Java tutorial
/* * * JAQPOT Quattro * * JAQPOT Quattro and the components shipped with it, in particular: * (i) JaqpotCoreServices * (ii) JaqpotAlgorithmServices * (iii) JaqpotDB * (iv) JaqpotDomain * (v) JaqpotEAR * are licensed by GPL v3 as specified hereafter. Additional components may ship * with some other licence as will be specified therein. * * Copyright (C) 2014-2015 KinkyDesign (Charalampos Chomenidis, Pantelis Sopasakis) * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. * * Source code: * The source code of JAQPOT Quattro is available on github at: * https://github.com/KinkyDesign/JaqpotQuattro * All source files of JAQPOT Quattro that are stored on github are licensed * with the aforementioned licence. */ package org.jaqpot.algorithm.resource; import java.io.IOException; import java.net.MalformedURLException; import java.net.URL; import java.util.Base64; import java.util.UUID; import javax.ws.rs.FormParam; import javax.ws.rs.HeaderParam; import javax.ws.rs.POST; import javax.ws.rs.Path; import javax.ws.rs.Produces; import javax.ws.rs.client.Entity; import javax.ws.rs.core.GenericEntity; import javax.ws.rs.core.MediaType; import javax.ws.rs.core.MultivaluedHashMap; import javax.ws.rs.core.MultivaluedMap; import javax.ws.rs.core.Response; import org.apache.commons.io.IOUtils; import org.jaqpot.core.model.dto.ambit.AmbitTask; import org.jaqpot.core.model.dto.ambit.AmbitTaskArray; import org.jaqpot.core.model.dto.dataset.Dataset; import org.jaqpot.core.model.factory.ErrorReportFactory; import org.jboss.resteasy.client.jaxrs.ResteasyClient; import org.jboss.resteasy.client.jaxrs.ResteasyClientBuilder; import org.jboss.resteasy.client.jaxrs.ResteasyWebTarget; import org.jboss.resteasy.plugins.providers.multipart.MultipartFormDataOutput; /** * * @author Charalampos Chomenidis * @author Pantelis Sopasakis */ @Path("mopac") @Produces(MediaType.APPLICATION_JSON) public class Mopac { @POST @Path("calculate") public Response calculate(@FormParam("pdbfile") String pdbFile, @HeaderParam("subjectid") String subjectId) { try { byte[] file; if (pdbFile.startsWith("data:")) { String base64pdb = pdbFile.split(",")[1]; file = Base64.getDecoder().decode(base64pdb.getBytes()); } else { URL pdbURL = new URL(pdbFile); file = IOUtils.toByteArray(pdbURL.openStream()); } ResteasyClient client = new ResteasyClientBuilder().disableTrustManager().build(); ResteasyWebTarget target = client.target("https://apps.ideaconsult.net/enmtest/dataset"); String fileName = UUID.randomUUID().toString() + ".pdb"; MultipartFormDataOutput mdo = new MultipartFormDataOutput(); mdo.addFormData("file", file, MediaType.APPLICATION_OCTET_STREAM_TYPE, fileName); GenericEntity<MultipartFormDataOutput> entity = new GenericEntity<MultipartFormDataOutput>(mdo) { }; Response response = target.request().header("subjectid", subjectId).accept(MediaType.APPLICATION_JSON) .post(Entity.entity(entity, MediaType.MULTIPART_FORM_DATA_TYPE)); AmbitTaskArray ambitTaskArray = response.readEntity(AmbitTaskArray.class); AmbitTask ambitTask = ambitTaskArray.getTask().get(0); String ambitTaskUri = ambitTask.getUri(); System.out.println("Task POST Dataset:" + ambitTaskUri); while (ambitTask.getStatus().equals("Running") || ambitTask.getStatus().equals("Queued")) { ambitTaskArray = client.target(ambitTaskUri).request().accept(MediaType.APPLICATION_JSON) .header("subjectid", subjectId).get(AmbitTaskArray.class); ambitTask = ambitTaskArray.getTask().get(0); try { Thread.sleep(500); } catch (InterruptedException ex) { continue; } } String datasetUri; if (ambitTask.getStatus().equals("Completed")) { datasetUri = ambitTask.getResult(); } else { return Response.status(Response.Status.BAD_GATEWAY).entity(ErrorReportFactory .remoteError(ambitTaskUri, ErrorReportFactory.internalServerError(), null)).build(); } System.out.println("New Dataset:" + datasetUri); MultivaluedMap algorithmFormData = new MultivaluedHashMap(); algorithmFormData.add("dataset_uri", datasetUri); algorithmFormData.add("mopac_commands", "PM3 NOINTER MMOK BONDS MULLIK GNORM=1.0 T=30.00M"); response = client .target("https://apps.ideaconsult.net/enmtest/algorithm/ambit2.mopac.MopacOriginalStructure") .request().header("subjectid", subjectId).accept(MediaType.APPLICATION_JSON) .post(Entity.form(algorithmFormData)); ambitTaskArray = response.readEntity(AmbitTaskArray.class); ambitTask = ambitTaskArray.getTask().get(0); ambitTaskUri = ambitTask.getUri(); System.out.println("Task POST Dataset:" + ambitTaskUri); while (ambitTask.getStatus().equals("Running") || ambitTask.getStatus().equals("Queued")) { ambitTaskArray = client.target(ambitTaskUri).request().accept(MediaType.APPLICATION_JSON) .header("subjectid", subjectId).get(AmbitTaskArray.class); ambitTask = ambitTaskArray.getTask().get(0); try { Thread.sleep(500); } catch (InterruptedException ex) { continue; } } if (ambitTask.getStatus().equals("Completed")) { datasetUri = ambitTask.getResult(); } else { return Response.status(Response.Status.BAD_GATEWAY).entity(ErrorReportFactory .remoteError(ambitTaskUri, ErrorReportFactory.internalServerError(), null)).build(); } System.out.println(datasetUri); response = client.target(datasetUri).request().header("subjectid", subjectId) .accept(MediaType.APPLICATION_JSON).get(); Dataset dataset = response.readEntity(Dataset.class); return Response.ok(dataset.getDataEntry().get(0).getValues()).build(); } catch (MalformedURLException ex) { return Response.status(Response.Status.BAD_REQUEST) .entity(ErrorReportFactory.badRequest(ex.getMessage(), "Bad pdb file:" + pdbFile)).build(); } catch (IOException ex) { return Response.status(Response.Status.BAD_GATEWAY).entity( ErrorReportFactory.remoteError(ex.getMessage(), ErrorReportFactory.internalServerError(), ex)) .build(); } } }