163 lines
4.9 KiB
Java
163 lines
4.9 KiB
Java
package org.gcube.data.transfer.plugins.sis;
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import java.io.File;
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import java.io.FileInputStream;
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import java.io.FileOutputStream;
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import java.io.IOException;
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import java.io.InputStream;
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import java.io.OutputStream;
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import java.net.URL;
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import java.nio.file.Files;
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import java.nio.file.StandardCopyOption;
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import java.security.MessageDigest;
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import java.security.NoSuchAlgorithmException;
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import javax.xml.bind.JAXBException;
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import org.apache.sis.storage.DataStoreException;
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import org.apache.sis.storage.UnsupportedStorageException;
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import org.gcube.data.transfer.plugins.thredds.ISOMetadataMarshalling;
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import org.gcube.data.transfer.plugins.thredds.sis.SisPlugin;
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import ucar.nc2.NetcdfFile;
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import ucar.nc2.dataset.NetcdfDataset;
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public class TestGetMetadata {
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public static void main(String[] args) throws UnsupportedStorageException, DataStoreException, IOException, NoSuchAlgorithmException, JAXBException {
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String[] toCheckFiles=new String[] {
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// ********** HDF - NETCDF 4
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"/Users/FabioISTI/Downloads/NASA_Surface_Air_Temperature_1950_2100_rcp45.nc",
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// "https://thredds.d4science.org/thredds/fileServer/public/netcdf/ClimateChange/NASA_Precipitations_1950_2100_rcp45.nc",
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// "https://thredds.d4science.org/thredds/fileServer/public/netcdf/ClimateChange/NASA_Precipitations_1950_2100_rcp85.nc",
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// "https://thredds.d4science.org/thredds/fileServer/public/netcdf/ClimateChange/NASA_Surface_Air_Temperature_1950_2100_rcp45.nc",
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// "https://thredds.d4science.org/thredds/fileServer/public/netcdf/ClimateChange/NASA_Surface_Air_Temperature_1950_2100_rcp85.nc",
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// "https://thredds.d4science.org/thredds/fileServer/public/netcdf/ClimateChange/hcaf_v6_1950_2100.nc",
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// *********** NETCDF 3
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"/Users/FabioISTI/Downloads/Aaptos_aaptos.nc",
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"/Users/FabioISTI/Downloads/dataset-armor-3d-rep-monthly_20181115T1200Z_P20190301T0000Z.nc",
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//"/Users/FabioISTI/Downloads/data_retro_Run_10026_911.nc",
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//"/Users/FabioISTI/Downloads/2BPR6_2021_a_NRT_Gosud_V3.nc",
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"/Users/FabioISTI/Downloads/GO_WTEP_2015_TRAJ.nc"
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};
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for(String f:toCheckFiles) {
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System.out.println("checking "+f);
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try{
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check(false,f);
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}catch(Exception e) {
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System.err.println(e.getMessage());
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System.out.println("Trying opening "+f+" manually");
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open(f);
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}
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}
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System.out.println("Done");
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}
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private static void open(String path) throws IOException, UnsupportedStorageException, DataStoreException {
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System.out.println("Opening "+path);
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NetcdfFile f=NetcdfFile.open(path);
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System.out.println(f.getFileTypeDescription()+"\t"+f.getFileTypeId());
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NetcdfDataset ncDs=NetcdfDataset.openDataset(path);
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// NcMLReaderNew.
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//
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System.out.println(ncDs.getFileTypeDescription()+"\t"+ncDs.getFileTypeId());
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// NetcdfDatasets.openFile(path,null);
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}
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private static void check(boolean checkCopy,String src) throws UnsupportedStorageException, DataStoreException, IOException, NoSuchAlgorithmException, JAXBException {
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File original=new File(src);
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File dataset=original;
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if(checkCopy) {
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File temp=File.createTempFile("temp", ".temp");
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File copied=File.createTempFile("copied", ".nc");
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transferStream(new FileInputStream(original),new FileOutputStream(temp));
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System.out.println("copied. Moving..");
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System.out.println("Checksum original : "+getChecksum(original));
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System.out.println("Checksum temp : "+getChecksum(temp));
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Files.move(temp.toPath(), copied.toPath(),StandardCopyOption.ATOMIC_MOVE,StandardCopyOption.REPLACE_EXISTING);
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if(copied.length()<original.length()) throw new RuntimeException("Different size after moving");
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dataset=copied;
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}
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if(dataset.exists())
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System.out.println(
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ISOMetadataMarshalling.asXML(SisPlugin.getMetaFromFile(dataset)).getAbsolutePath());
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else {
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System.out.println(
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ISOMetadataMarshalling.asXML(SisPlugin.getMetaFromFile(new URL(src))).getAbsolutePath());
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}
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}
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private static String getChecksum(File datafile) throws NoSuchAlgorithmException, IOException {
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MessageDigest md = MessageDigest.getInstance("SHA1");
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FileInputStream fis = new FileInputStream(datafile);
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byte[] dataBytes = new byte[1024];
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int nread = 0;
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while ((nread = fis.read(dataBytes)) != -1) {
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md.update(dataBytes, 0, nread);
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};
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byte[] mdbytes = md.digest();
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//convert the byte to hex format
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StringBuffer sb = new StringBuffer("");
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for (int i = 0; i < mdbytes.length; i++) {
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sb.append(Integer.toString((mdbytes[i] & 0xff) + 0x100, 16).substring(1));
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}
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return sb.toString();
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}
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private static void transferStream(InputStream in, OutputStream out){
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long receivedTotal=0l;
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try{
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byte[] internalBuf=new byte[1024];
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int received=0;
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while ((received=in.read(internalBuf))!=-1){
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out.write(internalBuf,0,received);
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receivedTotal+=received;
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}
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out.flush();
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}catch(IOException e){
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throw new RuntimeException("Unable to read from source.");
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}
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}
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}
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