/** @param bioID */
private boolean setBioID(String bioID) {
boolean toRet = false;
try {
JsonFactory factory = new JsonFactory();
JsonParser jparser = factory.createParser(bioID);
String key = "";
// Get StartObject for JSON, after first {
jparser.nextToken();
while (jparser.nextToken() != JsonToken.END_OBJECT) {
key = jparser.getText();
if (key.equals("id")) {
key = jparser.nextTextValue();
// Set bioID in Experiment
selExp.setBioID(key);
toRet = true;
} else {
jparser.skipChildren();
}
}
jparser.close();
} catch (JsonParseException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
return toRet;
}
@Port(direction = Direction.INPUT, name = "Set Experiment to upload", order = 1)
public void setExperiment(IExperiment selExp) {
this.selExp = selExp;
if (this.selExp.getMapIntraExpsColors() != null) {
isInter = true;
} else {
isInter = false;
}
try {
// First step, send Experiment data
String json = generateJSON();
// Second step, receive Experiment bio_ID from BiofOmics
String bioID = getBioID(json);
if (!bioID.isEmpty()) {
// Third step, set bio_ID in the Experiment
boolean success = setBioID(bioID);
if (success) {
// Four step, create Experiment files and send them to
// BiofOmics
String zipPath = saveExpInTempFolder();
json = generateJSON(zipPath);
// Call webService to upload the file
int serverCode = uploadExperiment(json);
if (serverCode < 400) {
ShowDialog.showInfo(
I18n.get("updloadOkTitle"),
I18n.get("uploadOk1")
+ selExp.getName()
+ I18n.get("uploadOk2")
+ BewConstants.USER
+ ".");
} else {
if (serverCode == 401) {
ShowDialog.showError(I18n.get("updloadErrorTitle"), I18n.get("uploadBadLogin"));
} else if (serverCode == 500) {
ShowDialog.showError(I18n.get("updloadErrorTitle"), I18n.get("uploadServerError"));
}
}
} else {
ShowDialog.showError(I18n.get("updloadErrorTitle"), I18n.get("uploadIDError"));
}
} else {
ShowDialog.showError(I18n.get("updloadErrorTitle"), I18n.get("uploadIDError"));
}
} catch (UnknownHostException e) {
// TODO Auto-generated catch block
e.printStackTrace();
ShowDialog.showError(I18n.get("updloadErrorTitle"), I18n.get("webServicesConnection"));
} catch (Exception e) {
// TODO Auto-generated catch block
e.printStackTrace();
ShowDialog.showError(I18n.get("updloadErrorTitle"), I18n.get("updloadError"));
}
}
/**
* Method to fill the JSON with the experiment information. This JSON includes the files field.
*
* @param json Input JSON to fill with data.
* @param zipPath Path of the temporary zip files for the Experiment.
* @return String with the new JSON.
* @throws IOException
*/
private String getJSONExperiment(String json, String zipPath) throws IOException {
// Get bioID
json += "\"id\":\"" + selExp.getBioID() + "\"";
// Set zip file
Path path = FileSystems.getDefault().getPath(zipPath);
json += ",\"file\":\"" + new String(Base64Coder.encode(Files.readAllBytes(path))) + "\"}";
return json;
}
/**
* Method to save the selected Experiment, in xml and xls (if possible), in a temporary folder.
* The files will be contained inside a zip.
*
* @return String with the path of the zip file.
* @throws IOException
*/
private String saveExpInTempFolder() throws IOException {
String toRet = "";
// Create temporary File
String filePath = Files.createTempDirectory("").toString() + "/";
filePath = filePath.replace("\\", "/");
// Get bioID
String bioID = selExp.getBioID();
if (bioID.isEmpty()) {
bioID = "bio_";
}
DataToFile.saveXMLData(selExp, filePath + "xml");
// Only save in XLS if the Experiment is an IntraExperiment
if (!isInter) {
DataToFile.saveXLSData(selExp, filePath + "xls");
}
// Generate ZIP file with Java 7
Map<String, String> zipProperties = new HashMap<>();
zipProperties.put("create", "true");
zipProperties.put("encoding", "UTF-8");
// Create zip file
URI zipDisk;
toRet = filePath + bioID + ".zip";
if (toRet.startsWith("/")) {
zipDisk = URI.create("jar:file:" + toRet);
} else {
zipDisk = URI.create("jar:file:/" + toRet);
}
// Adding files to zip
try (FileSystem zipfs = FileSystems.newFileSystem(zipDisk, zipProperties)) {
// Create file inside zip
Path zipFilePath = zipfs.getPath(bioID + ".xml");
// Path where the file to be added resides
Path addNewFile = Paths.get(filePath + "xml.xml");
// Append file to ZIP File
Files.copy(addNewFile, zipFilePath);
if (!isInter) {
// Now go for the xls file
zipFilePath = zipfs.getPath(bioID + ".xls");
addNewFile = Paths.get(filePath + "xls.xls");
Files.copy(addNewFile, zipFilePath);
}
}
// Delete temp files
Files.deleteIfExists(Paths.get(filePath + "xml.xml"));
Files.deleteIfExists(Paths.get(filePath + "xls.xls"));
return toRet;
}
