MetadataNoConnection (SeqWare 1.1.2 API)

java.lang.Object
- net.sourceforge.seqware.common.metadata.MetadataNoConnection

All Implemented Interfaces:

Metadata
```
public class MetadataNoConnection
extends Object
implements Metadata
```
MetadataNoConnection class.

Version:

$Id: $Id

Author:

boconnor@oicr.on.ca This Metadata object essentially does nothing. It returns null, 0, or a successful ReturnValue for all methods. This lets us do absolutely no metadata writeback with objects that expect a validate Metadata object. Keep in mind this may break code that assumes it's talking to a Database- or WebService-backed Metadata object!

Constructor Summary

Constructors
Constructor and Description

MetadataNoConnection()

Constructors
Constructor and Description
`MetadataNoConnection()`

Method Summary

Methods
Modifier and Type	Method and Description
`ReturnValue`	`add_empty_processing_event_by_parent_accession(int[] parentAccessions)` add_empty_processing_event_by_parent_accession.
`ReturnValue`	`add_empty_processing_event(int[] parentIDs)` add_empty_processing_event.
`ReturnValue`	`add_task_group(int[] parentIDs, int[] childIDs, String algorithm, String description)` add_task_group.
`void`	`add_workflow_run_ancestor(int workflowRunAccession, int processingId)` add_workflow_run_ancestor.
`int`	`add_workflow_run(int workflowAccession)` add_workflow_run.
`ReturnValue`	`addExperiment(Integer studySwAccession, Integer platformId, String description, String title, Integer experimentLibraryDesignId, Integer experimentSpotDesignId)` addExperiment.
`ReturnValue`	`addIUS(Integer laneAccession, Integer sampleAccession, String name, String description, String barcode, boolean skip)` addSample.
`ReturnValue`	`addLane(Integer sequencerRunAccession, Integer studyTypeId, Integer libraryStrategyId, Integer librarySelectionId, Integer librarySourceId, String name, String description, String cycleDescriptor, boolean skip, Integer laneNumber)` addSample.
`ReturnValue`	`addSample(Integer experimentAccession, Integer parentSampleAccession, Integer organismId, String description, String title)` addSample.
`ReturnValue`	`addSequencerRun(Integer platformAccession, String name, String description, boolean pairdEnd, boolean skip, String filePath, SequencerRunStatus status)` addSample.
`ReturnValue`	`addStudy(String title, String description, String centerName, String centerProjectName, Integer studyTypeId)` addStudy.
`ReturnValue`	`addWorkflow(String name, String version, String description, String baseCommand, String configFile, String templateFile, String provisionDir, boolean storeProvisionDir, String archiveZip, boolean storeArchiveZip, String workflowClass, String workflowType, String workflowEngine, String seqwareVersion)` addWorkflow.
`void`	`annotateExperiment(int experimentSWID, ExperimentAttribute att, Boolean skip)` annotateExperiment.
`void`	`annotateExperiment(int experimentSWID, Set<ExperimentAttribute> atts)` annotateExperiment.
`void`	`annotateFile(int laneSWID, FileAttribute iusAtt, Boolean skip)` annotateFile.
`void`	`annotateFile(int fileSWID, Set<FileAttribute> iusAtts)` annotateFile.
`void`	`annotateIUS(int iusSWID, IUSAttribute iusAtt, Boolean skip)` annotateIUS.
`void`	`annotateIUS(int laneSWID, Set<IUSAttribute> iusAtts)` annotateIUS.
`void`	`annotateLane(int laneSWID, LaneAttribute laneAtt, Boolean skip)` annotateLane.
`void`	`annotateLane(int laneSWID, Set<LaneAttribute> laneAtts)` annotateLane.
`void`	`annotateProcessing(int processingSWID, ProcessingAttribute att, Boolean skip)` annotateProcessing.
`void`	`annotateProcessing(int processingSWID, Set<ProcessingAttribute> atts)` annotateProcessing.
`void`	`annotateSample(int sampleSWID, SampleAttribute att, Boolean skip)` annotateSample.
`void`	`annotateSample(int sampleSWID, Set<SampleAttribute> atts)` annotateSample.
`void`	`annotateSequencerRun(int sequencerRunSWID, SequencerRunAttribute sequencerRunAtt, Boolean skip)` annotateSequencerRun.
`void`	`annotateSequencerRun(int sequencerRunSWID, Set<SequencerRunAttribute> sequencerRunAtts)` annotateSequencerRun.
`void`	`annotateStudy(int studySWID, Set<StudyAttribute> atts)` annotateStudy.
`void`	`annotateStudy(int studySWID, StudyAttribute att, Boolean skip)` annotateStudy.
`void`	`annotateWorkflow(int workflowSWID, Set<WorkflowAttribute> atts)` annotateWorkflow.
`void`	`annotateWorkflow(int workflowSWID, WorkflowAttribute att, Boolean skip)` annotateWorkflow.
`void`	`annotateWorkflowRun(int workflowSWID, Set<WorkflowRunAttribute> atts)` annotateWorkflowRun.
`void`	`annotateWorkflowRun(int workflowrunSWID, WorkflowRunAttribute att, Boolean skip)` annotateWorkflowRun.
`ReturnValue`	`associate_processing_event_with_parents_and_child(int processingID, int[] parentIDs, int[] childIDs)` associate_processing_event_with_parents_and_child.
`boolean`	`checkClientServerMatchingVersion()` Check to see if client seqware version matches server version
`ReturnValue`	`clean_up()` clean_up.
`List<Map<String,String>>`	`fileProvenanceReport(Map<FileProvenanceParam,List<String>> params)` Retrieves the file provenance report.
`void`	`fileProvenanceReport(Map<FileProvenanceParam,List<String>> params, Writer out)` Retrieves the file provenance report, writing it to the specified output stream as a TSV.
`void`	`fileProvenanceReportTrigger()` Triggers the file provenance report, this is a costly operation so it should be scheduled via a cron or similar
`Map<String,String>`	`get_workflow_info(int workflowAccession)` get_workflow_info.
`int`	`get_workflow_run_accession(int workflowRunId)` get_workflow_run_accession.
`int`	`get_workflow_run_id(int workflowRunAccession)` get_workflow_run_id.
`List<SequencerRun>`	`getAllSequencerRuns()` Get all of the sequencer runs in the DB.
`List<Study>`	`getAllStudies()` getAllStudies.
`List<Sample>`	`getChildSamplesFrom(int parentSampleAccession)` Get the child samples of a parent sample.
`Map<String,String>`	`getEnvironmentReport()` Retrieves all environmental information from the web-service
`Experiment`	`getExperiment(int swAccession)` getExperiment.
`List<ExperimentLibraryDesign>`	`getExperimentLibraryDesigns()` getExperimentLibraryDesigns.
`List<Experiment>`	`getExperimentsFrom(int studyAccession)` Get experiments from a study.
`List<ExperimentSpotDesignReadSpec>`	`getExperimentSpotDesignReadSpecs()` getPlatforms.
`List<ExperimentSpotDesign>`	`getExperimentSpotDesigns()` getExperimentSpotDesigns.
`File`	`getFile(int swAccession)` getFile.
`IUS`	`getIUS(int swAccession)` Get ius by sw accession
`List<IUS>`	`getIUSFrom(int laneOrSampleAccession)` Get IUSes (barcodes) from a lane or sample.
`Lane`	`getLane(int laneAccession)` getLane.
`List<Lane>`	`getLanesFrom(int sequencerRunAccession)` Get Lanes from a sequencer run.
`List<LibrarySelection>`	`getLibrarySelections()` getLibrarySelections.
`List<LibrarySource>`	`getLibrarySource()` getLibrarySource.
`List<LibraryStrategy>`	`getLibraryStrategies()` getLibraryStrategies.
`List<Organism>`	`getOrganisms()` getOrganisms.
`List<Sample>`	`getParentSamplesFrom(int childSampleAccession)` Get the parent samples of a sample.
`List<Platform>`	`getPlatforms()` getPlatforms.
`Processing`	`getProcessing(int processingAccession)` getProcessing.
`String`	`getProcessingRelations(String swAccession)` getProcessingRelations.
`Sample`	`getSample(int swAccession)` Get sample by swa
`List<Sample>`	`getSampleByName(String name)`
`List<Sample>`	`getSamplesFrom(int experimentAccession)` Get the samples from an experiment.
`SequencerRun`	`getSequencerRun(int sequencerRunAccession)` getSequencerRun.
`SequencerRun`	`getSequencerRunByName(String name)`
`String`	`getSequencerRunReport()` getSequencerRunReport.
`Study`	`getStudy(int swAccession)` Get study by swa
`List<Study>`	`getStudyByName(String name)`
`List<StudyType>`	`getStudyTypes()` getStudyTypes.
`List<Object>`	`getViaAccessions(int[] accessions)` Get the models corresponding to potential accessions
`List<ParentAccessionModel>`	`getViaParentAccessions(int[] potentialParentAccessions)` Get the models corresponding to potential parent accessions
`Workflow`	`getWorkflow(int workflowAccession)` Get a workflow
`int`	`getWorkflowAccession(String name, String version)` getWorkflowAccession.
`SortedSet<WorkflowParam>`	`getWorkflowParams(String swAccession)` getWorkflowParams.
`WorkflowRun`	`getWorkflowRun(int workflowRunAccession)` getWorkflowRun.
`String`	`getWorkflowRunReport(Date earliestDate, Date latestDate)` getWorkflowRunReport.
`String`	`getWorkflowRunReport(int workflowRunSWID)` getWorkflowRunReport.
`String`	`getWorkflowRunReport(int workflowSWID, Date earliestDate, Date latestDate)` getWorkflowRunReport.
`String`	`getWorkflowRunReport(Integer workflowSWID, WorkflowRunStatus status, Date earliestDate, Date latestDate)`
`String`	`getWorkflowRunReport(WorkflowRunStatus status, Date earliestDate, Date latestDate)` getWorkflowRunReport.
`String`	`getWorkflowRunReportStdErr(int workflowRunSWID)` getWorkflowRunReportStdErr.
`String`	`getWorkflowRunReportStdOut(int workflowRunSWID)` getWorkflowRunReportStdOut.
`List<WorkflowRun>`	`getWorkflowRunsAssociatedWithFiles(List<Integer> fileAccessions, String search_type)` Returns the workflow_runs associated with a group of files.
`List<WorkflowRun>`	`getWorkflowRunsAssociatedWithInputFiles(List<Integer> fileAccessions)` Returns the workflow_runs associated with a group of input files.
`List<WorkflowRun>`	`getWorkflowRunsAssociatedWithInputFiles(List<Integer> fileAccessions, List<Integer> workflowAccessions)` Returns the workflow_runs associated with a group of input files.
`List<WorkflowRun>`	`getWorkflowRunsByStatus(WorkflowRunStatus status)` getWorkflowRunsByStatus.
`List<WorkflowRun>`	`getWorkflowRunsByStatusCmd(String statusCmd)` Get workflow run by status cmd (oozie job id in oozie).
`WorkflowRun`	`getWorkflowRunWithWorkflow(String workflowRunAccession)` getWorkflowRunWithWorkflow.
`Boolean`	`isDuplicateFile(String filepath)` isDuplicateFile.
`boolean`	`linkWorkflowRunAndParent(int workflowRunId, int parentAccession)` linkWorkflowRunAndParent.
`String`	`listInstalledWorkflowParams(String workflowAccession)` listInstalledWorkflowParams.
`String`	`listInstalledWorkflows()` listInstalledWorkflows.
`int`	`mapProcessingIdToAccession(int processingId)` mapProcessingIdToAccession.
`ReturnValue`	`processing_event_to_task_group(int processingID, int[] parentIDs, int[] childIDs, String algorithm, String description)` processing_event_to_task_group.
`ReturnValue`	`update_processing_event(int processingID, ReturnValue retval)` update_processing_event.
`ReturnValue`	`update_processing_status(int processingID, ProcessingStatus status)` update_processing_status.
`ReturnValue`	`update_processing_workflow_run(int processingID, int workflowRunAccession)` update_processing_workflow_run.
`ReturnValue`	`update_workflow_run(int workflowRunId, String pegasusCmd, String workflowTemplate, WorkflowRunStatus status, String statusCmd, String workingDirectory, String dax, String ini, String host, String stdErr, String stdOut, String workflowEngine, Set<Integer> inputFiles)` update_workflow_run.
`ReturnValue`	`updateWorkflow(int workflowId, String permanentBundleLocation)` updateWorkflow.
`void`	`updateWorkflowRun(WorkflowRun wr)`

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

- Constructor Detail
  - MetadataNoConnection
```
public MetadataNoConnection()
```
- Method Detail
  - fileProvenanceReport
```
public void fileProvenanceReport(Map<FileProvenanceParam,List<String>> params,
                        Writer out)
```
    Description copied from interface: Metadata
    
    Retrieves the file provenance report, writing it to the specified output stream as a TSV.
    
    Specified by:
    
    fileProvenanceReport in interface Metadata
    
    Parameters:
    params - the parameters to filter the results
    out - where the TSV content will be written
  - fileProvenanceReport
```
public List<Map<String,String>> fileProvenanceReport(Map<FileProvenanceParam,List<String>> params)
```
    Description copied from interface: Metadata
    
    Retrieves the file provenance report.
    
    Specified by:
    
    fileProvenanceReport in interface Metadata
    
    Parameters:
    params - the parameters to filter the results
    
    Returns:
    the list of each file provenance entry
  - addStudy
```
public ReturnValue addStudy(String title,
                   String description,
                   String centerName,
                   String centerProjectName,
                   Integer studyTypeId)
```
    addStudy.
    
    Specified by:
    
    addStudy in interface Metadata
    
    Parameters:
    title - a String object.
    description - a String object.
    centerName - a String object.
    centerProjectName - a String object.
    studyTypeId - a Integer object.
    
    Returns:
    a ReturnValue object.
  - addExperiment
```
public ReturnValue addExperiment(Integer studySwAccession,
                        Integer platformId,
                        String description,
                        String title,
                        Integer experimentLibraryDesignId,
                        Integer experimentSpotDesignId)
```
    addExperiment.
    
    Specified by:
    
    addExperiment in interface Metadata
    
    Parameters:
    experimentLibraryDesignId - the value of experimentLibraryDesignId
    experimentSpotDesignId - the value of experimentSpotDesignId
    studySwAccession - a Integer object.
    platformId - a Integer object.
    description - a String object.
    title - a String object.
    
    Returns:
    a ReturnValue object.
  - addSample
```
public ReturnValue addSample(Integer experimentAccession,
                    Integer parentSampleAccession,
                    Integer organismId,
                    String description,
                    String title)
```
    addSample.
    
    Specified by:
    
    addSample in interface Metadata
    
    Parameters:
    parentSampleAccession -
    experimentAccession - a Integer object.
    organismId - a Integer object.
    description - a String object.
    title - a String object.
    
    Returns:
    a ReturnValue object.
  - addSequencerRun
```
public ReturnValue addSequencerRun(Integer platformAccession,
                          String name,
                          String description,
                          boolean pairdEnd,
                          boolean skip,
                          String filePath,
                          SequencerRunStatus status)
```
    Description copied from interface: Metadata
    
    addSample.
    
    Specified by:
    
    addSequencerRun in interface Metadata
    
    description - a String object.
    status - the value of status
    
    Returns:
    a ReturnValue object.
  - addLane
```
public ReturnValue addLane(Integer sequencerRunAccession,
                  Integer studyTypeId,
                  Integer libraryStrategyId,
                  Integer librarySelectionId,
                  Integer librarySourceId,
                  String name,
                  String description,
                  String cycleDescriptor,
                  boolean skip,
                  Integer laneNumber)
```
    Description copied from interface: Metadata
    
    addSample.
    
    Specified by:
    
    addLane in interface Metadata
    
    description - a String object.
    
    Returns:
    a ReturnValue object.
  - addIUS
```
public ReturnValue addIUS(Integer laneAccession,
                 Integer sampleAccession,
                 String name,
                 String description,
                 String barcode,
                 boolean skip)
```
    Description copied from interface: Metadata
    
    addSample.
    
    Specified by:
    
    addIUS in interface Metadata
    
    Returns:
    a ReturnValue object.
  - getPlatforms
```
public List<Platform> getPlatforms()
```
    Description copied from interface: Metadata
    
    getPlatforms.
    
    Specified by:
    
    getPlatforms in interface Metadata
    
    Returns:
    a Platform object.
  - getOrganisms
```
public List<Organism> getOrganisms()
```
    Description copied from interface: Metadata
    
    getOrganisms.
    
    Specified by:
    
    getOrganisms in interface Metadata
    
    Returns:
    a Organism object.
  - getStudyTypes
```
public List<StudyType> getStudyTypes()
```
    Description copied from interface: Metadata
    
    getStudyTypes.
    
    Specified by:
    
    getStudyTypes in interface Metadata
    
    Returns:
    a StudyType object.
  - getLibraryStrategies
```
public List<LibraryStrategy> getLibraryStrategies()
```
    Description copied from interface: Metadata
    
    getLibraryStrategies.
    
    Specified by:
    
    getLibraryStrategies in interface Metadata
    
    Returns:
    a LibraryStrategy object.
  - getLibrarySelections
```
public List<LibrarySelection> getLibrarySelections()
```
    Description copied from interface: Metadata
    
    getLibrarySelections.
    
    Specified by:
    
    getLibrarySelections in interface Metadata
    
    Returns:
    a LibrarySelection object.
  - getLibrarySource
```
public List<LibrarySource> getLibrarySource()
```
    Description copied from interface: Metadata
    
    getLibrarySource.
    
    Specified by:
    
    getLibrarySource in interface Metadata
    
    Returns:
    a LibrarySource object.
  - add_empty_processing_event
```
public ReturnValue add_empty_processing_event(int[] parentIDs)
```
    add_empty_processing_event.
    
    Specified by:
    
    add_empty_processing_event in interface Metadata
    
    Parameters:
    parentIDs - an array of int.
    
    Returns:
    a ReturnValue object.
  - add_empty_processing_event_by_parent_accession
```
public ReturnValue add_empty_processing_event_by_parent_accession(int[] parentAccessions)
```
    add_empty_processing_event_by_parent_accession.
    
    Specified by:
    
    add_empty_processing_event_by_parent_accession in interface Metadata
    
    Parameters:
    parentAccessions - an array of int.
    
    Returns:
    a ReturnValue object.
  - mapProcessingIdToAccession
```
public int mapProcessingIdToAccession(int processingId)
```
    mapProcessingIdToAccession.
    This maps processing_id to sw_accession for that event.
    
    Specified by:
    
    mapProcessingIdToAccession in interface Metadata
    
    Parameters:
    processingId - a int.
    
    Returns:
    a int.
  - linkWorkflowRunAndParent
```
public boolean linkWorkflowRunAndParent(int workflowRunId,
                               int parentAccession)
                                 throws SQLException
```
    linkWorkflowRunAndParent.
    TODO: needs to support more relationship types, but will need to add to the SQL schema to support this
    
    Specified by:
    
    linkWorkflowRunAndParent in interface Metadata
    
    Parameters:
    workflowRunId - a int.
    parentAccession - a int.
    
    Returns:
    a boolean.
    
    Throws:
    
    SQLException - if any.
  - processing_event_to_task_group
```
public ReturnValue processing_event_to_task_group(int processingID,
                                         int[] parentIDs,
                                         int[] childIDs,
                                         String algorithm,
                                         String description)
```
    processing_event_to_task_group.
    
    Specified by:
    
    processing_event_to_task_group in interface Metadata
    
    Parameters:
    processingID - a int.
    parentIDs - an array of int.
    childIDs - an array of int.
    algorithm - a String object.
    description - a String object.
    
    Returns:
    a ReturnValue object.
  - add_task_group
```
public ReturnValue add_task_group(int[] parentIDs,
                         int[] childIDs,
                         String algorithm,
                         String description)
```
    add_task_group.
    
    Specified by:
    
    add_task_group in interface Metadata
    
    Parameters:
    parentIDs - an array of int.
    childIDs - an array of int.
    algorithm - a String object.
    description - a String object.
    
    Returns:
    a ReturnValue object.
  - associate_processing_event_with_parents_and_child
```
public ReturnValue associate_processing_event_with_parents_and_child(int processingID,
                                                            int[] parentIDs,
                                                            int[] childIDs)
```
    associate_processing_event_with_parents_and_child.
    
    Specified by:
    
    associate_processing_event_with_parents_and_child in interface Metadata
    
    Parameters:
    processingID - a int.
    parentIDs - an array of int.
    childIDs - an array of int.
    
    Returns:
    a ReturnValue object.
  - update_processing_status
```
public ReturnValue update_processing_status(int processingID,
                                   ProcessingStatus status)
```
    update_processing_status.
    
    Specified by:
    
    update_processing_status in interface Metadata
    
    Parameters:
    processingID - a int.
    status - a String object.
    
    Returns:
    a ReturnValue object.
  - add_workflow_run
```
public int add_workflow_run(int workflowAccession)
```
    add_workflow_run.
    
    Specified by:
    
    add_workflow_run in interface Metadata
    
    Parameters:
    workflowAccession - a int.
    
    Returns:
    a int.
  - get_workflow_run_accession
```
public int get_workflow_run_accession(int workflowRunId)
```
    get_workflow_run_accession.
    
    Specified by:
    
    get_workflow_run_accession in interface Metadata
    
    Parameters:
    workflowRunId - a int.
    
    Returns:
    a int.
  - get_workflow_run_id
```
public int get_workflow_run_id(int workflowRunAccession)
```
    get_workflow_run_id.
    
    Specified by:
    
    get_workflow_run_id in interface Metadata
    
    Parameters:
    workflowRunAccession - a int.
    
    Returns:
    a int.
  - getWorkflowRun
```
public WorkflowRun getWorkflowRun(int workflowRunAccession)
```
    getWorkflowRun.
    
    Specified by:
    
    getWorkflowRun in interface Metadata
    
    Parameters:
    workflowRunAccession - a int.
    
    Returns:
    a WorkflowRun object.
  - add_workflow_run_ancestor
```
public void add_workflow_run_ancestor(int workflowRunAccession,
                             int processingId)
```
    add_workflow_run_ancestor.
    
    Specified by:
    
    add_workflow_run_ancestor in interface Metadata
    
    Parameters:
    workflowRunAccession - a int.
    processingId - a int.
  - update_processing_workflow_run
```
public ReturnValue update_processing_workflow_run(int processingID,
                                         int workflowRunAccession)
```
    update_processing_workflow_run.
    
    Specified by:
    
    update_processing_workflow_run in interface Metadata
    
    Parameters:
    workflowRunAccession -
    processingID - a int.
    
    Returns:
    a ReturnValue object.
  - update_workflow_run
```
public ReturnValue update_workflow_run(int workflowRunId,
                              String pegasusCmd,
                              String workflowTemplate,
                              WorkflowRunStatus status,
                              String statusCmd,
                              String workingDirectory,
                              String dax,
                              String ini,
                              String host,
                              String stdErr,
                              String stdOut,
                              String workflowEngine,
                              Set<Integer> inputFiles)
```
    update_workflow_run.
    
    Specified by:
    
    update_workflow_run in interface Metadata
    
    Parameters:
    inputFiles -
    workflowRunId - a int.
    pegasusCmd - a String object.
    workflowTemplate - a String object.
    status - a String object.
    statusCmd - a String object.
    workingDirectory - a String object.
    dax - a String object.
    ini - a String object.
    host - a String object.
    stdErr - a String object.
    stdOut - a String object.
    workflowEngine - the value of workflowEngine
    
    Returns:
    a ReturnValue object.
  - updateWorkflowRun
```
public void updateWorkflowRun(WorkflowRun wr)
```
    Specified by:
    
    updateWorkflowRun in interface Metadata
  - update_processing_event
```
public ReturnValue update_processing_event(int processingID,
                                  ReturnValue retval)
```
    update_processing_event.
    
    Specified by:
    
    update_processing_event in interface Metadata
    
    Parameters:
    processingID - a int.
    retval - a ReturnValue object.
    
    Returns:
    a ReturnValue object.
  - clean_up
```
public ReturnValue clean_up()
```
    clean_up.
    
    Specified by:
    
    clean_up in interface Metadata
    
    Returns:
    a ReturnValue object.
  - addWorkflow
```
public ReturnValue addWorkflow(String name,
                      String version,
                      String description,
                      String baseCommand,
                      String configFile,
                      String templateFile,
                      String provisionDir,
                      boolean storeProvisionDir,
                      String archiveZip,
                      boolean storeArchiveZip,
                      String workflowClass,
                      String workflowType,
                      String workflowEngine,
                      String seqwareVersion)
```
    addWorkflow.
    
    Specified by:
    
    addWorkflow in interface Metadata
    
    Parameters:
    name - a String object.
    version - a String object.
    description - a String object.
    baseCommand - a String object.
    configFile - a String object.
    templateFile - a String object.
    provisionDir - a String object.
    storeProvisionDir - a boolean.
    archiveZip - a String object.
    storeArchiveZip - a boolean.
    
    Returns:
    a ReturnValue object.
  - get_workflow_info
```
public Map<String,String> get_workflow_info(int workflowAccession)
```
    get_workflow_info.
    
    Specified by:
    
    get_workflow_info in interface Metadata
    
    Parameters:
    workflowAccession - a int.
    
    Returns:
    a Map object.
  - isDuplicateFile
```
public Boolean isDuplicateFile(String filepath)
```
    isDuplicateFile.
    
    Specified by:
    
    isDuplicateFile in interface Metadata
    
    Parameters:
    filepath - a String object.
    
    Returns:
    a Boolean object.
  - updateWorkflow
```
public ReturnValue updateWorkflow(int workflowId,
                         String permanentBundleLocation)
```
    updateWorkflow.
    
    Specified by:
    
    updateWorkflow in interface Metadata
    
    Parameters:
    workflowId - a int.
    permanentBundleLocation - a String object.
    
    Returns:
    a ReturnValue object.
  - listInstalledWorkflows
```
public String listInstalledWorkflows()
```
    listInstalledWorkflows.
    
    Specified by:
    
    listInstalledWorkflows in interface Metadata
    
    Returns:
    a String object.
  - listInstalledWorkflowParams
```
public String listInstalledWorkflowParams(String workflowAccession)
```
    listInstalledWorkflowParams.
    
    Specified by:
    
    listInstalledWorkflowParams in interface Metadata
    
    Parameters:
    workflowAccession - a String object.
    
    Returns:
    a String object.
  - getWorkflowAccession
```
public int getWorkflowAccession(String name,
                       String version)
```
    getWorkflowAccession.
    
    Specified by:
    
    getWorkflowAccession in interface Metadata
    
    Parameters:
    name - a String object.
    version - a String object.
    
    Returns:
    a int.
  - getWorkflowRunsByStatus
```
public List<WorkflowRun> getWorkflowRunsByStatus(WorkflowRunStatus status)
```
    getWorkflowRunsByStatus.
    
    Specified by:
    
    getWorkflowRunsByStatus in interface Metadata
    
    Parameters:
    status - a String object.
    
    Returns:
    a List object.
  - getWorkflowRunWithWorkflow
```
public WorkflowRun getWorkflowRunWithWorkflow(String workflowRunAccession)
```
    getWorkflowRunWithWorkflow.
    
    Specified by:
    
    getWorkflowRunWithWorkflow in interface Metadata
    
    Parameters:
    workflowRunAccession - a String object.
    
    Returns:
    a WorkflowRun object.
  - getAllStudies
```
public List<Study> getAllStudies()
```
    getAllStudies.
    
    Specified by:
    
    getAllStudies in interface Metadata
    
    Returns:
    a List object.
  - getSequencerRunReport
```
public String getSequencerRunReport()
```
    getSequencerRunReport.
    
    Specified by:
    
    getSequencerRunReport in interface Metadata
    
    Returns:
    a String object.
  - annotateIUS
```
public void annotateIUS(int iusSWID,
               IUSAttribute iusAtt,
               Boolean skip)
```
    annotateIUS.
    
    Specified by:
    
    annotateIUS in interface Metadata
    
    Parameters:
    iusSWID -
    iusAtt - a IUSAttribute object.
    skip - a Boolean object.
  - annotateLane
```
public void annotateLane(int laneSWID,
                LaneAttribute laneAtt,
                Boolean skip)
```
    annotateLane.
    
    Specified by:
    
    annotateLane in interface Metadata
    
    Parameters:
    laneSWID - a int.
    laneAtt - a LaneAttribute object.
    skip - a Boolean object.
  - annotateSequencerRun
```
public void annotateSequencerRun(int sequencerRunSWID,
                        SequencerRunAttribute sequencerRunAtt,
                        Boolean skip)
```
    annotateSequencerRun.
    
    Specified by:
    
    annotateSequencerRun in interface Metadata
    
    Parameters:
    sequencerRunSWID - a int.
    sequencerRunAtt - a SequencerRunAttribute object.
    skip - a Boolean object.
  - annotateExperiment
```
public void annotateExperiment(int experimentSWID,
                      ExperimentAttribute att,
                      Boolean skip)
```
    annotateExperiment.
    
    Specified by:
    
    annotateExperiment in interface Metadata
    
    Parameters:
    experimentSWID - a int.
    att - a ExperimentAttribute object.
    skip - a Boolean object.
  - annotateProcessing
```
public void annotateProcessing(int processingSWID,
                      ProcessingAttribute att,
                      Boolean skip)
```
    annotateProcessing.
    
    Specified by:
    
    annotateProcessing in interface Metadata
    
    Parameters:
    processingSWID - a int.
    att - a ProcessingAttribute object.
    skip - a Boolean object.
  - annotateSample
```
public void annotateSample(int sampleSWID,
                  SampleAttribute att,
                  Boolean skip)
```
    annotateSample.
    
    Specified by:
    
    annotateSample in interface Metadata
    
    Parameters:
    sampleSWID - a int.
    att - a SampleAttribute object.
    skip - a Boolean object.
  - annotateStudy
```
public void annotateStudy(int studySWID,
                 StudyAttribute att,
                 Boolean skip)
```
    annotateStudy.
    
    Specified by:
    
    annotateStudy in interface Metadata
    
    Parameters:
    studySWID - a int.
    att - a StudyAttribute object.
    skip - a Boolean object.
  - getWorkflowRunReport
```
public String getWorkflowRunReport(int workflowRunSWID)
```
    getWorkflowRunReport.
    
    Specified by:
    
    getWorkflowRunReport in interface Metadata
    
    Parameters:
    workflowRunSWID - a int.
    
    Returns:
    a String object.
  - getWorkflowRunReport
```
public String getWorkflowRunReport(int workflowSWID,
                          Date earliestDate,
                          Date latestDate)
```
    getWorkflowRunReport.
    
    Specified by:
    
    getWorkflowRunReport in interface Metadata
    
    Parameters:
    workflowSWID - a int.
    earliestDate - a Date object.
    latestDate - a Date object.
    
    Returns:
    a String object.
  - getWorkflowRunReport
```
public String getWorkflowRunReport(Date earliestDate,
                          Date latestDate)
```
    getWorkflowRunReport.
    
    Specified by:
    
    getWorkflowRunReport in interface Metadata
    
    Parameters:
    earliestDate - a Date object.
    latestDate - a Date object.
    
    Returns:
    a String object.
  - getFile
```
public File getFile(int swAccession)
```
    getFile.
    
    Specified by:
    
    getFile in interface Metadata
    
    Parameters:
    swAccession - a int.
    
    Returns:
    a File object.
  - getWorkflowParams
```
public SortedSet<WorkflowParam> getWorkflowParams(String swAccession)
```
    getWorkflowParams.
    
    Specified by:
    
    getWorkflowParams in interface Metadata
    
    Parameters:
    swAccession - a String object.
    
    Returns:
    a SortedSet object.
  - annotateWorkflow
```
public void annotateWorkflow(int workflowSWID,
                    WorkflowAttribute att,
                    Boolean skip)
```
    annotateWorkflow.
    
    Specified by:
    
    annotateWorkflow in interface Metadata
    
    Parameters:
    workflowSWID - a int.
    att - a WorkflowAttribute object.
    skip - a Boolean object.
  - annotateWorkflowRun
```
public void annotateWorkflowRun(int workflowrunSWID,
                       WorkflowRunAttribute att,
                       Boolean skip)
```
    annotateWorkflowRun.
    
    Specified by:
    
    annotateWorkflowRun in interface Metadata
    
    Parameters:
    workflowrunSWID - a int.
    att - a WorkflowRunAttribute object.
    skip - a Boolean object.
  - annotateIUS
```
public void annotateIUS(int laneSWID,
               Set<IUSAttribute> iusAtts)
```
    annotateIUS.
    
    Specified by:
    
    annotateIUS in interface Metadata
    
    Parameters:
    laneSWID - a int.
    iusAtts - a Set object.
  - annotateLane
```
public void annotateLane(int laneSWID,
                Set<LaneAttribute> laneAtts)
```
    annotateLane.
    
    Specified by:
    
    annotateLane in interface Metadata
    
    Parameters:
    laneSWID - a int.
    laneAtts - a Set object.
  - annotateSequencerRun
```
public void annotateSequencerRun(int sequencerRunSWID,
                        Set<SequencerRunAttribute> sequencerRunAtts)
```
    annotateSequencerRun.
    
    Specified by:
    
    annotateSequencerRun in interface Metadata
    
    Parameters:
    sequencerRunSWID - a int.
    sequencerRunAtts - a Set object.
  - annotateExperiment
```
public void annotateExperiment(int experimentSWID,
                      Set<ExperimentAttribute> atts)
```
    annotateExperiment.
    
    Specified by:
    
    annotateExperiment in interface Metadata
    
    Parameters:
    experimentSWID - a int.
    atts - a Set object.
  - annotateProcessing
```
public void annotateProcessing(int processingSWID,
                      Set<ProcessingAttribute> atts)
```
    annotateProcessing.
    
    Specified by:
    
    annotateProcessing in interface Metadata
    
    Parameters:
    processingSWID - a int.
    atts - a Set object.
  - annotateSample
```
public void annotateSample(int sampleSWID,
                  Set<SampleAttribute> atts)
```
    annotateSample.
    
    Specified by:
    
    annotateSample in interface Metadata
    
    Parameters:
    sampleSWID - a int.
    atts - a Set object.
  - annotateStudy
```
public void annotateStudy(int studySWID,
                 Set<StudyAttribute> atts)
```
    annotateStudy.
    
    Specified by:
    
    annotateStudy in interface Metadata
    
    Parameters:
    studySWID - a int.
    atts - a Set object.
  - annotateWorkflow
```
public void annotateWorkflow(int workflowSWID,
                    Set<WorkflowAttribute> atts)
```
    annotateWorkflow.
    
    Specified by:
    
    annotateWorkflow in interface Metadata
    
    Parameters:
    workflowSWID - a int.
    atts - a Set object.
  - annotateWorkflowRun
```
public void annotateWorkflowRun(int workflowSWID,
                       Set<WorkflowRunAttribute> atts)
```
    annotateWorkflowRun.
    
    Specified by:
    
    annotateWorkflowRun in interface Metadata
    
    Parameters:
    workflowSWID - a int.
    atts - a Set object.
  - getProcessingRelations
```
public String getProcessingRelations(String swAccession)
```
    Description copied from interface: Metadata
    
    getProcessingRelations.
    
    Specified by:
    
    getProcessingRelations in interface Metadata
    
    Returns:
    a Dot format string
  - getWorkflowRunReportStdErr
```
public String getWorkflowRunReportStdErr(int workflowRunSWID)
```
    Description copied from interface: Metadata
    
    getWorkflowRunReportStdErr.
    
    Specified by:
    
    getWorkflowRunReportStdErr in interface Metadata
    
    Parameters:
    workflowRunSWID - a int.
    
    Returns:
    a String object.
  - getWorkflowRunReportStdOut
```
public String getWorkflowRunReportStdOut(int workflowRunSWID)
```
    Description copied from interface: Metadata
    
    getWorkflowRunReportStdOut.
    
    Specified by:
    
    getWorkflowRunReportStdOut in interface Metadata
    
    Parameters:
    workflowRunSWID - a int.
    
    Returns:
    a String object.
  - getWorkflow
```
public Workflow getWorkflow(int workflowAccession)
```
    Description copied from interface: Metadata
    
    Get a workflow
    
    Specified by:
    
    getWorkflow in interface Metadata
    
    Returns:
  - getAllSequencerRuns
```
public List<SequencerRun> getAllSequencerRuns()
```
    Description copied from interface: Metadata
    
    Get all of the sequencer runs in the DB.
    
    Specified by:
    
    getAllSequencerRuns in interface Metadata
    
    Returns:
    a list of Sequencer runs
  - getLanesFrom
```
public List<Lane> getLanesFrom(int sequencerRunAccession)
```
    Description copied from interface: Metadata
    
    Get Lanes from a sequencer run.
    
    Specified by:
    
    getLanesFrom in interface Metadata
    
    Parameters:
    sequencerRunAccession - the sw_accession of the sequencer run
    
    Returns:
    the lanes from the run
  - getIUSFrom
```
public List<IUS> getIUSFrom(int laneOrSampleAccession)
```
    Description copied from interface: Metadata
    
    Get IUSes (barcodes) from a lane or sample.
    
    Specified by:
    
    getIUSFrom in interface Metadata
    
    Parameters:
    laneOrSampleAccession - the sw_accession of the lane or sample
    
    Returns:
    a list of IUSes (barcodes)
  - getExperimentsFrom
```
public List<Experiment> getExperimentsFrom(int studyAccession)
```
    Description copied from interface: Metadata
    
    Get experiments from a study.
    
    Specified by:
    
    getExperimentsFrom in interface Metadata
    
    Parameters:
    studyAccession - the sw_accession of the study
    
    Returns:
    a list of Experiments
  - getSamplesFrom
```
public List<Sample> getSamplesFrom(int experimentAccession)
```
    Description copied from interface: Metadata
    
    Get the samples from an experiment.
    
    Specified by:
    
    getSamplesFrom in interface Metadata
    
    Parameters:
    experimentAccession - the sw_accession of the experiment
    
    Returns:
    a list of samples
  - getChildSamplesFrom
```
public List<Sample> getChildSamplesFrom(int parentSampleAccession)
```
    Description copied from interface: Metadata
    
    Get the child samples of a parent sample. These samples are further down the sample hierarchy (more specific). For example, if the parent sample or donor is ABC_001, the child sample would be ABC_001_Ref for the reference (blood) sample from the donor.
    
    Specified by:
    
    getChildSamplesFrom in interface Metadata
    
    Parameters:
    parentSampleAccession - the sw_accession of the parent sample / donor
    
    Returns:
    a list of child samples.
  - getParentSamplesFrom
```
public List<Sample> getParentSamplesFrom(int childSampleAccession)
```
    Description copied from interface: Metadata
    
    Get the parent samples of a sample. These samples are further up the sample hierarchy (less specific). For example, if the parent sample or donor is ABC_001, the child sample would be ABC_001_Ref for the reference (blood) sample from the donor.
    
    Specified by:
    
    getParentSamplesFrom in interface Metadata
    
    Parameters:
    childSampleAccession - the sw_accession of the child sample
    
    Returns:
    a list of parent samples / donors
  - getWorkflowRunsAssociatedWithInputFiles
```
public List<WorkflowRun> getWorkflowRunsAssociatedWithInputFiles(List<Integer> fileAccessions)
```
    Description copied from interface: Metadata
    
    Returns the workflow_runs associated with a group of input files. Specifically, this resource will return all workflow runs that use at least one of the input file accessions
    
    Specified by:
    
    getWorkflowRunsAssociatedWithInputFiles in interface Metadata
    
    Returns:
  - getWorkflowRunsAssociatedWithInputFiles
```
public List<WorkflowRun> getWorkflowRunsAssociatedWithInputFiles(List<Integer> fileAccessions,
                                                        List<Integer> workflowAccessions)
```
    Description copied from interface: Metadata
    
    Returns the workflow_runs associated with a group of input files. Specifically, this resource will return all workflow runs that use at least one of the input file accessions constrained to the provided list of workflow accessions
    
    Specified by:
    
    getWorkflowRunsAssociatedWithInputFiles in interface Metadata
    
    Returns:
  - getWorkflowRunsAssociatedWithFiles
```
public List<WorkflowRun> getWorkflowRunsAssociatedWithFiles(List<Integer> fileAccessions,
                                                   String search_type)
```
    Description copied from interface: Metadata
    
    Returns the workflow_runs associated with a group of files. Search types are defined as:
    
    Specified by:
    
    getWorkflowRunsAssociatedWithFiles in interface Metadata
    
    Returns:
  - annotateFile
```
public void annotateFile(int laneSWID,
                FileAttribute iusAtt,
                Boolean skip)
```
    Description copied from interface: Metadata
    
    annotateFile.
    
    Specified by:
    
    annotateFile in interface Metadata
    
    skip - a Boolean object.
  - annotateFile
```
public void annotateFile(int fileSWID,
                Set<FileAttribute> iusAtts)
```
    Description copied from interface: Metadata
    
    annotateFile.
    
    Specified by:
    
    annotateFile in interface Metadata
    
    Parameters:
    fileSWID - a int.
  - getLane
```
public Lane getLane(int laneAccession)
```
    Description copied from interface: Metadata
    
    getLane.
    
    Specified by:
    
    getLane in interface Metadata
    
    Parameters:
    laneAccession - a int.
    
    Returns:
    a Lane object.
  - getSequencerRun
```
public SequencerRun getSequencerRun(int sequencerRunAccession)
```
    Description copied from interface: Metadata
    
    getSequencerRun.
    
    Specified by:
    
    getSequencerRun in interface Metadata
    
    Parameters:
    sequencerRunAccession - a int.
    
    Returns:
    a SequencerRun object.
  - getExperimentLibraryDesigns
```
public List<ExperimentLibraryDesign> getExperimentLibraryDesigns()
```
    Description copied from interface: Metadata
    
    getExperimentLibraryDesigns.
    
    Specified by:
    
    getExperimentLibraryDesigns in interface Metadata
    
    Returns:
    a ExperimentLibraryDesign object.
  - getExperimentSpotDesignReadSpecs
```
public List<ExperimentSpotDesignReadSpec> getExperimentSpotDesignReadSpecs()
```
    Description copied from interface: Metadata
    
    getPlatforms.
    
    Specified by:
    
    getExperimentSpotDesignReadSpecs in interface Metadata
    
    Returns:
    a ExperimentSpotDesignReadSpec object.
  - getExperimentSpotDesigns
```
public List<ExperimentSpotDesign> getExperimentSpotDesigns()
```
    Description copied from interface: Metadata
    
    getExperimentSpotDesigns.
    
    Specified by:
    
    getExperimentSpotDesigns in interface Metadata
    
    Returns:
    a ExperimentSpotDesign object.
  - getExperiment
```
public Experiment getExperiment(int swAccession)
```
    Description copied from interface: Metadata
    
    getExperiment.
    
    Specified by:
    
    getExperiment in interface Metadata
    
    Parameters:
    swAccession - a int.
    
    Returns:
    a Experiment object.
  - getViaParentAccessions
```
public List<ParentAccessionModel> getViaParentAccessions(int[] potentialParentAccessions)
```
    Description copied from interface: Metadata
    
    Get the models corresponding to potential parent accessions
    
    Specified by:
    
    getViaParentAccessions in interface Metadata
    
    Returns:
    a list, with null when parent accessions are invalid
  - getViaAccessions
```
public List<Object> getViaAccessions(int[] accessions)
```
    Description copied from interface: Metadata
    
    Get the models corresponding to potential accessions
    
    Specified by:
    
    getViaAccessions in interface Metadata
    
    Returns:
    a list, with null when accessions are invalid
  - fileProvenanceReportTrigger
```
public void fileProvenanceReportTrigger()
```
    Description copied from interface: Metadata
    
    Triggers the file provenance report, this is a costly operation so it should be scheduled via a cron or similar
    
    Specified by:
    
    fileProvenanceReportTrigger in interface Metadata
  - getStudyByName
```
public List<Study> getStudyByName(String name)
```
    Specified by:
    
    getStudyByName in interface Metadata
  - getSampleByName
```
public List<Sample> getSampleByName(String name)
```
    Specified by:
    
    getSampleByName in interface Metadata
  - getSequencerRunByName
```
public SequencerRun getSequencerRunByName(String name)
```
    Specified by:
    
    getSequencerRunByName in interface Metadata
  - getProcessing
```
public Processing getProcessing(int processingAccession)
```
    Description copied from interface: Metadata
    
    getProcessing.
    
    Specified by:
    
    getProcessing in interface Metadata
    
    Parameters:
    processingAccession - a int.
    
    Returns:
    a Processing object.
  - getWorkflowRunReport
```
public String getWorkflowRunReport(WorkflowRunStatus status,
                          Date earliestDate,
                          Date latestDate)
```
    Description copied from interface: Metadata
    
    getWorkflowRunReport.
    
    Specified by:
    
    getWorkflowRunReport in interface Metadata
    
    Parameters:
    status - , can be null
    earliestDate - a Date object.
    latestDate - a Date object.
    
    Returns:
    a String object.
  - getWorkflowRunReport
```
public String getWorkflowRunReport(Integer workflowSWID,
                          WorkflowRunStatus status,
                          Date earliestDate,
                          Date latestDate)
```
    Specified by:
    
    getWorkflowRunReport in interface Metadata
  - getWorkflowRunsByStatusCmd
```
public List<WorkflowRun> getWorkflowRunsByStatusCmd(String statusCmd)
```
    Description copied from interface: Metadata
    
    Get workflow run by status cmd (oozie job id in oozie).
    
    Specified by:
    
    getWorkflowRunsByStatusCmd in interface Metadata
    
    Returns:
  - getEnvironmentReport
```
public Map<String,String> getEnvironmentReport()
```
    Description copied from interface: Metadata
    
    Retrieves all environmental information from the web-service
    
    Specified by:
    
    getEnvironmentReport in interface Metadata
    
    Returns:
  - checkClientServerMatchingVersion
```
public boolean checkClientServerMatchingVersion()
```
    Description copied from interface: Metadata
    
    Check to see if client seqware version matches server version
    
    Specified by:
    
    checkClientServerMatchingVersion in interface Metadata
    
    Returns:
  - getIUS
```
public IUS getIUS(int swAccession)
```
    Description copied from interface: Metadata
    
    Get ius by sw accession
    
    Specified by:
    
    getIUS in interface Metadata
    
    Returns:
  - getSample
```
public Sample getSample(int swAccession)
```
    Description copied from interface: Metadata
    
    Get sample by swa
    
    Specified by:
    
    getSample in interface Metadata
    
    Returns:
  - getStudy
```
public Study getStudy(int swAccession)
```
    Description copied from interface: Metadata
    
    Get study by swa
    
    Specified by:
    
    getStudy in interface Metadata
    
    Returns:

Class MetadataNoConnection

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

MetadataNoConnection

Method Detail

fileProvenanceReport

fileProvenanceReport

addStudy

addExperiment

addSample

addSequencerRun

addLane

addIUS

getPlatforms

getOrganisms

getStudyTypes

getLibraryStrategies

getLibrarySelections

getLibrarySource

add_empty_processing_event

add_empty_processing_event_by_parent_accession

mapProcessingIdToAccession

linkWorkflowRunAndParent

processing_event_to_task_group

add_task_group

associate_processing_event_with_parents_and_child

update_processing_status

add_workflow_run

get_workflow_run_accession

get_workflow_run_id

getWorkflowRun

add_workflow_run_ancestor

update_processing_workflow_run

update_workflow_run

updateWorkflowRun

update_processing_event

clean_up

addWorkflow

get_workflow_info

isDuplicateFile

updateWorkflow

listInstalledWorkflows

listInstalledWorkflowParams

getWorkflowAccession

getWorkflowRunsByStatus

getWorkflowRunWithWorkflow

getAllStudies

getSequencerRunReport

annotateIUS

annotateLane

annotateSequencerRun

annotateExperiment

annotateProcessing

annotateSample

annotateStudy

getWorkflowRunReport

getWorkflowRunReport

getWorkflowRunReport

getFile

getWorkflowParams

annotateWorkflow

annotateWorkflowRun

annotateIUS

annotateLane

annotateSequencerRun

annotateExperiment

annotateProcessing

annotateSample

annotateStudy

annotateWorkflow

annotateWorkflowRun

getProcessingRelations

getWorkflowRunReportStdErr

getWorkflowRunReportStdOut

getWorkflow

getAllSequencerRuns

getLanesFrom

getIUSFrom