copy phenopackets to output

src/main/java/org/monarchinitiative/phenopacket2prompt/cmd/GbtTranslateBatchCommand.java

@@ -9,6 +9,7 @@
 import org.monarchinitiative.phenopacket2prompt.model.PhenopacketDisease;
 import org.monarchinitiative.phenopacket2prompt.model.PpktIndividual;
 import org.monarchinitiative.phenopacket2prompt.output.CorrectResult;
+import org.monarchinitiative.phenopacket2prompt.output.PpktCopy;
 import org.monarchinitiative.phenopacket2prompt.output.PromptGenerator;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -41,6 +42,10 @@ public class GbtTranslateBatchCommand implements Callable<Integer> {
             description = "path to translations file")
     private String translationsPath = "data/hp-international.obo";
 
+    @CommandLine.Option(names = {"-o", "--outdir"},
+            description = "path to outdir")
+    private String outdirname = "prompts";
+
     @CommandLine.Option(names = {"-d", "--dir"}, description = "Path to directory with JSON phenopacket files", required = true)
     private String ppktDir;
 
@@ -61,10 +66,11 @@ public Integer call() throws Exception {
             return 1;
         }
         HpInternationalOboParser oboParser = new HpInternationalOboParser(translationsFile);
+
         Map<String, HpInternational> internationalMap = oboParser.getLanguageToInternationalMap();
         LOGGER.info("Got {} translations", internationalMap.size());
         List<File> ppktFiles = getAllPhenopacketJsonFiles();
-        createDir("prompts");
+        createDir(outdirname);
         List<CorrectResult>  correctResultList = outputPromptsEnglish(ppktFiles, hpo);
         // output all non-English languages here
 
@@ -86,7 +92,11 @@ public Integer call() throws Exception {
         PromptGenerator italian = PromptGenerator.italian(internationalMap.get("it"));
         outputPromptsInternational(ppktFiles, hpo, "it", italian);
         resetOutput("finished");
-
+        // output original phenopackets
+        PpktCopy pcopy = new PpktCopy(new File(outdirname));
+        for (var file : ppktFiles) {
+            pcopy.copyFile(file);
+        }
 
         // output file with correct diagnosis list
         outputCorrectResults(correctResultList);

src/main/java/org/monarchinitiative/phenopacket2prompt/output/PpktCopy.java

@@ -0,0 +1,53 @@
+package org.monarchinitiative.phenopacket2prompt.output;
+
+
+import org.monarchinitiative.phenol.base.PhenolRuntimeException;
+
+import java.io.*;
+
+/**
+ * Class to copy phenopackets from the input directory to an output directory so that we have all of the files
+ * used for an experiment in one place.
+ */
+public class PpktCopy {
+
+    private final File ppkt_out_dir;
+
+
+    public PpktCopy(File outdirectory) {
+        ppkt_out_dir = new File(outdirectory + File.separator + "original_phenopackets");
+        createDir(ppkt_out_dir);
+    }
+
+
+
+    private void createDir(File path) {
+        if (! path.exists() ) {
+            boolean result = path.mkdir();
+            if (! result) {
+                throw new PhenolRuntimeException("Could not create output directory at " + path);
+            }
+        }
+    }
+
+    public void copyFile(File sourceLocation) {
+        try {
+            String fname = sourceLocation.getName();
+            File outfile = new File(ppkt_out_dir + File.separator + fname);
+
+            InputStream in = new FileInputStream(sourceLocation);
+            OutputStream out = new FileOutputStream(outfile);
+
+            // Copy the bits from instream to outstream
+            byte[] buf = new byte[1024];
+            int len;
+            while ((len = in.read(buf)) > 0) {
+                out.write(buf, 0, len);
+            }
+            in.close();
+            out.close();
+        } catch (IOException e) {
+            throw new PhenolRuntimeException(e.getMessage());
+        }
+    }
+}

src/main/java/org/monarchinitiative/phenopacket2prompt/output/impl/dutch/DutchPromptGenerator.java

@@ -1,6 +1,5 @@
 package org.monarchinitiative.phenopacket2prompt.output.impl.dutch;
 
-import org.monarchinitiative.phenol.ontology.data.Ontology;
 import org.monarchinitiative.phenopacket2prompt.model.OntologyTerm;
 import org.monarchinitiative.phenopacket2prompt.model.PhenopacketAge;
 import org.monarchinitiative.phenopacket2prompt.model.PhenopacketSex;
@@ -15,9 +14,6 @@
 
 public class DutchPromptGenerator implements PromptGenerator {
 
-    private final Ontology hpo;
-
-
     private final PPKtIndividualInfoGenerator ppktAgeSexGenerator;
 
     private final PhenopacketTextGenerator ppktTextGenerator;
@@ -27,7 +23,6 @@ public class DutchPromptGenerator implements PromptGenerator {
 
 
     public DutchPromptGenerator(PpktPhenotypicFeatureGenerator pfgen) {
-        this.hpo = hpo;
         ppktAgeSexGenerator = new PpktIndividualDutch();
         ppktTextGenerator = new PpktTextDutch();
         this.ppktPhenotypicFeatureGenerator = pfgen;

src/main/java/org/monarchinitiative/phenopacket2prompt/output/impl/german/PpktIndividualGerman.java

@@ -1,6 +1,5 @@
 package org.monarchinitiative.phenopacket2prompt.output.impl.german;
 
-import com.sun.source.tree.BreakTree;
 import org.monarchinitiative.phenol.base.PhenolRuntimeException;
 import org.monarchinitiative.phenopacket2prompt.model.*;
 import org.monarchinitiative.phenopacket2prompt.output.PPKtIndividualInfoGenerator;
@@ -449,7 +448,10 @@ public String atAge(PhenopacketAge ppktAge) {
                 case "Neonatal onset"  -> "In der neugeborenen Zeit";
                 case "Congenital onset" -> "Zum Zeitpunkt der Geburt";
                 case "Adult onset" -> "Im Erwachsenenalter";
-                default-> String.format("TODO TODO el %s período", label.replace(" onset", ""));
+                case "Juvenile onset" -> "Im Jugendlichenalter";
+                default-> {
+                    throw new PhenolRuntimeException("No German translation for " + label);
+                }
             };
         } else {
             return ""; // should never get here

src/main/java/org/monarchinitiative/phenopacket2prompt/output/impl/spanish/PpktPhenotypicfeatureSpanish.java

@@ -95,9 +95,9 @@ public String formatFeatures(List<OntologyTerm> ontologyTerms) {
         } else {
             String exclusion;
             if (excludedLabels.size() == 1) {
-                exclusion = String.format(" En cambio, se descartó %s.", getOxfordCommaList(excludedLabels));
+                exclusion = String.format(". En cambio, se descartó %s.", getOxfordCommaList(excludedLabels));
             } else {
-                exclusion =  String.format(" En cambio, se descartaron %s.", getOxfordCommaList(excludedLabels));
+                exclusion =  String.format(". En cambio, se descartaron %s.", getOxfordCommaList(excludedLabels));
             }
             return getOxfordCommaList(observedLabels) +  exclusion;
         }