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From bil...@apache.org
Subject svn commit: r1297657 - in /incubator/accumulo/branches/1.4/src/core/src/main/java/org/apache/accumulo/core: client/ client/mapreduce/ iterators/user/ util/shell/commands/
Date Tue, 06 Mar 2012 19:18:07 GMT
Author: billie
Date: Tue Mar  6 19:18:06 2012
New Revision: 1297657

URL: http://svn.apache.org/viewvc?rev=1297657&view=rev
Log:
ACCUMULO-411 wrote some javadocs

Modified:
    incubator/accumulo/branches/1.4/src/core/src/main/java/org/apache/accumulo/core/client/BatchDeleter.java
    incubator/accumulo/branches/1.4/src/core/src/main/java/org/apache/accumulo/core/client/IteratorSetting.java
    incubator/accumulo/branches/1.4/src/core/src/main/java/org/apache/accumulo/core/client/RowIterator.java
    incubator/accumulo/branches/1.4/src/core/src/main/java/org/apache/accumulo/core/client/ZooKeeperInstance.java
    incubator/accumulo/branches/1.4/src/core/src/main/java/org/apache/accumulo/core/client/mapreduce/InputFormatBase.java
    incubator/accumulo/branches/1.4/src/core/src/main/java/org/apache/accumulo/core/iterators/user/IntersectingIterator.java
    incubator/accumulo/branches/1.4/src/core/src/main/java/org/apache/accumulo/core/util/shell/commands/SelectCommand.java
    incubator/accumulo/branches/1.4/src/core/src/main/java/org/apache/accumulo/core/util/shell/commands/SelectrowCommand.java

Modified: incubator/accumulo/branches/1.4/src/core/src/main/java/org/apache/accumulo/core/client/BatchDeleter.java
URL: http://svn.apache.org/viewvc/incubator/accumulo/branches/1.4/src/core/src/main/java/org/apache/accumulo/core/client/BatchDeleter.java?rev=1297657&r1=1297656&r2=1297657&view=diff
==============================================================================
--- incubator/accumulo/branches/1.4/src/core/src/main/java/org/apache/accumulo/core/client/BatchDeleter.java
(original)
+++ incubator/accumulo/branches/1.4/src/core/src/main/java/org/apache/accumulo/core/client/BatchDeleter.java
Tue Mar  6 19:18:06 2012
@@ -26,7 +26,14 @@ import org.apache.accumulo.core.data.Ran
  */
 
 public interface BatchDeleter extends ScannerBase {
-  
+  /**
+   * Deletes the ranges specified by {@link #setRanges}.
+   * 
+   * @throws MutationsRejectedException
+   *           this can be thrown when deletion mutations fail
+   * @throws TableNotFoundException
+   *           when the table does not exist
+   */
   public void delete() throws MutationsRejectedException, TableNotFoundException;
   
   /**
@@ -37,5 +44,8 @@ public interface BatchDeleter extends Sc
    */
   void setRanges(Collection<Range> ranges);
   
+  /**
+   * Releases any resources.
+   */
   void close();
 }

Modified: incubator/accumulo/branches/1.4/src/core/src/main/java/org/apache/accumulo/core/client/IteratorSetting.java
URL: http://svn.apache.org/viewvc/incubator/accumulo/branches/1.4/src/core/src/main/java/org/apache/accumulo/core/client/IteratorSetting.java?rev=1297657&r1=1297656&r2=1297657&view=diff
==============================================================================
--- incubator/accumulo/branches/1.4/src/core/src/main/java/org/apache/accumulo/core/client/IteratorSetting.java
(original)
+++ incubator/accumulo/branches/1.4/src/core/src/main/java/org/apache/accumulo/core/client/IteratorSetting.java
Tue Mar  6 19:18:06 2012
@@ -48,7 +48,7 @@ public class IteratorSetting {
   private Map<String,String> properties;
   
   /**
-   * Get layer at which this iterator applies. See {@link #setPriority(int) for how the priority
is used.}
+   * Get layer at which this iterator applies. See {@link #setPriority(int)} for how the
priority is used.
    * 
    * @return the priority of this Iterator
    */
@@ -138,7 +138,7 @@ public class IteratorSetting {
    * Constructs an iterator setting configured for the scan scope with no parameters. (Parameters
can be added later.)
    * 
    * @param priority
-   *          the priority for the iterator @see {@link #setPriority(int)}
+   *          the priority for the iterator (see {@link #setPriority(int)})
    * @param name
    *          the distinguishing name for the iterator
    * @param iteratorClass
@@ -152,7 +152,7 @@ public class IteratorSetting {
    * Constructs an iterator setting configured for the specified scopes with the specified
parameters.
    * 
    * @param priority
-   *          the priority for the iterator @see {@link #setPriority(int)}
+   *          the priority for the iterator (see {@link #setPriority(int)})
    * @param name
    *          the distinguishing name for the iterator
    * @param iteratorClass
@@ -173,7 +173,7 @@ public class IteratorSetting {
    * parameters.
    * 
    * @param priority
-   *          the priority for the iterator @see {@link #setPriority(int)}
+   *          the priority for the iterator (see {@link #setPriority(int)})
    * @param iteratorClass
    *          the class for the iterator
    */
@@ -182,19 +182,18 @@ public class IteratorSetting {
   }
   
   /**
-
+   * 
    * Constructs an iterator setting using the given class's SimpleName for the iterator name
and configured for the specified scopes with the specified
    * parameters.
    * 
    * @param priority
-   *          the priority for the iterator @see {@link #setPriority(int)}
+   *          the priority for the iterator (see {@link #setPriority(int)})
    * @param iteratorClass
    *          the class for the iterator
    * @param properties
    *          any properties for the iterator
    */
-  public IteratorSetting(int priority, Class<? extends SortedKeyValueIterator<Key,Value>>
iteratorClass,
-      Map<String,String> properties) {
+  public IteratorSetting(int priority, Class<? extends SortedKeyValueIterator<Key,Value>>
iteratorClass, Map<String,String> properties) {
     this(priority, iteratorClass.getSimpleName(), iteratorClass.getName(), properties);
   }
   
@@ -202,7 +201,7 @@ public class IteratorSetting {
    * Constructs an iterator setting configured for the scan scope with no parameters.
    * 
    * @param priority
-   *          the priority for the iterator @see {@link #setPriority(int)}
+   *          the priority for the iterator (see {@link #setPriority(int)})
    * @param name
    *          the distinguishing name for the iterator
    * @param iteratorClass
@@ -313,6 +312,6 @@ public class IteratorSetting {
     public Text getColumnQualifier() {
       return getSecond();
     }
-
+    
   }
 }

Modified: incubator/accumulo/branches/1.4/src/core/src/main/java/org/apache/accumulo/core/client/RowIterator.java
URL: http://svn.apache.org/viewvc/incubator/accumulo/branches/1.4/src/core/src/main/java/org/apache/accumulo/core/client/RowIterator.java?rev=1297657&r1=1297656&r2=1297657&view=diff
==============================================================================
--- incubator/accumulo/branches/1.4/src/core/src/main/java/org/apache/accumulo/core/client/RowIterator.java
(original)
+++ incubator/accumulo/branches/1.4/src/core/src/main/java/org/apache/accumulo/core/client/RowIterator.java
Tue Mar  6 19:18:06 2012
@@ -26,7 +26,11 @@ import org.apache.accumulo.core.util.Pee
 import org.apache.hadoop.io.Text;
 
 /**
- * Group Key/Value pairs into Iterators over rows.
+ * Group Key/Value pairs into Iterators over rows. Suggested usage:
+ * 
+ * <pre>
+ * RowIterator rowIterator = new RowIterator(connector.createScanner(tableName, authorizations));
+ * </pre>
  */
 public class RowIterator implements Iterator<Iterator<Entry<Key,Value>>>
{
   

Modified: incubator/accumulo/branches/1.4/src/core/src/main/java/org/apache/accumulo/core/client/ZooKeeperInstance.java
URL: http://svn.apache.org/viewvc/incubator/accumulo/branches/1.4/src/core/src/main/java/org/apache/accumulo/core/client/ZooKeeperInstance.java?rev=1297657&r1=1297656&r2=1297657&view=diff
==============================================================================
--- incubator/accumulo/branches/1.4/src/core/src/main/java/org/apache/accumulo/core/client/ZooKeeperInstance.java
(original)
+++ incubator/accumulo/branches/1.4/src/core/src/main/java/org/apache/accumulo/core/client/ZooKeeperInstance.java
Tue Mar  6 19:18:06 2012
@@ -232,6 +232,13 @@ public class ZooKeeperInstance implement
     this.conf = conf;
   }
   
+  /**
+   * Given a zooCache and instanceId, look up the instance name.
+   * 
+   * @param zooCache
+   * @param instanceId
+   * @return the instance name
+   */
   public static String lookupInstanceName(ZooCache zooCache, UUID instanceId) {
     ArgumentChecker.notNull(zooCache, instanceId);
     for (String name : zooCache.getChildren(Constants.ZROOT + Constants.ZINSTANCES)) {

Modified: incubator/accumulo/branches/1.4/src/core/src/main/java/org/apache/accumulo/core/client/mapreduce/InputFormatBase.java
URL: http://svn.apache.org/viewvc/incubator/accumulo/branches/1.4/src/core/src/main/java/org/apache/accumulo/core/client/mapreduce/InputFormatBase.java?rev=1297657&r1=1297656&r2=1297657&view=diff
==============================================================================
--- incubator/accumulo/branches/1.4/src/core/src/main/java/org/apache/accumulo/core/client/mapreduce/InputFormatBase.java
(original)
+++ incubator/accumulo/branches/1.4/src/core/src/main/java/org/apache/accumulo/core/client/mapreduce/InputFormatBase.java
Tue Mar  6 19:18:06 2012
@@ -140,12 +140,6 @@ public abstract class InputFormatBase<K,
   private static final String ITERATORS_DELIM = ",";
   
   /**
-   * Enable or disable use of the {@link IsolatedScanner}. By default it is not enabled.
-   * 
-   * @param job
-   *          The Hadoop job object
-   * @param enable
-   *          if true, enable usage of the IsolatedScanner. Otherwise, disable.
    * @deprecated Use {@link #setIsolated(Configuration,boolean)} instead
    */
   public static void setIsolated(JobContext job, boolean enable) {
@@ -153,7 +147,7 @@ public abstract class InputFormatBase<K,
   }
   
   /**
-   * Enable or disable use of the {@link IsolatedScanner}. By default it is not enabled.
+   * Enable or disable use of the {@link IsolatedScanner} in this configuration object. By
default it is not enabled.
    * 
    * @param conf
    *          The Hadoop configuration object
@@ -165,12 +159,6 @@ public abstract class InputFormatBase<K,
   }
   
   /**
-   * Enable or disable use of the {@link ClientSideIteratorScanner}. By default it is not
enabled.
-   * 
-   * @param job
-   *          The Hadoop job object
-   * @param enable
-   *          if true, enable usage of the ClientSideInteratorScanner. Otherwise, disable.
    * @deprecated Use {@link #setLocalIterators(Configuration,boolean)} instead
    */
   public static void setLocalIterators(JobContext job, boolean enable) {
@@ -178,7 +166,7 @@ public abstract class InputFormatBase<K,
   }
   
   /**
-   * Enable or disable use of the {@link ClientSideIteratorScanner}. By default it is not
enabled.
+   * Enable or disable use of the {@link ClientSideIteratorScanner} in this Configuration
object. By default it is not enabled.
    * 
    * @param conf
    *          The Hadoop configuration object
@@ -196,6 +184,20 @@ public abstract class InputFormatBase<K,
     setInputInfo(job.getConfiguration(), user, passwd, table, auths);
   }
   
+  /**
+   * Initialize the user, table, and authorization information for the configuration object
that will be used with an Accumulo InputFormat.
+   * 
+   * @param conf
+   *          the Hadoop configuration object
+   * @param user
+   *          a valid accumulo user
+   * @param passwd
+   *          the user's password
+   * @param table
+   *          the table to read
+   * @param auths
+   *          the authorizations used to restrict data read
+   */
   public static void setInputInfo(Configuration conf, String user, byte[] passwd, String
table, Authorizations auths) {
     if (conf.getBoolean(INPUT_INFO_HAS_BEEN_SET, false))
       throw new IllegalStateException("Input info can only be set once per job");
@@ -216,6 +218,16 @@ public abstract class InputFormatBase<K,
     setZooKeeperInstance(job.getConfiguration(), instanceName, zooKeepers);
   }
   
+  /**
+   * Configure a {@link ZooKeeperInstance} for this configuration object.
+   * 
+   * @param conf
+   *          the Hadoop configuration object
+   * @param instanceName
+   *          the accumulo instance name
+   * @param zooKeepers
+   *          a comma-separated list of zookeeper servers
+   */
   public static void setZooKeeperInstance(Configuration conf, String instanceName, String
zooKeepers) {
     if (conf.getBoolean(INSTANCE_HAS_BEEN_SET, false))
       throw new IllegalStateException("Instance info can only be set once per job");
@@ -233,6 +245,14 @@ public abstract class InputFormatBase<K,
     setMockInstance(job.getConfiguration(), instanceName);
   }
   
+  /**
+   * Configure a {@link MockInstance} for this configuration object.
+   * 
+   * @param conf
+   *          the Hadoop configuration object
+   * @param instanceName
+   *          the accumulo instance name
+   */
   public static void setMockInstance(Configuration conf, String instanceName) {
     conf.setBoolean(INSTANCE_HAS_BEEN_SET, true);
     conf.setBoolean(MOCK, true);
@@ -246,6 +266,14 @@ public abstract class InputFormatBase<K,
     setRanges(job.getConfiguration(), ranges);
   }
   
+  /**
+   * Set the ranges to map over for this configuration object.
+   * 
+   * @param conf
+   *          the Hadoop configuration object
+   * @param ranges
+   *          the ranges that will be mapped over
+   */
   public static void setRanges(Configuration conf, Collection<Range> ranges) {
     ArgumentChecker.notNull(ranges);
     ArrayList<String> rangeStrings = new ArrayList<String>(ranges.size());
@@ -268,16 +296,26 @@ public abstract class InputFormatBase<K,
     disableAutoAdjustRanges(job.getConfiguration());
   }
   
+  /**
+   * Disables the adjustment of ranges for this configuration object. By default, overlapping
ranges will be merged and ranges will be fit to existing tablet
+   * boundaries. Disabling this adjustment will cause there to be exactly one mapper per
range set using {@link #setRanges(Configuration, Collection)}.
+   * 
+   * @param conf
+   *          the Hadoop configuration object
+   */
   public static void disableAutoAdjustRanges(Configuration conf) {
     conf.setBoolean(AUTO_ADJUST_RANGES, false);
   }
   
+  /**
+   * @deprecated since 1.4 use {@link org.apache.accumulo.core.iterators.user.RegExFilter}
and {@link #addIterator(Configuration, IteratorSetting)}
+   */
   public static enum RegexType {
     ROW, COLUMN_FAMILY, COLUMN_QUALIFIER, VALUE
   }
   
   /**
-   * @deprecated since 1.4 {@link #addIterator(Configuration, IteratorSetting)}
+   * @deprecated since 1.4 use {@link #addIterator(Configuration, IteratorSetting)}
    * @see org.apache.accumulo.core.iterators.user.RegExFilter#setRegexs(IteratorSetting,
String, String, String, String, boolean)
    * @param job
    * @param type
@@ -311,14 +349,6 @@ public abstract class InputFormatBase<K,
   }
   
   /**
-   * Sets the max # of values that may be returned for an individual Accumulo cell. By default,
applied before all other Accumulo iterators (highest priority)
-   * leveraged in the scan by the record reader. To adjust priority use setIterator() &
setIteratorOptions() w/ the VersioningIterator type explicitly.
-   * 
-   * @param job
-   *          the job
-   * @param maxVersions
-   *          the max versions
-   * @throws IOException
    * @deprecated Use {@link #setMaxVersions(Configuration,int)} instead
    */
   public static void setMaxVersions(JobContext job, int maxVersions) throws IOException {
@@ -330,10 +360,11 @@ public abstract class InputFormatBase<K,
    * leveraged in the scan by the record reader. To adjust priority use setIterator() &
setIteratorOptions() w/ the VersioningIterator type explicitly.
    * 
    * @param conf
-   *          the job
+   *          the Hadoop configuration object
    * @param maxVersions
-   *          the max versions
+   *          the max number of versions per accumulo cell
    * @throws IOException
+   *           if maxVersions is < 1
    */
   public static void setMaxVersions(Configuration conf, int maxVersions) throws IOException
{
     if (maxVersions < 1)
@@ -342,10 +373,6 @@ public abstract class InputFormatBase<K,
   }
   
   /**
-   * 
-   * @param columnFamilyColumnQualifierPairs
-   *          A pair of {@link Text} objects corresponding to column family and column qualifier.
If the column qualifier is null, the entire column family is
-   *          selected. An empty set is the default and is equivalent to scanning the all
columns.
    * @deprecated Use {@link #fetchColumns(Configuration,Collection)} instead
    */
   public static void fetchColumns(JobContext job, Collection<Pair<Text,Text>>
columnFamilyColumnQualifierPairs) {
@@ -353,7 +380,10 @@ public abstract class InputFormatBase<K,
   }
   
   /**
+   * Restricts the columns that will be mapped over for this configuration object.
    * 
+   * @param conf
+   *          the Hadoop configuration object
    * @param columnFamilyColumnQualifierPairs
    *          A pair of {@link Text} objects corresponding to column family and column qualifier.
If the column qualifier is null, the entire column family is
    *          selected. An empty set is the default and is equivalent to scanning the all
columns.
@@ -380,6 +410,14 @@ public abstract class InputFormatBase<K,
     setLogLevel(job.getConfiguration(), level);
   }
   
+  /**
+   * Sets the log level for this configuration object.
+   * 
+   * @param conf
+   *          the Hadoop configuration object
+   * @param level
+   *          the logging level
+   */
   public static void setLogLevel(Configuration conf, Level level) {
     ArgumentChecker.notNull(level);
     log.setLevel(level);
@@ -387,12 +425,6 @@ public abstract class InputFormatBase<K,
   }
   
   /**
-   * Encode an iterator on the input.
-   * 
-   * @param job
-   *          The job in which to save the iterator configuration
-   * @param cfg
-   *          The configuration of the iterator
    * @deprecated Use {@link #addIterator(Configuration,IteratorSetting)} instead
    */
   public static void addIterator(JobContext job, IteratorSetting cfg) {
@@ -400,10 +432,10 @@ public abstract class InputFormatBase<K,
   }
   
   /**
-   * Encode an iterator on the input.
+   * Encode an iterator on the input for this configuration object.
    * 
    * @param conf
-   *          The job in which to save the iterator configuration
+   *          The Hadoop configuration in which to save the iterator configuration
    * @param cfg
    *          The configuration of the iterator
    */
@@ -440,7 +472,7 @@ public abstract class InputFormatBase<K,
   }
   
   /**
-   * Specify an Accumulo iterator type to manage the behavior of the underlying table scan
this InputFormat's Record Reader will conduct, w/ priority dictating
+   * Specify an Accumulo iterator type to manage the behavior of the underlying table scan
this InputFormat's RecordReader will conduct, w/ priority dictating
    * the order in which specified iterators are applied. Repeat calls to specify multiple
iterators are allowed.
    * 
    * @param job
@@ -509,6 +541,14 @@ public abstract class InputFormatBase<K,
     return isIsolated(job.getConfiguration());
   }
   
+  /**
+   * Determines whether a configuration has isolation enabled.
+   * 
+   * @param conf
+   *          the Hadoop configuration object
+   * @return true if isolation is enabled, false otherwise
+   * @see #setIsolated(Configuration, boolean)
+   */
   protected static boolean isIsolated(Configuration conf) {
     return conf.getBoolean(ISOLATED, false);
   }
@@ -520,6 +560,14 @@ public abstract class InputFormatBase<K,
     return usesLocalIterators(job.getConfiguration());
   }
   
+  /**
+   * Determines whether a configuration uses local iterators.
+   * 
+   * @param conf
+   *          the Hadoop configuration object
+   * @return true if uses local iterators, false otherwise
+   * @see #setLocalIterators(Configuration, boolean)
+   */
   protected static boolean usesLocalIterators(Configuration conf) {
     return conf.getBoolean(LOCAL_ITERATORS, false);
   }
@@ -531,6 +579,14 @@ public abstract class InputFormatBase<K,
     return getUsername(job.getConfiguration());
   }
   
+  /**
+   * Gets the user name from the configuration.
+   * 
+   * @param conf
+   *          the Hadoop configuration object
+   * @return the user name
+   * @see #setInputInfo(Configuration, String, byte[], String, Authorizations)
+   */
   protected static String getUsername(Configuration conf) {
     return conf.get(USERNAME);
   }
@@ -546,8 +602,13 @@ public abstract class InputFormatBase<K,
   }
   
   /**
-   * WARNING: The password is stored in the Configuration and shared with all MapReduce tasks;
It is BASE64 encoded to provide a charset safe conversion to a
-   * string, and is not intended to be secure.
+   * Gets the password from the configuration. WARNING: The password is stored in the Configuration
and shared with all MapReduce tasks; It is BASE64 encoded to
+   * provide a charset safe conversion to a string, and is not intended to be secure.
+   * 
+   * @param conf
+   *          the Hadoop configuration object
+   * @return the BASE64-encoded password
+   * @see #setInputInfo(Configuration, String, byte[], String, Authorizations)
    */
   protected static byte[] getPassword(Configuration conf) {
     return Base64.decodeBase64(conf.get(PASSWORD, "").getBytes());
@@ -560,6 +621,14 @@ public abstract class InputFormatBase<K,
     return getTablename(job.getConfiguration());
   }
   
+  /**
+   * Gets the table name from the configuration.
+   * 
+   * @param conf
+   *          the Hadoop configuration object
+   * @return the table name
+   * @see #setInputInfo(Configuration, String, byte[], String, Authorizations)
+   */
   protected static String getTablename(Configuration conf) {
     return conf.get(TABLE_NAME);
   }
@@ -571,6 +640,14 @@ public abstract class InputFormatBase<K,
     return getAuthorizations(job.getConfiguration());
   }
   
+  /**
+   * Gets the authorizations to set for the scans from the configuration.
+   * 
+   * @param conf
+   *          the Hadoop configuration object
+   * @return the accumulo scan authorizations
+   * @see #setInputInfo(Configuration, String, byte[], String, Authorizations)
+   */
   protected static Authorizations getAuthorizations(Configuration conf) {
     String authString = conf.get(AUTHORIZATIONS);
     return authString == null ? Constants.NO_AUTHS : new Authorizations(authString.split(","));
@@ -583,6 +660,15 @@ public abstract class InputFormatBase<K,
     return getInstance(job.getConfiguration());
   }
   
+  /**
+   * Initializes an Accumulo {@link Instance} based on the configuration.
+   * 
+   * @param conf
+   *          the Hadoop configuration object
+   * @return an accumulo instance
+   * @see #setZooKeeperInstance(Configuration, String, String)
+   * @see #setMockInstance(Configuration, String)
+   */
   protected static Instance getInstance(Configuration conf) {
     if (conf.getBoolean(MOCK, false))
       return new MockInstance(conf.get(INSTANCE_NAME));
@@ -596,6 +682,15 @@ public abstract class InputFormatBase<K,
     return getTabletLocator(job.getConfiguration());
   }
   
+  /**
+   * Initializes an Accumulo {@link TabletLocator} based on the configuration.
+   * 
+   * @param conf
+   *          the Hadoop configuration object
+   * @return an accumulo tablet locator
+   * @throws TableNotFoundException
+   *           if the table name set on the configuration doesn't exist
+   */
   protected static TabletLocator getTabletLocator(Configuration conf) throws TableNotFoundException
{
     if (conf.getBoolean(MOCK, false))
       return new MockTabletLocator();
@@ -614,6 +709,16 @@ public abstract class InputFormatBase<K,
     return getRanges(job.getConfiguration());
   }
   
+  /**
+   * Gets the ranges to scan over from a configuration object.
+   * 
+   * @param conf
+   *          the Hadoop configuration object
+   * @return the ranges
+   * @throws IOException
+   *           if the ranges have been encoded improperly
+   * @see #setRanges(Configuration, Collection)
+   */
   protected static List<Range> getRanges(Configuration conf) throws IOException {
     ArrayList<Range> ranges = new ArrayList<Range>();
     for (String rangeString : conf.getStringCollection(RANGES)) {
@@ -626,13 +731,10 @@ public abstract class InputFormatBase<K,
   }
   
   /**
-   * @deprecated Use {@link #getRegex(Configuration,RegexType)} instead
+   * @deprecated since 1.4 use {@link org.apache.accumulo.core.iterators.user.RegExFilter}
and {@link #addIterator(Configuration, IteratorSetting)}
+   * @see #setRegex(JobContext, RegexType, String)
    */
   protected static String getRegex(JobContext job, RegexType type) {
-    return getRegex(job.getConfiguration(), type);
-  }
-  
-  protected static String getRegex(Configuration conf, RegexType type) {
     String key = null;
     switch (type) {
       case ROW:
@@ -651,7 +753,7 @@ public abstract class InputFormatBase<K,
         throw new NoSuchElementException();
     }
     try {
-      String s = conf.get(key);
+      String s = job.getConfiguration().get(key);
       if (s == null)
         return null;
       return URLDecoder.decode(s, "UTF-8");
@@ -668,6 +770,14 @@ public abstract class InputFormatBase<K,
     return getFetchedColumns(job.getConfiguration());
   }
   
+  /**
+   * Gets the columns to be mapped over from this configuration object.
+   * 
+   * @param conf
+   *          the Hadoop configuration object
+   * @return a set of columns
+   * @see #fetchColumns(Configuration, Collection)
+   */
   protected static Set<Pair<Text,Text>> getFetchedColumns(Configuration conf)
{
     Set<Pair<Text,Text>> columns = new HashSet<Pair<Text,Text>>();
     for (String col : conf.getStringCollection(COLUMNS)) {
@@ -686,6 +796,14 @@ public abstract class InputFormatBase<K,
     return getAutoAdjustRanges(job.getConfiguration());
   }
   
+  /**
+   * Determines whether a configuration has auto-adjust ranges enabled.
+   * 
+   * @param conf
+   *          the Hadoop configuration object
+   * @return true if auto-adjust is enabled, false otherwise
+   * @see #disableAutoAdjustRanges(Configuration)
+   */
   protected static boolean getAutoAdjustRanges(Configuration conf) {
     return conf.getBoolean(AUTO_ADJUST_RANGES, true);
   }
@@ -697,6 +815,14 @@ public abstract class InputFormatBase<K,
     return getLogLevel(job.getConfiguration());
   }
   
+  /**
+   * Gets the log level from this configuration.
+   * 
+   * @param conf
+   *          the Hadoop configuration object
+   * @return the log level
+   * @see #setLogLevel(Configuration, Level)
+   */
   protected static Level getLogLevel(Configuration conf) {
     return Level.toLevel(conf.getInt(LOGLEVEL, Level.INFO.toInt()));
   }
@@ -712,6 +838,14 @@ public abstract class InputFormatBase<K,
   
   // InputFormat doesn't have the equivalent of OutputFormat's
   // checkOutputSpecs(JobContext job)
+  /**
+   * Check whether a configuration is fully configured to be used with an Accumulo {@link
org.apache.hadoop.mapreduce.InputFormat}.
+   * 
+   * @param conf
+   *          the Hadoop configuration object
+   * @throws IOException
+   *           if the configuration is improperly configured
+   */
   protected static void validateOptions(Configuration conf) throws IOException {
     if (!conf.getBoolean(INPUT_INFO_HAS_BEEN_SET, false))
       throw new IOException("Input info has not been set.");
@@ -740,7 +874,6 @@ public abstract class InputFormatBase<K,
     }
   }
   
-  // Get the maxVersions the VersionsIterator should be configured with. Return -1 if none.
   /**
    * @deprecated Use {@link #getMaxVersions(Configuration)} instead
    */
@@ -748,12 +881,18 @@ public abstract class InputFormatBase<K,
     return getMaxVersions(job.getConfiguration());
   }
   
-  // Get the maxVersions the VersionsIterator should be configured with. Return -1 if none.
+  /**
+   * Gets the maxVersions to use for the {@link VersioningIterator} from this configuration.
+   * 
+   * @param conf
+   *          the Hadoop configuration object
+   * @return the max versions, -1 if not configured
+   * @see #setMaxVersions(Configuration, int)
+   */
   protected static int getMaxVersions(Configuration conf) {
     return conf.getInt(MAX_VERSIONS, -1);
   }
   
-  // Return a list of the iterator settings (for iterators to apply to a scanner)
   /**
    * @deprecated Use {@link #getIterators(Configuration)} instead
    */
@@ -761,7 +900,14 @@ public abstract class InputFormatBase<K,
     return getIterators(job.getConfiguration());
   }
   
-  // Return a list of the iterator settings (for iterators to apply to a scanner)
+  /**
+   * Gets a list of the iterator settings (for iterators to apply to a scanner) from this
configuration.
+   * 
+   * @param conf
+   *          the Hadoop configuration object
+   * @return a list of iterators
+   * @see #addIterator(Configuration, IteratorSetting)
+   */
   protected static List<AccumuloIterator> getIterators(Configuration conf) {
     
     String iterators = conf.get(ITERATORS);
@@ -780,7 +926,6 @@ public abstract class InputFormatBase<K,
     return list;
   }
   
-  // Return a list of the iterator options specified
   /**
    * @deprecated Use {@link #getIteratorOptions(Configuration)} instead
    */
@@ -788,7 +933,14 @@ public abstract class InputFormatBase<K,
     return getIteratorOptions(job.getConfiguration());
   }
   
-  // Return a list of the iterator options specified
+  /**
+   * Gets a list of the iterator options specified on this configuration.
+   * 
+   * @param conf
+   *          the Hadoop configuration object
+   * @return a list of iterator options
+   * @see #addIterator(Configuration, IteratorSetting)
+   */
   protected static List<AccumuloIteratorOption> getIteratorOptions(Configuration conf)
{
     String iteratorOptions = conf.get(ITERATORS_OPTIONS);
     
@@ -812,7 +964,9 @@ public abstract class InputFormatBase<K,
     private boolean scannerRegexEnabled = false;
     protected RangeInputSplit split;
     
-    @SuppressWarnings("deprecation")
+    /**
+     * @deprecated since 1.4, configure {@link org.apache.accumulo.core.iterators.user.RegExFilter}
instead.
+     */
     private void checkAndEnableRegex(String regex, Scanner scanner, String methodName) throws
IllegalArgumentException, SecurityException,
         IllegalAccessException, InvocationTargetException, NoSuchMethodException, IOException
{
       if (regex != null) {
@@ -826,18 +980,14 @@ public abstract class InputFormatBase<K,
     }
     
     /**
-     * @deprecated Use {@link #setupRegex(Configuration,Scanner)} instead
+     * @deprecated since 1.4, configure {@link org.apache.accumulo.core.iterators.user.RegExFilter}
instead.
      */
     protected boolean setupRegex(TaskAttemptContext attempt, Scanner scanner) throws AccumuloException
{
-      return setupRegex(attempt.getConfiguration(), scanner);
-    }
-    
-    protected boolean setupRegex(Configuration conf, Scanner scanner) throws AccumuloException
{
       try {
-        checkAndEnableRegex(getRegex(conf, RegexType.ROW), scanner, "setRowRegex");
-        checkAndEnableRegex(getRegex(conf, RegexType.COLUMN_FAMILY), scanner, "setColumnFamilyRegex");
-        checkAndEnableRegex(getRegex(conf, RegexType.COLUMN_QUALIFIER), scanner, "setColumnQualifierRegex");
-        checkAndEnableRegex(getRegex(conf, RegexType.VALUE), scanner, "setValueRegex");
+        checkAndEnableRegex(getRegex(attempt, RegexType.ROW), scanner, "setRowRegex");
+        checkAndEnableRegex(getRegex(attempt, RegexType.COLUMN_FAMILY), scanner, "setColumnFamilyRegex");
+        checkAndEnableRegex(getRegex(attempt, RegexType.COLUMN_QUALIFIER), scanner, "setColumnQualifierRegex");
+        checkAndEnableRegex(getRegex(attempt, RegexType.VALUE), scanner, "setValueRegex");
         return true;
       } catch (Exception e) {
         throw new AccumuloException("Can't set up regex for scanner");
@@ -852,7 +1002,15 @@ public abstract class InputFormatBase<K,
       setupIterators(attempt.getConfiguration(), scanner);
     }
     
-    // Apply the configured iterators from the job to the scanner
+    /**
+     * Apply the configured iterators from the configuration to the scanner.
+     * 
+     * @param conf
+     *          the Hadoop configuration object
+     * @param scanner
+     *          the scanner to configure
+     * @throws AccumuloException
+     */
     protected void setupIterators(Configuration conf, Scanner scanner) throws AccumuloException
{
       List<AccumuloIterator> iterators = getIterators(conf);
       List<AccumuloIteratorOption> options = getIteratorOptions(conf);
@@ -869,7 +1027,6 @@ public abstract class InputFormatBase<K,
       }
     }
     
-    // Apply the VersioningIterator at priority 0 based on the job config
     /**
      * @deprecated Use {@link #setupMaxVersions(Configuration,Scanner)} instead
      */
@@ -877,7 +1034,14 @@ public abstract class InputFormatBase<K,
       setupMaxVersions(attempt.getConfiguration(), scanner);
     }
     
-    // Apply the VersioningIterator at priority 0 based on the job config
+    /**
+     * If maxVersions has been set, configure a {@link VersioningIterator} at priority 0
for this scanner.
+     * 
+     * @param conf
+     *          the Hadoop configuration object
+     * @param scanner
+     *          the scanner to configure
+     */
     protected void setupMaxVersions(Configuration conf, Scanner scanner) {
       int maxVersions = getMaxVersions(conf);
       // Check to make sure its a legit value
@@ -888,6 +1052,9 @@ public abstract class InputFormatBase<K,
       }
     }
     
+    /**
+     * Initialize a scanner over the given input split using this task attempt configuration.
+     */
     public void initialize(InputSplit inSplit, TaskAttemptContext attempt) throws IOException
{
       Scanner scanner;
       split = (RangeInputSplit) inSplit;
@@ -912,7 +1079,7 @@ public abstract class InputFormatBase<K,
           scanner = new ClientSideIteratorScanner(scanner);
         }
         setupMaxVersions(attempt.getConfiguration(), scanner);
-        setupRegex(attempt.getConfiguration(), scanner);
+        setupRegex(attempt, scanner);
         setupIterators(attempt.getConfiguration(), scanner);
       } catch (Exception e) {
         throw new IOException(e);
@@ -962,7 +1129,7 @@ public abstract class InputFormatBase<K,
   }
   
   /**
-   * read the metadata table to get tablets of interest these each become a split
+   * Read the metadata table to get tablets and match up ranges to them.
    */
   public List<InputSplit> getSplits(JobContext job) throws IOException {
     log.setLevel(getLogLevel(job.getConfiguration()));

Modified: incubator/accumulo/branches/1.4/src/core/src/main/java/org/apache/accumulo/core/iterators/user/IntersectingIterator.java
URL: http://svn.apache.org/viewvc/incubator/accumulo/branches/1.4/src/core/src/main/java/org/apache/accumulo/core/iterators/user/IntersectingIterator.java?rev=1297657&r1=1297656&r2=1297657&view=diff
==============================================================================
--- incubator/accumulo/branches/1.4/src/core/src/main/java/org/apache/accumulo/core/iterators/user/IntersectingIterator.java
(original)
+++ incubator/accumulo/branches/1.4/src/core/src/main/java/org/apache/accumulo/core/iterators/user/IntersectingIterator.java
Tue Mar  6 19:18:06 2012
@@ -382,11 +382,10 @@ public class IntersectingIterator implem
   private static final String notFlagOptionName = "notFlag";
   
   /**
-   * to be made protected
-   * 
    * @param columns
    * @return encoded columns
-   * @deprecated since 1.4 {@link #setColumnFamilies(IteratorSetting, Text[] columns)}
+   * @deprecated since 1.4. To be made protected. Do not interact with flags string directly,
just use
+   *             {@link #setColumnFamilies(IteratorSetting, Text[], boolean[])}.
    */
   public static String encodeColumns(Text[] columns) {
     StringBuilder sb = new StringBuilder();
@@ -398,11 +397,10 @@ public class IntersectingIterator implem
   }
   
   /**
-   * to be made protected
-   * 
    * @param flags
    * @return encoded flags
-   * @deprecated since 1.4 {@link #setColumnFamilies(IteratorSetting, Text[] columns, boolean[]
flags)}
+   * @deprecated since 1.4. To be made protected. Do not interact with flags string directly,
just use
+   *             {@link #setColumnFamilies(IteratorSetting, Text[], boolean[])}.
    */
   public static String encodeBooleans(boolean[] flags) {
     byte[] bytes = new byte[flags.length];
@@ -429,7 +427,8 @@ public class IntersectingIterator implem
    * 
    * @param flags
    * @return decoded flags
-   * @deprecated since 1.4
+   * @deprecated since 1.4. To be made protected. Do not interact with flags string directly,
just use
+   *             {@link #setColumnFamilies(IteratorSetting, Text[], boolean[])}.
    */
   public static boolean[] decodeBooleans(String flags) {
     // return null of there were no flags

Modified: incubator/accumulo/branches/1.4/src/core/src/main/java/org/apache/accumulo/core/util/shell/commands/SelectCommand.java
URL: http://svn.apache.org/viewvc/incubator/accumulo/branches/1.4/src/core/src/main/java/org/apache/accumulo/core/util/shell/commands/SelectCommand.java?rev=1297657&r1=1297656&r2=1297657&view=diff
==============================================================================
--- incubator/accumulo/branches/1.4/src/core/src/main/java/org/apache/accumulo/core/util/shell/commands/SelectCommand.java
(original)
+++ incubator/accumulo/branches/1.4/src/core/src/main/java/org/apache/accumulo/core/util/shell/commands/SelectCommand.java
Tue Mar  6 19:18:06 2012
@@ -34,8 +34,9 @@ import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
 import org.apache.hadoop.io.Text;
 
-@Deprecated
-// deprecated since 1.4
+/**
+ * @deprecated since 1.4, use {@code scan -r <row> -c <columnfamily>[:<columnqualifier>]}
instead.
+ */
 public class SelectCommand extends Command {
   
   private Option selectOptAuths, timestampOpt, disablePaginationOpt, tableOpt;
@@ -44,8 +45,8 @@ public class SelectCommand extends Comma
       IOException {
     String tableName;
     
-    shellState.log.warn("select is deprecated, use 'scan -r <row> -c <columnfamily>[:<columnqualifier>]'");
-
+    Shell.log.warn("select is deprecated, use scan -r <row> -c <columnfamily>[:<columnqualifier>]'");
+    
     if (cl.hasOption(tableOpt.getOpt())) {
       tableName = cl.getOptionValue(tableOpt.getOpt());
       if (!shellState.getConnector().tableOperations().exists(tableName))
@@ -102,4 +103,4 @@ public class SelectCommand extends Comma
   public int numArgs() {
     return 3;
   }
-}
\ No newline at end of file
+}

Modified: incubator/accumulo/branches/1.4/src/core/src/main/java/org/apache/accumulo/core/util/shell/commands/SelectrowCommand.java
URL: http://svn.apache.org/viewvc/incubator/accumulo/branches/1.4/src/core/src/main/java/org/apache/accumulo/core/util/shell/commands/SelectrowCommand.java?rev=1297657&r1=1297656&r2=1297657&view=diff
==============================================================================
--- incubator/accumulo/branches/1.4/src/core/src/main/java/org/apache/accumulo/core/util/shell/commands/SelectrowCommand.java
(original)
+++ incubator/accumulo/branches/1.4/src/core/src/main/java/org/apache/accumulo/core/util/shell/commands/SelectrowCommand.java
Tue Mar  6 19:18:06 2012
@@ -32,8 +32,9 @@ import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
 import org.apache.hadoop.io.Text;
 
-@Deprecated
-// deprecated since 1.4
+/**
+ * @deprecated since 1.4, use {@code scan -r <row>} instead.
+ */
 public class SelectrowCommand extends Command {
   
   private Option selectrowOptAuths, timestampOpt, disablePaginationOpt, tableOpt;
@@ -43,8 +44,8 @@ public class SelectrowCommand extends Co
     
     String tableName;
     
-    shellState.log.warn("selectrow is deprecated, use 'scan -r <row>'");
-
+    Shell.log.warn("selectrow is deprecated, use 'scan -r <row>'");
+    
     if (cl.hasOption(tableOpt.getOpt())) {
       tableName = cl.getOptionValue(tableOpt.getOpt());
       if (!shellState.getConnector().tableOperations().exists(tableName))
@@ -103,4 +104,4 @@ public class SelectrowCommand extends Co
   public int numArgs() {
     return 1;
   }
-}
\ No newline at end of file
+}



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