Change default picomolarity to 5, and allow overriding the default

via the htsworkflow ini file.
closes [ticket:120] and [ticket:83]

diff --git a/htsworkflow/frontend/experiments/models.py b/htsworkflow/frontend/experiments/models.py
index 0ac386eea254b0e72cfe13a44b52b95bb3e0edb2..a6635c5d3c1077f809f099de437c24f96aca2dd0 100755 (executable)
--- a/htsworkflow/frontend/experiments/models.py
+++ b/htsworkflow/frontend/experiments/models.py
@@ -1,6 +1,8 @@
 from django.db import models
 from htsworkflow.frontend.samples.models import *
+from htsworkflow.frontend.settings import options
 from django.core.exceptions import ObjectDoesNotExist
+import logging
 
 class ClusterStation(models.Model):
   name = models.CharField(max_length=50, unique=True)
@@ -14,6 +16,12 @@ class Sequencer(models.Model):
   def __unicode__(self):
     return unicode(self.name)
 
+default_pM = 5
+try:
+  default_pM = int(options.get('frontend', 'default_pm'))
+except ValueError,e:
+  logging.error("invalid value for frontend.default_pm")
+
 class FlowCell(models.Model):
   
   flowcell_id = models.CharField(max_length=20, unique=True, db_index=True)
@@ -31,14 +39,14 @@ class FlowCell(models.Model):
   lane_7_library = models.ForeignKey(Library, related_name="lane_7_library")
   lane_8_library = models.ForeignKey(Library, related_name="lane_8_library")
 
-  lane_1_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
-  lane_2_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
-  lane_3_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
-  lane_4_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
-  lane_5_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
-  lane_6_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
-  lane_7_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
-  lane_8_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=2.5)
+  lane_1_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=default_pM)
+  lane_2_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=default_pM)
+  lane_3_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=default_pM)
+  lane_4_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=default_pM)
+  lane_5_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=default_pM)
+  lane_6_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=default_pM)
+  lane_7_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=default_pM)
+  lane_8_pM = models.DecimalField(max_digits=5, decimal_places=2,blank=False, null=False,default=default_pM)
   
   lane_1_cluster_estimate = models.IntegerField(blank=True, null=True)
   lane_2_cluster_estimate = models.IntegerField(blank=True, null=True)

diff --git a/htsworkflow/frontend/settings.py b/htsworkflow/frontend/settings.py
index 01ec35aa3002ef7b5c971692a4c5931bf3a3c3e1..eb30b90b07b6b155cacc16a62a9a6d83d349cce7 100644 (file)
--- a/htsworkflow/frontend/settings.py
+++ b/htsworkflow/frontend/settings.py
@@ -54,6 +54,7 @@ options = ConfigParser.SafeConfigParser(
              'database_name': 
                os.path.abspath('/htsworkflow/htswfrontend/dev_fctracker.db'),
              'time_zone': 'America/Los_Angeles',
+             'default_pm': '5'
            })
 
 options.read([os.path.expanduser("~/.htsworkflow.ini"),