Prevent NPEs in YAML parsing.

Signed-off-by: Daniel Danis <[email protected]>

lirical-cli/src/examples/phenotype-only.yml

@@ -0,0 +1,13 @@
+## LIRICAL Analysis Template.
+# Use this as a template for your own set-up.
+---
+sampleId: Sample ID
+hpoIds: ['HP:0002352', 'HP:0002490', 'HP:0001290']
+negatedHpoIds: ['HP:0000486']
+
+# Age in ISO8601 notation (e.g. 'P12Y6M5D' to indicate 12 years, 6 months, and 5 days).
+#age:
+# Choose from {MALE, FEMALE}
+#sex:
+# Path to a VCF file (optional)
+#vcf:

lirical-io/src/main/java/org/monarchinitiative/lirical/io/analysis/YamlAnalysisDataParser.java

@@ -58,6 +58,9 @@ public AnalysisData parse(InputStream is) throws LiricalParseException {
 
 
     private static Sex parseSex(String sex) {
+        if (sex == null)
+            return Sex.UNKNOWN;
+
         return switch (sex.toLowerCase()) {
             case "male" -> Sex.MALE;
             case "female" -> Sex.FEMALE;

lirical-io/src/main/java/org/monarchinitiative/lirical/io/analysis/YamlConfig.java

@@ -10,11 +10,11 @@
  */
 public class YamlConfig {
 
-    private String sampleId;
-    private List<String> hpoIds;
-    private List<String> negatedHpoIds;
+    private String sampleId = "Sample ID";
+    private List<String> hpoIds = List.of();
+    private List<String> negatedHpoIds = List.of();
     private String age;
-    private String sex;
+    private String sex = "UNKNOWN";
     private String vcf;
 
     public void setSampleId(String sampleId) {
@@ -66,7 +66,7 @@ public String vcf() {
     }
 
     public Optional<Path> vcfPath() {
-        return vcf == null ?
+        return vcf == null || vcf.isBlank() ?
                 Optional.empty()
                 : Optional.of(Path.of(vcf));
     }