Metadata (SeqWare 1.1.2 API)

All Known Implementing Classes:

MetadataDB, MetadataInMemory, MetadataNoConnection, MetadataWS
```
public interface Metadata
```

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 laneSWID, 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[] potentialAccessions)` 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 workflowRunID)` 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)`

Method Detail

clean_up
```
ReturnValue clean_up()
```
clean_up.

Returns:
a ReturnValue object.

mapProcessingIdToAccession
```
int mapProcessingIdToAccession(int processingId)
```
mapProcessingIdToAccession.

Parameters:
processingId - a int.

Returns:
a int.

addStudy

ReturnValue addStudy(String title,
                   String description,
                   String centerName,
                   String centerProjectName,
                   Integer studyTypeId)

addStudy.

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

ReturnValue addExperiment(Integer studySwAccession,
                        Integer platformId,
                        String description,
                        String title,
                        Integer experimentLibraryDesignId,
                        Integer experimentSpotDesignId)

addExperiment.

Parameters:: studySwAccession - a Integer object.; platformId - a Integer object.; description - a String object.; title - a String object.; experimentLibraryDesignId - the value of experimentLibraryDesignId; experimentSpotDesignId - the value of experimentSpotDesignId
Returns:: a ReturnValue object.

addSample

ReturnValue addSample(Integer experimentAccession,
                    Integer parentSampleAccession,
                    Integer organismId,
                    String description,
                    String title)

addSample.

Parameters:: experimentAccession - a Integer object.; parentSampleAccession -; organismId - a Integer object.; description - a String object.; title - a String object.
Returns:: a ReturnValue object.

addSequencerRun

ReturnValue addSequencerRun(Integer platformAccession,
                          String name,
                          String description,
                          boolean pairdEnd,
                          boolean skip,
                          String filePath,
                          SequencerRunStatus status)

addSample.

Parameters:: platformAccession -; name -; description - a String object.; status - the value of status; pairdEnd -; filePath -; skip -
Returns:: a ReturnValue object.

addLane

ReturnValue addLane(Integer sequencerRunAccession,
                  Integer studyTypeId,
                  Integer libraryStrategyId,
                  Integer librarySelectionId,
                  Integer librarySourceId,
                  String name,
                  String description,
                  String cycleDescriptor,
                  boolean skip,
                  Integer laneNumber)

addSample.

Parameters:: sequencerRunAccession -; studyTypeId -; libraryStrategyId -; librarySelectionId -; description - a String object.; laneNumber -; librarySourceId -; name -; skip -; cycleDescriptor -
Returns:: a ReturnValue object.

addIUS

ReturnValue addIUS(Integer laneAccession,
                 Integer sampleAccession,
                 String name,
                 String description,
                 String barcode,
                 boolean skip)

addSample.

Parameters:: laneAccession -; sampleAccession -; skip -; name -; barcode -; description -
Returns:: a ReturnValue object.

getPlatforms
```
List<Platform> getPlatforms()
```
getPlatforms.

Returns:
a Platform object.

getExperiment
```
Experiment getExperiment(int swAccession)
```
getExperiment.

Parameters:
swAccession - a int.

Returns:
a Experiment object.

getExperimentLibraryDesigns
```
List<ExperimentLibraryDesign> getExperimentLibraryDesigns()
```
getExperimentLibraryDesigns.

Returns:
a ExperimentLibraryDesign object.

getExperimentSpotDesignReadSpecs
```
List<ExperimentSpotDesignReadSpec> getExperimentSpotDesignReadSpecs()
```
getPlatforms.

Returns:
a ExperimentSpotDesignReadSpec object.

getExperimentSpotDesigns
```
List<ExperimentSpotDesign> getExperimentSpotDesigns()
```
getExperimentSpotDesigns.

Returns:
a ExperimentSpotDesign object.

getOrganisms
```
List<Organism> getOrganisms()
```
getOrganisms.

Returns:
a Organism object.

getStudyTypes
```
List<StudyType> getStudyTypes()
```
getStudyTypes.

Returns:
a StudyType object.

getLibraryStrategies
```
List<LibraryStrategy> getLibraryStrategies()
```
getLibraryStrategies.

Returns:
a LibraryStrategy object.

getLibrarySelections
```
List<LibrarySelection> getLibrarySelections()
```
getLibrarySelections.

Returns:
a LibrarySelection object.

getLibrarySource
```
List<LibrarySource> getLibrarySource()
```
getLibrarySource.

Returns:
a LibrarySource object.

add_empty_processing_event
```
ReturnValue add_empty_processing_event(int[] parentIDs)
```
add_empty_processing_event.

Parameters:
parentIDs - an array of int.

Returns:
a ReturnValue object.

add_empty_processing_event_by_parent_accession
```
ReturnValue add_empty_processing_event_by_parent_accession(int[] parentAccessions)
```
add_empty_processing_event_by_parent_accession.

Parameters:
parentAccessions - an array of int.

Returns:
a ReturnValue object.

add_task_group

ReturnValue add_task_group(int[] parentIDs,
                         int[] childIDs,
                         String algorithm,
                         String description)

add_task_group.

Parameters:: parentIDs - an array of int.; childIDs - an array of int.; algorithm - a String object.; description - a String object.
Returns:: a ReturnValue object.

processing_event_to_task_group

ReturnValue processing_event_to_task_group(int processingID,
                                         int[] parentIDs,
                                         int[] childIDs,
                                         String algorithm,
                                         String description)

processing_event_to_task_group.

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.

update_processing_event

ReturnValue update_processing_event(int processingID,
                                  ReturnValue retval)

update_processing_event.

Parameters:: processingID - a int.; retval - a ReturnValue object.
Returns:: a ReturnValue object.

update_processing_status

ReturnValue update_processing_status(int processingID,
                                   ProcessingStatus status)

update_processing_status.

Parameters:: processingID - a int.; status - a String object.
Returns:: a ReturnValue object.

associate_processing_event_with_parents_and_child

ReturnValue associate_processing_event_with_parents_and_child(int processingID,
                                                            int[] parentIDs,
                                                            int[] childIDs)

associate_processing_event_with_parents_and_child.

Parameters:: processingID - a int.; parentIDs - an array of int.; childIDs - an array of int.
Returns:: a ReturnValue object.

add_workflow_run
```
int add_workflow_run(int workflowAccession)
```
add_workflow_run.

Parameters:
workflowAccession - a int.

Returns:
a int.

update_processing_workflow_run
```
ReturnValue update_processing_workflow_run(int processingID,
                                         int workflowRunID)
```
update_processing_workflow_run.

Parameters:
processingID - a int.
workflowRunID - a int.

Returns:
a ReturnValue object.

add_workflow_run_ancestor
```
void add_workflow_run_ancestor(int workflowRunAccession,
                             int processingId)
```
add_workflow_run_ancestor.

Parameters:
workflowRunAccession - a int.
processingId - a int.

get_workflow_run_accession
```
int get_workflow_run_accession(int workflowRunId)
```
get_workflow_run_accession.

Parameters:
workflowRunId - a int.

Returns:
a int.

get_workflow_run_id
```
int get_workflow_run_id(int workflowRunAccession)
```
get_workflow_run_id.

Parameters:
workflowRunAccession - a int.

Returns:
a int.

getWorkflowRun
```
WorkflowRun getWorkflowRun(int workflowRunAccession)
```
getWorkflowRun.

Parameters:
workflowRunAccession - a int.

Returns:
a WorkflowRun object.

getWorkflowRunsByStatusCmd
```
List<WorkflowRun> getWorkflowRunsByStatusCmd(String statusCmd)
```
Get workflow run by status cmd (oozie job id in oozie).

Parameters:
statusCmd -

Returns:

getWorkflowRunsAssociatedWithInputFiles
```
List<WorkflowRun> getWorkflowRunsAssociatedWithInputFiles(List<Integer> fileAccessions)
```
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

Parameters:
fileAccessions -

Returns:

getWorkflowRunsAssociatedWithInputFiles
```
List<WorkflowRun> getWorkflowRunsAssociatedWithInputFiles(List<Integer> fileAccessions,
                                                        List<Integer> workflowAccessions)
```
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

Parameters:
fileAccessions -
workflowAccessions -

Returns:

getWorkflowRunsAssociatedWithFiles

List<WorkflowRun> getWorkflowRunsAssociatedWithFiles(List<Integer> fileAccessions,
                                                   String search_type)

Returns the workflow_runs associated with a group of files. Search types are defined as:

Parameters:: fileAccessions -; search_type -
Returns:

get_workflow_info
```
Map<String,String> get_workflow_info(int workflowAccession)
```
get_workflow_info.

Parameters:
workflowAccession - a int.

Returns:
a Map object.

linkWorkflowRunAndParent

boolean linkWorkflowRunAndParent(int workflowRunId,
                               int parentAccession)
                                 throws SQLException

linkWorkflowRunAndParent.

Parameters:: workflowRunId - a int.; parentAccession - a int.
Returns:: a boolean.
Throws:: SQLException - if any.

update_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.

Parameters:: 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; inputFiles -
Returns:: a ReturnValue object.

updateWorkflowRun

void updateWorkflowRun(WorkflowRun wr)

addWorkflow

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.

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.; workflowClass -; workflowEngine -; workflowType -; seqwareVersion -
Returns:: a ReturnValue object.

updateWorkflow

ReturnValue updateWorkflow(int workflowId,
                         String permanentBundleLocation)

updateWorkflow.

Parameters:: workflowId - a int.; permanentBundleLocation - a String object.
Returns:: a ReturnValue object.

listInstalledWorkflows
```
String listInstalledWorkflows()
```
listInstalledWorkflows.

Returns:
a String object.

listInstalledWorkflowParams
```
String listInstalledWorkflowParams(String workflowAccession)
```
listInstalledWorkflowParams.

Parameters:
workflowAccession - a String object.

Returns:
a String object.

getWorkflowAccession
```
int getWorkflowAccession(String name,
                       String version)
```
getWorkflowAccession.

Parameters:
name - a String object.
version - a String object.

Returns:
a int.

fileProvenanceReportTrigger
```
void fileProvenanceReportTrigger()
```
Triggers the file provenance report, this is a costly operation so it should be scheduled via a cron or similar

fileProvenanceReport
```
void fileProvenanceReport(Map<FileProvenanceParam,List<String>> params,
                        Writer out)
```
Retrieves the file provenance report, writing it to the specified output stream as a TSV.

Parameters:
params - the parameters to filter the results
out - where the TSV content will be written

fileProvenanceReport
```
List<Map<String,String>> fileProvenanceReport(Map<FileProvenanceParam,List<String>> params)
```
Retrieves the file provenance report.

Parameters:
params - the parameters to filter the results

Returns:
the list of each file provenance entry

getEnvironmentReport
```
Map<String,String> getEnvironmentReport()
```
Retrieves all environmental information from the web-service

Returns:

checkClientServerMatchingVersion
```
boolean checkClientServerMatchingVersion()
```
Check to see if client seqware version matches server version

Returns:

isDuplicateFile
```
Boolean isDuplicateFile(String filepath)
```
isDuplicateFile.

Parameters:
filepath - a String object.

Returns:
a Boolean object.

getWorkflowRunsByStatus
```
List<WorkflowRun> getWorkflowRunsByStatus(WorkflowRunStatus status)
```
getWorkflowRunsByStatus.

Parameters:
status - a String object.

Returns:
a List object.

getWorkflowRunWithWorkflow
```
WorkflowRun getWorkflowRunWithWorkflow(String workflowRunAccession)
```
getWorkflowRunWithWorkflow.

Parameters:
workflowRunAccession - a String object.

Returns:
a WorkflowRun object.

getAllStudies
```
List<Study> getAllStudies()
```
getAllStudies.

Returns:
a List object.

getSequencerRunReport
```
String getSequencerRunReport()
```
getSequencerRunReport.

Returns:
a String object.

annotateFile

void annotateFile(int laneSWID,
                FileAttribute iusAtt,
                Boolean skip)

annotateFile.

Parameters:: laneSWID -; iusAtt -; skip - a Boolean object.

annotateFile

void annotateFile(int fileSWID,
                Set<FileAttribute> iusAtts)

annotateFile.

Parameters:: fileSWID - a int.; iusAtts -

annotateIUS

void annotateIUS(int laneSWID,
               IUSAttribute iusAtt,
               Boolean skip)

annotateIUS.

Parameters:: laneSWID - a int.; iusAtt - a IUSAttribute object.; skip - a Boolean object.

annotateIUS

void annotateIUS(int laneSWID,
               Set<IUSAttribute> iusAtts)

annotateIUS.

Parameters:: laneSWID - a int.; iusAtts - a Set object.

annotateLane

void annotateLane(int laneSWID,
                LaneAttribute laneAtt,
                Boolean skip)

annotateLane.

Parameters:: laneSWID - a int.; laneAtt - a LaneAttribute object.; skip - a Boolean object.

annotateLane

void annotateLane(int laneSWID,
                Set<LaneAttribute> laneAtts)

annotateLane.

Parameters:: laneSWID - a int.; laneAtts - a Set object.

annotateSequencerRun

void annotateSequencerRun(int sequencerRunSWID,
                        SequencerRunAttribute sequencerRunAtt,
                        Boolean skip)

annotateSequencerRun.

Parameters:: sequencerRunSWID - a int.; sequencerRunAtt - a SequencerRunAttribute object.; skip - a Boolean object.

annotateSequencerRun

void annotateSequencerRun(int sequencerRunSWID,
                        Set<SequencerRunAttribute> sequencerRunAtts)

annotateSequencerRun.

Parameters:: sequencerRunSWID - a int.; sequencerRunAtts - a Set object.

annotateExperiment

void annotateExperiment(int experimentSWID,
                      ExperimentAttribute att,
                      Boolean skip)

annotateExperiment.

Parameters:: experimentSWID - a int.; att - a ExperimentAttribute object.; skip - a Boolean object.

annotateExperiment

void annotateExperiment(int experimentSWID,
                      Set<ExperimentAttribute> atts)

annotateExperiment.

Parameters:: experimentSWID - a int.; atts - a Set object.

annotateProcessing

void annotateProcessing(int processingSWID,
                      ProcessingAttribute att,
                      Boolean skip)

annotateProcessing.

Parameters:: processingSWID - a int.; att - a ProcessingAttribute object.; skip - a Boolean object.

annotateProcessing

void annotateProcessing(int processingSWID,
                      Set<ProcessingAttribute> atts)

annotateProcessing.

Parameters:: processingSWID - a int.; atts - a Set object.

annotateSample

void annotateSample(int sampleSWID,
                  SampleAttribute att,
                  Boolean skip)

annotateSample.

Parameters:: sampleSWID - a int.; att - a SampleAttribute object.; skip - a Boolean object.

annotateSample

void annotateSample(int sampleSWID,
                  Set<SampleAttribute> atts)

annotateSample.

Parameters:: sampleSWID - a int.; atts - a Set object.

annotateStudy

void annotateStudy(int studySWID,
                 StudyAttribute att,
                 Boolean skip)

annotateStudy.

Parameters:: studySWID - a int.; att - a StudyAttribute object.; skip - a Boolean object.

annotateStudy

void annotateStudy(int studySWID,
                 Set<StudyAttribute> atts)

annotateStudy.

Parameters:: studySWID - a int.; atts - a Set object.

annotateWorkflow

void annotateWorkflow(int workflowSWID,
                    WorkflowAttribute att,
                    Boolean skip)

annotateWorkflow.

Parameters:: workflowSWID - a int.; att - a WorkflowAttribute object.; skip - a Boolean object.

annotateWorkflow

void annotateWorkflow(int workflowSWID,
                    Set<WorkflowAttribute> atts)

annotateWorkflow.

Parameters:: workflowSWID - a int.; atts - a Set object.

annotateWorkflowRun

void annotateWorkflowRun(int workflowrunSWID,
                       WorkflowRunAttribute att,
                       Boolean skip)

annotateWorkflowRun.

Parameters:: workflowrunSWID - a int.; att - a WorkflowRunAttribute object.; skip - a Boolean object.

annotateWorkflowRun

void annotateWorkflowRun(int workflowSWID,
                       Set<WorkflowRunAttribute> atts)

annotateWorkflowRun.

Parameters:: workflowSWID - a int.; atts - a Set object.

getWorkflowRunReport
```
String getWorkflowRunReport(int workflowRunSWID)
```
getWorkflowRunReport.

Parameters:
workflowRunSWID - a int.

Returns:
a String object.

getWorkflowRunReportStdErr
```
String getWorkflowRunReportStdErr(int workflowRunSWID)
```
getWorkflowRunReportStdErr.

Parameters:
workflowRunSWID - a int.

Returns:
a String object.

getWorkflowRunReportStdOut
```
String getWorkflowRunReportStdOut(int workflowRunSWID)
```
getWorkflowRunReportStdOut.

Parameters:
workflowRunSWID - a int.

Returns:
a String object.

getWorkflowRunReport

String getWorkflowRunReport(int workflowSWID,
                          Date earliestDate,
                          Date latestDate)

getWorkflowRunReport.

Parameters:: workflowSWID - a int.; earliestDate - a Date object.; latestDate - a Date object.
Returns:: a String object.

getWorkflowRunReport

String getWorkflowRunReport(WorkflowRunStatus status,
                          Date earliestDate,
                          Date latestDate)

getWorkflowRunReport.

Parameters:: status - , can be null; earliestDate - a Date object.; latestDate - a Date object.
Returns:: a String object.

getWorkflowRunReport

String getWorkflowRunReport(Integer workflowSWID,
                          WorkflowRunStatus status,
                          Date earliestDate,
                          Date latestDate)

getWorkflowRunReport

String getWorkflowRunReport(Date earliestDate,
                          Date latestDate)

getWorkflowRunReport.

Parameters:: earliestDate - a Date object.; latestDate - a Date object.
Returns:: a String object.

getFile
```
File getFile(int swAccession)
```
getFile.

Parameters:
swAccession - a int.

Returns:
a File object.

getWorkflowParams
```
SortedSet<WorkflowParam> getWorkflowParams(String swAccession)
```
getWorkflowParams.

Parameters:
swAccession - a String object.

Returns:
a SortedSet object.

getProcessingRelations
```
String getProcessingRelations(String swAccession)
```
getProcessingRelations.

Parameters:
swAccession -

Returns:
a Dot format string

getWorkflow
```
Workflow getWorkflow(int workflowAccession)
```
Get a workflow

Parameters:
workflowAccession -

Returns:

getAllSequencerRuns
```
List<SequencerRun> getAllSequencerRuns()
```
Get all of the sequencer runs in the DB.

Returns:
a list of Sequencer runs

getLane
```
Lane getLane(int laneAccession)
```
getLane.

Parameters:
laneAccession - a int.

Returns:
a Lane object.

getProcessing
```
Processing getProcessing(int processingAccession)
```
getProcessing.

Parameters:
processingAccession - a int.

Returns:
a Processing object.

getSequencerRun
```
SequencerRun getSequencerRun(int sequencerRunAccession)
```
getSequencerRun.

Parameters:
sequencerRunAccession - a int.

Returns:
a SequencerRun object.

getLanesFrom
```
List<Lane> getLanesFrom(int sequencerRunAccession)
```
Get Lanes from a sequencer run.

Parameters:
sequencerRunAccession - the sw_accession of the sequencer run

Returns:
the lanes from the run

getIUSFrom
```
List<IUS> getIUSFrom(int laneOrSampleAccession)
```
Get IUSes (barcodes) from a lane or sample.

Parameters:
laneOrSampleAccession - the sw_accession of the lane or sample

Returns:
a list of IUSes (barcodes)

getExperimentsFrom
```
List<Experiment> getExperimentsFrom(int studyAccession)
```
Get experiments from a study.

Parameters:
studyAccession - the sw_accession of the study

Returns:
a list of Experiments

getSamplesFrom
```
List<Sample> getSamplesFrom(int experimentAccession)
```
Get the samples from an experiment.

Parameters:
experimentAccession - the sw_accession of the experiment

Returns:
a list of samples

getChildSamplesFrom
```
List<Sample> getChildSamplesFrom(int parentSampleAccession)
```
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.

Parameters:
parentSampleAccession - the sw_accession of the parent sample / donor

Returns:
a list of child samples.

getParentSamplesFrom
```
List<Sample> getParentSamplesFrom(int childSampleAccession)
```
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.

Parameters:
childSampleAccession - the sw_accession of the child sample

Returns:
a list of parent samples / donors

getViaParentAccessions
```
List<ParentAccessionModel> getViaParentAccessions(int[] potentialParentAccessions)
```
Get the models corresponding to potential parent accessions

Parameters:
potentialParentAccessions -

Returns:
a list, with null when parent accessions are invalid

getViaAccessions
```
List<Object> getViaAccessions(int[] potentialAccessions)
```
Get the models corresponding to potential accessions

Parameters:
potentialAccessions -

Returns:
a list, with null when accessions are invalid

getStudyByName

List<Study> getStudyByName(String name)

getSampleByName

List<Sample> getSampleByName(String name)

getSequencerRunByName

SequencerRun getSequencerRunByName(String name)

getIUS
```
IUS getIUS(int swAccession)
```
Get ius by sw accession

Parameters:
swAccession -

Returns:

getSample
```
Sample getSample(int swAccession)
```
Get sample by swa

Parameters:
swAccession -

Returns:

getStudy
```
Study getStudy(int swAccession)
```
Get study by swa

Parameters:
swAccession -

Returns:

Interface Metadata

Method Summary

Method Detail

clean_up

mapProcessingIdToAccession

addStudy

addExperiment

addSample

addSequencerRun

addLane

addIUS

getPlatforms

getExperiment

getExperimentLibraryDesigns

getExperimentSpotDesignReadSpecs

getExperimentSpotDesigns

getOrganisms

getStudyTypes

getLibraryStrategies

getLibrarySelections

getLibrarySource

add_empty_processing_event

add_empty_processing_event_by_parent_accession

add_task_group

processing_event_to_task_group

update_processing_event

update_processing_status

associate_processing_event_with_parents_and_child

add_workflow_run

update_processing_workflow_run

add_workflow_run_ancestor

get_workflow_run_accession

get_workflow_run_id

getWorkflowRun

getWorkflowRunsByStatusCmd

getWorkflowRunsAssociatedWithInputFiles

getWorkflowRunsAssociatedWithInputFiles

getWorkflowRunsAssociatedWithFiles

get_workflow_info

linkWorkflowRunAndParent

update_workflow_run

updateWorkflowRun

addWorkflow

updateWorkflow

listInstalledWorkflows

listInstalledWorkflowParams

getWorkflowAccession

fileProvenanceReportTrigger

fileProvenanceReport

fileProvenanceReport

getEnvironmentReport

checkClientServerMatchingVersion

isDuplicateFile

getWorkflowRunsByStatus

getWorkflowRunWithWorkflow

getAllStudies

getSequencerRunReport

annotateFile

annotateFile

annotateIUS

annotateIUS

annotateLane

annotateLane

annotateSequencerRun

annotateSequencerRun

annotateExperiment

annotateExperiment

annotateProcessing

annotateProcessing

annotateSample

annotateSample

annotateStudy

annotateStudy

annotateWorkflow

annotateWorkflow

annotateWorkflowRun

annotateWorkflowRun

getWorkflowRunReport

getWorkflowRunReportStdErr

getWorkflowRunReportStdOut