Merge pull request #32 from monarch-initiative/update_docs

Fixes #29

src/main/java/org/monarchinitiative/phenopacket2prompt/Main.java

@@ -2,15 +2,12 @@
 
 
 import org.monarchinitiative.phenopacket2prompt.cmd.*;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 import picocli.CommandLine;
 
 import java.util.concurrent.Callable;
 @CommandLine.Command(name = "phenopacket2prompt", mixinStandardHelpOptions = true, version = "0.2.0",
         description = "Convert phenopacket to prompt for GPT")
 public class Main implements Callable<Integer> {
-    private static final Logger logger = LoggerFactory.getLogger(Main.class);
 
     public static void main(String[] args){
         if (args.length == 0) {
@@ -21,6 +18,7 @@ public static void main(String[] args){
         CommandLine cline = new CommandLine(new Main())
                 .addSubcommand("batch", new GbtTranslateBatchCommand())
                 .addSubcommand("download", new DownloadCommand())
+                .addSubcommand("prompt", new PromptCommand())
                 .addSubcommand("mine", new TextMineCommand())
                 .addSubcommand("translate", new GptTranslateCommand())
                 ;

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

@@ -0,0 +1,57 @@
+package org.monarchinitiative.phenopacket2prompt.cmd;
+
+
+import org.monarchinitiative.phenol.base.PhenolRuntimeException;
+import org.monarchinitiative.phenol.io.OntologyLoader;
+import org.monarchinitiative.phenol.ontology.data.Ontology;
+import org.monarchinitiative.phenopacket2prompt.model.PpktIndividual;
+import org.monarchinitiative.phenopacket2prompt.output.PromptGenerator;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import picocli.CommandLine;
+
+import java.io.File;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.concurrent.Callable;
+
+@CommandLine.Command(name = "prompt", aliases = {"P"},
+        mixinStandardHelpOptions = true,
+        description = "Create a prompt from one phenopacket")
+public class PromptCommand implements Callable<Integer> {
+    private final static Logger LOGGER = LoggerFactory.getLogger(PromptCommand.class);
+
+
+    @CommandLine.Option(names = {"--hp"},
+            description = "path to HP json file")
+    private String hpoJsonPath = "data/hp.json";
+
+
+    @CommandLine.Option(names = {"-p", "--ppkt"}, description = "Path to JSON phenopacket file", required = true)
+    private String ppkt;
+
+    @CommandLine.Option(names = {"-o", "--out"}, description = "Name of output prompt file")
+    private String outfile = null;
+
+
+
+    @Override
+    public Integer call() throws Exception {
+        File hpJsonFile = new File(hpoJsonPath);
+        if (! hpJsonFile.isFile()) {
+            throw new PhenolRuntimeException("Could not find hp.json at " + hpJsonFile.getAbsolutePath());
+        }
+        Ontology hpo = OntologyLoader.loadOntology(hpJsonFile);
+        LOGGER.info("HPO version {}", hpo.version().orElse("n/a"));
+        PromptGenerator generator = PromptGenerator.english();
+        PpktIndividual individual = PpktIndividual.fromFile(new File(ppkt));
+        String prompt = generator.createPrompt(individual);
+        System.out.println(prompt);
+        if (outfile != null) {
+            LOGGER.trace("Writing prompt to {}", outfile);
+            Path path = Path.of(outfile);
+            Files.writeString(path, prompt);
+        }
+        return 0;
+    }
+}

src/main/java/org/monarchinitiative/phenopacket2prompt/model/AgeNotSpecified.java

@@ -28,6 +28,11 @@ public boolean isInfant() {
         return false;
     }
 
+    @Override
+    public boolean isNeonate() {
+        return false;
+    }
+
     @Override
     public boolean isFetus() {
         return false;

src/main/java/org/monarchinitiative/phenopacket2prompt/model/HpoOnsetAge.java

@@ -38,23 +38,41 @@ public final class HpoOnsetAge implements PhenopacketAge {
     private final static Set<TermId> fetalIds = Set.of(TermId.of(" HP:0030674"), TermId.of("HP:0011461"), TermId.of("HP:0034199"),
             TermId.of("HP:0034197"), TermId.of("HP:0034198"), TermId.of("HP:0011460*"));
 
-    /**
-     * Childhood onset
-     */
-    private final static TermId childhoodOnset = TermId.of("HP:0011463");
-
-    private final static TermId juvenileOnset = TermId.of("HP:0003621");
+    public static HpoOnsetAge congenital() {
+        return new HpoOnsetAge(congenitalOnset.getValue(), "Congenital onset");
+    }
+    public static HpoOnsetAge infantile() {
+        return new HpoOnsetAge(infantileOnset.getValue(), "Infantile onset");
+    }
+    public static HpoOnsetAge childhood() {
+        return new HpoOnsetAge(childhoodOnset.getValue(), "Childhood onset");
+    }
+    public static HpoOnsetAge juvenile() {
+        return new HpoOnsetAge(juvenileOnset.getValue(), "Juvenile onset");
+    }
 
-    /**
-     * Infantile onset
-     */
-    private final static TermId infantileOnset = TermId.of("HP:0003593");
 
-    /**
-     * Congenital onset
-     */
+    private final static TermId neonatalOnset = TermId.of("HP:0003623");
     private final static TermId congenitalOnset = TermId.of("HP:0003577");
-
+    private final static TermId infantileOnset = TermId.of("HP:0003593");
+    private final static TermId childhoodOnset = TermId.of("HP:0011463");
+    private final static TermId juvenileOnset = TermId.of("HP:0003621");
+    /** Adult onset*/
+    private final static TermId adultOnset = TermId.of("HP:0003581");
+    /** Young adult onset HP:0011462 */
+    private final static TermId youngAdultOnset = TermId.of("HP:0011462");
+    /** Early young adult onset HP:0025708*/
+    private final static TermId earlyYoungAdultAnset = TermId.of("HP:0025708");
+    /** Intermediate young adult onset HP:0025709 */
+    private final static TermId intermediateYoungAdultOnset = TermId.of("HP:0025709");
+    /** Late young adult onset HP:0025710 */
+    private final static TermId lateYoungAdultOnset = TermId.of("HP:0025710");
+    /** Middle age onset HP:0003596 */
+    private final static TermId middleAgeOnset = TermId.of("HP:0003596");
+    /** Late onset HP:0003584 */
+    private final static TermId lateOnset = TermId.of("HP:0003584");
+    private final static Set<TermId> adultTermIds = Set.of(adultOnset, youngAdultOnset, earlyYoungAdultAnset,
+    intermediateYoungAdultOnset, lateYoungAdultOnset, middleAgeOnset, lateOnset);
 
     public HpoOnsetAge(String id, String label) {
         this.tid = TermId.of(id);
@@ -66,7 +84,6 @@ public HpoOnsetAge(String id, String label) {
         } else {
             totalDays = Integer.MAX_VALUE;
         }
-
     }
 
     @Override
@@ -83,24 +100,29 @@ public PhenopacketAgeType ageType() {
     public boolean isJuvenile() {
         return tid.equals(juvenileOnset);
     }
-
-
     @Override
     public boolean isChild() {
         return tid.equals(childhoodOnset);
     }
-
     @Override
     public boolean isInfant() {
         return tid.equals(infantileOnset);
     }
 
+    @Override
+    public boolean isNeonate() {
+        return tid.equals(neonatalOnset);
+    }
+
     @Override
     public boolean isCongenital() {
         return tid.equals(congenitalOnset);
     }
 
     @Override
+    public boolean isAdult() {
+        return adultTermIds.contains(tid);
+
     public boolean isYoungAdult() {
         return youngAdultIds.contains(tid);
     }
@@ -115,17 +137,10 @@ public boolean isLateAdultAge() {
         return tid.equals(lateAgeOnset);
     }
 
-    @Override
-    public boolean isAdult() {
-        return youngAdultIds.contains(tid) || otherAdult.contains(tid);
-    }
-
     @Override
     public boolean isFetus() {
         return fetalIds.contains(tid);
     }
-
-
     @Override
     public int totalDays() {
         return totalDays;
@@ -136,23 +151,6 @@ public TermId getTid() {
     }
 
 
-    public static HpoOnsetAge childhood() {
-        return new HpoOnsetAge(childhoodOnset.getValue(), "Childhood onset");
-    }
-
-    public static HpoOnsetAge juvenile() {
-        return new HpoOnsetAge(juvenileOnset.getValue(), "Juvenile onset");
-    }
-
-
-    public static HpoOnsetAge infantile() {
-        return new HpoOnsetAge(infantileOnset.getValue(), "Infantile onset");
-    }
-
-
-    public static HpoOnsetAge congenital() {
-        return new HpoOnsetAge(congenitalOnset.getValue(), "Congenital onset");
-    }
 
     @Override
     public int hashCode() {

src/main/java/org/monarchinitiative/phenopacket2prompt/model/Iso8601Age.java

@@ -78,7 +78,7 @@ public PhenopacketAgeType ageType() {
 
     @Override
     public boolean isJuvenile() {
-        return years >= 6 && years < 18;
+        return years >= 6 && years < 16;
     }
 
     @Override
@@ -91,6 +91,11 @@ public boolean isInfant() {
         return years < 1;
     }
 
+    @Override
+    public boolean isNeonate() {
+        return years == 0 && months < 1;
+    }
+
     @Override
     public boolean isFetus() {
         // always false because we cannot express prenatal ages with iso

src/main/java/org/monarchinitiative/phenopacket2prompt/model/PhenopacketAge.java

@@ -11,6 +11,8 @@ public sealed interface PhenopacketAge permits AgeNotSpecified, HpoOnsetAge, Iso
 
     boolean isInfant();
 
+    boolean isNeonate();
+
     boolean isFetus();
 
     boolean isCongenital();

src/main/java/org/monarchinitiative/phenopacket2prompt/output/impl/english/PpktIndividualEnglish.java

@@ -116,9 +116,13 @@ private String onsetTermAtAgeOf(HpoOnsetAge hpoOnsetTermAge) {
         } else if (hpoOnsetTermAge.isChild()) {
             return buildBlocks.inChildhood();
         } else if (hpoOnsetTermAge.isJuvenile()) {
-            return buildBlocks.asAdolescent();
+            return "as an adolescent";
+        } else if (hpoOnsetTermAge.isNeonate()){
+            return "as a neonate";
+        } else if (hpoOnsetTermAge.isAdult()){
+            return "in adulthood";
         } else {
-            return buildBlocks.inAdulthoold();
+            throw new PhenolRuntimeException("Could not identify onset age for HpoOnsetAge " + hpoOnsetTermAge);
         }
     }