[project @ Massive change to DB structure; complete library table]

Primary change to the DB is the library table and supporting changes to the flowcell table.
They should both be properly linked now; you'll have to pull species information from the
linked library field. In addition, I added a common name to the Species table. Most interface
changes are via the meta and admin classes in each model, and are fairly straightforward. I
also added databrowse support; go to /databrowse instead of /admin to play with it.

diff --git a/elandifier/fctracker/models.py b/elandifier/fctracker/models.py
index 95ad1a5a8616c07e3649217d5202b9f1589d6eec..099edb10697611e1401dc4465f2811c67a5eb66a 100644 (file)
--- a/elandifier/fctracker/models.py
+++ b/elandifier/fctracker/models.py
@@ -3,67 +3,133 @@ from elandifier import settings
 
 # Create your models here.
 
-
-class Specie(models.Model):
-  
-  class Admin: pass
+class Species(models.Model):
   
-  scientific_name = models.CharField(maxlength=256, unique=True, db_index=True)
-
+  scientific_name = models.CharField(max_length=256, unique=True, db_index=True, core=True)
+  common_name = models.CharField(max_length=256, blank=True)
 
   def __str__(self):
-    return self.scientific_name
-
-#class BedFilePack(models.Model):
+    return '%s (%s)' % (self.scientific_name, self.common_name)
+  
+  class Meta:
+    verbose_name_plural = "species"
+    ordering = ["scientific_name"]
+  
+  class Admin:
+      fields = (
+        (None, {
+            'fields': (('scientific_name', 'common_name'),)
+        }),
+      )
 
 class Library(models.Model):
-  class Admin: pass
-  
-  library_id = models.IntegerField(unique=True, db_index=True)
-  library_name = models.CharField(maxlength=100, unique=True)
-  library_species = models.ForeignKey(Specie)
   
-  made_from_sample = models.ForeignKey('self', blank=True)
+  library_id = models.IntegerField(primary_key=True, db_index=True, core=True)
+  library_name = models.CharField(max_length=100, unique=True, core=True)
+  library_species = models.ForeignKey(Species, core=True)
+  RNAseq = models.BooleanField()
   
-  made_by = models.CharField(maxlength=50, blank=True)
+  made_by = models.CharField(max_length=50, blank=True, default="Lorian")
   creation_date = models.DateField(blank=True, null=True)
+  made_for = models.CharField(max_length=50, blank=True)
+  
+  PROTOCOL_END_POINTS = (
+      ('?', 'Unknown'),
+      ('Sample', 'Raw sample'),
+      ('Gel', 'Ran gel'),
+      ('1A', 'Gel purification'),
+      ('2A', '2nd PCR'),
+      ('Progress', 'In progress'),
+    )
+  stopping_point = models.CharField(max_length=50, choices=PROTOCOL_END_POINTS)
+  amplified_from_sample = models.ForeignKey('self', blank=True, null=True)
+  
+  undiluted_concentration = models.DecimalField(max_digits=5, decimal_places=2, blank=True, null=True)
+  ten_nM_dilution = models.BooleanField()
+  successful_pM = models.IntegerField(blank=True, null=True)
+  
   notes = models.TextField(blank=True)
   
   def __str__(self):
-    return self.library_name
-
-
-class FlowCell(models.Model):
+    return '#%s: %s' % (self.library_id, self.library_name)
   
-  class Admin: pass
+  class Meta:
+    verbose_name_plural = "libraries"
+    ordering = ["-library_id"]
   
-  flowcell_id = models.CharField(maxlength=20, unique=True, db_index=True)
+  class Admin:
+    date_hierarchy = "creation_date"
+    save_as = True
+    save_on_top = True
+    search_fields = ['library_name']
+    list_display = ('library_id', 'library_name', 'made_for', 'creation_date', 'ten_nM_dilution', 'stopping_point', 'successful_pM')
+    list_display_links = ('library_id', 'library_name')
+    list_filter = ('stopping_point', 'ten_nM_dilution', 'library_species', 'made_for', 'made_by')
+    fields = (
+        (None, {
+            'fields': (('library_id', 'library_name'), ('library_species', 'RNAseq'),)
+        }),
+        ('Creation Information:', {
+            'fields' : (('made_for', 'made_by', 'creation_date'), ('stopping_point', 'amplified_from_sample'), ('undiluted_concentration', 'ten_nM_dilution', 'successful_pM'), 'notes',)
+        }),
+    )
+
+class FlowCell(models.Model):
   
-  run_date = models.DateTimeField()
+  flowcell_id = models.CharField(max_length=20, unique=True, db_index=True, core=True)
+  run_date = models.DateTimeField(core=True)
   
-  lane1_sample = models.CharField(maxlength=500)
-  lane1_species = models.ForeignKey(Specie, related_name="lane1_species")
-  lane2_sample = models.CharField(maxlength=500)
-  lane2_species = models.ForeignKey(Specie, related_name="lane2_species")
-  lane3_sample = models.CharField(maxlength=500)
-  lane3_species = models.ForeignKey(Specie, related_name="lane3_species")
-  lane4_sample = models.CharField(maxlength=500)
-  lane4_species = models.ForeignKey(Specie, related_name="lane4_species")
+  lane_1_library = models.ForeignKey(Library, related_name="lane_1_library")
+  lane_2_library = models.ForeignKey(Library, related_name="lane_2_library")
+  lane_3_library = models.ForeignKey(Library, related_name="lane_3_library")
+  lane_4_library = models.ForeignKey(Library, related_name="lane_4_library")
+  lane_5_library = models.ForeignKey(Library, related_name="lane_5_library")
+  lane_6_library = models.ForeignKey(Library, related_name="lane_6_library")
+  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.IntegerField(default=4)
+  lane_2_pM = models.IntegerField(default=4)
+  lane_3_pM = models.IntegerField(default=4)
+  lane_4_pM = models.IntegerField(default=4)
+  lane_5_pM = models.IntegerField(default=4)
+  lane_6_pM = models.IntegerField(default=4)
+  lane_7_pM = models.IntegerField(default=4)
+  lane_8_pM = models.IntegerField(default=4)
   
-  lane5_sample = models.CharField(maxlength=500)
-  lane5_species = models.ForeignKey(Specie, related_name="lane5_species")
-  lane6_sample = models.CharField(maxlength=500)
-  lane6_species = models.ForeignKey(Specie, related_name="lane6_species")
-  lane7_sample = models.CharField(maxlength=500)
-  lane7_species = models.ForeignKey(Specie, related_name="lane7_species")
-  lane8_sample = models.CharField(maxlength=500)
-  lane8_species = models.ForeignKey(Specie, related_name="lane8_species")
+  lane_1_cluster_estimate = models.IntegerField(blank=True, null=True)
+  lane_2_cluster_estimate = models.IntegerField(blank=True, null=True)
+  lane_3_cluster_estimate = models.IntegerField(blank=True, null=True)
+  lane_4_cluster_estimate = models.IntegerField(blank=True, null=True)
+  lane_5_cluster_estimate = models.IntegerField(blank=True, null=True)
+  lane_6_cluster_estimate = models.IntegerField(blank=True, null=True)
+  lane_7_cluster_estimate = models.IntegerField(blank=True, null=True)
+  lane_8_cluster_estimate = models.IntegerField(blank=True, null=True)
   
   notes = models.TextField(blank=True)
 
   def __str__(self):
-    return self.flowcell_id
-
+    return '%s (%s)' % (self.flowcell_id, self.run_date) 
+  
+  class Meta:
+    ordering = ["run_date"]
+  
+  class Admin:
+    date_hierarchy = "run_date"
+    save_on_top = True
+    search_fields = ['lane_1_library', 'lane_2_library', 'lane_3_library', 'lane_4_library', 'lane_5_library', 'lane_6_library', 'lane_7_library', 'lane_8_library']
+    list_display = ('flowcell_id', 'run_date', 'lane_1_library', 'lane_2_library', 'lane_3_library', 'lane_4_library', 'lane_5_library', 'lane_6_library', 'lane_7_library', 'lane_8_library')
+    fields = (
+        (None, {
+            'fields': ('run_date', 'flowcell_id',)
+        }),
+        ('Lanes:', {
+            'fields' : (('lane_1_library', 'lane_1_pM', 'lane_1_cluster_estimate'), ('lane_2_library', 'lane_2_pM', 'lane_2_cluster_estimate'), ('lane_3_library', 'lane_3_pM', 'lane_3_cluster_estimate'), ('lane_4_library', 'lane_4_pM', 'lane_4_cluster_estimate'), ('lane_5_library', 'lane_5_pM', 'lane_5_cluster_estimate'), ('lane_6_library', 'lane_6_pM', 'lane_6_cluster_estimate'), ('lane_7_library', 'lane_7_pM', 'lane_7_cluster_estimate'), ('lane_8_library', 'lane_8_pM', 'lane_8_cluster_estimate'),)
+        }),
+       (None, {
+           'fields' : ('notes',)
+       }),
+    )
 
 class ElandResult(models.Model):
   

diff --git a/elandifier/settings.py b/elandifier/settings.py
index 860699a835e7d4b1d71fb75ee1fd8954787f3abe..778dae9a463203464c132beafeee0cc280c83edf 100644 (file)
--- a/elandifier/settings.py
+++ b/elandifier/settings.py
@@ -12,7 +12,7 @@ ADMINS = (
 MANAGERS = ADMINS
 
 DATABASE_ENGINE = 'sqlite3'           # 'postgresql_psycopg2', 'postgresql', 'mysql', 'sqlite3' or 'ado_mssql'.
-DATABASE_NAME = '/home/king/proj/solexa/elandifier/elandifier.db'             # Or path to database file if using sqlite3.
+DATABASE_NAME = '/home/lorian/Djangoproject/sequencer/elandifier/elandifier.db'             # Or path to database file if using sqlite3.
 DATABASE_USER = ''             # Not used with sqlite3.
 DATABASE_PASSWORD = ''         # Not used with sqlite3.
 DATABASE_HOST = ''             # Set to empty string for localhost. Not used with sqlite3.
@@ -82,7 +82,8 @@ INSTALLED_APPS = (
     'django.contrib.sessions',
     'django.contrib.sites',
     'elandifier.eland_config',
-    'elandifier.fctracker'
+    'elandifier.fctracker',
+    'django.contrib.databrowse',
 )
 
 # Project specific settings

diff --git a/elandifier/urls.py b/elandifier/urls.py
index 6e8b3b6093f81246fd89978634536c7614d6dd64..12676407715b8bffce72293dfe3e59a25ff5be50 100644 (file)
--- a/elandifier/urls.py
+++ b/elandifier/urls.py
@@ -1,9 +1,16 @@
 from django.conf.urls.defaults import *
 
+# Databrowser:
+from django.contrib import databrowse
+from fctracker.models import Library, FlowCell
+databrowse.site.register(Library)
+databrowse.site.register(FlowCell)
+
 urlpatterns = patterns('',
-    # Example:
+    # Base:
     (r'^elandifier/', include('elandifier.eland_config.urls')),
-
-    # Uncomment this for admin:
+    # Admin:
      (r'^admin/', include('django.contrib.admin.urls')),
+    # Databrowser:
+     (r'^databrowse/(.*)', databrowse.site.root),
 )