removed last changes, updated organiser-job.yaml

BBMRI-cz · Dec 14, 2024 · fa75a8f · fa75a8f
1 parent ec3745c
commit fa75a8f
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Showing 4 changed files with 4 additions and 30 deletions.
diff --git a/compose.yaml b/compose.yaml
@@ -6,11 +6,9 @@ services:
       dockerfile: Dockerfile.dev
     volumes:
       - /home/houfek/Work/MMCI/sequencing_pipeline/data-catalogue-playground/muni-sc/PseudonymizedRuns:/PseudonymizedRuns
-      - /home/houfek/Work/MMCI/sequencing_pipeline/data-catalogue-playground/muni-sc/NextSeqTemp/:/NextSeqTemp
       - /home/houfek/Work/MMCI/sequencing_pipeline/data-catalogue-playground/muni-sc/OrganisedRuns/:/OrganisedRuns
       - /home/houfek/Work/MMCI/sequencing_pipeline/data-catalogue-playground/muni-sc/Patients/:/Patients
     command: bash -c "python main.py
                               -r /PseudonymizedRuns/
-                              -n /NextSeqTemp/
                               -o /OrganisedRuns/
                               -p /Patients/"
diff --git a/kubernetes/organiser-job.yaml b/kubernetes/organiser-job.yaml
@@ -25,34 +25,12 @@ spec:
               capabilities:
                 drop:
                 - ALL
-            env:
-              - name: CATALOG_LOGIN
-                valueFrom:
-                  secretKeyRef:
-                    name: catalog-secret
-                    key: username
-              - name: CATALOG_PASSWORD
-                valueFrom:
-                  secretKeyRef:
-                    name: catalog-secret
-                    key: password
-              - name: HTTPS_PROXY
-                valueFrom:
-                  secretKeyRef:
-                    name: catalog-secret
-                    key: httpsproxy
-            command: ["python", "main.py", "-r", "/data/PSEUDONYMIZED", "-n", "data/NextSeqTemp/" ,"-o", "/data/OrganisedRuns/", "-p", "/data/Patients/"]
+            command: ["python", "main.py", "-r", "/data/PSEUDONYMIZED", "-o", "/data/OrganisedRuns/", "-p", "/data/Patients/"]
             volumeMounts:
             - name: storage-catalogue-volume
               mountPath: /data/
-            - name: data-wsi-volume
-              mountPath: /wsi/
-              subPath: tiff
           restartPolicy: "Never"
           volumes:
           - name: storage-catalogue-volume
             persistentVolumeClaim:
               claimName: pvc-storage-catalogue-secret
-          - name: data-wsi-volume
-            persistentVolumeClaim:
-              claimName: pvc-osd-secret
diff --git a/main.py b/main.py
@@ -9,8 +9,7 @@
 
     parser.add_argument("-r", "--runs", type=str, required=True, help="Path to pseudonymized runs")
     parser.add_argument("-o", "--output", type=str, required=True, help="Path to the organise file")
-    parser.add_argument("-n", "--nextseq_ouput", type=str, required=True, help="Temporary nextseq folder")
     parser.add_argument("-p", "--patients", type=str, required=True, help="Path to a patient folder")
     args = parser.parse_args()
 
-    Processor(args.runs, args.output, args.nextseq_output, args.patients).process_runs()
+    Processor(args.runs, args.output, args.patients).process_runs()
diff --git a/organiser/process/processor.py b/organiser/process/processor.py
@@ -12,10 +12,9 @@
 
 
 class Processor:
-    def __init__(self, pseudnymized_runs_folder, folder_for_organised_files, next_seq_temporary_folder, patient_folder):
+    def __init__(self, pseudnymized_runs_folder, folder_for_organised_files, patient_folder):
         self.psedunymized_runs_folder = pseudnymized_runs_folder
         self.organised_files_folder = folder_for_organised_files
-        self.next_seq_temporary_folder = next_seq_temporary_folder
         self.patient_folder = patient_folder
 
     def process_runs(self):
@@ -68,7 +67,7 @@ def _get_correct_organiser(self, run_path) -> OrganiseRun:
         elif self._is_run_nextseq(full_run_path):
             logging.info(f"{run_path} processed as NextSeq")
             return NextSeqRunOrganiser(self.psedunymized_runs_folder, run_path,
-                                       self.next_seq_temporary_folder, self.patient_folder)
+                                       self.organised_files_folder, self.patient_folder)
         else:
             logging.info(f"{run_path} processed as Old Miseq")
             return OldMiseqRunOrganiser(self.psedunymized_runs_folder, run_path,