java.lang.Object
- ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl

All Implemented Interfaces:

ExpressionDataFileService
```
@Service
@Transactional(propagation=NEVER)
public class ExpressionDataFileServiceImpl
extends Object
implements ExpressionDataFileService
```
Supports the creation and location of 'flat file' versions of data in the system, for download by users. Files are cached on the filesystem and reused if possible, rather than recreating them every time.
Never use this service in a Transactional context, it uses locks for files and spends significant time writing to disk.

Author:

paul

Constructor Summary

Constructors
Constructor Description

ExpressionDataFileServiceImpl()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`Path`	`copyMetadataFile(ExpressionExperiment ee, Path existingFile, String filename, boolean forceWrite)`	Copy a generic metadata file.
`Path`	`copyMetadataFile(ExpressionExperiment ee, Path existingFile, ExpressionExperimentMetaFileType type, boolean forceWrite)`	Copy a metadata file to the location of a given metadata type.
`int`	`deleteAllAnalysisFiles(ExpressionExperiment ee)`	Delete all analyses files for a given experiment.
`int`	`deleteAllAnnotatedFiles(ExpressionExperiment ee)`	Delete all files that contain platform annotations for a given experiment.
`int`	`deleteAllDataFiles(ExpressionExperiment ee, QuantitationType qt)`	Delete all data files for a given QT.
`int`	`deleteAllFiles(ExpressionExperiment ee)`	Delete any existing design, coexpression, data, or differential expression data files.
`int`	`deleteAllProcessedDataFiles(ExpressionExperiment ee)`	Delete all the processed files for a given experiment.
`boolean`	`deleteCoexpressionDataFile(ExpressionExperiment ee)`	Delete a coexpression data file if it exists.
`boolean`	`deleteDataFile(ExpressionExperiment ee, boolean filtered, ExpressionExperimentDataFileType type)`	Delete a processed data file if it exists.
`boolean`	`deleteDataFile(ExpressionExperiment ee, QuantitationType qt, ExpressionExperimentDataFileType type)`	Delete a raw or single-cell data file if it exists.
`boolean`	`deleteDesignFile(ExpressionExperiment ee)`	Delete the experimental design file for a given experiment.
`boolean`	`deleteDiffExArchiveFile(DifferentialExpressionAnalysis analysis)`	Delete a diff. ex. analysis archive file for a given analysis.
`boolean`	`deleteMetadataFile(ExpressionExperiment ee, ExpressionExperimentMetaFileType type)`	Delete a metadata file.
`LockedPath`	`getDataFile(String filename, boolean exclusive)`	Locate any data file in the data directory.
`LockedPath`	`getDataFile(String filename, boolean exclusive, long timeout, TimeUnit timeUnit)`
`LockedPath`	`getDataFile(ExpressionExperiment ee, QuantitationType qt, ExpressionExperimentDataFileType type, boolean exclusive, long timeout, TimeUnit timeUnit)`
`Optional<LockedPath>`	`getMetadataFile(ExpressionExperiment ee, String filename, boolean exclusive)`
`Optional<LockedPath>`	`getMetadataFile(ExpressionExperiment ee, String filename, boolean exclusive, long timeout, TimeUnit timeUnit)`
`Optional<LockedPath>`	`getMetadataFile(ExpressionExperiment ee, ExpressionExperimentMetaFileType type, boolean exclusive)`	Locate a metadata file.
`void`	`writeDesignMatrix(ExpressionExperiment ee, Writer writer)`	Writes out the experimental design for the given experiment.
`LockedPath`	`writeDiffExAnalysisArchiveFile(DifferentialExpressionAnalysis analysis, DifferentialExpressionAnalysisConfig config)`
`int`	`writeMexSingleCellExpressionData(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType qt, ScaleType scaleType, boolean useEnsemblIds, int fetchSize, boolean forceWrite, Path destDir)`
`int`	`writeMexSingleCellExpressionData(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType qt, ScaleType scaleType, boolean useEnsemblIds, OutputStream stream)`
`int`	`writeMexSingleCellExpressionData(ExpressionExperiment ee, QuantitationType qt, ScaleType scaleType, boolean useEnsemblIds, int fetchSize, boolean forceWrite, Path destDir)`	Write single-cell expression data to a given output stream for a given quantitation type.
`int`	`writeMexSingleCellExpressionData(ExpressionExperiment ee, QuantitationType qt, ScaleType scaleType, boolean useEnsemblIds, OutputStream stream)`	Write single-cell expression data to a given output stream for a given quantitation type.
`LockedPath`	`writeOrLocateCoexpressionDataFile(ExpressionExperiment ee, boolean forceWrite)`	Write or located the coexpression data file for a given experiment
`Optional<LockedPath>`	`writeOrLocateDesignFile(ExpressionExperiment ee, boolean forceWrite)`	Locate or create an experimental design file for a given experiment.
`Optional<LockedPath>`	`writeOrLocateDesignFile(ExpressionExperiment ee, boolean forceWrite, long timeout, TimeUnit timeUnit)`
`LockedPath`	`writeOrLocateDiffExArchiveFile(Long analysisId, boolean forceCreate)`	Locate or create the differential expression data file(s) for a given experiment.
`Collection<LockedPath>`	`writeOrLocateDiffExpressionDataFiles(ExpressionExperiment ee, boolean forceWrite)`	Locate or create the differential expression data file(s) for a given experiment.
`Optional<LockedPath>`	`writeOrLocateJSONProcessedExpressionDataFile(ExpressionExperiment ee, boolean forceWrite, boolean filtered)`
`LockedPath`	`writeOrLocateJSONRawExpressionDataFile(ExpressionExperiment ee, QuantitationType type, boolean forceWrite)`
`LockedPath`	`writeOrLocateMexSingleCellExpressionData(ExpressionExperiment ee, QuantitationType qt, int fetchSize, boolean forceWrite)`	Write single-cell expression data to a standard location for a given quantitation type.
`Future<Path>`	`writeOrLocateMexSingleCellExpressionDataAsync(ExpressionExperiment ee, QuantitationType qt, int fetchSize, boolean forceWrite)`
`Optional<LockedPath>`	`writeOrLocateProcessedDataFile(ExpressionExperiment ee, boolean filtered, boolean forceWrite)`	Locate or create a data file containing the 'preferred and masked' expression data matrix, with filtering for low expression applied (currently supports default settings only).
`Optional<LockedPath>`	`writeOrLocateProcessedDataFile(ExpressionExperiment ee, boolean filtered, boolean forceWrite, long timeout, TimeUnit timeUnit)`
`LockedPath`	`writeOrLocateRawExpressionDataFile(ExpressionExperiment ee, QuantitationType type, boolean forceWrite)`	Locate or create a new data file for the given quantitation type.
`LockedPath`	`writeOrLocateRawExpressionDataFile(ExpressionExperiment ee, QuantitationType type, boolean forceWrite, long timeout, TimeUnit timeUnit)`
`LockedPath`	`writeOrLocateTabularSingleCellExpressionData(ExpressionExperiment ee, QuantitationType qt, int fetchSize, boolean forceWrite)`	Write single-cell expression data to a standard location for a given quantitation type in tabular format.
`Future<Path>`	`writeOrLocateTabularSingleCellExpressionDataAsync(ExpressionExperiment ee, QuantitationType qt, int fetchSize, boolean forceWrite)`
`int`	`writeProcessedExpressionData(ExpressionExperiment ee, boolean filtered, ScaleType scaleType, Writer writer, boolean autoFlush)`	Write processed expression data to a given writer for a given quantitation type.
`int`	`writeProcessedExpressionData(ExpressionExperiment ee, List<BioAssay> samples, boolean filtered, ScaleType scaleType, Writer writer, boolean autoFlush)`
`int`	`writeRawExpressionData(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType qt, ScaleType scaleType, Writer writer, boolean autoFlush)`
`int`	`writeRawExpressionData(ExpressionExperiment ee, QuantitationType qt, ScaleType scaleType, Writer writer, boolean autoFlush)`	Write raw expression data to a given writer for a given quantitation type.
`int`	`writeTabularSingleCellExpressionData(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType qt, ScaleType scaleType, int fetchSize, Writer writer, boolean autoFlush)`
`int`	`writeTabularSingleCellExpressionData(ExpressionExperiment ee, QuantitationType qt, ScaleType scaleType, int fetchSize, Writer writer, boolean autoFlush)`	Write single-cell expression data to a given writer for a given quantitation type in tabular format.

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

Constructor Detail
- ExpressionDataFileServiceImpl
```
public ExpressionDataFileServiceImpl()
```

Method Detail

deleteAllFiles
```
public int deleteAllFiles(ExpressionExperiment ee)
```
Description copied from interface: ExpressionDataFileService

Delete any existing design, coexpression, data, or differential expression data files.
Experiment metadata are not deleted, use ExpressionDataFileService.deleteMetadataFile(ExpressionExperiment, ExpressionExperimentMetaFileType) for that purpose.

Specified by:

deleteAllFiles in interface ExpressionDataFileService

See Also:

ExpressionDataFileService.deleteDesignFile(ExpressionExperiment), ExpressionDataFileService.deleteAllDataFiles(ExpressionExperiment, QuantitationType), ExpressionDataFileService.deleteAllProcessedDataFiles(ExpressionExperiment), ExpressionDataFileService.deleteAllAnnotatedFiles(ExpressionExperiment)

deleteDesignFile
```
public boolean deleteDesignFile(ExpressionExperiment ee)
```
Description copied from interface: ExpressionDataFileService

Delete the experimental design file for a given experiment.

Specified by:

deleteDesignFile in interface ExpressionDataFileService

deleteAllAnnotatedFiles
```
public int deleteAllAnnotatedFiles(ExpressionExperiment ee)
```
Description copied from interface: ExpressionDataFileService

Delete all files that contain platform annotations for a given experiment.
This includes all the data and analysis files.

Specified by:

deleteAllAnnotatedFiles in interface ExpressionDataFileService

See Also:

ExpressionDataFileService.deleteAllDataFiles(ExpressionExperiment, QuantitationType), ExpressionDataFileService.deleteAllProcessedDataFiles(ExpressionExperiment), ExpressionDataFileService.deleteDiffExArchiveFile(DifferentialExpressionAnalysis)

deleteAllDataFiles
```
public int deleteAllDataFiles(ExpressionExperiment ee,
                              QuantitationType qt)
```
Description copied from interface: ExpressionDataFileService

Delete all data files for a given QT.
This includes all the possible file types enumerated in ExpressionExperimentDataFileType.

Specified by:

deleteAllDataFiles in interface ExpressionDataFileService

deleteAllProcessedDataFiles
```
public int deleteAllProcessedDataFiles(ExpressionExperiment ee)
```
Description copied from interface: ExpressionDataFileService

Delete all the processed files for a given experiment.
This includes all the possible file types enumerated in ExpressionExperimentDataFileType.

Specified by:

deleteAllProcessedDataFiles in interface ExpressionDataFileService

deleteAllAnalysisFiles
```
public int deleteAllAnalysisFiles(ExpressionExperiment ee)
```
Description copied from interface: ExpressionDataFileService

Delete all analyses files for a given experiment.

Specified by:

deleteAllAnalysisFiles in interface ExpressionDataFileService

See Also:

ExpressionDataFileService.deleteDiffExArchiveFile(DifferentialExpressionAnalysis), ExpressionDataFileService.deleteCoexpressionDataFile(ExpressionExperiment)

deleteDiffExArchiveFile
```
public boolean deleteDiffExArchiveFile(DifferentialExpressionAnalysis analysis)
```
Description copied from interface: ExpressionDataFileService

Delete a diff. ex. analysis archive file for a given analysis.

Specified by:

deleteDiffExArchiveFile in interface ExpressionDataFileService

Returns:

true if any file was deleted

deleteCoexpressionDataFile
```
public boolean deleteCoexpressionDataFile(ExpressionExperiment ee)
```
Description copied from interface: ExpressionDataFileService

Delete a coexpression data file if it exists.

Specified by:

deleteCoexpressionDataFile in interface ExpressionDataFileService

getMetadataFile
```
public Optional<LockedPath> getMetadataFile(ExpressionExperiment ee,
                                            ExpressionExperimentMetaFileType type,
                                            boolean exclusive)
                                     throws IOException
```
Description copied from interface: ExpressionDataFileService

Locate a metadata file. If the metadata file is represented by a directory (i.e. ExpressionExperimentMetaFileType.isDirectory() is true), then the latest file in the directory is returned. If no such file exists. Optional.empty() is returned.
If the data file is being written (i.e. with ExpressionDataFileService.copyMetadataFile(ExpressionExperiment, Path, ExpressionExperimentMetaFileType, boolean), this method will block until it is completed.

Specified by:

getMetadataFile in interface ExpressionDataFileService

Returns:

the metadata file or empty if none is present in the case of a directory-structured metadata

Throws:

IOException

getMetadataFile

public Optional<LockedPath> getMetadataFile(ExpressionExperiment ee,
                                            String filename,
                                            boolean exclusive)
                                     throws IOException

Specified by:: getMetadataFile in interface ExpressionDataFileService
Throws:: IOException

getMetadataFile

public Optional<LockedPath> getMetadataFile(ExpressionExperiment ee,
                                            String filename,
                                            boolean exclusive,
                                            long timeout,
                                            TimeUnit timeUnit)
                                     throws InterruptedException,
                                            TimeoutException,
                                            IOException

Specified by:: getMetadataFile in interface ExpressionDataFileService
Throws:: InterruptedException; TimeoutException; IOException

copyMetadataFile
```
public Path copyMetadataFile(ExpressionExperiment ee,
                             Path existingFile,
                             ExpressionExperimentMetaFileType type,
                             boolean forceWrite)
                      throws IOException
```
Description copied from interface: ExpressionDataFileService

Copy a metadata file to the location of a given metadata type.
Writing to a directory (i.e. ExpressionExperimentMetaFileType.isDirectory() is true) is not supported.
If the metadata file is in use, this method will block until it is released.

Specified by:

copyMetadataFile in interface ExpressionDataFileService

existingFile - file to copy, must exist

forceWrite - override any existing metadata file

Returns:

the resulting metadata file, which can also be retrieved with ExpressionDataFileService.getMetadataFile(ExpressionExperiment, ExpressionExperimentMetaFileType, boolean)

Throws:

IOException

copyMetadataFile
```
public Path copyMetadataFile(ExpressionExperiment ee,
                             Path existingFile,
                             String filename,
                             boolean forceWrite)
                      throws IOException
```
Description copied from interface: ExpressionDataFileService

Copy a generic metadata file.
This can only be used for metadata files that are not listed in ExpressionExperimentMetaFileType; using any of these reserved filenames will result in an exception. In addition, CHANGELOG.md is also reserved, use ExpressionMetadataChangelogFileService to manipulate it.

Specified by:

copyMetadataFile in interface ExpressionDataFileService

Throws:

IOException

deleteMetadataFile
```
public boolean deleteMetadataFile(ExpressionExperiment ee,
                                  ExpressionExperimentMetaFileType type)
                           throws IOException
```
Description copied from interface: ExpressionDataFileService

Delete a metadata file.
If the metadata file is organized as a directory, it is deleted recursively.
If the metadata file is in use, this method will block until it is released.

Specified by:

deleteMetadataFile in interface ExpressionDataFileService

type - the type of metadata file to delete

Returns:

true if a metadata file was deleted

Throws:

IOException

getDataFile
```
public LockedPath getDataFile(String filename,
                              boolean exclusive)
                       throws IOException
```
Description copied from interface: ExpressionDataFileService

Locate any data file in the data directory.

Specified by:

getDataFile in interface ExpressionDataFileService

exclusive - if true, acquire an exclusive lock on the file

Throws:

IOException

getDataFile

public LockedPath getDataFile(String filename,
                              boolean exclusive,
                              long timeout,
                              TimeUnit timeUnit)
                       throws IOException,
                              InterruptedException,
                              TimeoutException

Specified by:: getDataFile in interface ExpressionDataFileService
Throws:: IOException; InterruptedException; TimeoutException

getDataFile

public LockedPath getDataFile(ExpressionExperiment ee,
                              QuantitationType qt,
                              ExpressionExperimentDataFileType type,
                              boolean exclusive,
                              long timeout,
                              TimeUnit timeUnit)
                       throws InterruptedException,
                              TimeoutException,
                              IOException

Specified by:: getDataFile in interface ExpressionDataFileService
Throws:: InterruptedException; TimeoutException; IOException

deleteDataFile
```
public boolean deleteDataFile(ExpressionExperiment ee,
                              QuantitationType qt,
                              ExpressionExperimentDataFileType type)
                       throws IOException
```
Description copied from interface: ExpressionDataFileService

Delete a raw or single-cell data file if it exists.
If the data file is in use, this method will block until it is released.

Specified by:

deleteDataFile in interface ExpressionDataFileService

Returns:

true if the file was deleted, false if it did not exist

Throws:

IOException

deleteDataFile
```
public boolean deleteDataFile(ExpressionExperiment ee,
                              boolean filtered,
                              ExpressionExperimentDataFileType type)
                       throws IOException
```
Description copied from interface: ExpressionDataFileService

Delete a processed data file if it exists.
If the data file is in use, this method will block until it is released.

Specified by:

deleteDataFile in interface ExpressionDataFileService

Returns:

true if the file was deleted, false if it did not exist

Throws:

IOException

writeTabularSingleCellExpressionData

public int writeTabularSingleCellExpressionData(ExpressionExperiment ee,
                                                QuantitationType qt,
                                                @Nullable
                                                ScaleType scaleType,
                                                int fetchSize,
                                                Writer writer,
                                                boolean autoFlush)
                                         throws IOException

Description copied from interface: ExpressionDataFileService

Write single-cell expression data to a given writer for a given quantitation type in tabular format.

Specified by:: writeTabularSingleCellExpressionData in interface ExpressionDataFileService
Parameters:: ee - the experiment to use; qt - the quantitation type to retrieve; scaleType - a scale type to use or null to leave the data untransformed; fetchSize - retrieve data in a streaming fashion
Throws:: IOException
See Also:: TabularMatrixWriter

writeTabularSingleCellExpressionData

public int writeTabularSingleCellExpressionData(ExpressionExperiment ee,
                                                List<BioAssay> samples,
                                                QuantitationType qt,
                                                @Nullable
                                                ScaleType scaleType,
                                                int fetchSize,
                                                Writer writer,
                                                boolean autoFlush)
                                         throws IOException

Specified by:: writeTabularSingleCellExpressionData in interface ExpressionDataFileService
Throws:: IOException

writeOrLocateTabularSingleCellExpressionData
```
public LockedPath writeOrLocateTabularSingleCellExpressionData(ExpressionExperiment ee,
                                                               QuantitationType qt,
                                                               int fetchSize,
                                                               boolean forceWrite)
                                                        throws IOException
```
Description copied from interface: ExpressionDataFileService

Write single-cell expression data to a standard location for a given quantitation type in tabular format.

Specified by:

writeOrLocateTabularSingleCellExpressionData in interface ExpressionDataFileService

Returns:

a path where the vectors were written

Throws:

IOException

See Also:

ExpressionDataFileService.writeTabularSingleCellExpressionData(ExpressionExperiment, QuantitationType, ScaleType, int, Writer, boolean), TabularMatrixWriter

writeOrLocateTabularSingleCellExpressionDataAsync

public Future<Path> writeOrLocateTabularSingleCellExpressionDataAsync(ExpressionExperiment ee,
                                                                      QuantitationType qt,
                                                                      int fetchSize,
                                                                      boolean forceWrite)

Specified by:: writeOrLocateTabularSingleCellExpressionDataAsync in interface ExpressionDataFileService
See Also:: ExpressionDataFileService.writeOrLocateTabularSingleCellExpressionData(ExpressionExperiment, QuantitationType, int, boolean)

writeMexSingleCellExpressionData
```
public int writeMexSingleCellExpressionData(ExpressionExperiment ee,
                                            QuantitationType qt,
                                            @Nullable
                                            ScaleType scaleType,
                                            boolean useEnsemblIds,
                                            OutputStream stream)
                                     throws IOException
```
Description copied from interface: ExpressionDataFileService

Write single-cell expression data to a given output stream for a given quantitation type.
Note: this method is memory intensive because the whole matrix needs to be in-memory to write each individual sample matrices. Thus, no streaming is possible.

Specified by:

writeMexSingleCellExpressionData in interface ExpressionDataFileService

Parameters:

ee - the experiment to use

qt - the quantitation type to retrieve

scaleType - a scale type to use or null to leave the data untransformed

useEnsemblIds - use Ensembl IDs instead of official gene symbols

Throws:

IOException

See Also:

MexMatrixWriter

writeMexSingleCellExpressionData

public int writeMexSingleCellExpressionData(ExpressionExperiment ee,
                                            List<BioAssay> samples,
                                            QuantitationType qt,
                                            @Nullable
                                            ScaleType scaleType,
                                            boolean useEnsemblIds,
                                            OutputStream stream)
                                     throws IOException

Specified by:: writeMexSingleCellExpressionData in interface ExpressionDataFileService
Throws:: IOException

writeMexSingleCellExpressionData

public int writeMexSingleCellExpressionData(ExpressionExperiment ee,
                                            QuantitationType qt,
                                            @Nullable
                                            ScaleType scaleType,
                                            boolean useEnsemblIds,
                                            int fetchSize,
                                            boolean forceWrite,
                                            Path destDir)
                                     throws IOException

Description copied from interface: ExpressionDataFileService

Write single-cell expression data to a given output stream for a given quantitation type.

Specified by:: writeMexSingleCellExpressionData in interface ExpressionDataFileService
Parameters:: ee - the experiment to use; qt - the quantitation type to retrieve; scaleType - a scale type to use or null to leave the data untransformed; useEnsemblIds - use Ensembl IDs instead of official gene symbols; fetchSize - fetch size to use for streaming, or load everything in memory of zero or less; forceWrite - whether to force write and ignore any pre-existing directory
Throws:: IOException
See Also:: MexMatrixWriter

writeMexSingleCellExpressionData

public int writeMexSingleCellExpressionData(ExpressionExperiment ee,
                                            List<BioAssay> samples,
                                            QuantitationType qt,
                                            @Nullable
                                            ScaleType scaleType,
                                            boolean useEnsemblIds,
                                            int fetchSize,
                                            boolean forceWrite,
                                            Path destDir)
                                     throws IOException

Specified by:: writeMexSingleCellExpressionData in interface ExpressionDataFileService
Throws:: IOException

writeOrLocateMexSingleCellExpressionData
```
public LockedPath writeOrLocateMexSingleCellExpressionData(ExpressionExperiment ee,
                                                           QuantitationType qt,
                                                           int fetchSize,
                                                           boolean forceWrite)
                                                    throws IOException
```
Description copied from interface: ExpressionDataFileService

Write single-cell expression data to a standard location for a given quantitation type.

Specified by:

writeOrLocateMexSingleCellExpressionData in interface ExpressionDataFileService

Returns:

a path where the vectors were written

Throws:

IOException

See Also:

ExpressionDataFileService.writeMexSingleCellExpressionData(ExpressionExperiment, QuantitationType, ScaleType, boolean, int, boolean, Path), MexMatrixWriter

writeOrLocateMexSingleCellExpressionDataAsync

public Future<Path> writeOrLocateMexSingleCellExpressionDataAsync(ExpressionExperiment ee,
                                                                  QuantitationType qt,
                                                                  int fetchSize,
                                                                  boolean forceWrite)

Specified by:: writeOrLocateMexSingleCellExpressionDataAsync in interface ExpressionDataFileService
See Also:: ExpressionDataFileService.writeOrLocateMexSingleCellExpressionData(ExpressionExperiment, QuantitationType, int, boolean)

writeRawExpressionData
```
public int writeRawExpressionData(ExpressionExperiment ee,
                                  QuantitationType qt,
                                  @Nullable
                                  ScaleType scaleType,
                                  Writer writer,
                                  boolean autoFlush)
                           throws IOException
```
Description copied from interface: ExpressionDataFileService

Write raw expression data to a given writer for a given quantitation type.
Note: For compression, wrap a GZIPOutputStream with a OutputStreamWriter. To write to a string, consider using StringWriter.

Specified by:

writeRawExpressionData in interface ExpressionDataFileService

Parameters:

ee - the expression experiment

qt - a quantitation type to use

scaleType - a scale type to use or null to leave the data untransformed

writer - the destination for the raw expression data

Throws:

IOException - if operations with the writer fails

writeRawExpressionData

public int writeRawExpressionData(ExpressionExperiment ee,
                                  List<BioAssay> samples,
                                  QuantitationType qt,
                                  @Nullable
                                  ScaleType scaleType,
                                  Writer writer,
                                  boolean autoFlush)
                           throws IOException

Specified by:: writeRawExpressionData in interface ExpressionDataFileService
Throws:: IOException

writeDesignMatrix
```
public void writeDesignMatrix(ExpressionExperiment ee,
                              Writer writer)
                       throws IOException
```
Description copied from interface: ExpressionDataFileService

Writes out the experimental design for the given experiment.
The bioassays (col 0) matches the header row of the data matrix printed out by the MatrixWriter.

Specified by:

writeDesignMatrix in interface ExpressionDataFileService

Throws:

IOException

See Also:

ExperimentalDesignWriter

writeProcessedExpressionData

public int writeProcessedExpressionData(ExpressionExperiment ee,
                                        boolean filtered,
                                        @Nullable
                                        ScaleType scaleType,
                                        Writer writer,
                                        boolean autoFlush)
                                 throws FilteringException,
                                        IOException

Description copied from interface: ExpressionDataFileService

Write processed expression data to a given writer for a given quantitation type.

Note: For compression, wrap a GZIPOutputStream with a OutputStreamWriter. To write to a string, consider using StringWriter.

Specified by:: writeProcessedExpressionData in interface ExpressionDataFileService
Parameters:: ee - the expression experiment; writer - the destination for the raw expression data
Throws:: IOException - if operations with the writer fails; FilteringException

writeProcessedExpressionData

public int writeProcessedExpressionData(ExpressionExperiment ee,
                                        List<BioAssay> samples,
                                        boolean filtered,
                                        @Nullable
                                        ScaleType scaleType,
                                        Writer writer,
                                        boolean autoFlush)
                                 throws FilteringException,
                                        IOException

Specified by:: writeProcessedExpressionData in interface ExpressionDataFileService
Throws:: FilteringException; IOException

writeOrLocateCoexpressionDataFile
```
public LockedPath writeOrLocateCoexpressionDataFile(ExpressionExperiment ee,
                                                    boolean forceWrite)
                                             throws IOException
```
Description copied from interface: ExpressionDataFileService

Write or located the coexpression data file for a given experiment

Specified by:

writeOrLocateCoexpressionDataFile in interface ExpressionDataFileService

Parameters:

ee - the experiment

forceWrite - whether to force write

Returns:

file

Throws:

IOException

writeOrLocateProcessedDataFile
```
public Optional<LockedPath> writeOrLocateProcessedDataFile(ExpressionExperiment ee,
                                                           boolean filtered,
                                                           boolean forceWrite)
                                                    throws IOException,
                                                           FilteringException
```
Description copied from interface: ExpressionDataFileService

Locate or create a data file containing the 'preferred and masked' expression data matrix, with filtering for low expression applied (currently supports default settings only). It will be gzip-compressed. The file will be regenerated even if one already exists if the forceWrite parameter is true, or if there was a recent change (more recent than the last modified date of the existing file) to any of the experiments platforms.

Specified by:

writeOrLocateProcessedDataFile in interface ExpressionDataFileService

Parameters:

ee - the experiment

filtered - filtered

forceWrite - force re-write even if file already exists and is up to date.

Returns:

file, or empty if the experiment has no processed vectors

Throws:

IOException

FilteringException

writeOrLocateProcessedDataFile

public Optional<LockedPath> writeOrLocateProcessedDataFile(ExpressionExperiment ee,
                                                           boolean filtered,
                                                           boolean forceWrite,
                                                           long timeout,
                                                           TimeUnit timeUnit)
                                                    throws TimeoutException,
                                                           IOException,
                                                           InterruptedException,
                                                           FilteringException

Specified by:: writeOrLocateProcessedDataFile in interface ExpressionDataFileService
Throws:: TimeoutException; IOException; InterruptedException; FilteringException

writeOrLocateRawExpressionDataFile
```
public LockedPath writeOrLocateRawExpressionDataFile(ExpressionExperiment ee,
                                                     QuantitationType type,
                                                     boolean forceWrite)
                                              throws IOException
```
Description copied from interface: ExpressionDataFileService

Locate or create a new data file for the given quantitation type. The output will include gene information if it can be located from its own file.

Specified by:

writeOrLocateRawExpressionDataFile in interface ExpressionDataFileService

type - the quantitation type

forceWrite - To not return the existing file, but create it anew.

Returns:

file

Throws:

IOException

writeOrLocateRawExpressionDataFile

public LockedPath writeOrLocateRawExpressionDataFile(ExpressionExperiment ee,
                                                     QuantitationType type,
                                                     boolean forceWrite,
                                                     long timeout,
                                                     TimeUnit timeUnit)
                                              throws TimeoutException,
                                                     IOException,
                                                     InterruptedException

Specified by:: writeOrLocateRawExpressionDataFile in interface ExpressionDataFileService
Throws:: TimeoutException; IOException; InterruptedException

writeOrLocateDesignFile
```
public Optional<LockedPath> writeOrLocateDesignFile(ExpressionExperiment ee,
                                                    boolean forceWrite)
                                             throws IOException
```
Description copied from interface: ExpressionDataFileService

Locate or create an experimental design file for a given experiment. The file will be regenerated even if one already exists if the forceWrite parameter is true, or if there was a recent change (more recent than the last modified date of the existing file) to any of the experiments platforms.

Specified by:

writeOrLocateDesignFile in interface ExpressionDataFileService

Parameters:

ee - the experiment

forceWrite - force re-write even if file already exists and is up to date

Returns:

a file or empty if the experiment does not have a design

Throws:

IOException

See Also:

ExpressionDataFileService.writeDesignMatrix(ExpressionExperiment, Writer)

writeOrLocateDesignFile

public Optional<LockedPath> writeOrLocateDesignFile(ExpressionExperiment ee,
                                                    boolean forceWrite,
                                                    long timeout,
                                                    TimeUnit timeUnit)
                                             throws TimeoutException,
                                                    IOException,
                                                    InterruptedException

Specified by:: writeOrLocateDesignFile in interface ExpressionDataFileService
Throws:: TimeoutException; IOException; InterruptedException

writeOrLocateDiffExpressionDataFiles
```
public Collection<LockedPath> writeOrLocateDiffExpressionDataFiles(ExpressionExperiment ee,
                                                                   boolean forceWrite)
                                                            throws IOException
```
Description copied from interface: ExpressionDataFileService

Locate or create the differential expression data file(s) for a given experiment.

Specified by:

writeOrLocateDiffExpressionDataFiles in interface ExpressionDataFileService

Parameters:

ee - the experiment

forceWrite - whether to force write

Returns:

collection of files, one per analysis.

Throws:

IOException

writeOrLocateDiffExArchiveFile
```
public LockedPath writeOrLocateDiffExArchiveFile(Long analysisId,
                                                 boolean forceCreate)
                                          throws IOException
```
Description copied from interface: ExpressionDataFileService

Locate or create the differential expression data file(s) for a given experiment. We generate an archive that contains following files: - differential expression analysis file (q-values per factor) - file for each result set with contrasts info (such as fold change for each factor value)

Specified by:

writeOrLocateDiffExArchiveFile in interface ExpressionDataFileService

Parameters:

analysisId - analysis ID

forceCreate - whether to force creation

Returns:

file

Throws:

IOException

writeDiffExAnalysisArchiveFile

public LockedPath writeDiffExAnalysisArchiveFile(DifferentialExpressionAnalysis analysis,
                                                 @Nullable
                                                 DifferentialExpressionAnalysisConfig config)
                                          throws IOException

Specified by:: writeDiffExAnalysisArchiveFile in interface ExpressionDataFileService
Throws:: IOException

writeOrLocateJSONProcessedExpressionDataFile

public Optional<LockedPath> writeOrLocateJSONProcessedExpressionDataFile(ExpressionExperiment ee,
                                                                         boolean forceWrite,
                                                                         boolean filtered)
                                                                  throws FilteringException,
                                                                         IOException

Specified by:: writeOrLocateJSONProcessedExpressionDataFile in interface ExpressionDataFileService
Throws:: FilteringException; IOException
See Also:: ExpressionDataFileService.writeOrLocateProcessedDataFile(ExpressionExperiment, boolean, boolean)

writeOrLocateJSONRawExpressionDataFile

public LockedPath writeOrLocateJSONRawExpressionDataFile(ExpressionExperiment ee,
                                                         QuantitationType type,
                                                         boolean forceWrite)
                                                  throws IOException

Specified by:: writeOrLocateJSONRawExpressionDataFile in interface ExpressionDataFileService
Throws:: IOException
See Also:: ExpressionDataFileService.writeOrLocateRawExpressionDataFile(ExpressionExperiment, QuantitationType, boolean)

Class ExpressionDataFileServiceImpl

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

ExpressionDataFileServiceImpl

Method Detail

deleteAllFiles

deleteDesignFile

deleteAllAnnotatedFiles

deleteAllDataFiles

deleteAllProcessedDataFiles

deleteAllAnalysisFiles

deleteDiffExArchiveFile

deleteCoexpressionDataFile

getMetadataFile

getMetadataFile

getMetadataFile

copyMetadataFile

copyMetadataFile

deleteMetadataFile

getDataFile

getDataFile

getDataFile

deleteDataFile

deleteDataFile

writeTabularSingleCellExpressionData

writeTabularSingleCellExpressionData

writeOrLocateTabularSingleCellExpressionData

writeOrLocateTabularSingleCellExpressionDataAsync

writeMexSingleCellExpressionData

writeMexSingleCellExpressionData

writeMexSingleCellExpressionData

writeMexSingleCellExpressionData

writeOrLocateMexSingleCellExpressionData

writeOrLocateMexSingleCellExpressionDataAsync

writeRawExpressionData

writeRawExpressionData

writeDesignMatrix

writeProcessedExpressionData

writeProcessedExpressionData

writeOrLocateCoexpressionDataFile

writeOrLocateProcessedDataFile

writeOrLocateProcessedDataFile

writeOrLocateRawExpressionDataFile

writeOrLocateRawExpressionDataFile

writeOrLocateDesignFile

writeOrLocateDesignFile

writeOrLocateDiffExpressionDataFiles

writeOrLocateDiffExArchiveFile

writeDiffExAnalysisArchiveFile

writeOrLocateJSONProcessedExpressionDataFile

writeOrLocateJSONRawExpressionDataFile