Spanish translations

docs/cases/PMID_28183707.txt

@@ -0,0 +1,36 @@
+[source]
+pmid = PMID:28183707
+title = Chédiak-Higashi syndrome with novel gene mutation
+[diagnosis]
+disease_id = OMIM:214500
+disease_label = Chediak-Higashi syndrome
+[text]
+A boy aged 2½ years was admitted with right-sided pneumonia, which did not improve on antibiotics. Prior to admission,
+the child had a history of fever and poor appetite of 2 weeks duration. He had no cough, sweating, vomiting, diarrhoea or urinary symptoms.
+The child had a history of recurrent wheezing which was managed by nebulised bronchodilators. Moreover, there was a history of skin
+discolouration and weight loss for the past 8 months. The child was under treatment for infantile eczema. One year back,
+he had scalp abscess, which was resolved by oral antibiotics. The child was born term by Lower segment Caesarean section (LSCS)
+due to previous LSCS and Placenta Previa. His mother had gestational diabetes. He had an uneventful prenatal, natal and postnatal
+history. His birth weight was 3kg. He was born to consanguineous parents; his parents are cousins. He has two healthy
+elder brothers and a sister. His vaccination schedule was up to date. There was a history of contact with a caregiver who had old treated tuberculosis.
+On examination, he was afebrile with normal vital signs. His general condition was good apart from pallor with good nutritional status.
+No lymph nodes were palpable. He has greyish short sparse hair. There was a hyperpigmented area at the forehead with other
+hypopigmented patches on the face, behind the ear (figure 1A), at the trunk, the scapular area (figure 1B), the dorsum of the hand (figure 1C),
+and extremities, especially the dorsum of the foot and upper inner thighs (figure 1D). The scrotum, flexural areas and creases were spared.
+There was no joint swelling or tenderness. His weight was between the 3rd and 10th centile, and his height was between the 50th and 75th centile.
+Systemic examination was normal apart from reduced air entry on the right side, mainly the posterior lower zone of the chest.
+There was no hepatosplenomegaly or bleeding tendency and nor was there neurological or developmental impairment.
+Preliminary investigation revealed anaemia with an elevated acute phase reactant. The relevant haematological findings were haemoglobin of
+8.8g %, and total white cell count was within the normal range of a healthy population with no leucopenia, neutropenia or lymphopenia.
+The total leucocyte count was 11900/μL and the platelet count 531000/μL. Differential leucocyte counts showed 60% lymphocytes, 26% neutrophils,
+10% monocytes and eosinophils 4%. C reactive protein: 12mg/L. Serum ferritin: 14.1ng/mL (N: 9.29–58.7).
+T-Spot Tuberculosis test: non-reactive. Acid-fast bacilli (AFB) Smear only: AFB not seen. AFB culture and sensitivity (gastric aspirate): not seen.
+CXR showed right middle lobe consolidation. Repeated chest X-ray after 1week revealed patchy opacities, noted in the right lung and left lower lobe,
+suggestive of progressive pneumonic consolidation.
+Immune status screen showed a non-specific reactive picture: CD4,8 RATIO 1.729% (normal range (N) 1.20–2.40),
+TOTAL T CELLS 67.7% (N:62.0–72.0), CD3 ABS 6119.0 CELL/μL (N:812–2318), CD4% 37.7% (N:35.0–55.0), CD4 ABS 3408.0 CELL/μL (N:589–1505)
+CD8% 21.8% (N:16.0–28.0), CD8 ABS 1971.0 CELL/μL (N:325–995), CD56% 2.3% (N:5.00–13.0), CD56 ABS 208.0 CELL/μL (N:78–602, CD19% 21.6% (N:12.0–28.0)
+CD19 ABS 1952.0 CELL/μL (N: 99–426).
+Immunoglobulins assay showed elevated immunoglobulin E (IgE) 2680.0KU/L (N: 0–64), IGG 21.80g/L (N: 4.07–10.09), IGA 2.01g/L (N: 0.14–1.22),
+IGM 1.94g/L (N:0.46–1.60).
+Liver and renal function tests were normal.

docs/cases/PMID_28503313.txt

@@ -0,0 +1,24 @@
+[source]
+pmid = PMID:28503313
+title = Novel DHCR7 mutation in a case of Smith-Lemli-Opitz syndrome showing 46,XY disorder of sex development
+[diagnosis]
+disease_id = OMIM:270400
+disease_label = Smith-Lemli-Opitz syndrome
+[text]
+The patient was born at 38 weeks of gestation to non-consanguineous Japanese parents. Birth weight, length and head
+circumference were 2,59Z g (−0.92 s.d.), 45 cm (−1.7 s.d.) and 33 cm (−0.1 s.d.), respectively.
+Ambiguous genitalia, low set ears, a short nose and Y-shaped 2–3 toe syndactyly were detected at birth (Figure 1a and b).
+Examination of the patient’s genitalia revealed a micropenis (stretch length: 1.5 cm),
+left lateral testicular hypoplasia (right and left diameters: 10 and 5 mm, respectively), hypospadias and a bifid scrotum (Figure 1c).
+Echography and magnetic resonance imaging failed to detect the presence of a uterus or ovaries.
+Blood examination revealed a relatively low total cholesterol (T. Chol) level (46 mg/dl) (reference: 129–232),
+normal testosterone and slightly low anti-mullerian hormone level for males.
+Urine steroid profile was normal.
+G-banding analysis confirmed a normal 46,XY male karyotype. From these results, the patient was recorded in public office documents as male.
+We performed cholesterol analysis with high-performance liquid chromatography.
+This analysis revealed relative hypocholesterolemia and high 7-DHC and 8-dehydrocholesterol levels in the patient and normal levels
+(undetectable) in his parents (Table 1). T.
+Chol/7-DHC was significantly lower in the patient than in his parents.
+Therefore, he was biochemically diagnosed with SLOS.
+The patient also presented with allergies for milk and eggs, and eczema throughout his body.
+His eczema, considered to be atopic dermatitis, was treated with corticosteroid ointment.

pom.xml

@@ -6,7 +6,7 @@
 
     <groupId>org.monarchinitiative</groupId>
     <artifactId>phenopacket2prompt</artifactId>
-    <version>0.4.4</version>
+    <version>0.4.6</version>
 
     <name>phenopacket2prompt</name>
     <url>https://github.com/monarch-initiative/phenopacket2prompt</url>

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

@@ -10,7 +10,7 @@ public interface PpktPhenotypicFeatureGenerator {
 
     String formatFeatures(List<OntologyTerm> ontologyTerms);
 
-    default String featuresAtEncounter(List<OntologyTerm> ontologyTerms) {
+    default String featuresAtEncounter(String personString, String ageString, List<OntologyTerm> ontologyTerms) {
         return ""; //TODO - implement and make this not default
     }
 

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

@@ -50,8 +50,12 @@ public String formatFeatures(List<OntologyTerm> ontologyTerms) {
     @Override
     public String getVignetteAtAge(PhenopacketAge page, PhenopacketSex psex, List<OntologyTerm> terms) {
         String ageString = this.ppktAgeSexGenerator.atAgeForVignette(page);
-        String features = formatFeatures(terms);
-        return String.format("%s, präsentierte %s mit den folgenden Symptomen: %s", ageString, ppktAgeSexGenerator.heSheIndividual(psex), features);
+        String person = switch (psex) {
+            case MALE -> "er";
+            case FEMALE -> "sie";
+            default -> "die betroffene Person";
+        };
+        return this.ppktPhenotypicFeatureGenerator.featuresAtEncounter(person, ageString, terms);
     }
 
     @Override

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

@@ -1,5 +1,6 @@
 package org.monarchinitiative.phenopacket2prompt.output.impl.german;
 
+import org.monarchinitiative.phenol.base.PhenolRuntimeException;
 import org.monarchinitiative.phenopacket2prompt.international.HpInternational;
 import org.monarchinitiative.phenopacket2prompt.model.OntologyTerm;
 import org.monarchinitiative.phenopacket2prompt.output.PpktPhenotypicFeatureGenerator;
@@ -82,13 +83,41 @@ public Set<String> getMissingTranslations() {
     }
 
 
+    @Override
+    public String featuresAtEncounter(String personString, String ageString, List<OntologyTerm> ontologyTerms) {
+        List<OntologyTerm> observed = getObservedFeatures(ontologyTerms);
+        List<OntologyTerm> excluded = getExcludedFeatures(ontologyTerms);
+        List<String> observedGerman = getTranslations(observed);
+        List<String> excludedGerman = getTranslations(excluded);
+        var observedStr = getCommaList(observedGerman);
+        var excludedStr = getCommaList(excludedGerman);
+        if (!observed.isEmpty() && ! excluded.isEmpty()) {
+            return String.format("%s präsentierte %s mit den folgenden Symptomen: %s. Im Gegensatz %s die folgenden Symptome ausgeschlossen: %s.",
+                    ageString,
+                    personString,
+                    observedStr,
+                    excluded.size()>1? "wurden":"wurde",
+                    excludedStr);
+        } else if (!observed.isEmpty()) {
+            return String.format("%s präsentierte %s mit den folgenden Symptomen: %s.", ageString, personString,  observedStr);
+        } else if (!excluded.isEmpty()) {
+            return String.format("%s %s die folgenden Symptome ausgeschlossen: %s.",
+                    ageString,
+                    excluded.size()>1? "wurden":"wurde", excludedStr);
+        } else {
+            throw new PhenolRuntimeException("No features found for time point " + ageString); // should never happen
+        }
+    }
 
     @Override
     public String featuresAtOnset(String personString, List<OntologyTerm> ontologyTerms) {
-        List<String> observed = getObservedFeaturesAsStr(ontologyTerms);
-        List<String> excluded = getExcludedFeaturesAsStr(ontologyTerms);
-        var observedStr = getCommaList(observed);
-        var excludedStr = getCommaList(excluded);
+        List<OntologyTerm> observed = getObservedFeatures(ontologyTerms);
+        List<OntologyTerm> excluded = getExcludedFeatures(ontologyTerms);
+        List<String> observedGerman = getTranslations(observed);
+        List<String> excludedGerman = getTranslations(excluded);
+        var observedStr = getCommaList(observedGerman);
+        var excludedStr = getCommaList(excludedGerman);
+
         if (!observed.isEmpty() && ! excluded.isEmpty()) {
             return String.format("%s präsentierte mit den folgenden Symptomen: %s. Im Gegensatz %s die folgenden Symptome ausgeschlossen: %s.",
                     personString,