Implement experiment type as a seperate table.

closes [ticket:107]
also initialize the experiment type table with the conversion script

diff --git a/docs/conv_caltech_v0.1_to_htsw.py b/docs/conv_caltech_v0.1_to_htsw.py
index 15e6d84cd0a8cf8282db3e27c65c8da7e40b482c..2adb0364cf964bdb002d353997c83548f3ed296d 100644 (file)
--- a/docs/conv_caltech_v0.1_to_htsw.py
+++ b/docs/conv_caltech_v0.1_to_htsw.py
@@ -97,6 +97,19 @@ def main(cmdline=None):
     "notes" text NOT NULL);''')
     c.execute('''insert into samples_condition (condition_name,notes) values("Unknown","Unknown");''')
 
+    # create samples.experiment type
+    c.execute('''CREATE TABLE "samples_experimenttype" (
+          "id" integer NOT NULL PRIMARY KEY,
+          "name" varchar(50) NOT NULL UNIQUE);''')
+    for et in [ ('Unknown',),
+                ('ChIP-seq',),
+                ('Sheared',),
+                ('RNA-seq',),
+                ('Methyl-seq',),
+                ('DIP-seq',),
+                ('De Novo',)]:
+        c.execute('insert into samples_experimenttype (name) values (?)', et)
+
     # create samples.library
     c.execute('''CREATE TABLE "samples_library" (
     "id" integer NOT NULL PRIMARY KEY,
@@ -107,7 +120,7 @@ def main(cmdline=None):
     "condition_id" integer NOT NULL REFERENCES "samples_condition" ("id"),
     "antibody_id" integer NULL REFERENCES "samples_antibody" ("id"),
     "replicate" smallint unsigned NOT NULL,
-    "experiment_type" varchar(50) NOT NULL,
+    "experiment_type_id" NOT NULL REFERENCES "samples_experimenttype" ("id"),
     "creation_date" date NULL,
     "made_for" varchar(50) NOT NULL,
     "made_by" varchar(50) NOT NULL,
@@ -119,17 +132,19 @@ def main(cmdline=None):
     "avg_lib_size" integer NULL,
     "notes" text NOT NULL);''')
     c.execute('''INSERT INTO samples_library 
-      (id,library_id,library_name,library_species_id, experiment_type,
+      (id,library_id,library_name,library_species_id, experiment_type_id,
        cell_line_id,condition_id,replicate,made_by,creation_date,
        made_for,stopping_point,amplified_from_sample_id,
        undiluted_concentration,ten_nM_dilution,successful_pM,
        avg_lib_size,notes) 
-select library_id,library_id,library_name,library_species_id,"unknown",
+select library_id,library_id,library_name,library_species_id, 1,
        1,           1,           1,        made_by,creation_date,
        made_for,stopping_point,amplified_from_sample_id,
        undiluted_concentration,ten_nM_dilution,successful_pM,
        0,notes from fctracker_library;''');
-    c.execute('''update samples_library set experiment_type="RNA-seq" where library_id in (select library_id from fctracker_library where RNASeq = 1);''')
+    c.execute('select id from samples_experimenttype where name = "RNA-seq";')
+    rna_seq_id = list(c)[0]
+    c.execute('''update samples_library set experiment_type_id=?  where library_id in (select library_id from fctracker_library where RNASeq = 1);''', rna_seq_id)
     #c.execute('''drop table fctracker_library;''') 
     # add many to many tables
     c.execute('''CREATE TABLE "samples_library_affiliations" (

diff --git a/htsworkflow/frontend/samples/admin.py b/htsworkflow/frontend/samples/admin.py
index a8494f6e4928b41320979d0a96f9f1a8b5b9d710..5967e32974c04dfc6fcef3d823e6fa1b769394a6 100644 (file)
--- a/htsworkflow/frontend/samples/admin.py
+++ b/htsworkflow/frontend/samples/admin.py
@@ -1,4 +1,4 @@
-from htsworkflow.frontend.samples.models import Antibody, Cellline, Condition, Species, Affiliation, Library, Tag
+from htsworkflow.frontend.samples.models import Antibody, Cellline, Condition, ExperimentType, Species, Affiliation, Library, Tag
 from django.contrib import admin
 from django.utils.translation import ugettext_lazy as _
 
@@ -14,6 +14,11 @@ class CelllineOptions(admin.ModelAdmin):
       }),
      )
 
+class ExperimentTypeOptions(admin.ModelAdmin):
+  model = ExperimentType
+  #list_display = ('name',)
+  #fieldsets = ( (None, { 'fields': ('name',) }), )
+
 class LibraryOptions(admin.ModelAdmin):
     date_hierarchy = "creation_date"
     save_as = True
@@ -121,6 +126,7 @@ admin.site.register(Affiliation, AffiliationOptions)
 admin.site.register(Antibody, AntibodyOptions)
 admin.site.register(Cellline, CelllineOptions)
 admin.site.register(Condition, ConditionOptions)
+admin.site.register(ExperimentType, ExperimentTypeOptions)
 admin.site.register(Library, LibraryOptions)
 admin.site.register(Species, SpeciesOptions)
 admin.site.register(Tag, TagOptions)

diff --git a/htsworkflow/frontend/samples/models.py b/htsworkflow/frontend/samples/models.py
index 2845e81d93317031d2e263765c82200a231e5d63..9301d4f3eb788d5c1d3d63d493a671059dea38e3 100644 (file)
--- a/htsworkflow/frontend/samples/models.py
+++ b/htsworkflow/frontend/samples/models.py
@@ -59,6 +59,12 @@ class Condition(models.Model):
     class Meta:
         ordering = ["condition_name"]
 
+class ExperimentType(models.Model):
+  name = models.CharField(max_length=50, unique=True)
+
+  def __unicode__(self):
+    return unicode(self.name)
+
 class Tag(models.Model): 
   tag_name = models.CharField(max_length=100, db_index=True,blank=False,null=False) 
   TAG_CONTEXT = ( 
@@ -123,18 +129,7 @@ class Library(models.Model):
   # SQL to add column: alter table fctracker_library add column "replicate" smallint unsigned NULL;
   REPLICATE_NUM = ((1,1),(2,2),(3,3),(4,4))
   replicate =  models.PositiveSmallIntegerField(choices=REPLICATE_NUM,default=1) 
-
-  EXPERIMENT_TYPES = (
-      ('INPUT_RXLCh','INPUT_RXLCh'),
-      ('ChIP-seq', 'ChIP-seq'),
-      ('Sheared', 'Sheared'),
-      ('RNA-seq', 'RNA-seq'),
-      ('Methyl-seq', 'Methyl-seq'),
-      ('DIP-seq', 'DIP-seq'),
-    ) 
-  experiment_type = models.CharField(max_length=50, choices=EXPERIMENT_TYPES,
-                                     default='RNA-seq')
-  
+  experiment_type = models.ForeignKey(ExperimentType)
   creation_date = models.DateField(blank=True, null=True)
   made_for = models.CharField(max_length=50, blank=True, 
       verbose_name='ChIP/DNA/RNA Made By')