Merge pull request #92 from fscheel/RemoveLabelListUsageFromJavaClient

Remove label list usage from java client

client/java/freq-client/.swagger-codegen-ignore

@@ -21,3 +21,5 @@
 #docs/*.md
 # Then explicitly reverse the ignore rule for a single file:
 #!docs/README.md
+
+.gitignore

client/java/freq-tools/src/main/java/org/dash/freq/PostPopulationFrequencies.java

@@ -55,7 +55,6 @@
 import io.swagger.client.model.HaplotypeFrequencyData;
 import io.swagger.client.model.Label;
 import io.swagger.client.model.LabelData;
-import io.swagger.client.model.LabelList;
 import io.swagger.client.model.License;
 import io.swagger.client.model.License.TypeOfLicenseEnum;
 import io.swagger.client.model.PopulationData;
@@ -67,172 +66,169 @@
  */
 public class PostPopulationFrequencies implements Callable<Integer> {
 
-	private final File inputFile;
-	private final String gtRegistry;
-	private final String estEntity;
-	private final URL url;
-
-	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
-	 * @throws MalformedURLException
-	 */
-	public PostPopulationFrequencies(File inputFile, String gtRegistry, String estEntity, URL url)
-			throws MalformedURLException {
-		this.inputFile = inputFile;
-		this.gtRegistry = gtRegistry;
-		this.estEntity = estEntity;
-		if (url == null) {
-			this.url = new URL("http://localhost:8080");
-		} else {
-			this.url = url;
-		}
-	}
-
-	@Override
-	public Integer call() throws Exception {
-		postPopulationFrequencies(reader(inputFile));
-
-		return 0;
-	}
-
-	public void postPopulationFrequencies(BufferedReader reader) throws IOException, ApiException {
-		String row;
-		String[] columns;
-
-		HashMap<String, HaplotypeFrequencyData> populationMap = new HashMap<String, HaplotypeFrequencyData>();
-		HaplotypeFrequencyData haplotypeFrequencyData;
-
-		License license = new License();
-		license.setTypeOfLicense(TypeOfLicenseEnum.CC0);
-
-		while ((row = reader.readLine()) != null) {
-			columns = row.split(",");
-
-			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 HaplotypeFrequencyData();
-				haplotypeFrequencyData.setLicense(license);
-			}
-
-			HaplotypeFrequency hapFrequency = new HaplotypeFrequency();
-			hapFrequency.setFrequency(new Double(frequency));
-			hapFrequency.setHaplotypeString(haplotype);
-			haplotypeFrequencyData.addHaplotypeFrequencyListItem(hapFrequency);
-
-			populationMap.put(race, haplotypeFrequencyData);
-		}
-
-		reader.close();
-
-		ApiClient apiClient = new ApiClient();
-		apiClient.setConnectTimeout(60000);
-		apiClient.setReadTimeout(60000);
-		apiClient.setWriteTimeout(60000);
-		apiClient.setBasePath(url.toString());
-		DefaultApi api = new DefaultApi(apiClient);
-		PopulationApi popApi = new PopulationApi(apiClient);
-		CohortApi cohortApi = new CohortApi(apiClient);
-
-		CohortRequest cohortRequest = new CohortRequest();
-
-		CohortData cohortData = new CohortData();
-		cohortData.setName(inputFile.getName());
-		cohortData.setGenotypeList(new GenotypeList());
-
-		cohortRequest.setCohortData(cohortData);
-
-		System.out.println("Creating cohort: " + cohortData.getName());
-
-		cohortData = cohortApi.createCohort(cohortRequest);
-
-		LabelData labelData = new LabelData();
-		LabelList labelList = new LabelList();
-		Label registryLabel = new Label();
-		registryLabel.setTypeOfLabel("GT_REGISTRY");
-		registryLabel.setValue(gtRegistry);
-		labelList.addLabelItem(registryLabel);
-
-		Label estimatorLabel = new Label();
-		estimatorLabel.setTypeOfLabel("HT_ESTIMATION_ENT");
-		estimatorLabel.setValue(estEntity);
-		labelList.addLabelItem(estimatorLabel);
-
-		labelData.setLabelList(labelList);
-
-		for (String populationName : populationMap.keySet()) {
-			HFCurationRequest hfCurationRequest = new HFCurationRequest();
-			PopulationRequest populationRequest = new PopulationRequest();
-
-			populationRequest.setName(populationName);
-
-			System.out.println("Creating population: " + populationRequest.getName());
-
-			PopulationData populationData = popApi.createPopulation(populationRequest);
-
-			hfCurationRequest.setPopulationID(populationData.getId());
-			hfCurationRequest.setCohortID(cohortData.getId());
-			hfCurationRequest.setHaplotypeFrequencyData(populationMap.get(populationName));
-
-			hfCurationRequest.setLabelData(labelData);
-
-			System.out.println("Submitting frequencies for population: " + populationData.getName());
-			HFCurationResponse response = api.hfcPost(hfCurationRequest);
-		}		
-	}
-
-	/**
-	 * Main.
-	 *
-	 * @param args
-	 *            command line args
-	 * @throws MalformedURLException
-	 */
-	public static void main(final String[] args) throws MalformedURLException {
-		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 gtRegistry = new StringArgument("r", "registry", "genotype registry", false);
-		StringArgument estEntity = new StringArgument("e", "estimator", "haplotype frequency estimating entity", false);
-		URLArgument url = new URLArgument("u", "url", "frequency service url", false);
-
-		ArgumentList arguments = new ArgumentList(about, help, inputFile, gtRegistry, estEntity, url);
-		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(), gtRegistry.getValue(),
-					estEntity.getValue(), url.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);
-		}
-	}
+  private final File inputFile;
+  private final String gtRegistry;
+  private final String estEntity;
+  private final URL url;
+
+  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
+   * @throws MalformedURLException
+   */
+  public PostPopulationFrequencies(File inputFile, String gtRegistry, String estEntity, URL url)
+      throws MalformedURLException {
+    this.inputFile = inputFile;
+    this.gtRegistry = gtRegistry;
+                this.estEntity = estEntity;
+    if (url == null) {
+      this.url = new URL("http://localhost:8080");
+    } else {
+      this.url = url;
+    }
+  }
+
+  @Override
+  public Integer call() throws Exception {
+    postPopulationFrequencies(reader(inputFile));
+
+    return 0;
+  }
+
+  public void postPopulationFrequencies(BufferedReader reader) throws IOException, ApiException {
+    String row;
+    String[] columns;
+
+    HashMap<String, HaplotypeFrequencyData> populationMap = new HashMap<String, HaplotypeFrequencyData>();
+    HaplotypeFrequencyData haplotypeFrequencyData;
+
+    License license = new License();
+    license.setTypeOfLicense(TypeOfLicenseEnum.CC0);
+
+    while ((row = reader.readLine()) != null) {
+      columns = row.split(",");
+
+      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 HaplotypeFrequencyData();
+        haplotypeFrequencyData.setLicense(license);
+      }
+
+      HaplotypeFrequency hapFrequency = new HaplotypeFrequency();
+      hapFrequency.setFrequency(new Double(frequency));
+      hapFrequency.setHaplotypeString(haplotype);
+      haplotypeFrequencyData.addHaplotypeFrequencyListItem(hapFrequency);
+
+      populationMap.put(race, haplotypeFrequencyData);
+    }
+
+    reader.close();
+
+    ApiClient apiClient = new ApiClient();
+    apiClient.setConnectTimeout(60000);
+    apiClient.setReadTimeout(60000);
+    apiClient.setWriteTimeout(60000);
+    apiClient.setBasePath(url.toString());
+    DefaultApi api = new DefaultApi(apiClient);
+    PopulationApi popApi = new PopulationApi(apiClient);
+    CohortApi cohortApi = new CohortApi(apiClient);
+
+    CohortRequest cohortRequest = new CohortRequest();
+
+    CohortData cohortData = new CohortData();
+    cohortData.setName(inputFile.getName());
+    cohortData.setGenotypeList(new GenotypeList());
+
+    cohortRequest.setCohortData(cohortData);
+
+    System.out.println("Creating cohort: " + cohortData.getName());
+
+    cohortData = cohortApi.createCohort(cohortRequest);
+
+    LabelData labelData = new LabelData();
+    Label registryLabel = new Label();
+    registryLabel.setTypeOfLabel("GT_REGISTRY");
+    registryLabel.setValue(gtRegistry);
+    labelData.addLabelListItem(registryLabel);
+
+    Label estimatorLabel = new Label();
+    estimatorLabel.setTypeOfLabel("HT_ESTIMATION_ENT");
+    estimatorLabel.setValue(estEntity);
+    labelData.addLabelListItem(estimatorLabel);
+
+    for (String populationName : populationMap.keySet()) {
+      HFCurationRequest hfCurationRequest = new HFCurationRequest();
+      PopulationRequest populationRequest = new PopulationRequest();
+
+      populationRequest.setName(populationName);
+
+      System.out.println("Creating population: " + populationRequest.getName());
+
+      PopulationData populationData = popApi.createPopulation(populationRequest);
+
+      hfCurationRequest.setPopulationID(populationData.getId());
+      hfCurationRequest.setCohortID(cohortData.getId());
+      hfCurationRequest.setHaplotypeFrequencyData(populationMap.get(populationName));
+
+      hfCurationRequest.setLabelData(labelData);
+
+      System.out.println("Submitting frequencies for population: " + populationData.getName());
+      HFCurationResponse response = api.hfcPost(hfCurationRequest);
+    }
+  }
+
+  /**
+   * Main.
+   *
+   * @param args
+   *            command line args
+   * @throws MalformedURLException
+   */
+  public static void main(final String[] args) throws MalformedURLException {
+    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 gtRegistry = new StringArgument("r", "registry", "genotype registry", false);
+    StringArgument estEntity = new StringArgument("e", "estimator", "haplotype frequency estimating entity", false);
+    URLArgument url = new URLArgument("u", "url", "frequency service url", false);
+
+    ArgumentList arguments = new ArgumentList(about, help, inputFile, gtRegistry, estEntity, url);
+    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(), gtRegistry.getValue(),
+          estEntity.getValue(), url.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);
+    }
+  }
 
 }

client/testDataFiles/README.md

@@ -0,0 +1,10 @@
+# Data requirements
+
+This is a work in progress determining how to format data for upload.
+
+* Do not include a header
+* There can be no empty lines in the middle of the data. (A blank line at the end seems to be fine.)
+* It currently doesn't care if the frequencies add up to one. (Working on that.)
+* Haplotypes should be separated by tildas (~).
+
+See demo_PHYCUS_HFs.csv for an example.

client/testDataFiles/demo_PHYCUS_HFs.csv

@@ -0,0 +1,10 @@
+OTH,DRB1*07:01:01:01~DQB1*02:02:01,0.082586969
+OTH,DRB1*15:01:01:01~DQB1*03:03:02:03,0.175318163
+OTH,DRB1*01:01:01~DQB1*05:03:01:01,0.053289506
+OTH,DRB1*03:01:02~DQB1*06:02:01,0.120375512
+OTH,DRB1*03:01:01:01~DQB1*05:01:01:01,0.099318824
+OTH,DRB1*04:01:01~DQB1*04:01:01,0.056614833
+OTH,DRB1*15:01:01:01~DQB1*03:02:12,0.106412321
+OTH,DRB1*08:01:03~DQB1*03:02:01,0.188099248
+OTH,DRB1*13:01:01~DQB1*03:01:01:01,0.000557303
+OTH,DRB1*15:01:01:01~DQB1*06:05:01,0.117427322

client/testDataFiles/proto_hap_data.csv

@@ -0,0 +1,4 @@
+Beer License
+AFA, ABCDE, 0.25
+AFA, FGHIJ, 0.25
+AFA, KLMNO, 0.50