Merge pull request #14 from johandahlberg/samplesheet_naming

arteria_samplesheet.csv -> Samplesheet.csv

bcl2fastq/__init__.py

@@ -1 +1 @@
-__version__ = "1.0.0"
+__version__ = "1.1.0"

bcl2fastq/lib/bcl2fastq_utils.py

@@ -2,6 +2,8 @@
 import os
 from itertools import groupby
 import logging
+import shutil
+import time
 
 from illuminate.metadata import InteropMetadata
 
@@ -51,7 +53,11 @@ def __init__(self,
             self.samplesheet_file = runfolder_input + "/SampleSheet.csv"
         else:
             log.debug("Got a new samplesheet. Will use that instead of the one found in the runfolder.")
-            new_samplesheet_file = runfolder_input + "/arteria_samplesheet.csv"
+            new_samplesheet_file = runfolder_input + "/SampleSheet.csv"
+
+            if os.path.exists(new_samplesheet_file):
+                Bcl2FastqConfig.copy_old_samplesheet(new_samplesheet_file)
+
             Bcl2FastqConfig.write_samplesheet(samplesheet, new_samplesheet_file)
             self.samplesheet_file = new_samplesheet_file
 
@@ -83,6 +89,13 @@ def __init__(self,
             import multiprocessing
             self.nbr_of_cores = multiprocessing.cpu_count()
 
+    @staticmethod
+    def copy_old_samplesheet(new_samplesheet_file):
+        new_path_for_old_samplesheet = new_samplesheet_file + time.strftime("%Y%m%d-%H%M%S")
+        log.debug("Original samplesheet: {} copied to: {}. ".
+                  format(new_samplesheet_file, new_path_for_old_samplesheet))
+        shutil.copy(new_samplesheet_file,  new_path_for_old_samplesheet)
+
     @staticmethod
     def write_samplesheet(samplesheet_string, new_samplesheet_file):
         with open(new_samplesheet_file, "w") as f:

tests/test_bcl2fastq_handlers.py

@@ -106,7 +106,7 @@ def test_start_providing_samplesheet(self):
             self.assertEqual(json.loads(response.body)["link"], expected_link)
             self.assertEqual(json.loads(response.body)["bcl2fastq_version"], "2.15.2")
             self.assertEqual(json.loads(response.body)["state"], "started")
-            ws.assert_called_once_with(TestUtils.DUMMY_SAMPLESHEET_STRING, "/data/biotank3/runfolders/150415_D00457_0091_AC6281ANXX/arteria_samplesheet.csv")
+            ws.assert_called_once_with(TestUtils.DUMMY_SAMPLESHEET_STRING, "/data/biotank3/runfolders/150415_D00457_0091_AC6281ANXX/SampleSheet.csv")
 
     def test_status_with_id(self):
         #TODO Add real tests here!