public void parseStatsMessage(Message<Map<String, Map<String, byte[]>>> message)
throws IOException {
Map<String, Map<String, byte[]>> a = message.getPayload();
for (String type : a.keySet()) {
Map<String, byte[]> b = a.get(type);
for (String filename : b.keySet()) {
log.info("Processing stats for: " + filename);
BufferedInputStream bis =
new BufferedInputStream(new ByteArrayInputStream(b.get(filename)));
File outFile = null;
OutputStream out = null;
try {
outFile = new File(new File("/tmp/"), filename);
try {
out = new FileOutputStream(outFile);
byte[] buf = new byte[16884];
int len;
while ((len = bis.read(buf)) > 0) {
out.write(buf, 0, len);
}
} catch (IOException e) {
log.error("Could not write temporary file: " + outFile.getAbsolutePath());
e.printStackTrace();
} finally {
try {
bis.close();
} catch (IOException e) {
// ignore
}
}
} finally {
if (out != null) {
out.close();
}
if (outFile != null) {
File newFile = misoFileManager.storeFile(Run.class, "stats", outFile);
if (newFile != null && outFile.delete()) {
File destination = new File(newFile.getParentFile(), newFile.getName().split("-")[0]);
if (LimsUtils.checkDirectory(destination, true)) {
if (LimsUtils.unzipFile(newFile, destination)) {
newFile.delete();
}
}
}
}
}
}
}
}
public JSONObject getPlateBarcode(HttpSession session, JSONObject json) {
Long plateId = json.getLong("plateId");
File temploc = new File(session.getServletContext().getRealPath("/") + "temp/");
try {
// Plate<LinkedList<Plateable>, Plateable> plate = requestManager.<LinkedList<Plateable>,
// Plateable> getPlateById(plateId);
Plate<? extends List<? extends Plateable>, ? extends Plateable> plate =
requestManager.getPlateById(plateId);
barcodeFactory.setPointPixels(1.5f);
barcodeFactory.setBitmapResolution(600);
RenderedImage bi = null;
if (json.has("barcodeGenerator")) {
BarcodeDimension dim = new BarcodeDimension(100, 100);
if (json.has("dimensionWidth") && json.has("dimensionHeight")) {
dim =
new BarcodeDimension(
json.getDouble("dimensionWidth"), json.getDouble("dimensionHeight"));
}
BarcodeGenerator bg = BarcodeFactory.lookupGenerator(json.getString("barcodeGenerator"));
if (bg != null) {
bi = barcodeFactory.generateBarcode(plate, bg, dim);
} else {
return JSONUtils.SimpleJSONError(
"'" + json.getString("barcodeGenerator") + "' is not a valid barcode generator type");
}
} else {
bi = barcodeFactory.generateSquareDataMatrix(plate, 400);
}
if (bi != null) {
File tempimage = misoFileManager.generateTemporaryFile("barcode-", ".png", temploc);
if (ImageIO.write(bi, "png", tempimage)) {
return JSONUtils.JSONObjectResponse("img", tempimage.getName());
}
return JSONUtils.SimpleJSONError("Writing temp image file failed.");
} else {
return JSONUtils.SimpleJSONError("Plate has no parseable barcode");
}
} catch (IOException e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError(
e.getMessage() + ": Cannot seem to access " + temploc.getAbsolutePath());
}
}
public JSONObject downloadPlateInputForm(HttpSession session, JSONObject json) {
if (json.has("documentFormat")) {
String documentFormat = json.getString("documentFormat");
try {
File f =
misoFileManager.getNewFile(
Plate.class,
"forms",
"PlateInputForm-" + LimsUtils.getCurrentDateAsString() + "." + documentFormat);
FormUtils.createPlateInputSpreadsheet(f);
return JSONUtils.SimpleJSONResponse("" + f.getName().hashCode());
} catch (Exception e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError("Failed to get plate input form: " + e.getMessage());
}
} else {
return JSONUtils.SimpleJSONError("Missing project ID or document format supplied.");
}
}