org.hl7.fhir.r4.utils.BatchLoader Maven / Gradle / Ivy

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Builds the hapi fhir r4. Requires hapi-fhir-base and hapi-fhir-utilities be built first and be excluded from any other poms requiring it.
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package org.hl7.fhir.r4.utils;

/*
  Copyright (c) 2011+, HL7, Inc.
  All rights reserved.
  
  Redistribution and use in source and binary forms, with or without modification, 
  are permitted provided that the following conditions are met:
    
   * Redistributions of source code must retain the above copyright notice, this 
     list of conditions and the following disclaimer.
   * Redistributions in binary form must reproduce the above copyright notice, 
     this list of conditions and the following disclaimer in the documentation 
     and/or other materials provided with the distribution.
   * Neither the name of HL7 nor the names of its contributors may be used to 
     endorse or promote products derived from this software without specific 
     prior written permission.
  
  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
  ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
  WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. 
  IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, 
  INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT 
  NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 
  PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, 
  WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
  ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
  POSSIBILITY OF SUCH DAMAGE.
  
 */

import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.text.SimpleDateFormat;
import java.util.Date;
import java.util.UUID;

import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r4.formats.IParser;
import org.hl7.fhir.r4.formats.JsonParser;
import org.hl7.fhir.r4.formats.XmlParser;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.r4.model.Bundle.BundleType;
import org.hl7.fhir.r4.model.Bundle.HTTPVerb;
import org.hl7.fhir.r4.model.Resource;
import org.hl7.fhir.r4.utils.client.FHIRToolingClient;
import org.hl7.fhir.utilities.IniFile;
import org.hl7.fhir.utilities.Utilities;

public class BatchLoader {

  public static void main(String[] args) throws IOException, Exception {
    if (args.length < 3) {
      System.out.println(
          "Batch uploader takes 3 parameters in order: server base url, file/folder to upload, and batch size");
    } else {
      String server = args[0];
      String file = args[1];
      int size = Integer.parseInt(args[2]);
      if (file.endsWith(".xml")) {
        throw new FHIRException("Unimplemented file type " + file);
      } else if (file.endsWith(".json")) {
        throw new FHIRException("Unimplemented file type " + file);
//	  	} else if (file.endsWith(".zip")) {
//	  		LoadZipFile(server, file, p, size, 0, -1);
      } else if (new File(file).isDirectory()) {
        LoadDirectory(server, file, size);
      } else
        throw new FHIRException("Unknown file type " + file);
    }
  }

  private static void LoadDirectory(String server, String folder, int size) throws IOException, Exception {
    System.out.print("Connecting to " + server + ".. ");
    FHIRToolingClient client = new FHIRToolingClient(server, "fhir/batch-loader");
    System.out.println("Done");

    IniFile ini = new IniFile(Utilities.path(folder, "batch-load-progress.ini"));
    for (File f : new File(folder).listFiles()) {
      if (f.getName().endsWith(".json") || f.getName().endsWith(".xml")) {
        if (!ini.getBooleanProperty("finished", f.getName())) {
          sendFile(client, f, size, ini);
        }
      }
    }
  }

  private static void sendFile(FHIRToolingClient client, File f, int size, IniFile ini)
      throws FHIRFormatError, FileNotFoundException, IOException {
    long ms = System.currentTimeMillis();
    System.out.print("Loading " + f.getName() + ".. ");
    IParser parser = f.getName().endsWith(".json") ? new JsonParser() : new XmlParser();
    Resource res = parser.parse(new FileInputStream(f));
    System.out.println("  done: (" + Long.toString(System.currentTimeMillis() - ms) + " ms)");

    if (res instanceof Bundle) {
      Bundle bnd = (Bundle) res;
      int cursor = ini.hasProperty("progress", f.getName()) ? ini.getIntegerProperty("progress", f.getName()) : 0;
      while (cursor < bnd.getEntry().size()) {
        Bundle bt = new Bundle();
        bt.setType(BundleType.BATCH);
        bt.setId(UUID.randomUUID().toString().toLowerCase());
        for (int i = cursor; i < Math.min(bnd.getEntry().size(), cursor + size); i++) {
          BundleEntryComponent be = bt.addEntry();
          be.setResource(bnd.getEntry().get(i).getResource());
          be.getRequest().setMethod(HTTPVerb.PUT);
          be.getRequest().setUrl(be.getResource().getResourceType().toString() + "/" + be.getResource().getId());
        }
        System.out.print(f.getName() + " (" + cursor + "/" + bnd.getEntry().size() + "): ");
        ms = System.currentTimeMillis();
        Bundle resp = client.transaction(bt);

        int ncursor = cursor + size;
        for (int i = 0; i < resp.getEntry().size(); i++) {
          BundleEntryComponent t = resp.getEntry().get(i);
          if (!t.getResponse().getStatus().startsWith("2")) {
            System.out.println("failed status at " + Integer.toString(i) + ": " + t.getResponse().getStatus());
            ncursor = cursor + i - 1;
            break;
          }
        }
        cursor = ncursor;
        System.out.println("  .. done: (" + Long.toString(System.currentTimeMillis() - ms) + " ms) "
            + SimpleDateFormat.getInstance().format(new Date()));
        ini.setIntegerProperty("progress", f.getName(), cursor, null);
        ini.save();
      }
      ini.setBooleanProperty("finished", f.getName(), true, null);
      ini.save();
    } else {
      client.update(res);
      ini.setBooleanProperty("finished", f.getName(), true, null);
      ini.save();
    }
  }
//
//  private static void LoadZipFile(String server, String file, IParser p, int size, int start, int end) throws IOException, Exception {
//		System.out.println("Load Zip file "+file);
//	 	Bundle b = new Bundle();
//	 	b.setType(BundleType.COLLECTION);
//	 	b.setId(UUID.randomUUID().toString().toLowerCase());
//	 	ZipInputStream zip = new ZipInputStream(new FileInputStream(file));
//	 	ZipEntry entry;
//    while((entry = zip.getNextEntry())!=null)
//    {
//    	try {
//    	  Resource r = p.parse(zip);
//    	  b.addEntry().setResource(r);
//    	} catch (Exception e) {
//    		throw new Exception("Error parsing "+entry.getName()+": "+e.getMessage(), e);
//    	}
//    }
//	 	loadBundle(server, b, size, start, end);
//	}
//
//  
//	private static int loadBundle(String server, Bundle b, int size, int start, int end) throws URISyntaxException {
//		System.out.println("Post to "+server+". size = "+Integer.toString(size)+", start = "+Integer.toString(start)+", total = "+Integer.toString(b.getEntry().size()));
//		FHIRToolingClient client = new FHIRToolingClient(server);
//	  int c = start;
//	  if (end == -1)
//	    end = b.getEntry().size();
//	  while (c < end) {
//		 	Bundle bt = new Bundle();
//		 	bt.setType(BundleType.BATCH);		 	
//		 	bt.setId(UUID.randomUUID().toString().toLowerCase());
//		 	for (int i = c; i < Math.min(b.getEntry().size(), c+size); i++) {
//		 		BundleEntryComponent be = bt.addEntry();
//		 		be.setResource(b.getEntry().get(i).getResource());
//		 		be.getRequest().setMethod(HTTPVerb.PUT);
//		 		be.getRequest().setUrl(be.getResource().getResourceType().toString()+"/"+be.getResource().getId());
//		 	}
//			System.out.print("  posting..");
//			long ms = System.currentTimeMillis();
//		 	Bundle resp = client.transaction(bt);
//		 	
//		 	for (int i = 0; i < resp.getEntry().size(); i++) {
//		 	  BundleEntryComponent t = resp.getEntry().get(i);
//		 	  if (!t.getResponse().getStatus().startsWith("2")) { 
//		 	    System.out.println("failed status at "+Integer.toString(i)+": "+t.getResponse().getStatus());
//		 	    return c+i;
//		 	  }
//		 	}
//		 	c = c + size;
//      System.out.println("  ..done: "+Integer.toString(c)+". ("+Long.toString(System.currentTimeMillis()-ms)+" ms)");
//	  }
//		System.out.println(" done");
//		return c;
//	}

}