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Repaired reporting order of linkages and now express as a haplotype.
Remove multiple xml headers from single output.
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178 changes: 178 additions & 0 deletions
178
ld-tools/src/main/java/org/nmdp/validation/tools/PostPopulationFrequencies.java
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| ///* | ||
| // | ||
| // Copyright (c) 2014-2015 National Marrow Donor Program (NMDP) | ||
| // | ||
| // This library is free software; you can redistribute it and/or modify it | ||
| // under the terms of the GNU Lesser General Public License as published | ||
| // by the Free Software Foundation; either version 3 of the License, or (at | ||
| // your option) any later version. | ||
| // | ||
| // This library is distributed in the hope that it will be useful, but WITHOUT | ||
| // ANY WARRANTY; with out even the implied warranty of MERCHANTABILITY or | ||
| // FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public | ||
| // License for more details. | ||
| // | ||
| // You should have received a copy of the GNU Lesser General Public License | ||
| // along with this library; if not, write to the Free Software Foundation, | ||
| // Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA. | ||
| // | ||
| // > http://www.gnu.org/licenses/lgpl.html | ||
| // | ||
| //*/ | ||
| //package org.nmdp.validation.tools; | ||
| // | ||
| //import static org.dishevelled.compress.Readers.reader; | ||
| // | ||
| //import java.io.BufferedReader; | ||
| //import java.io.File; | ||
| //import java.io.IOException; | ||
| //import java.math.BigDecimal; | ||
| //import java.util.HashMap; | ||
| //import java.util.concurrent.Callable; | ||
| // | ||
| //import org.dash.valid.gl.GLStringConstants; | ||
| //import org.dishevelled.commandline.ArgumentList; | ||
| //import org.dishevelled.commandline.CommandLine; | ||
| //import org.dishevelled.commandline.CommandLineParseException; | ||
| //import org.dishevelled.commandline.CommandLineParser; | ||
| //import org.dishevelled.commandline.Switch; | ||
| //import org.dishevelled.commandline.Usage; | ||
| //import org.dishevelled.commandline.argument.FileArgument; | ||
| //import org.dishevelled.commandline.argument.StringArgument; | ||
| // | ||
| //import io.swagger.client.model.HFCurationRequest1; | ||
| //import io.swagger.client.model.HaplotypeFrequency1; | ||
| //import io.swagger.client.model.HaplotypeFrequencyData1; | ||
| //import io.swagger.client.model.License1; | ||
| // | ||
| ///** | ||
| // * PostPopulationFrequencies | ||
| // * | ||
| // */ | ||
| //public class PostPopulationFrequencies implements Callable<Integer> { | ||
| // | ||
| // private final File inputFile; | ||
| // private final String accessId; | ||
| // private final String cohortId; | ||
| // | ||
| // private static final String USAGE = "post-population-frequencies [args]"; | ||
| // | ||
| // | ||
| // /** | ||
| // * Post population frequencies to the frequency curation service | ||
| // * | ||
| // * @param inputFile input file | ||
| // * @param accessId | ||
| // * @param cohortId | ||
| // */ | ||
| // public PostPopulationFrequencies(File inputFile, String accessId, String cohortId) { | ||
| // this.inputFile = inputFile; | ||
| // this.accessId = accessId; | ||
| // this.cohortId = cohortId; | ||
| // } | ||
| // | ||
| // @Override | ||
| // public Integer call() throws Exception { | ||
| // postPopulationFrequencies(reader(inputFile)); | ||
| // | ||
| // return 0; | ||
| // } | ||
| // | ||
| // public void postPopulationFrequencies(BufferedReader reader) throws IOException { | ||
| // String row; | ||
| // String[] columns; | ||
| // | ||
| // HashMap<String, HaplotypeFrequencyData1> populationMap = new HashMap<String, HaplotypeFrequencyData1>(); | ||
| // HaplotypeFrequencyData1 haplotypeFrequencyData; | ||
| // | ||
| // License1 license = new License1(); | ||
| // license.setTypeOfLicense(io.swagger.client.model.License1.TypeOfLicenseEnum.CC0); | ||
| // | ||
| // while ((row = reader.readLine()) != null) { | ||
| // columns = row.split(GLStringConstants.COMMA); | ||
| // | ||
| // String race = columns[0]; | ||
| // String haplotype = columns[1]; | ||
| // Double frequency = new Double(columns[2]); | ||
| // | ||
| // if (populationMap.containsKey(race)) { | ||
| // haplotypeFrequencyData = populationMap.get(race); | ||
| // } | ||
| // else { | ||
| // haplotypeFrequencyData = new HaplotypeFrequencyData1(); | ||
| // haplotypeFrequencyData.setLicense(license); | ||
| // } | ||
| // | ||
| // HaplotypeFrequency1 hapFrequency = new HaplotypeFrequency1(); | ||
| // hapFrequency.setFrequency(new BigDecimal(frequency)); | ||
| // hapFrequency.setHaplotypeString(haplotype); | ||
| // haplotypeFrequencyData.addHaplotypeFrequencyListItem(hapFrequency); | ||
| // | ||
| // populationMap.put(race, haplotypeFrequencyData); | ||
| // } | ||
| // | ||
| // reader.close(); | ||
| // | ||
| // for (String populationId : populationMap.keySet()) { | ||
| // HFCurationRequest1 hfCurationRequest = new HFCurationRequest1(); | ||
| // | ||
| // hfCurationRequest.setAccessID(accessId); | ||
| // hfCurationRequest.setPopulationID(populationId); | ||
| // hfCurationRequest.setHaplotypeFrequencyData(populationMap.get(populationId)); | ||
| // hfCurationRequest.setCohortID(cohortId); | ||
| // | ||
| // //HFCurationResponse1 response = api.hfcPost(hfCurationRequest); | ||
| // //System.out.println(response); | ||
| // | ||
| // System.out.println("Population: " + hfCurationRequest.getPopulationID() + " and haplotypes: " + hfCurationRequest.getHaplotypeFrequencyData().getHaplotypeFrequencyList().size()); | ||
| // | ||
| // System.out.println("Here's the first two..."); | ||
| // | ||
| // System.out.println(hfCurationRequest.getHaplotypeFrequencyData().getHaplotypeFrequencyList().get(0)); | ||
| // System.out.println(hfCurationRequest.getHaplotypeFrequencyData().getHaplotypeFrequencyList().get(1)); | ||
| // } | ||
| // } | ||
| // | ||
| // /** | ||
| // * Main. | ||
| // * | ||
| // * @param args command line args | ||
| // */ | ||
| // public static void main(final String[] args) { | ||
| // Switch about = new Switch("a", "about", "display about message"); | ||
| // Switch help = new Switch("h", "help", "display help message"); | ||
| // FileArgument inputFile = new FileArgument("i", "input-file", "input file, default stdin", true); | ||
| // StringArgument accessId = new StringArgument("s", "accessId", "accessId", true); | ||
| // StringArgument cohortId = new StringArgument("c", "cohortId", "cohortId", true); | ||
| // | ||
| // ArgumentList arguments = new ArgumentList(about, help, inputFile, accessId, cohortId); | ||
| // CommandLine commandLine = new CommandLine(args); | ||
| // | ||
| // PostPopulationFrequencies postPopulationFrequencies = null; | ||
| // try | ||
| // { | ||
| // CommandLineParser.parse(commandLine, arguments); | ||
| // if (about.wasFound()) { | ||
| // About.about(System.out); | ||
| // System.exit(0); | ||
| // } | ||
| // if (help.wasFound()) { | ||
| // Usage.usage(USAGE, null, commandLine, arguments, System.out); | ||
| // System.exit(0); | ||
| // } | ||
| // postPopulationFrequencies = new PostPopulationFrequencies(inputFile.getValue(), accessId.getValue(), cohortId.getValue()); | ||
| // } | ||
| // catch (CommandLineParseException | IllegalArgumentException e) { | ||
| // Usage.usage(USAGE, e, commandLine, arguments, System.err); | ||
| // System.exit(-1); | ||
| // } | ||
| // try { | ||
| // System.exit(postPopulationFrequencies.call()); | ||
| // } | ||
| // catch (Exception e) { | ||
| // e.printStackTrace(); | ||
| // System.exit(1); | ||
| // } | ||
| // } | ||
| // | ||
| //} |
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21 changes: 21 additions & 0 deletions
21
ld-validation/src/main/java/org/dash/valid/report/DetectedLinkageFindingsList.java
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| package org.dash.valid.report; | ||
|
|
||
| import java.util.List; | ||
|
|
||
| import javax.xml.bind.annotation.XmlElement; | ||
| import javax.xml.bind.annotation.XmlRootElement; | ||
|
|
||
| @XmlRootElement(name="gl-freqs") | ||
| public class DetectedLinkageFindingsList { | ||
|
|
||
| private List<DetectedLinkageFindings> findings = null; | ||
|
|
||
| @XmlElement(name="gl-freq") | ||
| public List<DetectedLinkageFindings> getFindings() { | ||
| return findings; | ||
| } | ||
|
|
||
| public void setFindings(List<DetectedLinkageFindings> findings) { | ||
| this.findings = findings; | ||
| } | ||
| } |
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