cg 76.0.0__py3-none-any.whl → 83.14.0__py3-none-any.whl

cg/services/illumina/backup/backup_service.py

@@ -114,7 +114,10 @@ class IlluminaBackupService:
         """Process a flow cell from backup. Return elapsed time."""
         start_time: float = get_start_time()
         run_dir = Path(self.sequencing_runs_dir)
-        sequencing_run_output_dir = Path(run_dir, archived_run.name.split(".")[0])
+        is_current: bool = self._is_archiving_directory_current(archived_run)
+        sequencing_run_output_dir: Path = self._get_sequencing_run_output_dir(
+            archived_run=archived_run, is_current=is_current
+        )
         self.retrieve_archived_key(
             archived_key=archived_key, sequencing_run=sequencing_run, run_dir=run_dir
         )
@@ -128,9 +131,12 @@ class IlluminaBackupService:
                 encryption_key,
                 retrieved_run,
                 retrieved_key,
-            ) = self.decrypt_sequencing_run(archived_run, archived_key, run_dir)
-
-            self.extract_sequencing_run(decrypted_run, run_dir)
+            ) = self.decrypt_sequencing_run(
+                archived_run=archived_run, archived_key=archived_key, run_dir=run_dir
+            )
+            self.extract_sequencing_run(
+                decrypted_run=decrypted_run, is_current=is_current, run_dir=run_dir
+            )
             self.create_rta_complete(sequencing_run_output_dir)
             self.create_copy_complete(sequencing_run_output_dir)
             self.unlink_files(decrypted_run, encryption_key, retrieved_run, retrieved_key)
@@ -145,6 +151,20 @@ class IlluminaBackupService:
 
         return get_elapsed_time(start_time=start_time)
 
+    def _get_sequencing_run_output_dir(self, archived_run: Path, is_current: bool) -> Path:
+        """Return the path to the sequencing run based on the archived run path."""
+        if is_current:
+            run_full_name: str = archived_run.parent.name
+        else:
+            run_full_name: str = archived_run.name.split(".")[0]
+        return Path(self.sequencing_runs_dir, run_full_name)
+
+    def _is_archiving_directory_current(self, archived_run: Path) -> bool:
+        """Check if the archived run is in the current archiving directory."""
+        return archived_run.as_posix().startswith(
+            Path(self.pdc_archiving_directory.current).parent.as_posix()
+        )
+
     def unlink_files(
         self,
         decrypted_run: Path,
@@ -184,10 +204,12 @@ class IlluminaBackupService:
         """Create a CopyComplete.txt file in the flow cell run directory."""
         Path(flow_cell_directory, DemultiplexingDirsAndFiles.COPY_COMPLETE).touch()
 
-    def extract_sequencing_run(self, decrypted_run, run_dir):
+    def extract_sequencing_run(self, decrypted_run: Path, is_current: bool, run_dir: Path) -> None:
         """Extract the sequencing run tar archive."""
-        extraction_command = self.tar_api.get_extract_file_command(
-            input_file=decrypted_run, output_dir=run_dir
+        extraction_command: list[str] = self.tar_api.get_extract_file_command(
+            input_file=decrypted_run,
+            output_dir=run_dir,
+            is_current=is_current,
         )
         LOG.debug(f"Extract sequencing run command: {extraction_command}")
         self.tar_api.run_tar_command(extraction_command)

cg/services/orders/validation/constants.py

@@ -30,6 +30,7 @@ class ExtractionMethod(StrEnum):
 
 
 class IndexEnum(StrEnum):
+    ARCHER_SET_B = "Archer Set B"
     AVIDA_INDEX_PLATE = "Avida Index plate"
     AVIDA_INDEX_STRIP = "Avida Index strip"
     IDT_DS_B = "IDT DupSeq 10 bp Set B"
@@ -37,6 +38,7 @@ class IndexEnum(StrEnum):
     IDT_XGEN_UDI = "IDT xGen UDI Adapters"
     IDT10_UDI_NIPT = "IDT10 UDI NIPT"
     KAPA_UDI_NIPT = "KAPA UDI NIPT"
+    NEBNEXT_LV_Unique_Dual_2A = "NEBNext LV Unique Dual Index Primers Set 2A"
     NEXTERA_XT = "Nextera XT Dual"
     NEXTFLEX_UDI_96 = "NEXTflex® Unique Dual Index Barcodes 1 - 96"
     NEXTFLEX_V2_UDI_96 = "NEXTflex® v2 UDI Barcodes 1 - 96"
@@ -46,4 +48,5 @@ class IndexEnum(StrEnum):
     TWIST_UDI_B = "TWIST UDI Set B"
     TWIST_UDI_C = "TWIST UDI Set C"
     TRUSEQ_DNA_HT = "TruSeq DNA HT Dual-index (D7-D5)"
+    XGEN_UDI_10_1_4 = "xGen UDI 10nt Primer Plates 1-4"
     NO_INDEX = "NoIndex"