From: Diane Trout <diane@caltech.edu>
Date: Fri, 13 Aug 2010 22:49:09 +0000 (+0000)
Subject: This patch adds in fields to support storing bioanalyzer results. [ticket:166]
X-Git-Tag: 0.4.4~2
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=145d10cddf64a7741bf755be3991f25056ca352a

This patch adds in fields to support storing bioanalyzer results. [ticket:166]
---

diff --git a/docs/upgrade_v0.4.3_to_v0.4.4.py b/docs/upgrade_v0.4.3_to_v0.4.4.py
new file mode 100644
index 0000000..44e2baf
--- /dev/null
+++ b/docs/upgrade_v0.4.3_to_v0.4.4.py
@@ -0,0 +1,37 @@
+"""
+This renames avg_lib_size to gel_cut_size and adds an insert length field 
+to samples_library.
+"""
+
+import shutil
+import sqlite3
+import sys
+
+def main(cmdline=None):
+    if len(cmdline) == 1:
+       dest='/tmp/fctracker.db'
+    else:
+      dest = cmdline[1]
+    shutil.copy(cmdline[0], dest)
+    conn = sqlite3.connect(dest)
+    c = conn.cursor()
+    
+    c.execute("""
+alter table samples_library 
+add column "bioanalyzer_concentration" decimal;
+""")
+    
+    c.execute("""
+alter table samples_library 
+add column "bioanalyzer_summary" text NOT NULL default "";
+""")
+
+    c.execute("""
+alter table samples_library 
+add column "bioanalyzer_image_url" varchar(200) NOT NULL default "";
+""")
+
+    conn.commit()
+
+if __name__ == "__main__":
+    main(sys.argv[1:])
diff --git a/htsworkflow/frontend/samples/admin.py b/htsworkflow/frontend/samples/admin.py
index 393bfa2..4b46a22 100644
--- a/htsworkflow/frontend/samples/admin.py
+++ b/htsworkflow/frontend/samples/admin.py
@@ -148,7 +148,14 @@ class LibraryOptions(admin.ModelAdmin):
           ('cell_line','condition','antibody'),)
          }),
          ('Creation Information:', {
-             'fields' : (('made_for', 'made_by', 'creation_date'), ('stopping_point', 'amplified_from_sample'), ('gel_cut_size', 'insert_size', 'undiluted_concentration', 'ten_nM_dilution', 'successful_pM'), 'account_number', 'notes',)
+             'fields' : (('made_for', 'made_by', 'creation_date'), 
+                         ('stopping_point', 'amplified_from_sample'), 
+                         ('gel_cut_size', 'insert_size', 
+                          'undiluted_concentration', 'ten_nM_dilution', 
+                          'successful_pM'), 
+                         ('bioanalyzer_concentration','bioanalyzer_image_url'),
+                         ('bioanalyzer_summary'), 
+                         ('account_number', 'notes',))
          }),
          ('Library/Project Affiliation:', {
              'fields' : (('affiliations'), ('tags'),)
@@ -159,7 +166,6 @@ class LibraryOptions(admin.ModelAdmin):
     ]
     actions = ['action_print_library_labels']
     
-    
     def action_print_library_labels(self, request, queryset):
         """
         Django action which prints labels for the selected set of labels from the
@@ -200,19 +206,20 @@ class LibraryOptions(admin.ModelAdmin):
                           
     action_print_library_labels.short_description = "Print Labels"
 
-
-
-    # some post 1.0.2 version of django has formfield_overrides 
-    # which would replace this code with:
-    # formfield_overrids = {
-    #    models.ManyToMany: { 'widget': widgets.FilteredSelectMultiple }
-    #}
     def formfield_for_dbfield(self, db_field, **kwargs):
-      if db_field.name in ('affiliations', 'tags'):
-        kwargs['widget'] = widgets.FilteredSelectMultiple(db_field.verbose_name,
-                                                          (db_field.name in self.filter_vertical))
-      rv = super(LibraryOptions, self).formfield_for_dbfield(db_field, **kwargs)
-      return rv
+        # Override Field type
+        if db_field.name in ('affiliations', 'tags'):
+            kwargs['widget'] = widgets.FilteredSelectMultiple(
+                db_field.verbose_name,
+                (db_field.name in self.filter_vertical)
+            )
+        field = super(LibraryOptions, self).formfield_for_dbfield(db_field,
+                                                                  **kwargs)
+        # Override field attributes
+        if db_field.name == "bioanalyzer_summary":
+            print field.widget.attrs.items()
+            field.widget.attrs["rows"] = "5"
+        return field
 
 class SpeciesOptions(admin.ModelAdmin):
     fieldsets = (
diff --git a/htsworkflow/frontend/samples/models.py b/htsworkflow/frontend/samples/models.py
index b6fb4eb..0a65651 100644
--- a/htsworkflow/frontend/samples/models.py
+++ b/htsworkflow/frontend/samples/models.py
@@ -177,6 +177,12 @@ class Library(models.Model):
   gel_cut_size = models.IntegerField(default=225, blank=True, null=True)
   insert_size = models.IntegerField(blank=True, null=True)
   notes = models.TextField(blank=True)
+
+  bioanalyzer_summary = models.TextField(blank=True,default="")
+  bioanalyzer_concentration = models.DecimalField(max_digits=5, 
+                                decimal_places=2, blank=True, null=True,
+                                help_text=u"(ng/\u00b5l)")
+  bioanalyzer_image_url = models.URLField(blank=True,default="")
   
   def __unicode__(self):
     return u'#%s: %s' % (self.id, self.library_name)