From 3b30afa2f78483bb48d6b72b67da8090a27e0c9f Mon Sep 17 00:00:00 2001
From: Niklas Reimer <n.reimer@uni-luebeck.de>
Date: Tue, 22 Oct 2024 18:58:47 +0200
Subject: [PATCH] fix patient id resovling

---
 .../java/de/uzl/lied/mtbimporter/tasks/AddResourceData.java  | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/main/java/de/uzl/lied/mtbimporter/tasks/AddResourceData.java b/src/main/java/de/uzl/lied/mtbimporter/tasks/AddResourceData.java
index 860e837..0119f0a 100644
--- a/src/main/java/de/uzl/lied/mtbimporter/tasks/AddResourceData.java
+++ b/src/main/java/de/uzl/lied/mtbimporter/tasks/AddResourceData.java
@@ -39,9 +39,10 @@ private AddResourceData() {
     public static void processPdfFile(CbioPortalStudy study, File pdf) throws IOException {
         String sampleId = pdf.getName().replaceAll(
                 ".*_somaticGermline_|.*somatic_|.*tumorOnly_|_tumorOnly|_Report|_Slides|_Patho|_HumGen|.pdf", "");
+        sampleId = sampleId.replaceAll("somaticGermline_|somatic_|tumorOnly_", "");
         String patientId = pdf.getName().replaceAll("_somatic.*|_tumorOnly.*", "");
-        if (patientId == null || patientId.length() == 0) {
-            FhirResolver.resolvePatientFromSample(sampleId);
+        if (patientId == null || patientId.length() == 0 || patientId.equals(pdf.getName())) {
+            patientId = FhirResolver.resolvePatientFromSample(sampleId);
         }
         File target = new File(
                 Settings.getResourceFolder(), study.getStudyId() + "/" + patientId + "/" + pdf.getName());