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TASK-4150 - Role in cancer info missing from gene-census disease panel #245

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TASK-4150 - Role in cancer info missing from gene-census disease panel #245

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22 changes: 7 additions & 15 deletions biodata-tools/src/main/java/org/opencb/biodata/tools/clinical/DiseasePanelParsers.java
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Original file line number Diff line number Diff line change
Expand Up @@ -143,26 +143,18 @@ public static DiseasePanel parseCensus(Path censusTsvFile) throws IOException {
case "Role in Cancer":
if (StringUtils.isNotEmpty(value)) {
String[] roles = value.split(", ");
ClinicalProperty.RoleInCancer roleInCancer = null;
Set<ClinicalProperty.RoleInCancer> rolesInCancer = new HashSet<>();
for (String role : roles) {
ClinicalProperty.RoleInCancer tmpRole = null;
if ("TSG".equals(role)) {
tmpRole = ClinicalProperty.RoleInCancer.TUMOR_SUPPRESSOR_GENE;
rolesInCancer.add(ClinicalProperty.RoleInCancer.TUMOR_SUPPRESSOR_GENE);
} else if ("oncogene".equals(role)) {
tmpRole = ClinicalProperty.RoleInCancer.ONCOGENE;
}
if (tmpRole != null && roleInCancer == null) {
roleInCancer = tmpRole;
} else if (tmpRole != null) {
if (tmpRole != roleInCancer) {
roleInCancer = ClinicalProperty.RoleInCancer.BOTH;
} else {
System.out.println("Found repeated roles?");
}
rolesInCancer.add(ClinicalProperty.RoleInCancer.ONCOGENE);
} else if ("fusion".equals(role)) {
rolesInCancer.add(ClinicalProperty.RoleInCancer.FUSION);
}
}
if (roleInCancer != null) {
genePanel.getCancer().setRoles(Collections.singletonList(roleInCancer));
if (!rolesInCancer.isEmpty()) {
genePanel.getCancer().setRoles(new ArrayList<>(rolesInCancer));
}
}
break;
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