@ -0,0 +1,6 @@
+extensions:
+  - addsTo:
+      pack: codeql/java-all
+      extensible: neutralModel
+    data:
+      - ["java.lang.invoke", "MethodHandles", "lookup", "()", "manual"]

java/ql/lib/ext/java.lang.model.yml

@@ -117,6 +117,7 @@ extensions:
       - ["java.lang", "System", False, "getenv", "(String)", "", "Argument[-1].MapValue", "ReturnValue", "value", "manual"] # ! neutral instead?
       - ["java.lang", "System", False, "getenv", "(String)", "", "Argument[0]", "ReturnValue", "taint", "manual"]  # ! really unsure about this...; neutral instead? -- or unmodelled
       - ["java.lang", "Thread", False, "Thread", "(Runnable)", "", "Argument[0]", "Argument[-1]", "taint", "manual"] # ! neutral instead?
+      - ["java.lang", "Thread", True, "getName", "()", "", "Argument[-1].SyntheticField[java.lang.Thread.name]", "ReturnValue", "value", "manual"]
       - ["java.lang", "ThreadLocal", True, "get", "()", "", "Argument[-1].SyntheticField[java.lang.ThreadLocal.value]", "ReturnValue", "value", "manual"] # ! not sure if this model is correct, and if should be neutral model instead
       - ["java.lang", "Throwable", False, "Throwable", "(Throwable)", "", "Argument[0]", "Argument[this].SyntheticField[java.lang.Throwable.cause]", "value", "manual"]
       - ["java.lang", "Throwable", True, "getCause", "()", "", "Argument[this].SyntheticField[java.lang.Throwable.cause]", "ReturnValue", "value", "manual"]
@@ -128,11 +129,16 @@ extensions:
       extensible: neutralModel
     data:
       - ["java.lang", "AbstractStringBuilder", "length", "()", "manual"]
+      - ["java.lang", "AbstractStringBuilder", "setCharAt", "(int,char)", "manual"] # ! char manipulation not interesting? (or interesting since could set many chars... prbly switch to summary model)
+      - ["java.lang", "AbstractStringBuilder", "setLength", "(int)", "manual"] # ! summary?
       - ["java.lang", "Boolean", "equals", "(Object)", "manual"]
       - ["java.lang", "Boolean", "valueOf", "(boolean)", "manual"]
+      - ["java.lang", "CharSequence", "length", "()", "manual"]
       - ["java.lang", "Class", "forName", "(String)", "manual"]
       - ["java.lang", "Class", "getCanonicalName", "()", "manual"]
       - ["java.lang", "Class", "getClassLoader", "()", "manual"]
+      - ["java.lang", "Class", "getDeclaredConstructor", "(Class[])", "manual"]
+      - ["java.lang", "Class", "getDeclaredField", "(String)", "manual"]
       - ["java.lang", "Class", "getMethod", "(String,Class[])", "manual"]
       - ["java.lang", "Class", "getName", "()", "manual"]
       - ["java.lang", "Class", "getResource", "(String)", "manual"]
@@ -141,6 +147,8 @@ extensions:
       - ["java.lang", "Class", "isAssignableFrom", "(Class)", "manual"]
       - ["java.lang", "Class", "isInstance", "(Object)", "manual"]
       - ["java.lang", "Class", "toString", "()", "manual"]
+      - ["java.lang", "ClassLoader", "getResource", "(String)", "manual"]
+      - ["java.lang", "ClassLoader", "getResourceAsStream", "(String)", "manual"]
       - ["java.lang", "Enum", "Enum", "(String,int)", "manual"]
       - ["java.lang", "Enum", "equals", "(Object)", "manual"]
       - ["java.lang", "Enum", "hashCode", "()", "manual"]
@@ -154,6 +162,7 @@ extensions:
       - ["java.lang", "Object", "hashCode", "()", "manual"]
       - ["java.lang", "Object", "toString", "()", "manual"]
       - ["java.lang", "Runnable", "run", "()", "manual"]
+      - ["java.lang", "Runtime", "getRuntime", "()", "manual"]
       - ["java.lang", "String", "compareTo", "(String)", "manual"]
       - ["java.lang", "String", "contains", "(CharSequence)", "manual"]
       - ["java.lang", "String", "endsWith", "(String)", "manual"]
@@ -164,39 +173,49 @@ extensions:
       - ["java.lang", "String", "indexOf", "(String)", "manual"]
       - ["java.lang", "String", "isEmpty", "()", "manual"]
       - ["java.lang", "String", "lastIndexOf", "(int)", "manual"]
+      - ["java.lang", "String", "lastIndexOf", "(String)", "manual"]
       - ["java.lang", "String", "length", "()", "manual"]
       - ["java.lang", "String", "startsWith", "(String)", "manual"]
+      - ["java.lang", "String", "valueOf", "(boolean)", "manual"]
       - ["java.lang", "System", "currentTimeMillis", "()", "manual"]
       - ["java.lang", "System", "exit", "(int)", "manual"]
       - ["java.lang", "System", "identityHashCode", "(Object)", "manual"]
       - ["java.lang", "System", "lineSeparator", "()", "manual"] # ! double-check...
       - ["java.lang", "System", "nanoTime", "()", "manual"]
       - ["java.lang", "Thread", "currentThread", "()", "manual"]
+      - ["java.lang", "Thread", "getContextClassLoader", "()", "manual"] # ! summary instead?
       - ["java.lang", "Thread", "interrupt", "()", "manual"]
       - ["java.lang", "Thread", "sleep", "(long)", "manual"]
       - ["java.lang", "Thread", "start", "()", "manual"]
       # The below APIs have numeric flow and are currently being stored as neutral models.
       # These may be changed to summary models with kinds "value-numeric" and "taint-numeric" (or similar) in the future.
-      - ["java.lang", "Boolean", "booleanValue", "()", "manual"]       # taint-numeric
-      - ["java.lang", "Boolean", "parseBoolean", "(String)", "manual"] # taint-numeric
-      - ["java.lang", "Double", "parseDouble", "(String)", "manual"]   # taint-numeric
-      - ["java.lang", "Integer", "Integer", "(int)", "manual"]         # taint-numeric
-      - ["java.lang", "Integer", "intValue", "()", "manual"]           # taint-numeric
-      - ["java.lang", "Integer", "parseInt", "(String)", "manual"]     # taint-numeric
-      - ["java.lang", "Integer", "toHexString", "(int)", "manual"]     # taint-numeric
-      - ["java.lang", "Integer", "toString", "()", "manual"]           # taint-numeric
-      - ["java.lang", "Integer", "toString", "(int)", "manual"]        # taint-numeric
-      - ["java.lang", "Integer", "valueOf", "(int)", "manual"]         # taint-numeric
-      - ["java.lang", "Integer", "valueOf", "(String)", "manual"]      # taint-numeric # ! should probably make this and others like it have a "" signature instead...
-      - ["java.lang", "Long", "Long", "(long)", "manual"]              # taint-numeric
-      - ["java.lang", "Long", "intValue", "()", "manual"]              # taint-numeric
-      - ["java.lang", "Long", "longValue", "()", "manual"]             # taint-numeric
-      - ["java.lang", "Long", "parseLong", "(String)", "manual"]       # taint-numeric
-      - ["java.lang", "Long", "toString", "()", "manual"]              # taint-numeric
-      - ["java.lang", "Long", "toString", "(long)", "manual"]          # taint-numeric
-      - ["java.lang", "Long", "valueOf", "(long)", "manual"]           # taint-numeric
-      - ["java.lang", "Long", "valueOf", "(String)", "manual"]         # taint-numeric
-      - ["java.lang", "Math", "max", "(int,int)", "manual"]            # value-numeric
-      - ["java.lang", "Math", "min", "(int,int)", "manual"]            # value-numeric
-      - ["java.lang", "String", "valueOf", "(int)", "manual"]          # taint-numeric
-      - ["java.lang", "String", "valueOf", "(long)", "manual"]         # taint-numeric
+      - ["java.lang", "Boolean", "booleanValue", "()", "manual"]          # taint-numeric
+      - ["java.lang", "Boolean", "parseBoolean", "(String)", "manual"]    # taint-numeric
+      - ["java.lang", "Double", "doubleToLongBits", "(double)", "manual"] # taint-numeric
+      - ["java.lang", "Double", "parseDouble", "(String)", "manual"]      # taint-numeric
+      - ["java.lang", "Double", "valueOf", "(double)", "manual"]          # taint-numeric
+      - ["java.lang", "Integer", "Integer", "(int)", "manual"]            # taint-numeric
+      - ["java.lang", "Integer", "intValue", "()", "manual"]              # taint-numeric
+      - ["java.lang", "Integer", "parseInt", "(String)", "manual"]        # taint-numeric
+      - ["java.lang", "Integer", "toHexString", "(int)", "manual"]        # taint-numeric
+      - ["java.lang", "Integer", "toString", "()", "manual"]              # taint-numeric
+      - ["java.lang", "Integer", "toString", "(int)", "manual"]           # taint-numeric
+      - ["java.lang", "Integer", "valueOf", "(int)", "manual"]            # taint-numeric
+      - ["java.lang", "Integer", "valueOf", "(String)", "manual"]         # taint-numeric # ! should probably make this and others like it have a "" signature instead...
+      - ["java.lang", "Long", "Long", "(long)", "manual"]                 # taint-numeric
+      - ["java.lang", "Long", "intValue", "()", "manual"]                 # taint-numeric
+      - ["java.lang", "Long", "longValue", "()", "manual"]                # taint-numeric
+      - ["java.lang", "Long", "parseLong", "(String)", "manual"]          # taint-numeric
+      - ["java.lang", "Long", "toString", "()", "manual"]                 # taint-numeric
+      - ["java.lang", "Long", "toString", "(long)", "manual"]             # taint-numeric
+      - ["java.lang", "Long", "valueOf", "(long)", "manual"]              # taint-numeric
+      - ["java.lang", "Long", "valueOf", "(String)", "manual"]            # taint-numeric
+      - ["java.lang", "Math", "max", "(int,int)", "manual"]               # value-numeric
+      - ["java.lang", "Math", "max", "(long,long)", "manual"]             # value-numeric
+      - ["java.lang", "Math", "min", "(int,int)", "manual"]               # value-numeric
+      - ["java.lang", "Math", "min", "(long,long)", "manual"]             # value-numeric
+      - ["java.lang", "Number", "doubleValue", "()", "manual"]            # taint-numeric # ! remove others that could rely on subtyping through Number instead? (e.g. Double, Integer, etc.)
+      - ["java.lang", "Number", "intValue", "()", "manual"]               # taint-numeric
+      - ["java.lang", "Number", "longValue", "()", "manual"]              # taint-numeric
+      - ["java.lang", "String", "valueOf", "(int)", "manual"]             # taint-numeric
+      - ["java.lang", "String", "valueOf", "(long)", "manual"]            # taint-numeric

java/ql/lib/ext/java.lang.reflect.model.yml

@@ -4,6 +4,7 @@ extensions:
       extensible: summaryModel
     data:
       - ["java.lang.reflect", "Constructor", False, "newInstance", "(Object[])", "", "Argument[0].ArrayElement", "ReturnValue.Parameter", "value", "manual"] # ! unsure about input/output
+      - ["java.lang.reflect", "Field", False, "get", "(Object)", "", "Argument[0].Field", "ReturnValue", "value", "manual"] # ! very unsure about
       - ["java.lang.reflect", "Method", False, "invoke", "(Object,Object[])", "", "Argument[1].ArrayElement", "Argument[-1].Parameter[0]", "value", "manual"] # ! very unsure if this model is correct...
 
   - addsTo:

java/ql/lib/ext/java.math.model.yml

@@ -11,9 +11,14 @@ extensions:
       - ["java.math", "BigDecimal", "BigDecimal", "(String)", "manual"]         # taint-numeric
       - ["java.math", "BigDecimal", "add", "(BigDecimal)", "manual"]            # taint-numeric
       - ["java.math", "BigDecimal", "doubleValue", "()", "manual"]              # taint-numeric
+      - ["java.math", "BigDecimal", "intValue", "()", "manual"]                 # taint-numeric
+      - ["java.math", "BigDecimal", "multiply", "(BigDecimal)", "manual"]       # taint-numeric
       - ["java.math", "BigDecimal", "setScale", "(int,RoundingMode)", "manual"] # taint-numeric
+      - ["java.math", "BigDecimal", "subtract", "(BigDecimal)", "manual"]       # taint-numeric
+      - ["java.math", "BigDecimal", "toBigInteger", "()", "manual"]             # taint-numeric
       - ["java.math", "BigDecimal", "toString", "()", "manual"]                 # taint-numeric
       - ["java.math", "BigDecimal", "valueOf", "(double)", "manual"]            # taint-numeric
       - ["java.math", "BigDecimal", "valueOf", "(long)", "manual"]              # taint-numeric
+      - ["java.math", "BigInteger", "BigInteger", "(String)", "manual"]         # taint-numeric
       - ["java.math", "BigInteger", "or", "(BigInteger)", "manual"]             # taint-numeric
       - ["java.math", "BigInteger", "valueOf", "(long)", "manual"]              # taint-numeric

java/ql/lib/ext/java.nio.file.model.yml

@@ -44,7 +44,9 @@ extensions:
       - ["java.nio.file", "FileSystem", True, "getPathMatcher", "(String)", "", "Argument[0]", "ReturnValue", "taint", "ai-generated"]
       - ["java.nio.file", "FileSystem", True, "getRootDirectories", "", "", "Argument[0]", "ReturnValue", "taint", "manual"]
       - ["java.nio.file", "Path", True, "getParent", "", "", "Argument[this]", "ReturnValue", "taint", "manual"]
+      # ! should Path have subtyping of False for all methods instead? Why is `toFile` different?
       - ["java.nio.file", "Path", True, "normalize", "", "", "Argument[this]", "ReturnValue", "taint", "manual"]
+      - ["java.nio.file", "Path", False, "getFileName", "()", "", "Argument[-1]", "ReturnValue", "taint", "manual"] # ! maybe need more field flow?
       - ["java.nio.file", "Path", True, "of", "(String,String[])", "", "Argument[0]", "ReturnValue", "taint", "ai-generated"]
       - ["java.nio.file", "Path", True, "of", "(String,String[])", "", "Argument[1]", "ReturnValue", "taint", "ai-generated"]
       - ["java.nio.file", "Path", True, "of", "(URI)", "", "Argument[0]", "ReturnValue", "taint", "ai-generated"]

java/ql/lib/ext/java.nio.model.yml

@@ -11,5 +11,6 @@ extensions:
       pack: codeql/java-all
       extensible: neutralModel
     data:
+      - ["java.nio", "Buffer", "position", "()", "manual"] # ! maybe should be summary?
       - ["java.nio", "Buffer", "remaining", "()", "manual"]
       - ["java.nio", "ByteBuffer", "allocate", "(int)", "manual"]

java/ql/lib/ext/java.sql.model.yml

@@ -24,16 +24,20 @@ extensions:
       - ["java.sql", "PreparedStatement", True, "executeQuery", "()", "", "Argument[-1]", "ReturnValue", "taint", "manual"] # ! this should maybe be a neutral model, not sure if this really counts as "flow through"...
       - ["java.sql", "PreparedStatement", True, "setString", "(int,String)", "", "Argument[1]", "Argument[this]", "value", "manual"]
       - ["java.sql", "ResultSet", True, "getString", "(String)", "", "Argument[this]", "ReturnValue", "taint", "manual"]
+      - ["java.sql", "ResultSet", True, "getTimestamp", "(String)", "", "Argument[-1]", "ReturnValue", "taint", "manual"]
+
   - addsTo:
       pack: codeql/java-all
       extensible: neutralModel
     data:
+      - ["java.sql", "Connection", "createStatement", "()", "manual"]
       - ["java.sql", "PreparedStatement", "executeUpdate", "()", "manual"]
       - ["java.sql", "ResultSet", "next", "()", "manual"]
       # The below APIs have numeric flow and are currently being stored as neutral models.
       # These may be changed to summary models with kinds "value-numeric" and "taint-numeric" (or similar) in the future.
       - ["java.sql", "PreparedStatement", "setInt", "(int,int)", "manual"]   # value-numeric
       - ["java.sql", "PreparedStatement", "setLong", "(int,long)", "manual"] # value-numeric
+      - ["java.sql", "ResultSet", "getInt", "(int)", "manual"]               # taint-numeric
       - ["java.sql", "ResultSet", "getInt", "(String)", "manual"]            # taint-numeric
       - ["java.sql", "ResultSet", "getLong", "(String)", "manual"]           # taint-numeric
       - ["java.sql", "ResultSet", "getString", "(int)", "manual"]            # taint-numeric

java/ql/lib/ext/java.text.model.yml

@@ -4,6 +4,7 @@ extensions:
       extensible: summaryModel
     data:
       - ["java.text", "DateFormat", True, "parse", "(String)", "", "Argument[0]", "ReturnValue", "taint", "manual"] # ! maybe not interesting flow and should be neutral model?
+      - ["java.text", "Format", True, "format", "(Object)", "", "Argument[0]", "ReturnValue", "taint", "manual"] # ! would cover DateFormat.format below through subtyping...
       - ["java.text", "MessageFormat", False, "format", "(String,Object[])", "", "Argument[0]", "ReturnValue", "taint", "manual"]              # ! not sure I did this right
       - ["java.text", "MessageFormat", False, "format", "(String,Object[])", "", "Argument[1].ArrayElement", "ReturnValue", "taint", "manual"] # ! not sure I did this right