more validations

docs/cases/PMID_29127725.txt

@@ -0,0 +1,36 @@
+[source]
+pmid = PMID:29127725
+title = A loss-of-function homozygous mutation in DDX59 implicates a conserved DEAD-box RNA helicase in nervous system development and function
+[diagnosis]
+disease_id = OMIM:174300
+disease_label = Orofaciodigital syndrome V
+[text]
+Patient 1  was the first born from healthy parents, non-consanguineous for their account.
+Family history was unremarkable, except for three prior spontaneous
+miscarriages. The pregnancy was complicated by intrauterine growth
+retardation. Delivery at term was normal, with a weight at birth of
+2,350 g (<3rd centile), length of 47 cm (3rd centile), and occipital–
+frontal circumference of 32 cm (5th centile). APGAR scores were 6 and
+9 at 1 and 5 min, respectively. He had bilateral postaxial extra-digits
+on his hands that were surgically removed in his late childhood. He
+also had bilateral cutaneous syndactyly of fingers 2–5, clinodactyly of
+the fifth fingers, and fingertip pads. His lower limbs were normal. Since
+the first months of life, he developed generalized seizures, which were
+controlled by anticonvulsant drugs. Developmental milestones were
+delayed and the patient showed cognitive difficulties during childhood,
+with an I.Q. of 70 (Terman-Merril scale) measured at the age
+of 9 years. For these reasons, he has undergone developmental and
+speech therapies since the age of 3 years. At the age of 17 years, his
+height was 165 cm (3rd centile), weight was 67 kg (50th centile), and
+head circumference 53 cm (10th centile). He had distinctive facial features,
+including prominent thick eyebrows, malocclusion, high-arched
+palate, and rounded prominent jaw (Figure 1G and H).
+A cerebral magnetic resonance imaging (MRI) disclosed thinning of the cerebral cortex
+in front of the ventricular collateral trigone (not shown).
+Wakefulness electroencephalograms showed diffuse high amplitude slow
+waves intermingled with sharp waves or spikes. Since early adulthood
+he started to complain of migraine. As part of his neurological presentation,
+he also presented lower limbs weakness and some walking difficulties. At the age of 30, after an episode of loss of consciousness
+associated with generalized seizures, he underwent a follow-up brain
+MRI scan, which showed diffuse white matter signal abnormalities and
+multifocal cortical–subcortical infarcts involving both cerebral hemispheres (Figure 1P and Q).

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

@@ -1,6 +1,8 @@
 package org.monarchinitiative.phenopacket2prompt.output;
 
 
+import org.monarchinitiative.phenopacket2prompt.model.Iso8601Age;
+
 /**
  * Provide the "building blocks" (i.e., text fragments) needed to generate the
  * texts in the various languages.
@@ -127,4 +129,6 @@ public interface PPKtBuildingBlockGenerator {
     String asMiddleAge();
 
     String asLateOnset();
+
+    String fromIso(Iso8601Age ppktAge);
 }

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

@@ -1,7 +1,11 @@
 package org.monarchinitiative.phenopacket2prompt.output.impl.english;
 
+import org.monarchinitiative.phenopacket2prompt.model.Iso8601Age;
 import org.monarchinitiative.phenopacket2prompt.output.PPKtBuildingBlockGenerator;
 
+import java.util.ArrayList;
+import java.util.List;
+
 public class PPKtEnglishBuildingBlocks implements PPKtBuildingBlockGenerator {
 
 
@@ -20,6 +24,26 @@ public String years(int y) {
         return y>1 ? "years" : "year";
     }
 
+
+
+    @Override
+    public String fromIso(Iso8601Age ppktAge) {
+        List<String> components = new ArrayList<>();
+        int y = ppktAge.getYears();
+        int m = ppktAge.getMonths();
+        int d = ppktAge.getDays();
+        if (y > 0) {
+            components.add(String.format("%d %s", y, years(y)));
+        }
+        if (m > 0) {
+            components.add(String.format("%d %s", m, months(y)));
+        }
+        if (d > 0) {
+            components.add(String.format("%d %s", d, days(y)));
+        }
+        return String.join(" ", components);
+    }
+
     @Override
     public String yearsOld(int y) {
         return String.format("%d-year-old", y);
@@ -42,7 +66,7 @@ public String monthDayOld(int m, int d) {
         } else if (d==0) {
             return monthsOld(m);
         }
-        return String.format("%d-%s, %d-%s old", m, months(m), d, days(d));
+        return String.format("%d-month, %d-day old", m,  d);
     }
 
     @Override
@@ -51,9 +75,9 @@ public String yearsMonthsDaysOld(int y, int m, int d) {
             return monthDayOld(m,d);
         }
         if (d==0) {
-            return String.format("%d-%s, %d-%s old", y, years(y), m, months(m));
+            return String.format("%d-year, %d-month old", y,  m);
         }
-        return String.format("%d-%s, %d-%s, %d-%s old", y, years(y), m, months(m), d, days(d));
+        return String.format("%d-year, %d-month, %d-day old", y, m, d);
     }
 
     @Override
@@ -299,4 +323,6 @@ public String asMiddleAge() {
     public String asLateOnset() {
         return "During old age";
     }
+
+
 }

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

@@ -218,21 +218,6 @@ private String iso8601individualDescription(PhenopacketSex psex, Iso8601Age iso8
     }
 
 
-    private String iso8601individualDescriptionAsA(PhenopacketSex psex, Iso8601Age iAge) {
-        String onsetWithSex = iso8601individualDescription(psex, iAge);
-        return String.format("as a %s", onsetWithSex);
-    }
-
-    private String hpoOnsetAsA(PhenopacketSex psex, HpoOnsetAge hpoOnsetTermAge) {
-        String onsetWithSex = hpoOnsetIndividualDescription(psex, hpoOnsetTermAge);
-        final Set<Character> vowels = Set.of('A', 'E', 'I', 'O', 'U');
-        if (vowels.contains(onsetWithSex.charAt(0))) {
-            return String.format("as an %s", onsetWithSex);
-        } else {
-            return String.format("as a %s", onsetWithSex);
-        }
-    }
-
     private String hpoOnsetIndividualDescription(PhenopacketSex psex, HpoOnsetAge hpoOnsetTermAge) {
         if (hpoOnsetTermAge.isFetus()) {
             return switch (psex) {
@@ -275,178 +260,11 @@ private String hpoOnsetIndividualDescription(PhenopacketSex psex, HpoOnsetAge hp
         }
     }
 
-    /**
-     * A sentence such as The proband was a 39-year-old woman who presented at the age of 12 years with
-     * HPO1, HPO2, and HPO3. HPO4 and HPO5 were excluded. This method returns the phrase that ends with "with"
-     *
-     * @param psex
-     * @param lastExamAge
-     * @param onsetAge
-     * @return
-
-    private String onsetAndLastEncounterAvailable(PhenopacketSex psex,
-                                                  PhenopacketAge lastExamAge,
-                                                  PhenopacketAge onsetAge) {
-        String individualDescription;
-        String onsetDescription;
-        if (lastExamAge.ageType().equals(PhenopacketAgeType.ISO8601_AGE_TYPE)) {
-            Iso8601Age isoAge = (Iso8601Age) lastExamAge;
-            individualDescription = iso8601individualDescription(psex, isoAge);
-        } else if (lastExamAge.ageType().equals(PhenopacketAgeType.HPO_ONSET_AGE_TYPE)) {
-            HpoOnsetAge hpoOnsetTermAge = (HpoOnsetAge) lastExamAge;
-            individualDescription = hpoOnsetAsA(psex, hpoOnsetTermAge);
-        } else {
-            // should never happen
-            throw new PhenolRuntimeException("Did not recognize last exam age type " + lastExamAge.ageType());
-        }
-        if (onsetAge.ageType().equals(PhenopacketAgeType.ISO8601_AGE_TYPE)) {
-            Iso8601Age isoAge = (Iso8601Age) onsetAge;
-            onsetDescription = iso8601AtAgeOf(isoAge);
-        } else if (onsetAge.ageType().equals(PhenopacketAgeType.HPO_ONSET_AGE_TYPE)) {
-            HpoOnsetAge hpoOnsetTermAge = (HpoOnsetAge) onsetAge;
-            onsetDescription = onsetTermAtAgeOf(hpoOnsetTermAge);
-        } else {
-            // should never happen
-            throw new PhenolRuntimeException("Did not recognize onset age type " + onsetAge.ageType());
-        }
-        return String.format("%s %s %s %s:",
-                buildBlocks.probandWasA(),
-                individualDescription,
-                buildBlocks.inWhomManifestationsWereExcluded(),
-                onsetDescription);
-
-    }
-     */
-
-    /**
-     * Age at last examination available but age of onset not available
-     * The proband was a 39-year-old woman who presented with HPO1, HPO2, and HPO3. HPO4 and HPO5 were excluded.
-     *
-     * @param psex
-     * @param lastExamAge
-
-    private String lastEncounterAvailable(PhenopacketSex psex,
-                                          PhenopacketAge lastExamAge) {
-        String individualDescription;
-        if (lastExamAge.ageType().equals(PhenopacketAgeType.ISO8601_AGE_TYPE)) {
-            Iso8601Age isoAge = (Iso8601Age) lastExamAge;
-            individualDescription = iso8601individualDescription(psex, isoAge);
-        } else if (lastExamAge.ageType().equals(PhenopacketAgeType.HPO_ONSET_AGE_TYPE)) {
-            HpoOnsetAge hpoOnsetTermAge = (HpoOnsetAge) lastExamAge;
-            individualDescription = hpoOnsetIndividualDescription(psex, hpoOnsetTermAge);
-        } else {
-            // should never happen
-            throw new PhenolRuntimeException("Did not recognize last exam age type " + lastExamAge.ageType());
-        }
-
-        return String.format("%s %s %s",
-                buildBlocks.probandWasA(),
-                individualDescription,
-                buildBlocks.inWhomManifestationsWereExcluded());
-
-    }*/
-
-    /**
-     * Age at last examination not available but age of onset available
-     * The proband  presented  at the age of 12 years with HPO1, HPO2, and HPO3. HPO4 and HPO5 were excluded.
-     *
-     * @param psex     sex of the proband
-     * @param onsetAge age at onset of disease
-     * @return
-
-    private String onsetAvailable(PhenopacketSex psex,
-                                  PhenopacketAge onsetAge) {
-        String onsetDescription;
-        String individualDescription;
-        if (onsetAge.ageType().equals(PhenopacketAgeType.ISO8601_AGE_TYPE)) {
-            Iso8601Age isoAge = (Iso8601Age) onsetAge;
-            individualDescription = iso8601individualDescriptionAsA(psex, isoAge);
-        } else if (onsetAge.ageType().equals(PhenopacketAgeType.HPO_ONSET_AGE_TYPE)) {
-            HpoOnsetAge hpoOnsetTermAge = (HpoOnsetAge) onsetAge;
-            individualDescription = hpoOnsetAsA(psex, hpoOnsetTermAge);
-        } else {
-            // should never happen
-            throw new PhenolRuntimeException("Did not recognize onset age type " + onsetAge.ageType());
-        }
-
-        return String.format("%s %s %s",
-                buildBlocks.probandNoAgePresented(),
-                individualDescription,
-                buildBlocks.inWhomManifestationsWereExcluded());
-
-
-    }*/
-
-    /**
-     * This method is called if we have no information at all about the age of the proband
-     *
-     * @param psex Sex of the proband
-     * @return A string such as  "The proband was a female who presented with";
-     */
-    private String ageNotAvailable(PhenopacketSex psex) {
-
-            return switch (psex) {
-                case FEMALE -> buildBlocks.probandWasAFemale();
-                case MALE -> buildBlocks.probandWasAMale();
-                default -> buildBlocks.probandWasAnIndividual();
-            };
-
-    }
-
-    /*
-    private String individualName(PpktIndividual individual) {
-        PhenopacketSex psex = individual.getSex();
-        Optional<PhenopacketAge> ageOpt = individual.getAgeAtLastExamination();
-        if (ageOpt.isEmpty()) {
-            ageOpt = individual.getAgeAtOnset();
-        }
-        if (ageOpt.isEmpty()) {
-            return switch (psex) {
-                case FEMALE -> "female";
-                case MALE -> "male";
-                default -> "individual";
-            };
-        }
-        PhenopacketAge age = ageOpt.get();;
-        if (age.isChild()) {
-            return switch (psex) {
-                case FEMALE -> buildBlocks.girl();
-                case MALE -> buildBlocks.boy();
-                default -> buildBlocks.child();
-            };
-        } else if (age.isCongenital()) {
-            return switch (psex) {
-                case FEMALE -> "female newborn";
-                case MALE -> "male newborn";
-                default -> "newborn";
-            };
-        } else if (age.isFetus()) {
-            return switch (psex) {
-                case FEMALE -> "female fetus";
-                case MALE -> "male fetus";
-                default -> "fetus";
-            };
-        } else if (age.isInfant()) {
-            return switch (psex) {
-                case FEMALE -> "female infant";
-                case MALE -> "male infant";
-                default -> "infant";
-            };
-        } else {
-            return switch (psex) {
-                case FEMALE -> buildBlocks.woman();
-                case MALE -> buildBlocks.man();
-                default -> buildBlocks.inAdulthoold();
-            };
-        }
-    }
-*/
-
 
     @Override
     public String atAgeForVignette(PhenopacketAge ppktAge) {
         if (ppktAge.ageType().equals(PhenopacketAgeType.ISO8601_AGE_TYPE)) {
-            return "At an age of " + ppktAge.age();
+            return "At an age of " + buildBlocks.fromIso((Iso8601Age)ppktAge);
         } else if (ppktAge.ageType().equals(PhenopacketAgeType.HPO_ONSET_AGE_TYPE)) {
             if (ppktAge.isFetus()) {
                 return buildBlocks.duringFetal();

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

@@ -110,7 +110,7 @@ public String featuresAtOnset(String personString, List<OntologyTerm> ontologyTe
         List<String> excluded = getExcludedFeaturesAsStr(ontologyTerms);
         var observedStr = getOxfordCommaList(observed);
         var excludedStr = getOxfordCommaList(excluded);
-        if (!observed.isEmpty() && excluded.isEmpty()) {
+        if (!observed.isEmpty() && ! excluded.isEmpty()) {
             return String.format("%s presented with %s. However, the following features were excluded: %s.",
                     personString, observedStr, excludedStr);
         } else if (!observed.isEmpty()) {

src/test/java/org/monarchinitiative/phenopacket2prompt/output/impl/english/PPKtEnglishBuildingBlocksTest.java

@@ -0,0 +1,22 @@
+package org.monarchinitiative.phenopacket2prompt.output.impl.english;
+
+import org.junit.jupiter.api.Test;
+import org.monarchinitiative.phenopacket2prompt.model.Iso8601Age;
+import org.monarchinitiative.phenopacket2prompt.output.PPKtBuildingBlockGenerator;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+public class PPKtEnglishBuildingBlocksTest {
+
+    public final static PPKtBuildingBlockGenerator generator = new PPKtEnglishBuildingBlocks();
+
+    @Test
+    public void oneMonth() {
+        String expected = "1 month";
+        Iso8601Age iso = new Iso8601Age("P1M");
+        String result = generator.fromIso(iso);
+        assertEquals(expected, result);
+    }
+
+
+}

src/test/java/org/monarchinitiative/phenopacket2prompt/output/impl/english/PpktIndividualEnglishTest.java

@@ -100,9 +100,9 @@ private static Stream<TestIdvlAtAge> testIndlAtAge() {
                 new TestIdvlAtAge("congenital",
                         congenital, new TestOutcome.Ok("At birth")),
                 new TestIdvlAtAge("infantile",
-                        infantile, new TestOutcome.Ok("During the infantile period")),
+                        infantile, new TestOutcome.Ok("As an infant")),
                 new TestIdvlAtAge("childhood age",
-                        childhood, new TestOutcome.Ok("During childhood")),
+                        childhood, new TestOutcome.Ok("As a child")),
                 new TestIdvlAtAge("46 years old",
                         p46y, new TestOutcome.Ok("At an age of 46 years"))
         );
@@ -121,8 +121,6 @@ void testPPKtSex(TestIdvlAtAge testCase) {
                             () -> generator.atAgeForVignette(testCase.ppktAge()),
                             "Incorrect error handling for: " + testCase.description());
         }
-
-
     }