org.labkey.remoteapi.assay.ImportRunCommand Maven / Gradle / Ivy
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The client-side library for Java developers is a separate JAR from the LabKey Server code base. It can be used by any Java program, including another Java web application.
/*
* Copyright (c) 2012-2018 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.labkey.remoteapi.assay;
import org.apache.http.client.methods.HttpPost;
import org.apache.http.client.methods.HttpUriRequest;
import org.apache.http.entity.ContentType;
import org.apache.http.entity.mime.MultipartEntityBuilder;
import org.json.simple.JSONArray;
import org.json.simple.JSONObject;
import org.labkey.remoteapi.PostCommand;
import java.io.File;
import java.net.URI;
import java.util.List;
import java.util.Map;
/**
* Import a new assay run. If no batch is specified, a new batch will be inserted.
*
* User: kevink
* Date: 9/12/12
*/
public class ImportRunCommand extends PostCommand
{
private boolean _useJson = false;
private int _batchId;
private int _assayId;
private String _name;
private String _comment;
private Map _properties;
private Map _batchProperties;
// Only one of the follow is allowed
private List> _dataRows;
private File _file;
private String _runFilePath;
private JSONObject _plateMetadata;
public ImportRunCommand(int assayId)
{
this(assayId, (File)null);
}
public ImportRunCommand(int assayId, File file)
{
super("assay", "importRun.api");
_assayId = assayId;
_file = file;
}
public ImportRunCommand(int assayId, List> dataRows)
{
super("assay", "importRun.api");
_assayId = assayId;
_dataRows = dataRows;
}
public void setUseJson(boolean useJson)
{
_useJson = useJson;
}
public void setName(String name)
{
_name = name;
}
public void setComment(String comment)
{
_comment = comment;
}
public void setFile(File file)
{
_file = file;
}
/**
* Absolute or relative path to assay data file to be imported.
* The file must exist under the file or pipeline root of the container.
* @param runFilePath the data file path
*/
public void setRunFilePath(String runFilePath)
{
_runFilePath = runFilePath;
}
public void setProperties(Map properties)
{
_properties = properties;
}
public void setBatchId(int batchId)
{
_batchId = batchId;
}
public void setBatchProperties(Map batchProperties)
{
_batchProperties = batchProperties;
}
public void setPlateMetadata(JSONObject plateMetadata)
{
_plateMetadata = plateMetadata;
}
@Override
public ImportRunCommand copy()
{
ImportRunCommand cmd = new ImportRunCommand(_assayId, _file);
cmd._useJson = _useJson;
cmd._name = _name;
cmd._comment = _comment;
cmd._properties = _properties;
cmd._batchId = _batchId;
cmd._batchProperties = _batchProperties;
cmd._runFilePath = _runFilePath;
cmd._plateMetadata = _plateMetadata;
return cmd;
}
@Override
protected ImportRunResponse createResponse(String text, int status, String contentType, JSONObject json)
{
return new ImportRunResponse(text, status, contentType, json, this);
}
@Override
protected HttpUriRequest createRequest(URI uri)
{
MultipartEntityBuilder builder = MultipartEntityBuilder.create();
if (_assayId == 0)
throw new IllegalArgumentException("assay id required");
if (_file == null && _runFilePath == null && _dataRows == null)
throw new IllegalArgumentException("At least one of 'file', 'runFilePath', or 'dataRows' is required");
if ((_file != null ? 1 : 0) + (_runFilePath != null ? 1 : 0) + (_dataRows != null ? 1 : 0) > 1)
throw new IllegalArgumentException("Only one of 'file', 'runFilePath', or 'dataRows' is allowed");
if (_useJson)
{
JSONObject json = new JSONObject();
json.put("apiVersion", getRequiredVersion());
json.put("assayId", _assayId);
if (_batchId > 0)
json.put("batchId", _batchId);
if (_name != null)
json.put("name", _name);
if (_comment != null)
json.put("comment", _comment);
if (_properties != null)
json.put("properties", _properties);
if (_batchProperties != null)
json.put("batchProperties", _batchProperties);
if (_dataRows != null)
json.put("dataRows", _dataRows);
if (_runFilePath != null)
json.put("runFilePath", _runFilePath);
if (_plateMetadata != null)
json.put("plateMetadata", _plateMetadata);
builder.addTextBody("json", json.toJSONString(), ContentType.APPLICATION_JSON);
}
else
{
builder.addTextBody("assayId", String.valueOf(_assayId));
if (_batchId > 0)
builder.addTextBody("batchId", String.valueOf(_batchId));
if (_name != null)
builder.addTextBody("name", String.valueOf(_name));
if (_comment != null)
builder.addTextBody("comment", String.valueOf(_comment));
if (_properties != null)
{
for (Map.Entry entry : _properties.entrySet())
{
builder.addTextBody("properties[" + entry.getKey() + "]", String.valueOf(entry.getValue()));
}
}
if (_batchProperties != null)
{
for (Map.Entry entry : _batchProperties.entrySet())
{
builder.addTextBody("batchProperties[" + entry.getKey() + "]", String.valueOf(entry.getValue()));
}
}
if (_dataRows != null)
builder.addTextBody("dataRows", JSONArray.toJSONString(_dataRows), ContentType.APPLICATION_JSON);
if (_runFilePath != null)
builder.addTextBody("runFilePath", _runFilePath);
if (_plateMetadata != null)
builder.addTextBody("plateMetadata", _plateMetadata.toJSONString());
}
// UNDONE: set content type based on extension
if (_file != null)
builder.addBinaryBody("file", _file, ContentType.APPLICATION_OCTET_STREAM, _file.getName());
HttpPost post = new HttpPost(uri);
post.setEntity(builder.build());
return post;
}
}