Checkstyle Results

The following document contains the results of Checkstyle. 

Summary

Files Infos  Warnings  Errors 
49 0 0 1178

Files

Files
org/galaxy/computing/ContextAware.java 0 0 5
org/galaxy/computing/ContextProvider.java 0 0 9
org/galaxy/computing/DataSet.java 0 0 33
org/galaxy/computing/DataSourceAware.java 0 0 4
org/galaxy/computing/DataSourceProvider.java 0 0 6
org/galaxy/computing/Defaults.java 0 0 7
org/galaxy/computing/Domain.java 0 0 10
org/galaxy/computing/Installable.java 0 0 14
org/galaxy/computing/InstallationException.java 0 0 13
org/galaxy/computing/Parameters.java 0 0 15
org/galaxy/computing/Processable.java 0 0 82
org/galaxy/computing/Processor.java 0 0 15
org/galaxy/computing/RemoteObservable.java 0 0 4
org/galaxy/computing/RemoteObserver.java 0 0 4
org/galaxy/computing/Worker.java 0 0 17
org/galaxy/computing/boot/Bootable.java 0 0 5
org/galaxy/computing/boot/BootableSystem.java 0 0 32
org/galaxy/computing/boot/package-info.java 0 0 2
org/galaxy/computing/dataset/AbstractDataSet.java 0 0 75
org/galaxy/computing/dataset/CacheableDataSet.java 0 0 24
org/galaxy/computing/dataset/ProcessableDataStorage.java 0 0 47
org/galaxy/computing/dataset/Storage.java 0 0 13
org/galaxy/computing/dataset/io/ChunkInputStream.java 0 0 24
org/galaxy/computing/dataset/io/ChunkOutputStream.java 0 0 26
org/galaxy/computing/dataset/io/ChunkUtils.java 0 0 67
org/galaxy/computing/dataset/io/CountingStream.java 0 0 12
org/galaxy/computing/dataset/io/ObjectStreamProvider.java 0 0 98
org/galaxy/computing/dataset/io/package-info.java 0 0 2
org/galaxy/computing/dataset/package-info.java 0 0 1
org/galaxy/computing/package-info.java 0 0 1
org/galaxy/computing/processor/AbstractContextAwareProcessor.java 0 0 14
org/galaxy/computing/processor/AbstractProcessor.java 0 0 19
org/galaxy/computing/processor/BenchmarkedProcessor.java 0 0 37
org/galaxy/computing/processor/BenchmarkedProcessorReporter.java 0 0 34
org/galaxy/computing/processor/DevNull.java 0 0 17
org/galaxy/computing/processor/Identity.java 0 0 12
org/galaxy/computing/processor/MultiProcessor.java 0 0 43
org/galaxy/computing/processor/ProcessingException.java 0 0 10
org/galaxy/computing/processor/package-info.java 0 0 3
org/galaxy/computing/utils/DistantParameterBuilder.java 0 0 45
org/galaxy/computing/utils/DistantParameterDecorator.java 0 0 63
org/galaxy/computing/utils/DomainResolver.java 0 0 7
org/galaxy/computing/utils/Lookup.java 0 0 48
org/galaxy/computing/utils/NuggetUtils.java 0 0 18
org/galaxy/computing/utils/VolumeMarker.java 0 0 29
org/galaxy/computing/utils/package-info.java 0 0 1
org/galaxy/computing/worker/AbstractWorker.java 0 0 98
org/galaxy/computing/worker/RemoteWorker.java 0 0 11
org/galaxy/computing/worker/package-info.java 0 0 2

Rules

Rules Violations Severity
JavadocPackage
  • allowLegacy: "true"
0  Error
NewlineAtEndOfFile 14  Error
Translation 0  Error
FileLength 0  Error
FileTabCharacter
  • eachLine: "true"
0  Error
RegexpSingleline
  • message: "Line has trailing spaces."
  • format: "\s+$"
234  Error
JavadocMethod 157  Error
JavadocType 20  Error
JavadocVariable 109  Error
JavadocStyle 11  Error
ConstantName 8  Error
LocalFinalVariableName 0  Error
LocalVariableName 0  Error
MemberName 2  Error
MethodName 0  Error
PackageName 0  Error
ParameterName 0  Error
StaticVariableName 0  Error
TypeName 0  Error
AvoidStarImport 0  Error
IllegalImport 0  Error
RedundantImport 0  Error
UnusedImports 6  Error
LineLength 145  Error
MethodLength 0  Error
ParameterNumber 0  Error
EmptyForIteratorPad 0  Error
MethodParamPad 0  Error
NoWhitespaceAfter 1  Error
NoWhitespaceBefore 0  Error
OperatorWrap 0  Error
ParenPad 0  Error
TypecastParenPad 0  Error
WhitespaceAfter 5  Error
WhitespaceAround 4  Error
ModifierOrder 0  Error
RedundantModifier 32  Error
AvoidNestedBlocks 0  Error
EmptyBlock 3  Error
LeftCurly 4  Error
NeedBraces 0  Error
RightCurly 0  Error
AvoidInlineConditionals 3  Error
EmptyStatement 0  Error
EqualsHashCode 0  Error
HiddenField 23  Error
IllegalInstantiation 0  Error
InnerAssignment 2  Error
MagicNumber 7  Error
MissingSwitchDefault 0  Error
RedundantThrows 18  Error
SimplifyBooleanExpression 0  Error
SimplifyBooleanReturn 0  Error
DesignForExtension 128  Error
FinalClass 0  Error
HideUtilityClassConstructor 3  Error
InterfaceIsType 0  Error
VisibilityModifier 16  Error
ArrayTypeStyle 0  Error
FinalParameters 214  Error
TodoComment 0  Error
UpperEll 10  Error

Details

org/galaxy/computing/ContextAware.java

Violation Message Line
Line has trailing spaces. 7
Line has trailing spaces. 8
Line has trailing spaces. 16
Redundant 'public' modifier. 21
Line has trailing spaces. 22

org/galaxy/computing/ContextProvider.java

Violation Message Line
Line has trailing spaces. 7
Line has trailing spaces. 8
Line has trailing spaces. 16
Redundant 'public' modifier. 20
Line has trailing spaces. 21
Line has trailing spaces. 24
Line has trailing spaces. 25
Redundant 'public' modifier. 28
Line has trailing spaces. 29

org/galaxy/computing/DataSet.java

Violation Message Line
Line has trailing spaces. 11
Type Javadoc comment is missing an @param <P> tag. 15
Line has trailing spaces. 19
Line is longer than 80 characters (found 94). 20
Line has trailing spaces. 21
Redundant 'public' modifier. 27
Line has trailing spaces. 28
Line has trailing spaces. 31
Line has trailing spaces. 34
Line has trailing spaces. 37
Line has trailing spaces. 38
Line has trailing spaces. 40
Redundant 'public' modifier. 46
Line has trailing spaces. 47
Line has trailing spaces. 50
Line has trailing spaces. 52
Redundant 'public' modifier. 56
Expected @param tag for 'batchSize'. 56
Expected @throws tag for 'IOException'. 56
Redundant throws: 'RemoteException' is subclass of 'IOException'. 56
Line has trailing spaces. 57
Line has trailing spaces. 60
Unused @param tag for 'entry'. 61
Line has trailing spaces. 62
Redundant 'public' modifier. 66
Expected @param tag for 'entries'. 66
Expected @throws tag for 'IOException'. 66
Redundant throws: 'RemoteException' is subclass of 'IOException'. 66
Line has trailing spaces. 67
Line has trailing spaces. 70
Line has trailing spaces. 72
Redundant 'public' modifier. 76
Line has trailing spaces. 77

org/galaxy/computing/DataSourceAware.java

Violation Message Line
Redundant 'public' modifier. 19
Redundant 'public' modifier. 26
Redundant 'public' modifier. 33
Redundant 'public' modifier. 41

org/galaxy/computing/DataSourceProvider.java

Violation Message Line
Line has trailing spaces. 6
Line has trailing spaces. 7
Line has trailing spaces. 8
Line has trailing spaces. 16
Redundant 'public' modifier. 20
Line has trailing spaces. 21

org/galaxy/computing/Defaults.java

Violation Message Line
Utility classes should not have a public or default constructor. 8
Line has trailing spaces. 12
Line has trailing spaces. 16
Line has trailing spaces. 18
Line has trailing spaces. 19
Line has trailing spaces. 23
Line has trailing spaces. 24

org/galaxy/computing/Domain.java

Violation Message Line
Line has trailing spaces. 10
Line has trailing spaces. 11
Line has trailing spaces. 12
Line has trailing spaces. 13
Line has trailing spaces. 15
Line has trailing spaces. 18
Line has trailing spaces. 29
Unused Javadoc tag. 30
Redundant 'public' modifier. 33
Line has trailing spaces. 34

org/galaxy/computing/Installable.java

Violation Message Line
Line has trailing spaces. 4
Line has trailing spaces. 5
Line has trailing spaces. 6
Line has trailing spaces. 7
Line has trailing spaces. 12
Line has trailing spaces. 15
Line is longer than 80 characters (found 88). 16
Redundant 'public' modifier. 19
Redundant throws: 'InstallationException' is unchecked exception. 19
Line has trailing spaces. 23
Line is longer than 80 characters (found 88). 24
Redundant 'public' modifier. 27
Redundant throws: 'InstallationException' is unchecked exception. 27
Line has trailing spaces. 28

org/galaxy/computing/InstallationException.java

Violation Message Line
Missing a Javadoc comment. 12
Line has trailing spaces. 13
Line has trailing spaces. 18
Line has trailing spaces. 26
Line has trailing spaces. 27
Parameter message should be final. 34
Line has trailing spaces. 39
Line has trailing spaces. 42
Line has trailing spaces. 46
Parameter cause should be final. 50
Parameter message should be final. 67
Parameter cause should be final. 67
Line has trailing spaces. 70

org/galaxy/computing/Parameters.java

Violation Message Line
Line has trailing spaces. 4
Line is longer than 80 characters (found 81). 4
Line has trailing spaces. 6
Unknown tag 'sicne'. 8
Missing a Javadoc comment. 12
Line has trailing spaces. 17
Line has trailing spaces. 21
Line has trailing spaces. 22
Line has trailing spaces. 24
Line has trailing spaces. 26
Line has trailing spaces. 28
Line has trailing spaces. 30
Line has trailing spaces. 34
Line has trailing spaces. 36
Line has trailing spaces. 40

org/galaxy/computing/Processable.java

Violation Message Line
Unused import - java.io.ObjectOutputStream. 7
Line has trailing spaces. 13
Line has trailing spaces. 14
Missing a Javadoc comment. 21
Line has trailing spaces. 22
Missing a Javadoc comment. 24
Line has trailing spaces. 25
Missing a Javadoc comment. 27
Missing a Javadoc comment. 30
Missing a Javadoc comment. 33
Line has trailing spaces. 34
Missing a Javadoc comment. 36
Line has trailing spaces. 37
Missing a Javadoc comment. 39
Missing a Javadoc comment. 50
Parameter processable should be final. 50
Line has trailing spaces. 57
Missing a Javadoc comment. 58
Parameter data should be final. 58
'data' hides a field. 58
Line has trailing spaces. 61
Missing a Javadoc comment. 62
Missing a Javadoc comment. 66
Parameter data should be final. 66
'data' hides a field. 66
Missing a Javadoc comment. 70
Parameter key should be final. 70
Parameter value should be final. 70
Line has trailing spaces. 72
Line has trailing spaces. 73
Missing a Javadoc comment. 74
Parameter key should be final. 74
Parameter value should be final. 74
Line has trailing spaces. 76
Line has trailing spaces. 77
Missing a Javadoc comment. 78
Parameter key should be final. 78
Parameter value should be final. 78
Line has trailing spaces. 80
Line has trailing spaces. 81
Missing a Javadoc comment. 82
Parameter key should be final. 82
Parameter value should be final. 82
Line has trailing spaces. 84
Line has trailing spaces. 85
Missing a Javadoc comment. 86
Parameter key should be final. 86
Missing a Javadoc comment. 90
Parameter key should be final. 90
Line has trailing spaces. 92
Avoid inline conditionals. 93
Method 'removeTextField' is not designed for extension - needs to be abstract, final or empty. 96
Missing a Javadoc comment. 96
Parameter key should be final. 96
Method 'removeLongField' is not designed for extension - needs to be abstract, final or empty. 100
Missing a Javadoc comment. 100
Parameter key should be final. 100
Method 'removeIntField' is not designed for extension - needs to be abstract, final or empty. 104
Missing a Javadoc comment. 104
Parameter key should be final. 104
Line has trailing spaces. 107
Missing a Javadoc comment. 108
Parameter key should be final. 108
Should use uppercase 'L'. 111
Missing a Javadoc comment. 117
Parameter key should be final. 117
Missing a Javadoc comment. 122
Parameter key should be final. 122
Missing a Javadoc comment. 126
Parameter key should be final. 126
Missing a Javadoc comment. 130
Parameter key should be final. 130
Line has trailing spaces. 133
Missing a Javadoc comment. 134
Parameter key should be final. 134
Line has trailing spaces. 137
Method 'writeExternal' is not designed for extension - needs to be abstract, final or empty. 138
Parameter out should be final. 139
Method 'readExternal' is not designed for extension - needs to be abstract, final or empty. 174
Line is longer than 80 characters (found 89). 175
Parameter in should be final. 175
Line has trailing spaces. 204

org/galaxy/computing/Processor.java

Violation Message Line
Line has trailing spaces. 7
Line is longer than 80 characters (found 87). 12
Type Javadoc comment is missing an @param <P> tag. 12
Line has trailing spaces. 13
Line has trailing spaces. 16
Line is longer than 80 characters (found 123). 18
Line is longer than 80 characters (found 85). 19
Redundant 'public' modifier. 22
Line has trailing spaces. 23
Line has trailing spaces. 25
Line is longer than 80 characters (found 83). 25
Line has trailing spaces. 26
Line is longer than 80 characters (found 84). 27
Redundant 'public' modifier. 30
Line has trailing spaces. 31

org/galaxy/computing/RemoteObservable.java

Violation Message Line
Line has trailing spaces. 9
Line has trailing spaces. 17
Redundant 'public' modifier. 21
Line has trailing spaces. 22

org/galaxy/computing/RemoteObserver.java

Violation Message Line
Line has trailing spaces. 8
Line has trailing spaces. 10
Redundant 'public' modifier. 23
Line has trailing spaces. 24

org/galaxy/computing/Worker.java

Violation Message Line
Line has trailing spaces. 11
Type Javadoc comment is missing an @param <P> tag. 15
Line has trailing spaces. 20
Redundant 'public' modifier. 25
Line has trailing spaces. 26
Line has trailing spaces. 29
Redundant 'public' modifier. 34
Line has trailing spaces. 35
Line has trailing spaces. 38
Line has trailing spaces. 44
Line has trailing spaces. 45
Expected an @return tag. 46
Line has trailing spaces. 46
Redundant 'public' modifier. 46
Expected @param tag for 'processables'. 46
Expected @throws tag for 'ProcessingException'. 47
Line has trailing spaces. 48

org/galaxy/computing/boot/Bootable.java

Violation Message Line
File does not end with a newline. 0
Line is longer than 80 characters (found 86). 19
Parameter parameters should be final. 42
'parameters' hides a field. 42
Line is longer than 80 characters (found 90). 43

org/galaxy/computing/boot/BootableSystem.java

Violation Message Line
File does not end with a newline. 0
First sentence should end with a period. 18
First sentence should end with a period. 26
Line is longer than 80 characters (found 87). 31
Name 'logger' must match pattern '^[A-Z][A-Z0-9]*(_[A-Z0-9]+)*$'. 31
Line has trailing spaces. 32
Variable 'context' must be private and have accessor methods. 55
Variable 'uuid' must be private and have accessor methods. 62
Variable 'domain' must be private and have accessor methods. 72
Parameter parameters should be final. 80
Method 'initialize' is not designed for extension - needs to be abstract, final or empty. 101
Parameter ctx should be final. 103
Method 'locateSharedVolume' is not designed for extension - needs to be abstract, final or empty. 129
Parameter label should be final. 129
Line has trailing spaces. 144
Line has trailing spaces. 149
Method 'lookup' is not designed for extension - needs to be abstract, final or empty. 152
Expected @param tag for '<T>'. 152
Parameter clazz should be final. 152
Parameter params should be final. 152
Line has trailing spaces. 155
Line has trailing spaces. 166
Line is longer than 80 characters (found 92). 169
Method 'lookup' is not designed for extension - needs to be abstract, final or empty. 169
Expected @param tag for '<T>'. 169
Parameter lookupDomain should be final. 169
Parameter clazz should be final. 169
Parameter params should be final. 169
Method 'initStubDirector' is not designed for extension - needs to be abstract, final or empty. 180
Missing a Javadoc comment. 180
Parameter clazz should be final. 180
'{' should be on the previous line. 182

org/galaxy/computing/boot/package-info.java

Violation Message Line
File does not end with a newline. 0
Line has trailing spaces. 3

org/galaxy/computing/dataset/AbstractDataSet.java

Violation Message Line
File does not end with a newline. 0
Unused import - java.rmi.UnknownHostException. 6
Line is longer than 80 characters (found 135). 32
Type Javadoc comment is missing an @param <P> tag. 32
Missing a Javadoc comment. 34
Missing a Javadoc comment. 35
Missing a Javadoc comment. 36
Missing a Javadoc comment. 37
Missing a Javadoc comment. 38
Missing a Javadoc comment. 39
Missing a Javadoc comment. 40
Missing a Javadoc comment. 41
Line is longer than 80 characters (found 88). 44
Missing a Javadoc comment. 44
Name 'logger' must match pattern '^[A-Z][A-Z0-9]*(_[A-Z0-9]+)*$'. 44
Line has trailing spaces. 45
Missing a Javadoc comment. 54
Missing a Javadoc comment. 55
Missing a Javadoc comment. 56
Missing a Javadoc comment. 57
Missing a Javadoc comment. 58
Missing a Javadoc comment. 59
Missing a Javadoc comment. 60
Missing a Javadoc comment. 61
Missing a Javadoc comment. 62
Missing a Javadoc comment. 63
Missing a Javadoc comment. 65
Parameter parameters should be final. 65
Should use uppercase 'L'. 69
Line is longer than 80 characters (found 84). 74
Line is longer than 80 characters (found 82). 77
Method 'getDatasetName' is not designed for extension - needs to be abstract, final or empty. 83
Missing a Javadoc comment. 83
Unused @param tag for 'ctx'. 90
Unused @throws tag for 'UnknownHostException'. 91
Method 'initialize' is not designed for extension - needs to be abstract, final or empty. 95
'10000' is a magic number. 95
Parameter context should be final. 98
Expected @param tag for 'context'. 98
Method 'initialize' is not designed for extension - needs to be abstract, final or empty. 102
Line is longer than 80 characters (found 96). 108
Line is longer than 80 characters (found 84). 115
Line is longer than 80 characters (found 88). 117
Line is longer than 80 characters (found 95). 124
Method 'run' is not designed for extension - needs to be abstract, final or empty. 133
'1000l' is a magic number. 137
Should use uppercase 'L'. 137
'1000000000l' is a magic number. 144
Should use uppercase 'L'. 144
Line is longer than 80 characters (found 90). 150
Method 'startup' is not designed for extension - needs to be abstract, final or empty. 163
Missing a Javadoc comment. 163
Method 'getName' is not designed for extension - needs to be abstract, final or empty. 172
Method 'getSignature' is not designed for extension - needs to be abstract, final or empty. 177
Method 'take' is not designed for extension - needs to be abstract, final or empty. 182
Parameter batchSize should be final. 183
Redundant throws: 'RemoteException' is subclass of 'IOException'. 183
Method 'put' is not designed for extension - needs to be abstract, final or empty. 193
Parameter entries should be final. 194
Redundant throws: 'RemoteException' is subclass of 'IOException'. 194
Method 'shutdown' is not designed for extension - needs to be abstract, final or empty. 204
Missing a Javadoc comment. 204
Method 'toString' is not designed for extension - needs to be abstract, final or empty. 210
Line is longer than 80 characters (found 94). 212
Method 'setEmpty' is not designed for extension - needs to be abstract, final or empty. 215
Missing a Javadoc comment. 215
Parameter value should be final. 215
Line is longer than 80 characters (found 88). 225
Method 'isEmpty' is not designed for extension - needs to be abstract, final or empty. 234
Missing a Javadoc comment. 234
Method 'notifyObservers' is not designed for extension - needs to be abstract, final or empty. 238
Method 'getObserverDomain' is not designed for extension - needs to be abstract, final or empty. 261
Missing a Javadoc comment. 261
Missing a Javadoc comment. 265
Method 'getLocalPath' is not designed for extension - needs to be abstract, final or empty. 267

org/galaxy/computing/dataset/CacheableDataSet.java

Violation Message Line
File does not end with a newline. 0
First sentence should end with a period. 16
Line is longer than 80 characters (found 90). 22
Type Javadoc comment is missing an @param <P> tag. 22
Line is longer than 80 characters (found 85). 24
Missing a Javadoc comment. 24
Name 'logger' must match pattern '^[A-Z][A-Z0-9]*(_[A-Z0-9]+)*$'. 24
Line has trailing spaces. 25
Missing a Javadoc comment. 40
Missing a Javadoc comment. 41
Name 'cache_size' must match pattern '^[a-z][a-zA-Z0-9]*$'. 41
Missing a Javadoc comment. 42
Missing a Javadoc comment. 44
Parameter parameters should be final. 44
Method 'take' is not designed for extension - needs to be abstract, final or empty. 54
Parameter batchSize should be final. 55
Redundant throws: 'RemoteException' is subclass of 'IOException'. 55
Method 'put' is not designed for extension - needs to be abstract, final or empty. 89
Parameter entries should be final. 90
Redundant throws: 'RemoteException' is subclass of 'IOException'. 90
Method 'setEmpty' is not designed for extension - needs to be abstract, final or empty. 112
Parameter value should be final. 113
Method 'shutdown' is not designed for extension - needs to be abstract, final or empty. 121
Line has trailing spaces. 126

org/galaxy/computing/dataset/ProcessableDataStorage.java

Violation Message Line
File does not end with a newline. 0
Line is longer than 80 characters (found 82). 19
Type Javadoc comment is missing an @param <P> tag. 19
Missing a Javadoc comment. 22
Name 'EMPTY_ARRAY' must match pattern '^[a-z][a-zA-Z0-9]*$'. 22
Line has trailing spaces. 23
Missing a Javadoc comment. 25
Missing a Javadoc comment. 28
Line has trailing spaces. 29
Missing a Javadoc comment. 31
Line has trailing spaces. 32
Line has trailing spaces. 34
Line has trailing spaces. 36
Line is longer than 80 characters (found 104). 39
Parameter directory should be final. 39
'directory' hides a field. 39
Expected @param tag for 'directory'. 39
Parameter chunkSize should be final. 39
Parameter gzipped should be final. 39
Expected @param tag for 'gzipped'. 39
Expected @throws tag for 'IOException'. 39
Line is longer than 80 characters (found 91). 41
Line has trailing spaces. 43
Line has trailing spaces. 47
Line has trailing spaces. 49
Parameter type should be final. 51
Line has trailing spaces. 54
Method 'load' is not designed for extension - needs to be abstract, final or empty. 55
Parameter batchSize should be final. 56
Line has trailing spaces. 60
Line has trailing spaces. 65
Method 'isEmpty' is not designed for extension - needs to be abstract, final or empty. 68
Line has trailing spaces. 75
Method 'save' is not designed for extension - needs to be abstract, final or empty. 76
Parameter processables should be final. 77
Method 'flush' is not designed for extension - needs to be abstract, final or empty. 87
Line has trailing spaces. 91
Method 'close' is not designed for extension - needs to be abstract, final or empty. 92
Line has trailing spaces. 98
Missing a Javadoc comment. 99
Parameter size should be final. 99
Line has trailing spaces. 102
'cast' is not followed by whitespace. 107
Line has trailing spaces. 119
Missing a Javadoc comment. 120
Line is longer than 80 characters (found 91). 122
Line has trailing spaces. 125

org/galaxy/computing/dataset/Storage.java

Violation Message Line
Type Javadoc comment is missing an @param <T> tag. 12
Missing a Javadoc comment. 14
Redundant 'public' modifier. 14
Line has trailing spaces. 15
Missing a Javadoc comment. 16
Redundant 'public' modifier. 16
Line has trailing spaces. 17
Missing a Javadoc comment. 18
Redundant 'public' modifier. 18
Line has trailing spaces. 19
Missing a Javadoc comment. 20
Redundant 'public' modifier. 20
Line has trailing spaces. 21

org/galaxy/computing/dataset/io/ChunkInputStream.java

Violation Message Line
Line is longer than 80 characters (found 92). 13
Missing a Javadoc comment. 15
Missing a Javadoc comment. 16
Missing a Javadoc comment. 17
Missing a Javadoc comment. 18
Line is longer than 80 characters (found 120). 20
Missing a Javadoc comment. 20
Parameter stream should be final. 20
Parameter chunk should be final. 20
'chunk' hides a field. 20
Parameter threshold should be final. 20
'threshold' hides a field. 20
Parameter file should be final. 20
'file' hides a field. 20
Method 'getChunk' is not designed for extension - needs to be abstract, final or empty. 31
Missing a Javadoc comment. 31
Method 'closeChunk' is not designed for extension - needs to be abstract, final or empty. 35
Missing a Javadoc comment. 35
Method 'getCount' is not designed for extension - needs to be abstract, final or empty. 39
Method 'incrementCount' is not designed for extension - needs to be abstract, final or empty. 44
Method 'resetCount' is not designed for extension - needs to be abstract, final or empty. 49
Method 'hasNext' is not designed for extension - needs to be abstract, final or empty. 54
Method 'getThreshold' is not designed for extension - needs to be abstract, final or empty. 59
Line has trailing spaces. 63

org/galaxy/computing/dataset/io/ChunkOutputStream.java

Violation Message Line
Line is longer than 80 characters (found 94). 13
Missing a Javadoc comment. 15
Missing a Javadoc comment. 16
Missing a Javadoc comment. 17
Missing a Javadoc comment. 18
Line is longer than 80 characters (found 122). 20
Missing a Javadoc comment. 20
Parameter stream should be final. 20
Parameter chunk should be final. 20
'chunk' hides a field. 20
Parameter threshold should be final. 20
'threshold' hides a field. 20
Parameter file should be final. 20
'file' hides a field. 20
Method 'getChunk' is not designed for extension - needs to be abstract, final or empty. 31
Missing a Javadoc comment. 31
Line has trailing spaces. 34
Method 'closeChunk' is not designed for extension - needs to be abstract, final or empty. 35
Missing a Javadoc comment. 35
Line has trailing spaces. 39
Method 'getCount' is not designed for extension - needs to be abstract, final or empty. 40
Method 'incrementCount' is not designed for extension - needs to be abstract, final or empty. 45
Method 'resetCount' is not designed for extension - needs to be abstract, final or empty. 50
Method 'hasNext' is not designed for extension - needs to be abstract, final or empty. 55
Method 'getThreshold' is not designed for extension - needs to be abstract, final or empty. 60
Line has trailing spaces. 64

org/galaxy/computing/dataset/io/ChunkUtils.java

Violation Message Line
Utility classes should not have a public or default constructor. 21
Line has trailing spaces. 26
Line has trailing spaces. 35
Line has trailing spaces. 39
Line has trailing spaces. 45
Line has trailing spaces. 47
Line has trailing spaces. 50
Line has trailing spaces. 53
Line is longer than 80 characters (found 100). 54
Line has trailing spaces. 55
Line has trailing spaces. 56
Line has trailing spaces. 58
Missing a Javadoc comment. 58
Missing a Javadoc comment. 61
Name 'rnd' must match pattern '^[A-Z][A-Z0-9]*(_[A-Z0-9]+)*$'. 61
Line has trailing spaces. 62
Missing a Javadoc comment. 63
Line has trailing spaces. 64
First sentence should end with a period. 65
Line has trailing spaces. 69
Expected an @return tag. 71
Parameter directory should be final. 71
Expected @param tag for 'directory'. 71
Line is longer than 80 characters (found 147). 75
Missing a Javadoc comment. 84
Parameter directory should be final. 84
Parameter filename should be final. 84
Line is longer than 80 characters (found 84). 88
Missing a Javadoc comment. 88
Parameter directory should be final. 88
Parameter filename should be final. 88
Parameter busy should be final. 88
Line is longer than 80 characters (found 97). 90
Line is longer than 80 characters (found 97). 92
Line is longer than 80 characters (found 100). 96
Missing a Javadoc comment. 96
Parameter directory should be final. 96
Parameter filename should be final. 96
Parameter writes should be final. 96
Line is longer than 80 characters (found 98). 97
Line is longer than 80 characters (found 86). 104
Missing a Javadoc comment. 104
Parameter directory should be final. 104
Parameter filename should be final. 104
Line is longer than 80 characters (found 96). 105
Line is longer than 80 characters (found 81). 112
Missing a Javadoc comment. 112
Parameter directory should be final. 112
Parameter chunk should be final. 112
Line is longer than 80 characters (found 86). 113
Line is longer than 80 characters (found 86). 114
Line is longer than 80 characters (found 81). 116
Line is longer than 80 characters (found 81). 119
Missing a Javadoc comment. 119
Parameter directory should be final. 119
Parameter chunk should be final. 119
Line is longer than 80 characters (found 86). 120
Line is longer than 80 characters (found 86). 121
Line is longer than 80 characters (found 81). 123
Line has trailing spaces. 125
Line has trailing spaces. 127
Line has trailing spaces. 129
Line is longer than 80 characters (found 82). 133
Parameter entry should be final. 136
Line is longer than 80 characters (found 92). 137
Line has trailing spaces. 139
Line has trailing spaces. 141

org/galaxy/computing/dataset/io/CountingStream.java

Violation Message Line
Missing a Javadoc comment. 10
Redundant 'public' modifier. 10
Line has trailing spaces. 11
Missing a Javadoc comment. 12
Redundant 'public' modifier. 12
Missing a Javadoc comment. 14
Redundant 'public' modifier. 14
Missing a Javadoc comment. 16
Redundant 'public' modifier. 16
Missing a Javadoc comment. 18
Redundant 'public' modifier. 18
Line has trailing spaces. 19

org/galaxy/computing/dataset/io/ObjectStreamProvider.java

Violation Message Line
File does not end with a newline. 0
Line has trailing spaces. 40
Missing a Javadoc comment. 42
Missing a Javadoc comment. 45
Line has trailing spaces. 46
Line has trailing spaces. 48
Missing a Javadoc comment. 48
Line has trailing spaces. 50
Line has trailing spaces. 52
Missing a Javadoc comment. 52
Line has trailing spaces. 54
Line has trailing spaces. 56
Missing a Javadoc comment. 56
Line has trailing spaces. 58
Line has trailing spaces. 60
Missing a Javadoc comment. 60
Missing a Javadoc comment. 64
Line has trailing spaces. 65
Missing a Javadoc comment. 67
Line has trailing spaces. 68
Missing a Javadoc comment. 70
Line has trailing spaces. 71
Missing a Javadoc comment. 73
Line has trailing spaces. 74
Missing a Javadoc comment. 76
Line has trailing spaces. 77
Missing a Javadoc comment. 78
Line is longer than 80 characters (found 81). 80
Missing a Javadoc comment. 80
Parameter directory should be final. 80
'directory' hides a field. 80
Parameter chunkSize should be final. 80
'chunkSize' hides a field. 80
Parameter gzipped should be final. 80
'gzipped' hides a field. 80
Line is longer than 80 characters (found 102). 91
Parameter directory should be final. 91
'directory' hides a field. 91
Parameter chunkSize should be final. 91
'chunkSize' hides a field. 91
Parameter maxOpenedChunks should be final. 91
'maxOpenedChunks' hides a field. 91
Expected @param tag for 'maxOpenedChunks'. 91
Parameter gzipped should be final. 91
'gzipped' hides a field. 91
Expected @param tag for 'gzipped'. 91
Method 'pollOutputStream' is not designed for extension - needs to be abstract, final or empty. 99
Missing a Javadoc comment. 99
Method 'pollInputStream' is not designed for extension - needs to be abstract, final or empty. 122
Missing a Javadoc comment. 122
Avoid inline conditionals. 137
Method 'getDirectory' is not designed for extension - needs to be abstract, final or empty. 149
Method 'validateState' is not designed for extension - needs to be abstract, final or empty. 160
Line is longer than 80 characters (found 98). 162
Method 'flush' is not designed for extension - needs to be abstract, final or empty. 166
Method 'close' is not designed for extension - needs to be abstract, final or empty. 179
Method 'waitForStream' is not designed for extension - needs to be abstract, final or empty. 203
Parameter condition should be final. 203
Expected @param tag for 'condition'. 203
'5' is a magic number. 205
Must have at least one statement. 205
Missing a Javadoc comment. 216
Must have at least one statement. 227
Line is longer than 80 characters (found 141). 238
'8192' is a magic number. 238
Line is longer than 80 characters (found 107). 240
Missing a Javadoc comment. 250
Line is longer than 80 characters (found 113). 251
Line is longer than 80 characters (found 83). 254
Line is longer than 80 characters (found 84). 265
Must have at least one statement. 274
Line is longer than 80 characters (found 83). 282
Line is longer than 80 characters (found 135). 285
'8192' is a magic number. 285
Line is longer than 80 characters (found 108). 287
Line is longer than 80 characters (found 97). 299
Missing a Javadoc comment. 299
Parameter stream should be final. 299
Parameter force should be final. 299
Line is longer than 80 characters (found 93). 304
Missing a Javadoc comment. 315
Parameter sis should be final. 315
Line is longer than 80 characters (found 116). 323
Line is longer than 80 characters (found 85). 325
Missing a Javadoc comment. 341
Line is longer than 80 characters (found 137). 343
Missing a Javadoc comment. 343
Parameter stream should be final. 343
Parameter chunk should be final. 343
Parameter maxWrites should be final. 343
Parameter file should be final. 343
Missing a Javadoc comment. 353
Line is longer than 80 characters (found 134). 355
Missing a Javadoc comment. 355
Parameter stream should be final. 355
Parameter chunk should be final. 355
Parameter maxReads should be final. 355
Parameter file should be final. 355

org/galaxy/computing/dataset/io/package-info.java

Violation Message Line
File does not end with a newline. 0
Line has trailing spaces. 3

org/galaxy/computing/dataset/package-info.java

Violation Message Line
Line has trailing spaces. 3

org/galaxy/computing/package-info.java

Violation Message Line
Line has trailing spaces. 3

org/galaxy/computing/processor/AbstractContextAwareProcessor.java

Violation Message Line
Line is longer than 80 characters (found 129). 13
Type Javadoc comment is missing an @param <P> tag. 13
First sentence should end with a period. 22
Variable 'ctx' must be private and have accessor methods. 28
First sentence should end with a period. 30
Variable 'domain' must be private and have accessor methods. 36
Parameter parameters should be final. 53
Method 'setContext' is not designed for extension - needs to be abstract, final or empty. 57
Parameter domain should be final. 58
'domain' hides a field. 58
Parameter ctx should be final. 58
'ctx' hides a field. 58
Method 'getContext' is not designed for extension - needs to be abstract, final or empty. 63
Method 'getDomain' is not designed for extension - needs to be abstract, final or empty. 68

org/galaxy/computing/processor/AbstractProcessor.java

Violation Message Line
File does not end with a newline. 0
Line is longer than 80 characters (found 123). 20
Type Javadoc comment is missing an @param <P> tag. 20
First sentence should end with a period. 22
Line is longer than 80 characters (found 92). 34
Name 'logger' must match pattern '^[A-Z][A-Z0-9]*(_[A-Z0-9]+)*$'. 34
Parameter parameters should be final. 61
Method 'install' is not designed for extension - needs to be abstract, final or empty. 70
Method 'setDataSource' is not designed for extension - needs to be abstract, final or empty. 87
Parameter dataSource should be final. 88
'dataSource' hides a field. 88
Method 'getDataSource' is not designed for extension - needs to be abstract, final or empty. 98
Method 'uninstall' is not designed for extension - needs to be abstract, final or empty. 109
Parameter out should be final. 115
Line is longer than 80 characters (found 89). 120
Parameter in should be final. 120
Method 'splitParameters' is not designed for extension - needs to be abstract, final or empty. 131
Parameter parameters should be final. 131
Method 'toString' is not designed for extension - needs to be abstract, final or empty. 140

org/galaxy/computing/processor/BenchmarkedProcessor.java

Violation Message Line
Line is longer than 80 characters (found 108). 11
Type Javadoc comment is missing an @param <P> tag. 11
First sentence should end with a period. 13
Missing a Javadoc comment. 38
Missing a Javadoc comment. 39
Missing a Javadoc comment. 43
Should use uppercase 'L'. 43
Missing a Javadoc comment. 46
Should use uppercase 'L'. 46
Missing a Javadoc comment. 49
Variable 'enableBenchmark' must be private and have accessor methods. 49
Missing a Javadoc comment. 60
Parameter parameters should be final. 60
Line is longer than 80 characters (found 103). 65
Method 'benchmarkStart' is not designed for extension - needs to be abstract, final or empty. 69
Missing a Javadoc comment. 69
Method 'benchmarkStop' is not designed for extension - needs to be abstract, final or empty. 75
Missing a Javadoc comment. 75
Parameter processable should be final. 75
Line is longer than 80 characters (found 81). 84
Line is longer than 80 characters (found 82). 85
Method 'getBenchmark' is not designed for extension - needs to be abstract, final or empty. 90
Missing a Javadoc comment. 90
Parameter clazz should be final. 90
Parameter processable should be final. 90
Method 'getBenchmark' is not designed for extension - needs to be abstract, final or empty. 94
Missing a Javadoc comment. 94
Parameter clazz should be final. 94
Parameter processable should be final. 94
Should use uppercase 'L'. 99
Method 'getBenchmarkDataSize' is not designed for extension - needs to be abstract, final or empty. 102
Missing a Javadoc comment. 102
Parameter clazz should be final. 102
Parameter processable should be final. 102
Should use uppercase 'L'. 107
Missing a Javadoc comment. 110
Parameter processable should be final. 110

org/galaxy/computing/processor/BenchmarkedProcessorReporter.java

Violation Message Line
Line is longer than 80 characters (found 98). 17
Type Javadoc comment is missing an @param <P> tag. 17
First sentence should end with a period. 19
Missing a Javadoc comment. 63
Missing a Javadoc comment. 66
Missing a Javadoc comment. 69
Missing a Javadoc comment. 72
Missing a Javadoc comment. 83
Parameter parameters should be final. 83
Line is longer than 80 characters (found 88). 88
Method 'process' is not designed for extension - needs to be abstract, final or empty. 100
Parameter processable should be final. 101
Should use uppercase 'L'. 105
Should use uppercase 'L'. 115
Method 'install' is not designed for extension - needs to be abstract, final or empty. 128
Redundant throws: 'InstallationException' is unchecked exception. 129
Line is longer than 80 characters (found 106). 141
Method 'uninstall' is not designed for extension - needs to be abstract, final or empty. 145
Redundant throws: 'InstallationException' is unchecked exception. 146
Method 'complete' is not designed for extension - needs to be abstract, final or empty. 155
Method 'writeExternal' is not designed for extension - needs to be abstract, final or empty. 162
Parameter out should be final. 163
Method 'readExternal' is not designed for extension - needs to be abstract, final or empty. 179
Line is longer than 80 characters (found 89). 180
Parameter in should be final. 180
'cast' is not followed by whitespace. 182
'=' is not preceded with whitespace. 186
'=' is not followed by whitespace. 186
'<' is not preceded with whitespace. 186
'<' is not followed by whitespace. 186
Method 'toString' is not designed for extension - needs to be abstract, final or empty. 193
Missing a Javadoc comment. 198
Parameter args should be final. 198
Line is longer than 80 characters (found 91). 199

org/galaxy/computing/processor/DevNull.java

Violation Message Line
File does not end with a newline. 0
Type Javadoc comment is missing an @param <P> tag. 15
First sentence should end with a period. 17
Missing a Javadoc comment. 24
Missing a Javadoc comment. 28
Parameter parameters should be final. 28
Unused @param tag for 'document'. 35
Expected an @return tag. 38
Method 'process' is not designed for extension - needs to be abstract, final or empty. 38
Parameter processable should be final. 39
Expected @param tag for 'processable'. 39
Expected @throws tag for 'ProcessingException'. 39
Inner assignments should be avoided. 40
Parameter out should be final. 49
Line is longer than 80 characters (found 89). 54
Parameter in should be final. 54
Method 'toString' is not designed for extension - needs to be abstract, final or empty. 58

org/galaxy/computing/processor/Identity.java

Violation Message Line
File does not end with a newline. 0
Type Javadoc comment is missing an @param <P> tag. 15
Missing a Javadoc comment. 24
Missing a Javadoc comment. 28
Parameter parameters should be final. 28
Method 'process' is not designed for extension - needs to be abstract, final or empty. 40
Parameter processable should be final. 41
Expected @param tag for 'processable'. 41
Parameter out should be final. 46
Line is longer than 80 characters (found 89). 51
Parameter in should be final. 51
Method 'toString' is not designed for extension - needs to be abstract, final or empty. 60

org/galaxy/computing/processor/MultiProcessor.java

Violation Message Line
Unused import - org.galaxy.computing.Installable. 13
Line is longer than 80 characters (found 93). 26
Type Javadoc comment is missing an @param <P> tag. 26
Missing a Javadoc comment. 29
Missing a Javadoc comment. 32
Missing a Javadoc comment. 35
Missing a Javadoc comment. 37
Missing a Javadoc comment. 41
Parameter parameters should be final. 41
Method 'register' is not designed for extension - needs to be abstract, final or empty. 55
Parameter classes should be final. 55
'classes' hides a field. 55
Line is longer than 80 characters (found 96). 66
Line is longer than 80 characters (found 136). 67
Line is longer than 80 characters (found 87). 69
Line is longer than 80 characters (found 83). 73
Line is longer than 80 characters (found 86). 77
Line is longer than 80 characters (found 84). 78
Line is longer than 80 characters (found 81). 82
Line is longer than 80 characters (found 90). 85
Line is longer than 80 characters (found 84). 87
Line is longer than 80 characters (found 84). 89
Line is longer than 80 characters (found 84). 91
Line is longer than 80 characters (found 84). 93
Method 'install' is not designed for extension - needs to be abstract, final or empty. 106
Redundant throws: 'InstallationException' is unchecked exception. 107
Method 'uninstall' is not designed for extension - needs to be abstract, final or empty. 121
Redundant throws: 'InstallationException' is unchecked exception. 122
Unused @param tag for 'document'. 132
Expected an @return tag. 135
Method 'process' is not designed for extension - needs to be abstract, final or empty. 135
Parameter processable should be final. 136
Expected @param tag for 'processable'. 136
Expected @throws tag for 'ProcessingException'. 137
Inner assignments should be avoided. 141
Line is longer than 80 characters (found 86). 145
Method 'complete' is not designed for extension - needs to be abstract, final or empty. 151
Method 'writeExternal' is not designed for extension - needs to be abstract, final or empty. 158
Parameter out should be final. 159
Method 'readExternal' is not designed for extension - needs to be abstract, final or empty. 168
Line is longer than 80 characters (found 89). 169
Parameter in should be final. 169
Method 'toString' is not designed for extension - needs to be abstract, final or empty. 179

org/galaxy/computing/processor/ProcessingException.java

Violation Message Line
Line has trailing spaces. 15
Line has trailing spaces. 19
Unused @param tag for 'processor'. 33
Parameter source should be final. 37
Expected @param tag for 'source'. 37
Parameter cause should be final. 54
Line is longer than 80 characters (found 87). 69
Parameter processor should be final. 69
Parameter cause should be final. 69
Line has trailing spaces. 72

org/galaxy/computing/processor/package-info.java

Violation Message Line
Line has trailing spaces. 2
Line is longer than 80 characters (found 93). 2
Line has trailing spaces. 4

org/galaxy/computing/utils/DistantParameterBuilder.java

Violation Message Line
Line has trailing spaces. 10
Missing a Javadoc comment. 17
Line has trailing spaces. 18
Missing a Javadoc comment. 20
Line has trailing spaces. 21
Line has trailing spaces. 24
Line has trailing spaces. 30
Method 'appaned' is not designed for extension - needs to be abstract, final or empty. 31
Missing a Javadoc comment. 31
Parameter name should be final. 31
Parameter value should be final. 31
Line has trailing spaces. 35
Method 'appaned' is not designed for extension - needs to be abstract, final or empty. 36
Missing a Javadoc comment. 36
Parameter name should be final. 36
Parameter value should be final. 36
Line has trailing spaces. 39
Method 'appaned' is not designed for extension - needs to be abstract, final or empty. 40
Missing a Javadoc comment. 40
Parameter name should be final. 40
Parameter value should be final. 40
Line has trailing spaces. 43
Method 'appaned' is not designed for extension - needs to be abstract, final or empty. 44
Missing a Javadoc comment. 44
Parameter name should be final. 44
Parameter value should be final. 44
Line has trailing spaces. 47
Method 'build' is not designed for extension - needs to be abstract, final or empty. 48
Missing a Javadoc comment. 48
Missing a Javadoc comment. 52
Parameter name should be final. 52
Parameter value should be final. 52
Line has trailing spaces. 57
Missing a Javadoc comment. 58
Parameter name should be final. 58
Parameter value should be final. 58
Line has trailing spaces. 63
Missing a Javadoc comment. 64
Parameter name should be final. 64
Parameter value should be final. 64
Line has trailing spaces. 69
Missing a Javadoc comment. 70
Parameter name should be final. 70
Parameter value should be final. 70
Line has trailing spaces. 75

org/galaxy/computing/utils/DistantParameterDecorator.java

Violation Message Line
File does not end with a newline. 0
Line is longer than 80 characters (found 82). 18
Missing a Javadoc comment. 18
Missing a Javadoc comment. 21
Missing a Javadoc comment. 24
Missing a Javadoc comment. 26
Line is longer than 80 characters (found 98). 34
Parameter parameters should be final. 34
'parameters' hides a field. 34
Parameter multiValuesSeparator should be final. 34
'multiValuesSeparator' hides a field. 34
Expected @param tag for 'multiValuesSeparator'. 34
Line is longer than 80 characters (found 81). 40
Method 'getDistantParameters' is not designed for extension - needs to be abstract, final or empty. 45
Missing a Javadoc comment. 45
Method 'selectPrefixedParameters' is not designed for extension - needs to be abstract, final or empty. 49
Missing a Javadoc comment. 49
Parameter prefix should be final. 49
Method 'get' is not designed for extension - needs to be abstract, final or empty. 66
Missing a Javadoc comment. 66
Parameter name should be final. 66
Line is longer than 80 characters (found 83). 69
Method 'getAsArray' is not designed for extension - needs to be abstract, final or empty. 74
Missing a Javadoc comment. 74
Parameter name should be final. 74
Line is longer than 80 characters (found 83). 77
Method 'get' is not designed for extension - needs to be abstract, final or empty. 82
Missing a Javadoc comment. 82
Parameter name should be final. 82
Parameter defaultValue should be final. 82
Avoid inline conditionals. 84
Method 'getInteger' is not designed for extension - needs to be abstract, final or empty. 87
Missing a Javadoc comment. 87
Parameter name should be final. 87
Redundant throws: 'NumberFormatException' is unchecked exception. 87
Line is longer than 80 characters (found 83). 90
Line is longer than 80 characters (found 87). 95
Method 'getInteger' is not designed for extension - needs to be abstract, final or empty. 95
Missing a Javadoc comment. 95
Parameter name should be final. 95
Parameter defaultValue should be final. 95
Redundant throws: 'NumberFormatException' is unchecked exception. 95
Method 'getLong' is not designed for extension - needs to be abstract, final or empty. 103
Missing a Javadoc comment. 103
Parameter name should be final. 103
Redundant throws: 'NumberFormatException' is unchecked exception. 103
Line is longer than 80 characters (found 83). 106
Line is longer than 80 characters (found 86). 111
Method 'getLong' is not designed for extension - needs to be abstract, final or empty. 111
Missing a Javadoc comment. 111
Parameter name should be final. 111
Parameter defaultValue should be final. 111
Redundant throws: 'NumberFormatException' is unchecked exception. 111
Method 'getBoolean' is not designed for extension - needs to be abstract, final or empty. 119
Missing a Javadoc comment. 119
Parameter name should be final. 119
Redundant throws: 'NumberFormatException' is unchecked exception. 119
Line is longer than 80 characters (found 95). 124
Method 'getBoolean' is not designed for extension - needs to be abstract, final or empty. 124
Missing a Javadoc comment. 124
Parameter name should be final. 124
Parameter defaultValue should be final. 124
Redundant throws: 'NumberFormatException' is unchecked exception. 124

org/galaxy/computing/utils/DomainResolver.java

Violation Message Line
Parameter domain should be final. 21
Parameter clazz should be final. 21
Expected @param tag for '<T>'. 31
Parameter clazz should be final. 31
Expected an @return tag. 48
Parameter domain should be final. 48
Parameter object should be final. 48

org/galaxy/computing/utils/Lookup.java

Violation Message Line
Line is longer than 80 characters (found 126). 17
Missing a Javadoc comment. 17
Parameter domain should be final. 17
Parameter name should be final. 17
Parameter ctx should be final. 17
Parameter clazz should be final. 17
Parameter parameters should be final. 17
Line has trailing spaces. 18
'{' should be on the previous line. 19
Line has trailing spaces. 22
'cast' is not followed by whitespace. 23
Line has trailing spaces. 25
Missing a Javadoc comment. 26
Parameter ctx should be final. 26
Parameter reference should be final. 26
'{' should be on the previous line. 28
Line has trailing spaces. 31
Line is longer than 80 characters (found 113). 32
Missing a Javadoc comment. 32
Parameter domain should be final. 32
Parameter ctx should be final. 32
Parameter clazz should be final. 32
Parameter parameters should be final. 32
Line has trailing spaces. 33
'{' should be on the previous line. 34
Line has trailing spaces. 37
'cast' is not followed by whitespace. 38
Line has trailing spaces. 40
Line has trailing spaces. 41
Line is longer than 80 characters (found 177). 42
Missing a Javadoc comment. 42
Parameter domain should be final. 42
Parameter ctx should be final. 42
Parameter clazz should be final. 42
Parameter parameters should be final. 42
Line has trailing spaces. 46
Line is longer than 80 characters (found 131). 50
Missing a Javadoc comment. 50
Parameter domain should be final. 50
Parameter jInterface should be final. 50
Line is longer than 80 characters (found 162). 54
Missing a Javadoc comment. 54
Parameter domain should be final. 54
Parameter jInterface should be final. 54
Parameter parameters should be final. 54
Line is longer than 80 characters (found 97). 56
'{' is followed by whitespace. 56
Line has trailing spaces. 58

org/galaxy/computing/utils/NuggetUtils.java

Violation Message Line
Unused import - kernel.cluster.NuggetImpl. 4
Utility classes should not have a public or default constructor. 17
Line is longer than 80 characters (found 84). 20
Missing a Javadoc comment. 20
Name 'logger' must match pattern '^[A-Z][A-Z0-9]*(_[A-Z0-9]+)*$'. 20
Line is longer than 80 characters (found 103). 22
Missing a Javadoc comment. 22
Parameter domain should be final. 22
Parameter program should be final. 22
Parameter startConsole should be final. 22
Line is longer than 80 characters (found 122). 29
Missing a Javadoc comment. 29
Parameter nuggetName should be final. 29
Parameter domain should be final. 29
Parameter program should be final. 29
Parameter startConsole should be final. 29
Line is longer than 80 characters (found 86). 31
Line is longer than 80 characters (found 81). 42

org/galaxy/computing/utils/VolumeMarker.java

Violation Message Line
Line has trailing spaces. 23
Missing a Javadoc comment. 29
Line is longer than 80 characters (found 110). 30
Line is longer than 80 characters (found 98). 32
Missing a Javadoc comment. 32
Line is longer than 80 characters (found 100). 34
Missing a Javadoc comment. 34
Line has trailing spaces. 35
Missing a Javadoc comment. 36
Line has trailing spaces. 38
Missing a Javadoc comment. 39
Parameter ctx should be final. 39
Parameter label should be final. 39
Missing a Javadoc comment. 43
Parameter path should be final. 43
Line has trailing spaces. 46
Line has trailing spaces. 50
Line has trailing spaces. 53
Missing a Javadoc comment. 54
Parameter path should be final. 54
Line has trailing spaces. 62
First sentence should end with a period. 63
Line has trailing spaces. 64
Line has trailing spaces. 65
Parameter args should be final. 67
Line is longer than 80 characters (found 91). 69
Line is longer than 80 characters (found 81). 73
Line is longer than 80 characters (found 91). 74
Line has trailing spaces. 80

org/galaxy/computing/utils/package-info.java

Violation Message Line
Line has trailing spaces. 3

org/galaxy/computing/worker/AbstractWorker.java

Violation Message Line
File does not end with a newline. 0
Unused import - java.util.ArrayDeque. 8
Unused import - java.util.concurrent.locks.Lock. 15
Line is longer than 80 characters (found 184). 46
Type Javadoc comment is missing an @param <P> tag. 46
Line is longer than 80 characters (found 87). 49
Missing a Javadoc comment. 49
Name 'logger' must match pattern '^[A-Z][A-Z0-9]*(_[A-Z0-9]+)*$'. 49
Missing a Javadoc comment. 52
Missing a Javadoc comment. 53
Variable 'conditionEmptySource' must be private and have accessor methods. 53
Missing a Javadoc comment. 54
Variable 'conditionAnyTarget' must be private and have accessor methods. 54
Line is longer than 80 characters (found 85). 55
Missing a Javadoc comment. 55
Missing a Javadoc comment. 68
Missing a Javadoc comment. 69
Missing a Javadoc comment. 70
Missing a Javadoc comment. 71
Missing a Javadoc comment. 72
Missing a Javadoc comment. 73
Missing a Javadoc comment. 76
Missing a Javadoc comment. 78
Missing a Javadoc comment. 79
Missing a Javadoc comment. 83
Missing a Javadoc comment. 85
Missing a Javadoc comment. 88
Missing a Javadoc comment. 89
Missing a Javadoc comment. 90
Variable 'batchSize' must be private and have accessor methods. 90
Missing a Javadoc comment. 91
Missing a Javadoc comment. 92
Variable 'sourceDataSet' must be private and have accessor methods. 92
Missing a Javadoc comment. 93
Variable 'targetDataSet' must be private and have accessor methods. 93
Missing a Javadoc comment. 94
Variable 'targetDataSetStub' must be private and have accessor methods. 94
Missing a Javadoc comment. 96
Variable 'processor' must be private and have accessor methods. 96
Missing a Javadoc comment. 98
Variable 'notifications' must be private and have accessor methods. 98
Missing a Javadoc comment. 100
Variable 'lock' must be private and have accessor methods. 100
Missing a Javadoc comment. 102
Variable 'notified' must be private and have accessor methods. 102
Parameter parameters should be final. 109
Line is longer than 80 characters (found 81). 124
Line is longer than 80 characters (found 87). 134
Method 'initialize' is not designed for extension - needs to be abstract, final or empty. 143
'20000' is a magic number. 145
Parameter ctx should be final. 146
Method 'initialize' is not designed for extension - needs to be abstract, final or empty. 150
Method 'getAccepts' is not designed for extension - needs to be abstract, final or empty. 156
Method 'getProvides' is not designed for extension - needs to be abstract, final or empty. 161
Method 'run' is not designed for extension - needs to be abstract, final or empty. 166
Line is longer than 80 characters (found 81). 189
Line has trailing spaces. 200
Line has trailing spaces. 205
Method 'initProcessor' is not designed for extension - needs to be abstract, final or empty. 218
Missing a Javadoc comment. 218
Missing a Javadoc comment. 238
Missing a Javadoc comment. 240
Missing a Javadoc comment. 242
Missing a Javadoc comment. 244
Method 'getSourceDataSetDomain' is not designed for extension - needs to be abstract, final or empty. 246
Missing a Javadoc comment. 246
Method 'getTargetDataSetDomain' is not designed for extension - needs to be abstract, final or empty. 250
Missing a Javadoc comment. 250
Method 'completeBatch' is not designed for extension - needs to be abstract, final or empty. 254
Missing a Javadoc comment. 254
Method 'obtainSourceDataSet' is not designed for extension - needs to be abstract, final or empty. 264
Missing a Javadoc comment. 264
Line is longer than 80 characters (found 127). 278
Method 'obtainTargetDataSet' is not designed for extension - needs to be abstract, final or empty. 293
Missing a Javadoc comment. 293
Line is longer than 80 characters (found 121). 300
Method 'process' is not designed for extension - needs to be abstract, final or empty. 307
Parameter processables should be final. 308
Method 'processData' is not designed for extension - needs to be abstract, final or empty. 312
Missing a Javadoc comment. 312
Parameter processables should be final. 312
Method 'waitForData' is not designed for extension - needs to be abstract, final or empty. 330
Missing a Javadoc comment. 330
Line is longer than 80 characters (found 83). 331
Method 'update' is not designed for extension - needs to be abstract, final or empty. 355
Parameter source should be final. 356
Method 'shutdown' is not designed for extension - needs to be abstract, final or empty. 382
Method 'getDomain' is not designed for extension - needs to be abstract, final or empty. 396
Method 'getContext' is not designed for extension - needs to be abstract, final or empty. 401
Method 'writeExternal' is not designed for extension - needs to be abstract, final or empty. 406
Parameter out should be final. 407
Line is longer than 80 characters (found 135). 408
Method 'readExternal' is not designed for extension - needs to be abstract, final or empty. 411
Line is longer than 80 characters (found 89). 412
Parameter in should be final. 412
Line is longer than 80 characters (found 135). 413
Method 'toString' is not designed for extension - needs to be abstract, final or empty. 416
Line is longer than 80 characters (found 105). 418

org/galaxy/computing/worker/RemoteWorker.java

Violation Message Line
Line is longer than 80 characters (found 85). 16
Type Javadoc comment is missing an @param <P> tag. 16
Line is longer than 80 characters (found 85). 19
Missing a Javadoc comment. 19
Name 'logger' must match pattern '^[A-Z][A-Z0-9]*(_[A-Z0-9]+)*$'. 19
Parameter parameters should be final. 26
Expected an @return tag. 35
Method 'loadData' is not designed for extension - needs to be abstract, final or empty. 35
Method 'saveData' is not designed for extension - needs to be abstract, final or empty. 56
Parameter data should be final. 57
Expected @param tag for 'data'. 57

org/galaxy/computing/worker/package-info.java

Violation Message Line
File does not end with a newline. 0
Line has trailing spaces. 3