Change cluster_mac_id and seq_mac_id from text fields holding

the contents of a drop down box to be seperate tables whose table names
are a bit closer to the official illumina names.
clust_mac_id -> cluster_station
seq_mac_id -> sequencer

diff --git a/docs/conv_caltech_v0.1_to_htsw.py b/docs/conv_caltech_v0.1_to_htsw.py
index 10f4e35862d181a19bf9303e573b7932d91d625f..15e6d84cd0a8cf8282db3e27c65c8da7e40b482c 100644 (file)
--- a/docs/conv_caltech_v0.1_to_htsw.py
+++ b/docs/conv_caltech_v0.1_to_htsw.py
@@ -11,6 +11,15 @@ def main(cmdline=None):
     conn = sqlite3.connect(dest)
     c = conn.cursor()
     c.execute('drop table fctracker_elandresult');
+    c.execute('''CREATE TABLE "experiments_clusterstation" (
+      "id" integer NOT NULL PRIMARY KEY,
+      "name" varchar(50) NOT NULL UNIQUE);''')
+    c.execute('''INSERT INTO experiments_clusterstation (name) values ("station");''')
+    c.execute('''CREATE TABLE "experiments_sequencer" (
+      "id" integer NOT NULL PRIMARY KEY,
+      "name" varchar(50) NOT NULL UNIQUE);''')
+    c.execute('''INSERT INTO experiments_sequencer (name) values ("HWI-EAS229");''')
+
     c.execute('''CREATE TABLE "experiments_flowcell" (
     "id" integer NOT NULL PRIMARY KEY,
     "flowcell_id" varchar(20) NOT NULL UNIQUE,
@@ -42,8 +51,8 @@ def main(cmdline=None):
     "lane_6_cluster_estimate" integer NULL,
     "lane_7_cluster_estimate" integer NULL,
     "lane_8_cluster_estimate" integer NULL,
-    "cluster_mac_id" varchar(50) NOT NULL,
-    "seq_mac_id" varchar(50) NOT NULL,
+    "cluster_station_id" integer NOT NULL REFERENCES "experiments_clusterstation" ("id"),
+    "sequencer_id" integer NOT NULL REFERENCES "experiments_sequencer" ("id"),
     "notes" text NOT NULL
 );''')
     c.execute('''insert into experiments_flowcell 
@@ -56,7 +65,7 @@ def main(cmdline=None):
          lane_2_cluster_estimate, lane_3_cluster_estimate, 
          lane_4_cluster_estimate, lane_5_cluster_estimate,
          lane_6_cluster_estimate, lane_7_cluster_estimate, 
-         lane_8_cluster_estimate, cluster_mac_id, seq_mac_id,
+         lane_8_cluster_estimate, cluster_station_id, sequencer_id,
          notes) 
       select
          id, flowcell_id, run_date, advanced_run, paired_end, read_length,
@@ -68,7 +77,7 @@ def main(cmdline=None):
          lane_2_cluster_estimate, lane_3_cluster_estimate, 
          lane_4_cluster_estimate, lane_5_cluster_estimate,
          lane_6_cluster_estimate, lane_7_cluster_estimate, 
-         lane_8_cluster_estimate, "", "",
+         lane_8_cluster_estimate, 1, 1,
          notes from fctracker_flowcell;''')
     c.execute('''drop table fctracker_flowcell;''')
 

diff --git a/htsworkflow/frontend/experiments/admin.py b/htsworkflow/frontend/experiments/admin.py
index 50b8e3f6b442cedddd0c89d0c81966e091840048..7432727038845f8308444b199394af4a1c52bdc2 100644 (file)
--- a/htsworkflow/frontend/experiments/admin.py
+++ b/htsworkflow/frontend/experiments/admin.py
@@ -1,4 +1,4 @@
-from htsworkflow.frontend.experiments.models import FlowCell, DataRun
+from htsworkflow.frontend.experiments.models import FlowCell, DataRun, ClusterStation, Sequencer
 from django.contrib import admin
 from django.utils.translation import ugettext_lazy as _
 
@@ -29,8 +29,8 @@ class FlowCellOptions(admin.ModelAdmin):
     date_hierarchy = "run_date"
     save_on_top = True
     search_fields = ('flowcell_id',
-        'seq_mac_id',
-        'cluster_mac_id',
+        'sequencer',
+        'cluster_station',
         '=lane_1_library__library_id',
         '=lane_2_library__library_id',
         '=lane_3_library__library_id',
@@ -40,16 +40,25 @@ class FlowCellOptions(admin.ModelAdmin):
         '=lane_7_library__library_id',
         '=lane_8_library__library_id')
     list_display = ('flowcell_id','run_date','Lanes')
-    list_filter = ('seq_mac_id','cluster_mac_id')
+    list_filter = ('sequencer','cluster_station')
     fieldsets = (
         (None, {
-            'fields': ('run_date', ('flowcell_id','cluster_mac_id','seq_mac_id'), ('read_length', 'paired_end'),)
+            'fields': ('run_date', ('flowcell_id','cluster_station','sequencer'), ('read_length', 'paired_end'),)
         }),
         ('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'),)
         }),
     )
 
+class ClusterStationOptions(admin.ModelAdmin):
+    list_display = ('name', )
+    fieldsets = ( ( None, { 'fields': ( 'name', ) } ), )
+
+class SequencerOptions(admin.ModelAdmin):
+    list_display = ('name', )
+    fieldsets = ( ( None, { 'fields': ( 'name', ) } ), )
+
 admin.site.register(DataRun, DataRunOptions)
 admin.site.register(FlowCell, FlowCellOptions)
-
+admin.site.register(ClusterStation, ClusterStationOptions)
+admin.site.register(Sequencer, SequencerOptions)

diff --git a/htsworkflow/frontend/experiments/models.py b/htsworkflow/frontend/experiments/models.py
index 5fdd7b25ce052564dc3caa152fdc5f159489c69a..0ac386eea254b0e72cfe13a44b52b95bb3e0edb2 100755 (executable)
--- a/htsworkflow/frontend/experiments/models.py
+++ b/htsworkflow/frontend/experiments/models.py
@@ -2,6 +2,18 @@ from django.db import models
 from htsworkflow.frontend.samples.models import *
 from django.core.exceptions import ObjectDoesNotExist
 
+class ClusterStation(models.Model):
+  name = models.CharField(max_length=50, unique=True)
+
+  def __unicode__(self):
+    return unicode(self.name)
+
+class Sequencer(models.Model):
+  name = models.CharField(max_length=50, unique=True)
+
+  def __unicode__(self):
+    return unicode(self.name)
+
 class FlowCell(models.Model):
   
   flowcell_id = models.CharField(max_length=20, unique=True, db_index=True)
@@ -46,23 +58,10 @@ class FlowCell(models.Model):
   # lane_7_primer = models.ForeignKey(Primer,blank=True,null=True,related_name="lane_7_primer")
   # lane_8_primer = models.ForeignKey(Primer,blank=True,null=True,related_name="lane_8_primer")
 
-  #Machine Names
-  CLUSTER_MAC = (
-      ('M304','Cardinal'),
-      ('R349','R349'),
-      ('Tinkerbell','Tinkerbell'),
-      ('BitBit','BitBit'),
-    )
-  
-  SEQ_MAC = (
-      ('EAS149','Stanford'),
-      ('EAS46','EAS46'),
-      ('EAS45','Paris'),
-      ('Britney','Britney'),
-    )
-  
-  cluster_mac_id = models.CharField(max_length=50, choices=CLUSTER_MAC, default='BitBit')
-  seq_mac_id = models.CharField(max_length=50, choices=SEQ_MAC, verbose_name = 'Sequencer', default='Britney')
+  #cluster_mac_id = models.CharField(max_length=50, choices=CLUSTER_MAC, default='BitBit')
+  #seq_mac_id = models.CharField(max_length=50, choices=SEQ_MAC, verbose_name = 'Sequencer', default='Britney')
+  cluster_station = models.ForeignKey(ClusterStation)
+  sequencer = models.ForeignKey(Sequencer)
   
   notes = models.TextField(blank=True)
 
@@ -95,7 +94,6 @@ class FlowCell(models.Model):
   class Meta:
     ordering = ["-run_date"]
   
-
 ### -----------------------
 class DataRun(models.Model):
   ConfTemplate = "CONFIG PARAMS WILL BE GENERATED BY THE PIPELINE SCRIPT.\nYOU'LL BE ABLE TO EDIT AFTER IF NEEDED."