ome.formats.importer.cli

Class CommandLineImporter

java.lang.Object

ome.formats.importer.cli.CommandLineImporter

public class CommandLineImporter
extends java.lang.Object

The base entry point for the CLI version of the OMERO importer.

Field Summary

Fields

Modifier and Type	Field and Description
protected ImportCandidates	candidates Candidates for import
ImportConfig	config Configuration used by all components
static int	DEFAULT_WAIT
java.util.List<FileExclusion>	exclusions FileExclusion mechanisms for skipping candidates
protected boolean	getUsedFiles If true, then only a report on used files will be produced
ErrorHandler	handler ErrorHandler which is also responsible for uploading files
protected ImportOutput	importOutput Format which should be preferred for standard out messages
ImportLibrary	library Base importer library, this is what we actually use to import.
protected OMEROWrapper	reader Bio-Formats reader wrapper customized for OMERO.
protected OMEROMetadataStoreClient	store Bio-Formats MetadataStore implementation for OMERO.
FileTransfer	transfer FileTransfer mechanism to be used for uploading

Constructor Summary

Constructors

Constructor and Description
CommandLineImporter(ImportConfig config, java.lang.String[] paths, boolean getUsedFiles) Legacy constructor which uses a UploadFileTransfer.
CommandLineImporter(ImportConfig config, java.lang.String[] paths, boolean getUsedFiles, FileTransfer transfer, int minutesToWait) Legacy constructor without any file exclusions.
CommandLineImporter(ImportConfig config, java.lang.String[] paths, boolean getUsedFiles, FileTransfer transfer, java.util.List<FileExclusion> exclusions, int minutesToWait) Main entry class for the application.

Method Summary

Modifier and Type	Method and Description
static void	advUsage() Prints advanced usage to STDERR and exits with return code 1.
protected void	checkLogin() Checks that requisite command line options for OMERO session creation have been provided and if not calls usage().
void	cleanup() Cleans up after a successful or unsuccessful image import.
static int	closeCompleted(ImportConfig config) Look for all ImportProcessPrx in the current session and close them if they return a non-null Response (i.e.
protected ImportLibrary	createImportLibrary(OMEROMetadataStoreClient client, OMEROWrapper reader, FileTransfer transfer, java.util.List<FileExclusion> exclusions, int minutesToWait) Creates the ImportLibrary that this command line importer will use to import data
static void	main(java.lang.String[] args) Command line application entry point which parses CLI arguments and passes them into the importer.
static void	setArgument(java.util.Map<java.lang.String,java.lang.Boolean> map, java.lang.String key) Set a conflicting argument and return the usage if the key is already set
ImportOutput	setImportOutput(ImportOutput importOutput) Set the current ImportOutput (defaulting to null if a null value is passed).
int	start()
static void	usage() Prints usage to STDERR and exits with return code 1.
static int	waitCompleted(ImportConfig config) Look for all ImportProcessPrx in the current session and close them if they return a non-null Response (i.e.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

DEFAULT_WAIT

public static final int DEFAULT_WAIT

See Also:

Constant Field Values

config

public final ImportConfig config

Configuration used by all components

transfer

public final FileTransfer transfer

FileTransfer mechanism to be used for uploading

exclusions

public final java.util.List<FileExclusion> exclusions

FileExclusion mechanisms for skipping candidates

library

public final ImportLibrary library

Base importer library, this is what we actually use to import.

handler

public final ErrorHandler handler

ErrorHandler which is also responsible for uploading files

reader

protected final OMEROWrapper reader

Bio-Formats reader wrapper customized for OMERO.

store

protected final OMEROMetadataStoreClient store

Bio-Formats MetadataStore implementation for OMERO.

candidates

protected final ImportCandidates candidates

Candidates for import

getUsedFiles

protected final boolean getUsedFiles

If true, then only a report on used files will be produced

importOutput

protected ImportOutput importOutput

Format which should be preferred for standard out messages

Constructor Detail

CommandLineImporter

public CommandLineImporter(ImportConfig config,
                           java.lang.String[] paths,
                           boolean getUsedFiles)
                    throws java.lang.Exception

Legacy constructor which uses a UploadFileTransfer.

Parameters:

config - the import configuration

paths - files or directories to search

getUsedFiles - if only getting a list of used files

Throws:

java.lang.Exception - if the import could not be set up

CommandLineImporter

public CommandLineImporter(ImportConfig config,
                           java.lang.String[] paths,
                           boolean getUsedFiles,
                           FileTransfer transfer,
                           int minutesToWait)
                    throws java.lang.Exception

Legacy constructor without any file exclusions.

Parameters:

config - the import configuration

paths - files or directories to search

getUsedFiles - if only getting a list of used files

transfer - how files are to be transferred to the server

minutesToWait - for how many minutes to wait for an import (negative for indefinitely)

Throws:

java.lang.Exception - if the import could not be set up

CommandLineImporter

public CommandLineImporter(ImportConfig config,
                           java.lang.String[] paths,
                           boolean getUsedFiles,
                           FileTransfer transfer,
                           java.util.List<FileExclusion> exclusions,
                           int minutesToWait)
                    throws java.lang.Exception

Main entry class for the application.

Parameters:

config - the import configuration

paths - files or directories to search

getUsedFiles - if only getting a list of used files

transfer - how files are to be transferred to the server

exclusions - mechanisms to be used for skipping candidates

minutesToWait - for how many minutes to wait for an import (negative for indefinitely)

Throws:

java.lang.Exception - if the import could not be set up

Method Detail

checkLogin

protected void checkLogin()

Checks that requisite command line options for OMERO session creation have been provided and if not calls usage().

createImportLibrary

protected ImportLibrary createImportLibrary(OMEROMetadataStoreClient client,
                                            OMEROWrapper reader,
                                            FileTransfer transfer,
                                            java.util.List<FileExclusion> exclusions,
                                            int minutesToWait)

Creates the ImportLibrary that this command line importer will use to import data

Parameters:

client - Bio-Formats MetadataStore implementation for OMERO

reader - Bio-Formats reader wrapper customized for OMERO

transfer - FileTransfer mechanism to be used for uploading

exclusions - FileExclusion mechanisms for skipping candidates

minutesToWait - for how many minutes to wait for an import (negative for indefinitely)

Returns:

See above.

closeCompleted

public static int closeCompleted(ImportConfig config)
                          throws java.lang.Exception

Look for all ImportProcessPrx in the current session and close them if they return a non-null Response (i.e. they are done).

Parameters:

config - the import configuration

Returns:

how many import processes could not be accessed

Throws:

java.lang.Exception - in the event of error

waitCompleted

public static int waitCompleted(ImportConfig config)
                         throws java.lang.Exception

Look for all ImportProcessPrx in the current session and close them if they return a non-null Response (i.e. they are done).

Parameters:

config - the import configuration

Returns:

exit code, 0 for success

Throws:

java.lang.Exception - in the event of error

setImportOutput

public ImportOutput setImportOutput(ImportOutput importOutput)

Set the current ImportOutput (defaulting to null if a null value is passed).

Parameters:

importOutput - possibly null enumeration value.

Returns:

previous value.

start

public int start()

cleanup

public void cleanup()

Cleans up after a successful or unsuccessful image import. This method only does the minimum required cleanup, so that it can be called during shutdown.

usage

public static void usage()

Prints usage to STDERR and exits with return code 1.

advUsage

public static void advUsage()

Prints advanced usage to STDERR and exits with return code 1.

main

public static void main(java.lang.String[] args)
                 throws java.lang.Exception

Command line application entry point which parses CLI arguments and passes them into the importer. Return codes for import are:

• 0 on success
• 1 on argument parsing failure
• 2 on exception during import

Return codes for the "-f" option (getUsedFiles) are:

• 0 on success, even if errors exist in the files
• 1 only if an exception propagates up the stack

Parameters:

args - Command line arguments.

Throws:

java.lang.Exception - in the event of error

setArgument

public static void setArgument(java.util.Map<java.lang.String,java.lang.Boolean> map,
                               java.lang.String key)

Set a conflicting argument and return the usage if the key is already set

Parameters:

map - map of conflicting properties

key - configuration property to be set