add support for patho and humgen reports

buschlab · Oct 22, 2024 · 87987fa · 87987fa
1 parent df7a6d0
commit 87987fa
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Showing 2 changed files with 21 additions and 5 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
@@ -37,17 +37,31 @@ private AddResourceData() {
      * @throws IOException
      */
     public static void processPdfFile(CbioPortalStudy study, File pdf) throws IOException {
-        String sampleId = pdf.getName()
-                .replaceAll("somaticGermline_|somatic_|tumorOnly_|_tumorOnly|_Report|_Slides|.pdf", "");
-        String patientId = FhirResolver.resolvePatientFromSample(sampleId);
+        String sampleId = pdf.getName().replaceAll(
+                ".*_somaticGermline_|.*somatic_|.*tumorOnly_|_tumorOnly|_Report|_Slides|_Patho|_HumGen|.pdf", "");
+        String patientId = pdf.getName().replaceAll("_somatic.*|_tumorOnly.*", "");
+        if (patientId == null || patientId.length() == 0) {
+            FhirResolver.resolvePatientFromSample(sampleId);
+        }
         File target = new File(
                 Settings.getResourceFolder(), study.getStudyId() + "/" + patientId + "/" + pdf.getName());
         FileUtils.copyFile(pdf, target);
         Files.setPosixFilePermissions(target.toPath(), PosixFilePermissions.fromString("rw-r--r--"));
         SampleResource sr = new SampleResource();
         sr.setPatientId(patientId);
         sr.setSampleId(sampleId);
-        sr.setResourceId(pdf.getName().contains("_Report") ? "PATHOLOGY_SLIDE" : "SLIDE");
+        if (pdf.getName().contains("_Report")) {
+            sr.setResourceId("PATHOLOGY_SLIDE");
+        }
+        if (pdf.getName().contains("_Slides")) {
+            sr.setResourceId("SLIDE");
+        }
+        if (pdf.getName().contains("_Patho")) {
+            sr.setResourceId("PATHOLOGY_REPORT");
+        }
+        if (pdf.getName().contains("_HumGen")) {
+            sr.setResourceId("HUMGEN_REPORT");
+        }
         try {
             sr.setUrl(Settings.getUrlBase() + "/" + study.getStudyId() + "/" + patientId + "/" + pdf.getName());
         } catch (MalformedURLException e) {

diff --git a/template/data_resource_definition.txt b/template/data_resource_definition.txt
@@ -1,3 +1,5 @@
 RESOURCE_ID	DISPLAY_NAME	RESOURCE_TYPE	DESCRIPTION	OPEN_BY_DEFAULT	PRIORITY
 PATHOLOGY_SLIDE	MIRACUM-Pipe Report	SAMPLE	The MIRACUM-Pipe report for the sample	TRUE	1
-SLIDE	Slides	SAMPLE	Slides	TRUE	1
+PATHOLOGY_REPORT	Pathology Report	SAMPLE	Pathology Report	TRUE	1
+SLIDE	Slides	SAMPLE	Slides	TRUE	1
+HUMGEN_REPORT	Human genetics	SAMPLE	Report of the human genetics	TRUE	1