Got show_trait running again for MrnaAssay traits

4 files changed, 80 insertions, 88 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 14e4055e..9f0f3fac 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -77,6 +77,9 @@ class DatasetGroup(object):
             self.name = "BXD"
         
         self.incparentsf1 = False
+        self.f1list = None
+        self.parlist = None
+        self.allsamples = None
             
             
     #def read_genotype(self):
@@ -95,39 +98,39 @@ class DatasetGroup(object):
         #genotype_1 is Dataset Object without parents and f1
         #genotype_2 is Dataset Object with parents and f1 (not for intercross)
 
-        self.genotype_1 = reaper.Dataset()
+        genotype_1 = reaper.Dataset()
         
         # reaper barfs on unicode filenames, so here we ensure it's a string
         full_filename = str(os.path.join(webqtlConfig.GENODIR, self.name + '.geno'))
-        self.genotype_1.read(full_filename)
+        genotype_1.read(full_filename)
 
         print("Got to after read")
 
         try:
             # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py;
-            _f1, _f12, _mat, _pat = webqtlUtil.ParInfo[self.name]
+            f1, f12, maternal, paternal = webqtlUtil.ParInfo[self.name]
         except KeyError:
-            _f1 = _f12 = _mat = _pat = None
+            f1 = f12 = maternal = paternal = None
 
-        self.genotype_2 = self.genotype_1
-        if self.genotype_1.type == "group" and _mat and _pat:
-            self.genotype_2 = self.genotype_1.add(Mat=_mat, Pat=_pat)       #, F1=_f1)
+
+        if genotype_1.type == "group" and maternal and paternal:
+            genotype_2 = genotype_1.add(Mat=maternal, Pat=paternal)       #, F1=_f1)
+        else:
+            genotype_2 = genotype_1
 
         #determine default genotype object
-        if self.incparentsf1 and self.genotype_1.type != "intercross":
-            self.genotype = self.genotype_2
+        if self.incparentsf1 and genotype_1.type != "intercross":
+            self.genotype = genotype_2
         else:
             self.incparentsf1 = 0
-            self.genotype = self.genotype_1
+            self.genotype = genotype_1
 
         self.samplelist = list(self.genotype.prgy)
-        self.f1list = []
-        self.parlist = []
 
-        if _f1 and _f12:
-            self.f1list = [_f1, _f12]
-        if _mat and _pat:
-            self.parlist = [_mat, _pat]
+        if f1 and f12:
+            self.f1list = [f1, f12]
+        if maternal and paternal:
+            self.parlist = [maternal, paternal]
 
 
 class DataSet(object):
@@ -169,8 +172,6 @@ class DataSet(object):
     #        self.get_group()
     #        
     #    return self._group
-    
-
 
 
 
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 53bb24fb..0c752617 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -1,5 +1,7 @@
 from __future__ import absolute_import, print_function, division
 
+from flask import Flask, g
+
 from base import webqtlCaseData
 from utility import webqtlUtil, Plot, Bunch
 from base.webqtlTrait import GeneralTrait
@@ -8,22 +10,19 @@ from pprint import pformat as pf
 
 class SampleList(object):
     def __init__(self,
-                 cursor,
                  dataset,
-                 variance_data_page,
                  sample_names,
                  this_trait,
                  sample_group_type,
                  header):
-        
-        self.cursor = cursor
+
         self.dataset = dataset
         self.this_trait = this_trait
         self.sample_group_type = sample_group_type    # primary or other
         self.header = header
 
         self.sample_list = [] # The actual list
-        
+
         self.get_attributes()
         
         print("camera: attributes are:", pf(self.attributes))
@@ -54,7 +53,7 @@ class SampleList(object):
                 sample.this_id = "Other_" + str(counter)
 
             #### For extra attribute columns; currently only used by several datasets - Zach
-            if self.this_trait and self.this_trait.db and self.this_trait.db.type == 'ProbeSet':
+            if self.this_trait and self.dataset and self.dataset.type == 'ProbeSet':
                 sample.extra_attributes = self.get_extra_attribute_values(sample_name)
                 print("sample.extra_attributes is", pf(sample.extra_attributes))
                 self.sample_list.append(sample)
@@ -88,27 +87,27 @@ class SampleList(object):
     def get_attributes(self):
         """Finds which extra attributes apply to this dataset"""
         
-        #ZS: Id and name values for this trait's extra attributes  
-        self.cursor.execute('''SELECT CaseAttribute.Id, CaseAttribute.Name
+        #ZS: Id and name values for this trait's extra attributes
+        case_attributes = g.db.execute('''SELECT CaseAttribute.Id, CaseAttribute.Name
                                         FROM CaseAttribute, CaseAttributeXRef
                                         WHERE CaseAttributeXRef.ProbeSetFreezeId = %s AND
                                             CaseAttribute.Id = CaseAttributeXRef.CaseAttributeId
                                                 group by CaseAttributeXRef.CaseAttributeId''',
-                                                (str(self.this_trait.db.id),))
+                                                (str(self.dataset.id),))
 
 
         self.attributes = {}
-        for key, value in self.cursor.fetchall():
+        for key, value in case_attributes.fetchall():
             print("radish: %s - %s" % (key, value))
             self.attributes[key] = Bunch()
             self.attributes[key].name = value
 
-            self.cursor.execute('''SELECT DISTINCT CaseAttributeXRef.Value
-                            FROM CaseAttribute, CaseAttributeXRef
-                            WHERE CaseAttribute.Name = %s AND
-                                CaseAttributeXRef.CaseAttributeId = CaseAttribute.Id''', (value,))            
+            attribute_values = g.db.execute('''SELECT DISTINCT CaseAttributeXRef.Value
+                                               FROM CaseAttribute, CaseAttributeXRef
+                                               WHERE CaseAttribute.Name = %s AND
+                                CaseAttributeXRef.CaseAttributeId = CaseAttribute.Id''', (value,))
 
-            self.attributes[key].distinct_values = [item[0] for item in self.cursor.fetchall()]
+            self.attributes[key].distinct_values = [item[0] for item in attribute_values.fetchall()]
             self.attributes[key].distinct_values.sort(key=natural_sort_key)
 
 
@@ -119,27 +118,28 @@ class SampleList(object):
         if self.attributes:
 
             #ZS: Get StrainId value for the next query
-            self.cursor.execute("""SELECT Strain.Id
+            result = g.db.execute("""SELECT Strain.Id
                                         FROM Strain, StrainXRef, InbredSet
                                         WHERE Strain.Name = %s and
                                             StrainXRef.StrainId = Strain.Id and
                                             InbredSet.Id = StrainXRef.InbredSetId and
-                                            InbredSet.Name = %s""", (sample_name, self.dataset.group.name))
+                                            InbredSet.Name = %s""", (sample_name,
+                                                                     self.dataset.group.name))
 
-            sample_id = self.cursor.fetchone()[0]
+            sample_id = result.fetchone().Id
 
             for attribute in self.attributes:
 
                 #ZS: Add extra case attribute values (if any)
-                self.cursor.execute("""SELECT Value
+                result = g.db.execute("""SELECT Value
                                                 FROM CaseAttributeXRef
-                                        WHERE ProbeSetFreezeId = '%s' AND
-                                                StrainId = '%s' AND
-                                                CaseAttributeId = '%s'
-                                        group by CaseAttributeXRef.CaseAttributeId""" % (
+                                        WHERE ProbeSetFreezeId = %s AND
+                                                StrainId = %s AND
+                                                CaseAttributeId = %s
+                                        group by CaseAttributeXRef.CaseAttributeId""", (
                                             self.this_trait.db.id, sample_id, str(attribute)))
 
-                attribute_value = self.cursor.fetchone()[0] #Trait-specific attributes, if any
+                attribute_value = result.fetchone().Value #Trait-specific attributes, if any
 
                 #ZS: If it's an int, turn it into one for sorting
                 #(for example, 101 would be lower than 80 if they're strings instead of ints)
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 73b438d0..cd61d70c 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -55,7 +55,7 @@ class ShowTrait(templatePage):
         #fd.readGenotype()
 
         if not self.dataset.group.genotype:
-            self.read_data(incf1=1)
+            self.read_data(include_f1=True)  #incf1=1)
 
         ## determine data editing page format
         #variance_data_page = 0
@@ -158,15 +158,15 @@ class ShowTrait(templatePage):
         #    print("Calling dispBasicStatistics")
         #    self.dispBasicStatistics(fd, this_trait)
 
-        self.build_correlation_tools(args, this_trait)
+        self.build_correlation_tools(this_trait)
 
-        self.make_sample_lists(args, variance_data_page, this_trait)
+        self.make_sample_lists(this_trait)
 
-        if args['allsamplelist']:
-            hddn['allsamplelist'] = string.join(args['allsamplelist'], ' ')
+        if self.dataset.group.allsamples:
+            hddn['allsamples'] = string.join(self.dataset.group.allsamples, ' ')
 
-        if args['varianceDispName'] != 'Variance':
-            hddn['isSE'] = "yes"
+        #if args['varianceDispName'] != 'Variance':
+        #    hddn['isSE'] = "yes"
 
         # We'll need access to this_trait and hddn in the Jinja2 Template, so we put it inside self
         self.this_trait = this_trait
@@ -215,22 +215,20 @@ class ShowTrait(templatePage):
         return this_trait
 
 
-    def read_data(self):
+    def read_data(self, include_f1=False):
         '''read user input data or from trait data and analysis form'''
 
-        if incf1 == None:
-            incf1 = []
+        #if incf1 == None:
+        #    incf1 = []
 
         if not self.genotype:
             self.dataset.read_genotype_file()
         if not samplelist:
-            if incf1:
+            if include_f1:
                 samplelist = self.f1list + self.samplelist
             else:
                 samplelist = self.samplelist
 
-        #print("before traitfiledata self.traitfile is:", pf(self.traitfile))
-
         traitfiledata = getattr(self, "traitfile", None)
         traitpastedata = getattr(self, "traitpaste", None)
         variancefiledata = getattr(self, "variancefile", None)
@@ -1174,39 +1172,34 @@ class ShowTrait(templatePage):
             dataset_menu = []
             print("[tape4] webqtlConfig.PUBLICTHRESH:", webqtlConfig.PUBLICTHRESH)
             print("[tape4] type webqtlConfig.PUBLICTHRESH:", type(webqtlConfig.PUBLICTHRESH))
-            query = 
-            self.cursor.execute('''SELECT PublishFreeze.FullName,PublishFreeze.Name FROM
+            results = g.db.execute("""SELECT PublishFreeze.FullName,PublishFreeze.Name FROM
                     PublishFreeze,InbredSet WHERE PublishFreeze.InbredSetId = InbredSet.Id
-                    and InbredSet.Name = %s and PublishFreeze.public > %s''',
+                    and InbredSet.Name = %s and PublishFreeze.public > %s""",
                     (this_group, webqtlConfig.PUBLICTHRESH))
-            for item in self.cursor.fetchall():
+            for item in results.fetchall():
                 dataset_menu.append(dict(tissue=None,
                                          datasets=[item]))
 
-            self.cursor.execute('''SELECT GenoFreeze.FullName,GenoFreeze.Name FROM GenoFreeze,
+            results = g.db.execute("""SELECT GenoFreeze.FullName,GenoFreeze.Name FROM GenoFreeze,
                     InbredSet WHERE GenoFreeze.InbredSetId = InbredSet.Id and InbredSet.Name =
-                    %s and GenoFreeze.public > %s''',
+                    %s and GenoFreeze.public > %s""",
                     (this_group, webqtlConfig.PUBLICTHRESH))
-            for item in self.cursor.fetchall():
+            for item in results.fetchall():
                 dataset_menu.append(dict(tissue=None,
                                     datasets=[item]))
 
             #03/09/2009: Xiaodong changed the SQL query to order by Name as requested by Rob.
-            self.cursor.execute('SELECT Id, Name FROM Tissue order by Name')
-            for item in self.cursor.fetchall():
+            tissues = g.db.execute("SELECT Id, Name FROM Tissue order by Name")
+            for item in tissues.fetchall():
                 tissue_id, tissue_name = item
                 #databaseMenuSub = HT.Optgroup(label = '%s ------' % tissue_name)
                 #dataset_sub_menu = []
-                print("phun9")
-                self.cursor.execute('''SELECT ProbeSetFreeze.FullName,ProbeSetFreeze.Name FROM ProbeSetFreeze, ProbeFreeze,
+                data_sets = g.db.execute('''SELECT ProbeSetFreeze.FullName,ProbeSetFreeze.Name FROM ProbeSetFreeze, ProbeFreeze,
                 InbredSet WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeFreeze.TissueId = %s and
                 ProbeSetFreeze.public > %s and ProbeFreeze.InbredSetId = InbredSet.Id and InbredSet.Name like %s
                 order by ProbeSetFreeze.CreateTime desc, ProbeSetFreeze.AvgId ''',
                 (tissue_id, webqtlConfig.PUBLICTHRESH, "%" + this_group + "%"))
-                print("phun8")
-                dataset_sub_menu = [item for item in self.cursor.fetchall() if item]
-                #for item2 in self.cursor.fetchall():
-                #    dataset_sub_menu.append(item2)
+                dataset_sub_menu = [item for item in data_sets.fetchall() if item]
                 if dataset_sub_menu:
                     dataset_menu.append(dict(tissue=tissue_name,
                                         datasets=dataset_sub_menu))
@@ -1612,11 +1605,13 @@ class ShowTrait(templatePage):
         title4Body.append(submitTable)
 
 
-    def make_sample_lists(self, fd, variance_data_page, this_trait):
-        if args['parlist']:
-            all_samples_ordered = args['parlist'] + args['f1list'] + args['samplelist']
+    def make_sample_lists(self, this_trait):
+        if self.dataset.group.parlist:
+            all_samples_ordered = (self.dataset.group.parlist +
+                                   self.dataset.group.f1list +
+                                   self.dataset.group.samplelist)
         else:
-            all_samples_ordered = args['f1list'] + args['samplelist']
+            all_samples_ordered = self.dataset.group.f1list + self.dataset.group.samplelist
 
         this_trait_samples = set(this_trait.data.keys())
 
@@ -1624,9 +1619,7 @@ class ShowTrait(templatePage):
 
         print("-*- primary_samplelist is:", pf(primary_sample_names))
 
-        primary_samples = SampleList(self.cursor,
-                                        args=args,
-                                        variance_data_page=variance_data_page,
+        primary_samples = SampleList(dataset = self.dataset,
                                         sample_names=primary_sample_names,
                                         this_trait=this_trait,
                                         sample_group_type='primary',
@@ -1640,18 +1633,16 @@ class ShowTrait(templatePage):
                 other_sample_names.append(sample)
 
         if other_sample_names:
-            par_f1_samples = fd.parlist + fd.f1list
+            parent_f1_samples = self.dataset.group.parlist + self.dataset.group.f1list
 
             other_sample_names.sort() #Sort other samples
-            other_sample_names = par_f1_samples + other_sample_names
+            other_sample_names = parent_f1_samples + other_sample_names
 
-            other_samples = SampleList(self.cursor,
-                                            fd=fd,
-                                            variance_data_page=variance_data_page,
-                                            sample_names=other_sample_names,
-                                            this_trait=this_trait,
-                                            sample_group_type='other',
-                                            header="Non-%s" % (fd.group))
+            other_samples = SampleList(dataset=self.dataset,
+                                        sample_names=other_sample_names,
+                                        this_trait=this_trait,
+                                        sample_group_type='other',
+                                        header="Non-%s" % (self.dataset.group.name))
 
             self.sample_groups = (primary_samples, other_samples)
         else:
@@ -1661,4 +1652,4 @@ class ShowTrait(templatePage):
         #if (other_sample_names or (fd.f1list and this_trait.data.has_key(fd.f1list[0]))
         #        or (fd.f1list and this_trait.data.has_key(fd.f1list[1]))):
         #    print("hjs")
-        fd.allsamplelist = all_samples_ordered
+        self.dataset.group.allsamples = all_samples_ordered
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index b5c1d6ac..163be69c 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -19,7 +19,7 @@
         <div class="container">
             <div class="page-header">
                 <h1>{{ this_trait.species.capitalize() }} -
-                    {{ fd.RISet }} -
+                    {{ dataset.group.name }} -
                     {{ this_trait.symbol }}
                 </h1>
             </div>