Cleanup a few warnings (#6764)

Author: labkey-jeckels

api/src/org/labkey/api/reader/BufferedReader.java

@@ -34,6 +34,8 @@ We use this implementation as it grows its buffer incrementally instead of alloc
  *  -Replaced StringBuilder with StringBuffer
  */
 
+import org.jetbrains.annotations.NotNull;
+
 import java.io.IOException;
 import java.io.Reader;
 
@@ -260,7 +262,7 @@ public int read() throws IOException {
      *             if this reader is closed or some other I/O error occurs.
      */
     @Override
-    public int read(char[] buffer, int offset, int length) throws IOException {
+    public int read(char @NotNull [] buffer, int offset, int length) throws IOException {
         synchronized (lock) {
             if (isClosed()) {
                 throw new IOException();

api/src/org/labkey/api/search/AbstractXMLDocumentParser.java

@@ -45,6 +45,7 @@ public void parseContent(InputStream stream, ContentHandler handler) throws IOEx
             SAXParser parser = SAXParserFactory.newInstance().newSAXParser();
             parser.getXMLReader().setFeature("http://xml.org/sax/features/validation", false);
             parser.getXMLReader().setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd", false);
+            parser.getXMLReader().setFeature("http://apache.org/xml/features/disallow-doctype-decl", true);
             parser.parse(stream, createSAXHandler(handler));
         }
         catch (ParserConfigurationException e)

api/src/org/labkey/api/security/Crypt.java

@@ -208,68 +208,10 @@ public boolean matches(String credentials, String digest)
         @Override
         public String digest(String credentials)
         {
-//            long n = System.nanoTime();
-            String ret = org.labkey.api.security.BCrypt.hashpw(credentials, org.labkey.api.security.BCrypt.gensalt(11));
-//            double d = (System.nanoTime() - n)/1000000000.0;
-            return ret;
+            return org.labkey.api.security.BCrypt.hashpw(credentials, org.labkey.api.security.BCrypt.gensalt(11));
         }
     }
 
-
-/*    public static class _saltaes extends Crypt
-    {
-        private static final String _algorithm = "AES";
-        private static final int _keylen = 24;
-        private static final String _text = "eUpeZclKWup36fRxihyIVcKf"; // don't change me!
-
-
-        public boolean matches(String credentials, String crypt)
-        {
-            return crypt.equals(_digest(credentials,crypt));
-        }
-
-        public String digest(String pwd)
-        {
-            return _digest(pwd, null);
-        }
-
-        private String _digest(String pwd, String salt)
-        {
-            pwd = StringUtils.trimToEmpty(pwd);
-            salt = makeSalt(salt);
-            
-            String crypt = "";
-
-            int[] keyInts = new int[_keylen];
-            for (int i = 0; i < pwd.length() ; i++)
-                keyInts[i % _keylen] = keyInts[i%_keylen] * 31 + pwd.charAt(i);
-            byte[] keyBytes = new byte[_keylen];
-            for (int i = 0; i < _keylen ; i++)
-                keyBytes[i] = (byte)keyInts[i];
-            byte[] textBytes = new byte[_keylen];
-            for (int i = 0; i < _keylen; i++)
-                textBytes[i] = (byte)(salt.charAt(i % salt.length()) ^ _text.charAt(i));
-
-            try
-            {
-                SecretKeySpec skey = new SecretKeySpec(keyBytes, _algorithm);
-                Cipher cipher = Cipher.getInstance(_algorithm);
-                cipher.init(Cipher.ENCRYPT_MODE, skey);
-                byte[] cipherBytes = cipher.doFinal(textBytes);
-                crypt = new String(Base64.encodeBase64(cipherBytes, false));
-            }
-            catch (Exception x)
-            {
-                x.printStackTrace(System.err);
-                return null;
-            }
-
-            return salt + crypt.substring(0, 32);
-        }
-    }
-*/
-
-
     private static String makeSalt(String salt)
     {
         if (null == salt) 
@@ -311,7 +253,7 @@ public static String encodeBase64(byte[] bytes)
 
     private static char _randChar()
     {
-        int i = (int) (Math.random() * 62);
+        int i = (int) (Encryption.SR.nextDouble() * 62);
         if (i > 52)
             return (char) ('0' + i - 52);
         return (char) (0 == (i & 0x0001)

api/src/org/labkey/api/security/Encryption.java

@@ -76,14 +76,23 @@ public class Encryption
     private static final Logger LOG = LogHelper.getLogger(Encryption.class, "Encryption operations");
     private static final String CATEGORY = "Encryption";
     private static final String SALT_KEY = "Salt";
-    private static final SecureRandom SR = new SecureRandom();
+    public static final SecureRandom SR;
     private static final String ENCRYPTION_PASS_PHRASE;
     private static final String KEY_CHANGE_GUIDANCE = "An administrator should change the encryption key back to the previous value, follow the official encryption key change process, or be prepared to re-enter and re-save all saved credentials.";
 
     static
     {
         ENCRYPTION_PASS_PHRASE = loadEncryptionPassPhrase();
 
+        try
+        {
+            SR = SecureRandom.getInstanceStrong();
+        }
+        catch (NoSuchAlgorithmException e)
+        {
+            throw new ConfigurationException("Could not initialize SecureRandom", e);
+        }
+
         WarningService.get().register(new WarningProvider() {
             @Override
             public void addDynamicWarnings(@NotNull Warnings warnings, @Nullable ViewContext context, boolean showAllWarnings)

api/src/org/labkey/api/util/XMLFileType.java

@@ -56,7 +56,7 @@ export class App extends React.Component<any, State> {
 
         // hack, if the returnUrl has stripped off the rowId because of encoding/decoding issues (see TODO in AbstractAssayProvider.getManageMenuNavTree()) add it back on
         let returnUrl = ActionURL.getReturnUrl();
-        if (rowId !== undefined && returnUrl && returnUrl.indexOf('rowId') === returnUrl.length - 5) {
+        if (rowId !== undefined && returnUrl && returnUrl.endsWith('rowId')) {
             returnUrl = returnUrl + '=' + rowId;
         }
 

core/src/client/AssayDesigner/AssayDesigner.tsx

@@ -22,7 +22,7 @@ function assayPublish_onLinkToStudy(el, fieldNames)
             var array = formData[e.name];
             if (!array)
                 array = formData[e.name] = [];
-            array.push(e.value.replace("\t"," "));
+            array.push(e.value.replace(/\t/g, " "));
         }
     }