Package ca.corefacility.bioinformatics.irida.service.sample

Interface SampleService

All Superinterfaces:

CRUDService<java.lang.Long,Sample>

All Known Implementing Classes:

SampleServiceImpl

public interface SampleService
extends CRUDService<java.lang.Long,Sample>

A service class for working with samples.

Method Summary

Modifier and Type	Method	Description
java.lang.Double	estimateCoverageForSample(Sample sample, long referenceFileLength)	Given the length of a reference file, estimate the total coverage for this sample.
java.lang.Double	estimateCoverageForSample(Sample sample, ReferenceFile referenceFile)	Given a ReferenceFile, estimate the total coverage for this sample.
java.util.Map<java.lang.Long,java.lang.Long>	getCoverageForSamplesInProject(Project project, java.util.List<java.lang.Long> sampleIds)	Get Coverage for samples within a project.
org.springframework.data.domain.Page<ProjectSampleJoin>	getFilteredProjectSamples(java.util.List<Project> projects, ProjectSampleJoinSpecification filterSpec, int currentPage, int pageSize, org.springframework.data.domain.Sort sort)	Get a Page of ProjectSampleJoin for samples from 1 or more projects based on filtering criteria.
org.springframework.data.domain.Page<ProjectSampleJoin>	getFilteredSamplesForProjects(java.util.List<Project> projects, java.util.List<java.lang.String> sampleNames, java.lang.String sampleName, java.lang.String searchTerm, java.lang.String organism, java.util.Date minDate, java.util.Date maxDate, int currentPage, int pageSize, org.springframework.data.domain.Sort sort)	Get a Page of ProjectSampleJoin for samples from 1 or more projects based on filtering criteria.
java.util.List<java.lang.Long>	getLockedSamplesInProject(Project project)	Get a list of Sample ids that are locked in this project.
ProjectMetadataResponse	getMetadataForProjectSamples(Project project, java.util.List<java.lang.Long> sampleIds, java.util.List<MetadataTemplateField> fields)	Get the metadata collections for a set of samples in a project.
java.util.Set<MetadataEntry>	getMetadataForSample(Sample sample)	Get the MetadataEntry set associated with the given Sample
java.lang.Long	getNumberOfSamplesForProject(Project project)	Get the number of Samples for a given Project.
java.util.List<QCEntry>	getQCEntriesForSample(Sample sample)	Find all the QCEntry associated with SequencingObjects in a given Sample
java.util.Map<java.lang.Long,java.util.List<QCEntry>>	getQCEntriesForSamples(java.util.List<Sample> samples)	Find all the QCEntry associated with SequencingObjects in a given Sample for a list of Samples
Sample	getSampleBySampleName(Project project, java.lang.String sampleName)	Get the Sample with the given sample name
ProjectSampleJoin	getSampleForProject(Project project, java.lang.Long identifier)	Get a specific instance of a Sample that belongs to a Project.
SampleSequencingObjectJoin	getSampleForSequencingObject(SequencingObject seqObject)	Find a Sample assocaited with a SequencingObject
java.util.Map<java.lang.String,java.util.List<java.lang.Long>>	getSampleIdsBySampleNameForProjects(java.util.List<java.lang.Long> projectIds, java.util.List<java.lang.String> sampleNames)	Get the Sample identifiers with the given list of sample names from a list of projects.
java.util.List<java.lang.String>	getSampleOrganismsForProject(Project project)	Get a list of the organism fields stored for all Samples in a Project
java.lang.Long	getSamplesCreated(java.util.Date createdDate)	Get count of samples created in the time period
java.util.List<GenericStatModel>	getSamplesCreatedGrouped(java.util.Date createdDate, StatisticTimePeriod statisticTimePeriod)	Get list of GenericStatModel of samples created in the past n time period grouped by the format provided.
java.util.Collection<Sample>	getSamplesForAnalysisSubmission(AnalysisSubmission submission)	Get a list of all Samples associated with a given AnalysisSubmission
java.util.List<Join<Project,Sample>>	getSamplesForProject(Project project)	Get the list of Sample that belongs to a specific project.
java.util.List<Sample>	getSamplesForProjectShallow(Project project)	Get a shallow listing of the Samples in a Project.
org.springframework.data.domain.Page<ProjectSampleJoin>	getSamplesForProjectWithName(Project project, java.lang.String name, int page, int size, org.springframework.data.domain.Sort.Direction order, java.lang.String... sortProperties)	Get the Samples for a Project in page form
java.util.List<Sample>	getSamplesInProject(Project project, java.util.List<java.lang.Long> sampleIds)	Get a list of Sample in a Project given some Sample ids.
java.lang.Long	getTotalBasesForSample(Sample sample)	Given a sample gets the total number of bases in all sequence files in this sample.
Sample	mergeSampleMetadata(Sample sample, java.util.Set<MetadataEntry> metadataToAdd)	Merge the given set of MetadataEntry into the given Sample.
Sample	mergeSamples(Project p, Sample mergeInto, java.util.Collection<Sample> toMerge)	Merge multiple samples into one.
void	removeSequencingObjectFromSample(Sample sample, SequencingObject object)	Remove a SequencingObject from a given Sample.
org.springframework.data.domain.Page<ProjectSampleJoin>	searchAllSamples(java.lang.String query, java.lang.Integer page, java.lang.Integer count, org.springframework.data.domain.Sort sort)	Search all Samples in the database on the given query
org.springframework.data.domain.Page<ProjectSampleJoin>	searchSamplesForUser(java.lang.String query, java.lang.Integer page, java.lang.Integer count, org.springframework.data.domain.Sort sort)	Search all Samples in projects the current logged in user has access to
Sample	updateSampleMetadata(Sample sample, java.util.Set<MetadataEntry> metadataToSet)	Set the given set of MetadataEntry on the given Sample and save it to the database

Methods inherited from interface ca.corefacility.bioinformatics.irida.service.CRUDService

count, create, delete, exists, findAll, findRevisions, findRevisions, list, list, list, read, readMultiple, search, search, update, updateFields, updateMultiple

Method Detail

getSampleForProject

ProjectSampleJoin getSampleForProject(Project project,
                                      java.lang.Long identifier)
                               throws EntityNotFoundException

Get a specific instance of a Sample that belongs to a Project. If the Sample is not associated to the Project (i.e., no relationship is shared between the Sample and Project, then an EntityNotFoundException will be thrown.

Parameters:

project - the Project to get the Sample for.

identifier - the identifier of the Sample

Returns:

the ProjectSampleJoin describing the relationship between projet and sample

Throws:

EntityNotFoundException - if no relationship exists between Sample and Project.

updateSampleMetadata

Sample updateSampleMetadata(Sample sample,
                            java.util.Set<MetadataEntry> metadataToSet)

Set the given set of MetadataEntry on the given Sample and save it to the database

Parameters:

sample - the Sample to save metadata for

metadataToSet - the metadata to save to the sample

Returns:

the updated Sample

mergeSampleMetadata

Sample mergeSampleMetadata(Sample sample,
                           java.util.Set<MetadataEntry> metadataToAdd)

Merge the given set of MetadataEntry into the given Sample. This will replace existing metadata that matches and add the new data to the sample.

Parameters:

sample - the sample to update

metadataToAdd - the metadata to add

Returns:

the updated Sample

getMetadataForSample

java.util.Set<MetadataEntry> getMetadataForSample(Sample sample)

Get the MetadataEntry set associated with the given Sample

Parameters:

sample - the Sample to get metadata for

Returns:

the metadata associated with the given sample

getLockedSamplesInProject

java.util.List<java.lang.Long> getLockedSamplesInProject(Project project)

Get a list of Sample ids that are locked in this project. This method exists as a faster way of determining ownership than getting the full ProjectSampleJoin

Parameters:

project - the Project to check

Returns:

a List of locked sample IDs.

getMetadataForProjectSamples

ProjectMetadataResponse getMetadataForProjectSamples(Project project,
                                                     java.util.List<java.lang.Long> sampleIds,
                                                     java.util.List<MetadataTemplateField> fields)

Get the metadata collections for a set of samples in a project. This will return a Map of Sample ID with a Set of the MetadataEntrys

Parameters:

project - the Project to get metadata for

sampleIds - the Sample ids to get metadata for

fields - the fields to get metadata from in the project. This must not be empty.

Returns:

a map of metadata

getSampleForSequencingObject

SampleSequencingObjectJoin getSampleForSequencingObject(SequencingObject seqObject)

Find a Sample assocaited with a SequencingObject

Parameters:

seqObject - the SequencingObject to get the Sample for

Returns:

the SampleSequencingObjectJoin describing the relationship

getSamplesForProject

java.util.List<Join<Project,Sample>> getSamplesForProject(Project project)

Get the list of Sample that belongs to a specific project.

Parameters:

project - the Project to get samples for.

Returns:

the collection of samples for the Project.

getSamplesForProjectShallow

java.util.List<Sample> getSamplesForProjectShallow(Project project)

Get a shallow listing of the Samples in a Project. Note: This method will not return any metadata or associated objects.

Parameters:

project - The Project to get samples for

Returns:

a List of Sample

getSamplesInProject

java.util.List<Sample> getSamplesInProject(Project project,
                                           java.util.List<java.lang.Long> sampleIds)

Get a list of Sample in a Project given some Sample ids.

Parameters:

project - Project to get samples for.

sampleIds - List of Sample ids.

Returns:

List of Samples from a Project.

getSampleOrganismsForProject

java.util.List<java.lang.String> getSampleOrganismsForProject(Project project)

Get a list of the organism fields stored for all Samples in a Project

Parameters:

project - the Project to get sample organisms for

Returns:

a list of sample organisms

getNumberOfSamplesForProject

java.lang.Long getNumberOfSamplesForProject(Project project)

Get the number of Samples for a given Project. This method will be faster than getSamplesForProjects

Parameters:

project - The project to get samples for

Returns:

The number of Samples in a given Project

getSamplesForProjectWithName

org.springframework.data.domain.Page<ProjectSampleJoin> getSamplesForProjectWithName(Project project,
                                                                                     java.lang.String name,
                                                                                     int page,
                                                                                     int size,
                                                                                     org.springframework.data.domain.Sort.Direction order,
                                                                                     java.lang.String... sortProperties)

Get the Samples for a Project in page form

Parameters:

project - The project to read from

name - The sample name to search

page - The page number

size - The size of the page

order - The order of the page

sortProperties - The properties to sort on

Returns:

A Page of Joins between Project and Sample

getSampleBySampleName

Sample getSampleBySampleName(Project project,
                             java.lang.String sampleName)

Get the Sample with the given sample name

Parameters:

project - the Project that the Sample belongs to.

sampleName - The name for the requested sample

Returns:

A Sample with the given ID

getSampleIdsBySampleNameForProjects

java.util.Map<java.lang.String,java.util.List<java.lang.Long>> getSampleIdsBySampleNameForProjects(java.util.List<java.lang.Long> projectIds,
                                                                                                         java.util.List<java.lang.String> sampleNames)

Get the Sample identifiers with the given list of sample names from a list of projects.

Parameters:

projectIds - The Project identifiers that the Sample belongs to.

sampleNames - The list of sample names

Returns:

A list of Sample identifiers

removeSequencingObjectFromSample

void removeSequencingObjectFromSample(Sample sample,
                                      SequencingObject object)

Remove a SequencingObject from a given Sample. This will delete the SampleSequencingObjectJoin object

Parameters:

sample - Sample to remove sequences from

object - SequencingObject to remove

mergeSamples

Sample mergeSamples(Project p,
                    Sample mergeInto,
                    java.util.Collection<Sample> toMerge)

Merge multiple samples into one. Merging samples copies the SequenceFile references from the set of samples into one sample. The collection of samples in toMerge are marked as deleted. All samples must be associated with the specified project. The relationship between each sample in toMerge and the project p will be deleted.

Parameters:

p - the Project that all samples must belong to.

mergeInto - the Sample to merge other samples into.

toMerge - the collection of Sample to merge.

Returns:

the completely merged Sample (the persisted version of mergeInto).

getTotalBasesForSample

java.lang.Long getTotalBasesForSample(Sample sample)
                               throws SequenceFileAnalysisException

Given a sample gets the total number of bases in all sequence files in this sample.

Parameters:

sample - The sample to find the total number of bases.

Returns:

The total number of bases in all sequence files in this sample.

Throws:

SequenceFileAnalysisException - If there was an error getting FastQC analyses for a sequence file.

estimateCoverageForSample

java.lang.Double estimateCoverageForSample(Sample sample,
                                           long referenceFileLength)
                                    throws SequenceFileAnalysisException

Given the length of a reference file, estimate the total coverage for this sample.

Parameters:

sample - The sample to estimate coverage for.

referenceFileLength - The length of the reference file in bases.

Returns:

The estimate coverage of all sequence data in this sample.

Throws:

SequenceFileAnalysisException - If there was an error getting FastQC analyses for a sequence file.

estimateCoverageForSample

java.lang.Double estimateCoverageForSample(Sample sample,
                                           ReferenceFile referenceFile)
                                    throws SequenceFileAnalysisException

Given a ReferenceFile, estimate the total coverage for this sample.

Parameters:

sample - The sample to estimate coverage for.

referenceFile - The ReferenceFile to estimate coverage for.

Returns:

The estimate coverage of all sequence data in this sample.

Throws:

SequenceFileAnalysisException - If there was an error getting FastQC analyses for a sequence file.

getFilteredProjectSamples

org.springframework.data.domain.Page<ProjectSampleJoin> getFilteredProjectSamples(java.util.List<Project> projects,
                                                                                  ProjectSampleJoinSpecification filterSpec,
                                                                                  int currentPage,
                                                                                  int pageSize,
                                                                                  org.springframework.data.domain.Sort sort)

Get a Page of ProjectSampleJoin for samples from 1 or more projects based on filtering criteria.

Parameters:

projects - List of Project the Samples must be found within.

filterSpec - ProjectSampleJoinSpecification

currentPage - Integer the current page the table is on.

pageSize - Integer the number of ProjectSampleJoin in the Page.

sort - Sort chained sort definitions to sort page by.

Returns:

a Page of ProjectSampleJoin that are filtered and sorted.

getFilteredSamplesForProjects

org.springframework.data.domain.Page<ProjectSampleJoin> getFilteredSamplesForProjects(java.util.List<Project> projects,
                                                                                      java.util.List<java.lang.String> sampleNames,
                                                                                      java.lang.String sampleName,
                                                                                      java.lang.String searchTerm,
                                                                                      java.lang.String organism,
                                                                                      java.util.Date minDate,
                                                                                      java.util.Date maxDate,
                                                                                      int currentPage,
                                                                                      int pageSize,
                                                                                      org.springframework.data.domain.Sort sort)

Get a Page of ProjectSampleJoin for samples from 1 or more projects based on filtering criteria.

Parameters:

projects - List of Project the Samples must be found within.

sampleNames - List of String of Sample names to search

sampleName - String exact name of a specific Sample

searchTerm - String search term to search for.

organism - String organism ter to search for.

minDate - Date minimum date the sample was modified.

maxDate - Date maximum date the sample was modified.

currentPage - Integer the current page the table is on.

pageSize - Integer the number of ProjectSampleJoin in the Page.

sort - Sort chained sort definitions to sort page by.

Returns:

a Page of ProjectSampleJoin that are filtered and sorted.

getSamplesForAnalysisSubmission

java.util.Collection<Sample> getSamplesForAnalysisSubmission(AnalysisSubmission submission)

Get a list of all Samples associated with a given AnalysisSubmission

Parameters:

submission - the AnalysisSubmission

Returns:

a Collection of Sample

getQCEntriesForSample

java.util.List<QCEntry> getQCEntriesForSample(Sample sample)

Find all the QCEntry associated with SequencingObjects in a given Sample

Parameters:

sample - the Sample to get QCEntry for

Returns:

a list of QCEntry

getQCEntriesForSamples

java.util.Map<java.lang.Long,java.util.List<QCEntry>> getQCEntriesForSamples(java.util.List<Sample> samples)

Find all the QCEntry associated with SequencingObjects in a given Sample for a list of Samples

Parameters:

samples - the Samples to get QCEntrys for

Returns:

a map of sample id to QCEntrys

searchSamplesForUser

org.springframework.data.domain.Page<ProjectSampleJoin> searchSamplesForUser(java.lang.String query,
                                                                             java.lang.Integer page,
                                                                             java.lang.Integer count,
                                                                             org.springframework.data.domain.Sort sort)

Search all Samples in projects the current logged in user has access to

Parameters:

query - the query string to search

page - which page to return

count - the number of entities to return

sort - how to sort the result

Returns:

a page of ProjectSampleJoin

searchAllSamples

org.springframework.data.domain.Page<ProjectSampleJoin> searchAllSamples(java.lang.String query,
                                                                         java.lang.Integer page,
                                                                         java.lang.Integer count,
                                                                         org.springframework.data.domain.Sort sort)

Search all Samples in the database on the given query

Parameters:

query - the query string to search

page - which page to return

count - the number of entities to return

sort - how to sort the result

Returns:

a page of ProjectSampleJoin

getSamplesCreated

java.lang.Long getSamplesCreated(java.util.Date createdDate)

Get count of samples created in the time period

Parameters:

createdDate - the minimum date for samples created

Returns:

An Long count of samples created

getSamplesCreatedGrouped

java.util.List<GenericStatModel> getSamplesCreatedGrouped(java.util.Date createdDate,
                                                          StatisticTimePeriod statisticTimePeriod)

Get list of GenericStatModel of samples created in the past n time period grouped by the format provided.

Parameters:

createdDate - the minimum date for samples created

statisticTimePeriod - the enum containing format for which to group the results by

Returns:

An GenericStatModel list

getCoverageForSamplesInProject

java.util.Map<java.lang.Long,java.lang.Long> getCoverageForSamplesInProject(Project project,
                                                                                  java.util.List<java.lang.Long> sampleIds)

Get Coverage for samples within a project.

Parameters:

project - the Project to use to calculate the coverage

sampleIds - the Sample ids to get coverage for

Returns:

a map of sample id to coverage value