Package com.biomatters.geneious.publicapi.plugin

Class DatabaseFolderImporter

java.lang.Object

com.biomatters.geneious.publicapi.plugin.DatabaseFolderImporter

public abstract class DatabaseFolderImporter
extends java.lang.Object

An importer for folders containing files that must be imported as a set, and cannot be handled by the normal DocumentFileImporter framework. If you need to import multiple files at once that may depend on one another, you should normally extend DocumentFileImporter. The advantage of extending DatabaseFolderImporter is that it provides the ability to reproduce the structure of a database or file system in the imported result. A plugin may provide a set of DatabaseFolderImporters via GeneiousPlugin.getDatabaseFolderImporters().

Since:

API 4.201920 (Geneious Prime 2019.2.0)

See Also:

DocumentFileImporter

Constructor Summary

Constructors

Constructor	Description
DatabaseFolderImporter()

Method Summary

Modifier and Type	Method	Description
abstract java.lang.String	getDatabaseTypeDescription()
abstract Options	getOptions(java.io.File folder, WritableDatabaseService destination, jebl.util.ProgressListener progress)	Provides some options applicable to this database importer to the user, or null if no user-specified options are required.
java.lang.String	getUniqueId()	Get a unique identifier for this DocumentFileImporter.
abstract WritableDatabaseService	importFolder(java.io.File folder, WritableDatabaseService destination, Options options, jebl.util.ProgressListener progress)	Import the external database to a Geneious WritableDatabaseService and report back the containing the added documents.
abstract DocumentFileImporter.AutoDetectStatus	tentativeAutoDetect(java.io.File folder)	Attempts to detect whether a folder has the right structure for this importer.

Methods inherited from class java.lang.Object

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

Constructor Detail

DatabaseFolderImporter

public DatabaseFolderImporter()

Method Detail

importFolder

public abstract WritableDatabaseService importFolder(java.io.File folder,
                                                     WritableDatabaseService destination,
                                                     Options options,
                                                     jebl.util.ProgressListener progress)
                                              throws DocumentImportException,
                                                     java.io.IOException

Import the external database to a Geneious WritableDatabaseService and report back the containing the added documents. The return value should normally be a newly-added folder.

Parameters:

folder - The folder containing the external database in the file system

destination - parent folder where the folder will be imported

Returns:

Geneious service containing the documents added to the Geneious database

Throws:

DocumentImportException

java.io.IOException

Since:

API 4.201920 (Geneious Prime 2019.2.0)

getOptions

public abstract Options getOptions(java.io.File folder,
                                   WritableDatabaseService destination,
                                   jebl.util.ProgressListener progress)
                            throws DocumentImportException

Provides some options applicable to this database importer to the user, or null if no user-specified options are required. This is guaranteed to be called before importFolder(File, WritableDatabaseService, Options, ProgressListener). The same Options object will be passed to importFolder(File, WritableDatabaseService, Options, ProgressListener) if the user clicks "Ok". The necessary values can then be extracted from it.

Parameters:

folder - The folder containing the external database in the file system

destination - parent folder where the folder will be imported

progress -

Returns:

Options to be used for importing the database folder

Throws:

DocumentImportException

Since:

API 4.201920 (Geneious Prime 2019.2.0)

tentativeAutoDetect

public abstract DocumentFileImporter.AutoDetectStatus tentativeAutoDetect(java.io.File folder)

Attempts to detect whether a folder has the right structure for this importer. This method should return quickly, and in particular it shouldn't normally attempt to parse any files in the folder. The folder parameter is provided to make it possible to quickly examine the directory structure to determine whether it appears to be correct. Parsing a small file to determine e.g., version compatibility, is permissible. Because this method shouldn't normally parse any files, it is also permissible in rare cases to return ACCEPT here even if the import will fail later on. However this method should never return REJECT if there is a chance that the file might be valid. This method also should not default to MAYBE in all cases where it cannot rightly return ACCEPT. It would then become the default importer for all folders it would be the only MAYBE returned for those files.

Returns:

Since:

API 4.201920 (Geneious Prime 2019.2.0)

getUniqueId

public java.lang.String getUniqueId()

Get a unique identifier for this DocumentFileImporter. This is so that PluginUtilities.getDatabaseFolderImporter(String) can be used to find this DocumentFileImporter. A unique identifier may consist of any valid Java indentifier characters (see Character.isJavaIdentifierPart(char) as well as to the space character.

Returns:

a unique identifier for this DocumentFileImporter. The default implementation returns the className.

Since:

API 4.201920 (Geneious Prime 2019.2.0)

getDatabaseTypeDescription

public abstract java.lang.String getDatabaseTypeDescription()

Returns:

The database type description. E.g.: "Some Application database"

Since:

API 4.201920 (Geneious Prime 2019.2.0)