From: Diane Trout <diane@caltech.edu>
Date: Fri, 5 Sep 2008 21:56:38 +0000 (+0000)
Subject: extract status field out of flowcell name.
X-Git-Tag: stanford.caltech-merged-database-2009-jan-15~38
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=738e532f82f6e19c32fc5a6123aedbfb8db4d5a5

extract status field out of flowcell name.

For gaworkflow we abused the schema and stored the flow cell status
in the flow cell name field, this patch updates my sqlite interface
to the fctracker db to split that field.
---

diff --git a/gaworkflow/util/fctracker.py b/gaworkflow/util/fctracker.py
index 2f07dce..57b5dcf 100644
--- a/gaworkflow/util/fctracker.py
+++ b/gaworkflow/util/fctracker.py
@@ -111,6 +111,10 @@ class fctracker:
         description = [ f[0] for f in c.description ]
         for row in c:
             row_dict = dict(zip(description, row))
+            fcid, status = self._parse_flowcell_id(row_dict)
+            row_dict['flowcell_id'] = fcid
+            row_dict['flowcell_status'] = status
+
             for lane in [ 'lane_%d_library' % (i) for i in range(1,9) ]:
                 lane_library = self.library[row_dict[lane+"_id"]]
                 species_id = lane_library['library_species_id']
@@ -125,23 +129,47 @@ class fctracker:
         self._add_lanes_to_libraries()
         return self.flowcells
 
+    def _parse_flowcell_id(self, flowcell_row):
+      """
+      Return flowcell id and status
+      
+      We stored the status information in the flowcell id name.
+      this was dumb, but database schemas are hard to update.
+      """
+      fields = flowcell_row['flowcell_id'].split()
+      fcid = None
+      status = None
+      if len(fields) > 0:
+        fcid = fields[0]
+      if len(fields) > 1:
+        status = fields[1]
+      return fcid, status
+      
+
+def flowcell_gone(cell):
+    """
+    Use a variety of heuristics to determine if the flowcell drive
+    has been deleted.
+    """
+    status = cell['flowcell_status']
+    if status is None:
+        return False
+    failures = ['failed', 'deleted', 'not run']
+    for f in failures:
+      if re.search(f, status):
+        return True
+    else:
+      return False
+
 def recoverable_drive_report(flowcells):
     """
     Attempt to report what flowcells are still on a hard drive
     """
-    def flowcell_gone(cell):
-        """
-        Use a variety of heuristics to determine if the flowcell drive
-        has been deleted.
-        """
-        name = cell['flowcell_id']
-        if 'failed' in name:
-            return True
-        if 'deleted' in name:
-            return True
-        if 'not run' in name:
-            return True
-        return False
+    def format_status(status):
+      if status is None:
+        return ""
+      else:
+        return status+" "
 
     # sort flowcells by run date
     flowcell_list = []
@@ -150,7 +178,7 @@ def recoverable_drive_report(flowcells):
     flowcell_list.sort()
 
     report = []
-    line = "%(date)s %(id)s %(lane)s %(library_name)s (%(library_id)s) "
+    line = "%(date)s %(id)s %(status)s%(lane)s %(library_name)s (%(library_id)s) "
     line += "%(species)s"
     for run_date, flowcell_id in flowcell_list:
         cell = flowcells[flowcell_id]
@@ -166,6 +194,7 @@ def recoverable_drive_report(flowcells):
               'library_name': cell_library['library_name'],
               'library_id': cell['%s_library_id'%(lane)],
               'species': cell_library['library_species']['scientific_name'],
+              'status': format_status(cell['flowcell_status']),
             }
             report.append(line % (fields))
     return os.linesep.join(report)