Hello BASE team,
We really enjoy the set of batch uploading plugins and were doing a
little training for our users in Bergen. Everything seemed great except
that they couldn't link freshly created scans with image files. I read
in the example spreadsheet that it is not supported and was very
surprised since similar 'file attaching' works very nice for raw
bioassays. I sat down, did some copy pasting from RawBioAssayImporter
and after little edits it worked (source attached).
I hope that you can make some use of it.
All the best,
Pawel
/**
$Id: ScanImporter.java 4551 2008-09-29 07:47:24Z nicklas $
Copyright (C) 2008 Nicklas Nordborg
This file is part of BASE - BioArray Software Environment.
Available at http://base.thep.lu.se/
BASE is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 3
of the License, or (at your option) any later version.
BASE is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with BASE. If not, see http://www.gnu.org/licenses/.
*/
package net.sf.basedb.plugins.batchimport;
import java.util.Collections;
import java.util.List;
import java.util.Set;
import net.sf.basedb.core.DbControl;
import net.sf.basedb.core.File;
import net.sf.basedb.core.Hardware;
import net.sf.basedb.core.Hybridization;
import net.sf.basedb.core.Image;
import net.sf.basedb.core.Item;
import net.sf.basedb.core.ItemQuery;
import net.sf.basedb.core.Path;
import net.sf.basedb.core.PathParameterType;
import net.sf.basedb.core.PluginParameter;
import net.sf.basedb.core.Protocol;
import net.sf.basedb.core.ProtocolType;
import net.sf.basedb.core.Scan;
import net.sf.basedb.core.SystemItems;
import net.sf.basedb.core.Version;
import net.sf.basedb.core.plugin.About;
import net.sf.basedb.core.plugin.AboutImpl;
import net.sf.basedb.core.plugin.GuiContext;
import net.sf.basedb.util.parser.FlatFileParser;
import net.sf.basedb.util.parser.Mapper;
/**
Plug-in for importing scan items in a batch. The plug-in can create new
items and updated existing items.
@author nicklas
@version 2.8
@base.modified $Date: 2008-09-29 09:47:24 +0200 (Mon, 29 Sep 2008) $
*/
public class ScanImporterNMC
extends AbstractItemImporterScan
{
private static final SetGuiContext guiContexts =
Collections.singleton(new GuiContext(Item.SCAN, GuiContext.Type.LIST));
private static final About about =
new AboutImpl
(
Scan importer with images,
Imports and updates scans in a batch (linking with images).,
Version.getMajor() + . + Version.getMinor() + . + Version.getMaintenance(),
2008, Base 2 development team,
null,
null,
http://base.thep.lu.se;
);
protected static final PluginParameterString hardwareColumnMapping = new PluginParameterString(
hardwareColumnMapping,
Scanner,
Mapping that picks the name or ID of the array slide scanner from the data columns. +
The plug-in will first try to find a scanner with the given name. If none is found and +
the value is numeric it will try to load by internal ID. +
Example: \\Scanner\\,
optionalColumnMapping
);
protected static final PluginParameterString hybridizationColumnMapping = new PluginParameterString(
hybridizationColumnMapping,
Hybridization,
Mapping that picks the name or ID of the hybridization from the data columns. +
The plug-in will first try to find a hybridization with the given name. If none is found and +
the value is numeric it will try to load by internal ID. +
Example: \\Hybridization\\,
optionalColumnMapping
);
// extra parameter needed for linking with image files
protected static final PluginParameterString fileColumnMapping = new PluginParameterString(
fileColumnMapping,
File,
Mapping that picks the path of a image file from the columns. +
The path can be an absolute path (starting with /) or relative +
to the 'Data directory' parameter. +
Example: \\File\\,
optionalColumnMapping
);
public ScanImporterNMC()
{}
/*
From the Plugin interface
*/
@Override
public About getAbout()
{
return about;
}
//
/*
From the InteractivePlugin interface
*/
@Override
public SetGuiContext getGuiContexts()
{
return guiContexts;
}
//
/*
From the AbstractItemImporter class
*/
private Mapper nameMapper;
private Mapper descriptionMapper;
private Mapper protocolMapper;
private Mapper hardwareMapper;
private Mapper hybridizationMapper;
//extra mappers for linking with image file
private
