BasicDecider (SeqWare 1.1.2 API)

java.lang.Object
- net.sourceforge.seqware.pipeline.plugin.Plugin
- - net.sourceforge.seqware.pipeline.deciders.BasicDecider

All Implemented Interfaces:

DeciderInterface, PluginInterface
```
public class BasicDecider
extends Plugin
implements DeciderInterface
```
Author:

mtaschuk

Nested Class Summary

Nested Classes
Modifier and Type	Class and Description
`protected static class`	`BasicDecider.FILE_STATUS` These file statuses reflect the discussion at https://wiki.oicr.on.ca/display/SEQWARE/BasicDecider+logic
`protected static class`	`BasicDecider.PREVIOUS_RUN_STATUS` We care about three types of status, an outright fail, other (pending, running, submitted, etc.), and completed

Field Summary

Fields
Modifier and Type Field and Description

protected Random random
- Fields inherited from class net.sourceforge.seqware.pipeline.plugin.Plugin
  config, metadata, options, params, parser

Fields
Modifier and Type	Field and Description
`protected Random`	`random`

Constructor Summary

Constructors
Constructor and Description

BasicDecider()

Constructors
Constructor and Description
`BasicDecider()`

Method Summary

Methods
Modifier and Type	Method and Description
`protected boolean`	`checkFileDetails(ReturnValue returnValue, FileMetadata fm)` Performs any additional checks on the file before adding it to the list of files to incorporate.
`ReturnValue`	`clean_up()` Perform post-task clean-up here.
`protected String`	`commaSeparateMy(Collection<String> list)`
`protected BasicDecider.FILE_STATUS`	`compareWorkflowRunFiles(Set<Integer> filesSWIDsHasRun, Collection<String> filesToRun)` Tests if the files from the workflow run (filesHasRun) are the same as those found in the database (filesToRun).
`protected ArrayList<String>`	`constructCommand()`
`protected BasicDecider.PREVIOUS_RUN_STATUS`	`determineStatus(WorkflowRunStatus generateStatus)` Map a normal status to whether a workflow run completed, failed, or other (submitted, pending, etc.) (the states that we care about for the decider)
`ReturnValue`	`do_run()` Performs the main tasks for the plugin.
`ReturnValue`	`do_summary()` Just returns a summary of what would be run.
`ReturnValue`	`do_test()` Perform any active system testing here.
`protected ReturnValue`	`doFinalCheck(String commaSeparatedFilePaths, String commaSeparatedParentAccessions)` allow to user to do the final check and decide to run or cancel the decider e.g.
`String`	`get_description()` Generates a short description of the plugin, preferably one line.
`Boolean`	`getForceRunAll()`
`FindAllTheFiles.Header`	`getGroupingStrategy()`
`FindAllTheFiles.Header`	`getHeader()` Deprecated.
`Boolean`	`getMetadataWriteback()`
`List<String>`	`getMetaType()`
`Set<String>`	`getParentWorkflowAccessions()`
`Boolean`	`getTest()`
`String`	`getWorkflowAccession()`
`Set<String>`	`getWorkflowAccessionsToCheck()`
`protected String`	`handleGroupByAttribute(String attribute)`
`ReturnValue`	`init()` Plugin initialization code goes here.
`protected static boolean`	`isCountAsFail(BasicDecider.FILE_STATUS fileStatus, BasicDecider.PREVIOUS_RUN_STATUS previousStatus)` We now use the guideline that we only count failures when they occur on the same number of files (with the same paths)
`protected static boolean`	`isDoRerun(BasicDecider.FILE_STATUS fileStatus, BasicDecider.PREVIOUS_RUN_STATUS previousStatus)` See https://wiki.oicr.on.ca/display/SEQWARE/BasicDecider+logic
`protected boolean`	`isToRunContained(Set<Integer> filesSWIDsHasRun, Collection<String> filesToRun)` Returns true if the filesToRun are totally contained by the files associated with the files in a given workflowRunAcc
`protected Map<String,String>`	`modifyIniFile(String commaSeparatedFilePaths, String commaSeparatedParentAccessions)`
`protected void`	`printFileMetadata(ReturnValue file, FileMetadata fm)`
`protected boolean`	`reportLaunch()` Report an actual launch of a workflow for testing purpose
`protected boolean`	`rerunWorkflowRun(Collection<String> filesToRun, Collection<Integer> fileSWIDs)` Returns true only if there are more files to run than have been run on any workflow so far, or if the filesToRun have different filepaths than those that have been run before.
`Map<String,List<ReturnValue>>`	`separateFiles(List<ReturnValue> vals, String groupBy)`
`void`	`setForceRunAll(Boolean forceRunAll)`
`void`	`setGroupingStrategy(FindAllTheFiles.Header strategy)`
`void`	`setHeader(FindAllTheFiles.Header header)` Deprecated.
`void`	`setMetadataWriteback(Boolean metadataWriteback)`
`void`	`setMetaType(List<String> metaType)`
`void`	`setMetaws(Metadata metaws)`
`void`	`setParentWorkflowAccessions(Set<String> parentWorkflowAccessions)`
`void`	`setTest(Boolean test)`
`void`	`setWorkflowAccession(String workflowAccession)`
`void`	`setWorkflowAccessionsToCheck(Set<String> workflowAccessions)`
`protected String`	`spaceSeparateMy(Collection<String> list)`

Methods inherited from class net.sourceforge.seqware.pipeline.plugin.Plugin
get_syntax, parse_parameters, print, println, setConfig, setMetadata, setParams

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface net.sourceforge.seqware.pipeline.decider.DeciderInterface
get_syntax, parse_parameters, setConfig, setMetadata, setParams

- Field Detail
  - random
```
protected Random random
```
- Constructor Detail
  - BasicDecider
```
public BasicDecider()
```
- Method Detail
  - get_description
```
public String get_description()
```
    Generates a short description of the plugin, preferably one line.
    
    Specified by:
    
    get_description in interface DeciderInterface
    
    Specified by:
    
    get_description in interface PluginInterface
    
    Overrides:
    
    get_description in class Plugin
    
    Returns:
    Description of the plugin.
  - init
```
public ReturnValue init()
```
    Description copied from interface: DeciderInterface
    
    Plugin initialization code goes here. This is the first phase of the plugin lifecycle run. Might do things here like set up database access, create temp files, define defaults, etc. Preprocessing can be done here, although normally processing should be done by/during do_run(). The SEQWARE_SETTINGS file contents is passed in here.
    
    Specified by:
    
    init in interface DeciderInterface
    
    Specified by:
    
    init in interface PluginInterface
    
    Returns:
    Success or failure info from this phase, along with any console output.
  - do_test
```
public ReturnValue do_test()
```
    Description copied from interface: DeciderInterface
    
    Perform any active system testing here. Use to make sure a DB is available, that a command line tools can be run, etc. You can even write functional tests that run the program you're wrapping on a small known good and then verify the output.
    
    Specified by:
    
    do_test in interface DeciderInterface
    
    Specified by:
    
    do_test in interface PluginInterface
    
    Returns:
    Success or failure info from this phase, along with any console output.
  - do_run
```
public ReturnValue do_run()
```
    Description copied from interface: DeciderInterface
    
    Performs the main tasks for the plugin. This is where you actually execute your task and where the bulk of your implementation will go.
    
    Specified by:
    
    do_run in interface DeciderInterface
    
    Specified by:
    
    do_run in interface PluginInterface
    
    Returns:
    Success or failure info from this phase, along with any console output.
  - constructCommand
```
protected ArrayList<String> constructCommand()
```
  - rerunWorkflowRun
```
protected boolean rerunWorkflowRun(Collection<String> filesToRun,
                       Collection<Integer> fileSWIDs)
```
    Returns true only if there are more files to run than have been run on any workflow so far, or if the filesToRun have different filepaths than those that have been run before.
    
    Parameters:
    filesToRun -
    fileSWIDs -
    
    Returns:
  - determineStatus
```
protected BasicDecider.PREVIOUS_RUN_STATUS determineStatus(WorkflowRunStatus generateStatus)
```
    Map a normal status to whether a workflow run completed, failed, or other (submitted, pending, etc.) (the states that we care about for the decider)
    
    Parameters:
    generateStatus -
    
    Returns:
  - isToRunContained
```
protected boolean isToRunContained(Set<Integer> filesSWIDsHasRun,
                       Collection<String> filesToRun)
```
    Returns true if the filesToRun are totally contained by the files associated with the files in a given workflowRunAcc
    
    Parameters:
    filesSWIDsHasRun -
    filesToRun - the files to check to see if they are contained by the past run
    
    Returns:
  - compareWorkflowRunFiles
```
protected BasicDecider.FILE_STATUS compareWorkflowRunFiles(Set<Integer> filesSWIDsHasRun,
                                               Collection<String> filesToRun)
```
    Tests if the files from the workflow run (filesHasRun) are the same as those found in the database (filesToRun). True if the filesToRun has more files than the workflow run. True if the filesToRun and the workflow run have the same number of files but with different filepaths. False if the filesToRun and the workflow run have the same number of files with the same file paths. False and prints an error message if there are more files in the workflow run than in the filesToRun.
    
    Parameters:
    filesSWIDsHasRun -
    filesToRun -
    
    Returns:
  - printFileMetadata
```
protected void printFileMetadata(ReturnValue file,
                     FileMetadata fm)
```
  - commaSeparateMy
```
protected String commaSeparateMy(Collection<String> list)
```
  - spaceSeparateMy
```
protected String spaceSeparateMy(Collection<String> list)
```
  - checkFileDetails
```
protected boolean checkFileDetails(ReturnValue returnValue,
                       FileMetadata fm)
```
    Performs any additional checks on the file before adding it to the list of files to incorporate. This method should be extended for future deciders for custom behaviour. You can also pull any details out of the file metadata here.
    
    Parameters:
    returnValue - The ReturnValue representing the Processing event. May have one or more files. The attributes table contains the information from FindAllTheFiles.Header.
    fm - the particular file that will be added
    
    Returns:
    true if the file can be added to the list, false otherwise
  - modifyIniFile
```
protected Map<String,String> modifyIniFile(String commaSeparatedFilePaths,
                               String commaSeparatedParentAccessions)
```
  - handleGroupByAttribute
```
protected String handleGroupByAttribute(String attribute)
```
  - separateFiles
```
public Map<String,List<ReturnValue>> separateFiles(List<ReturnValue> vals,
                                          String groupBy)
```
  - clean_up
```
public ReturnValue clean_up()
```
    Description copied from interface: DeciderInterface
    
    Perform post-task clean-up here. Use to remove temporary files and directories, flush buffers and close db connections, etc.
    
    Specified by:
    
    clean_up in interface DeciderInterface
    
    Specified by:
    
    clean_up in interface PluginInterface
    
    Returns:
    Success or failure info from this phase, along with any console output.
  - do_summary
```
public ReturnValue do_summary()
```
    Description copied from interface: DeciderInterface
    
    Just returns a summary of what would be run.
    
    Specified by:
    
    do_summary in interface DeciderInterface
    
    Returns:
    Success or failure info from this phase, along with any console output.
  - getForceRunAll
```
public Boolean getForceRunAll()
```
  - setForceRunAll
```
public void setForceRunAll(Boolean forceRunAll)
```
  - getHeader
```
@Deprecated
public FindAllTheFiles.Header getHeader()
```
    Deprecated.
    
    use getGroupingStrategy
    
    Returns:
  - getGroupingStrategy
```
public FindAllTheFiles.Header getGroupingStrategy()
```
  - setHeader
```
@Deprecated
public void setHeader(FindAllTheFiles.Header header)
```
    Deprecated.
    
    use setGroupingStrategy
    
    Parameters:
    header -
  - setGroupingStrategy
```
public void setGroupingStrategy(FindAllTheFiles.Header strategy)
```
  - getMetaType
```
public List<String> getMetaType()
```
  - setMetaType
```
public void setMetaType(List<String> metaType)
```
  - getMetadataWriteback
```
public Boolean getMetadataWriteback()
```
  - setMetadataWriteback
```
public void setMetadataWriteback(Boolean metadataWriteback)
```
  - getParentWorkflowAccessions
```
public Set<String> getParentWorkflowAccessions()
```
  - setParentWorkflowAccessions
```
public void setParentWorkflowAccessions(Set<String> parentWorkflowAccessions)
```
  - getTest
```
public Boolean getTest()
```
  - setTest
```
public void setTest(Boolean test)
```
  - getWorkflowAccession
```
public String getWorkflowAccession()
```
  - setWorkflowAccession
```
public void setWorkflowAccession(String workflowAccession)
```
  - getWorkflowAccessionsToCheck
```
public Set<String> getWorkflowAccessionsToCheck()
```
  - setWorkflowAccessionsToCheck
```
public void setWorkflowAccessionsToCheck(Set<String> workflowAccessions)
```
  - doFinalCheck
```
protected ReturnValue doFinalCheck(String commaSeparatedFilePaths,
                       String commaSeparatedParentAccessions)
```
    allow to user to do the final check and decide to run or cancel the decider e.g. check if all files are present
    
    Parameters:
    commaSeparatedFilePaths -
    commaSeparatedParentAccessions -
    
    Returns:
  - reportLaunch
```
protected boolean reportLaunch()
```
    Report an actual launch of a workflow for testing purpose
    
    Returns:
    false iff we don't actually want to launch
  - setMetaws
```
public void setMetaws(Metadata metaws)
```
  - isCountAsFail
```
protected static boolean isCountAsFail(BasicDecider.FILE_STATUS fileStatus,
                    BasicDecider.PREVIOUS_RUN_STATUS previousStatus)
```
    We now use the guideline that we only count failures when they occur on the same number of files (with the same paths)
    
    Parameters:
    fileStatus -
    previousStatus -
    
    Returns:
  - isDoRerun
```
protected static boolean isDoRerun(BasicDecider.FILE_STATUS fileStatus,
                BasicDecider.PREVIOUS_RUN_STATUS previousStatus)
```
    See https://wiki.oicr.on.ca/display/SEQWARE/BasicDecider+logic
    
    Parameters:
    fileStatus -
    previousStatus -
    
    Returns:

Class BasicDecider

Nested Class Summary

Field Summary

Fields inherited from class net.sourceforge.seqware.pipeline.plugin.Plugin

Constructor Summary

Method Summary

Methods inherited from class net.sourceforge.seqware.pipeline.plugin.Plugin

Methods inherited from class java.lang.Object

Methods inherited from interface net.sourceforge.seqware.pipeline.decider.DeciderInterface

Field Detail

random

Constructor Detail

BasicDecider

Method Detail

get_description

init

do_test

do_run

constructCommand

rerunWorkflowRun

determineStatus

isToRunContained

compareWorkflowRunFiles

printFileMetadata

commaSeparateMy

spaceSeparateMy

checkFileDetails

modifyIniFile

handleGroupByAttribute

separateFiles

clean_up

do_summary

getForceRunAll

setForceRunAll

getHeader

getGroupingStrategy

setHeader

setGroupingStrategy

getMetaType

setMetaType

getMetadataWriteback

setMetadataWriteback

getParentWorkflowAccessions

setParentWorkflowAccessions

getTest

setTest

getWorkflowAccession

setWorkflowAccession

getWorkflowAccessionsToCheck

setWorkflowAccessionsToCheck

doFinalCheck

reportLaunch

setMetaws

isCountAsFail

isDoRerun