diff options
| -rwxr-xr-x | wqflask/base/webqtlCaseData.py | 4 | ||||
| -rwxr-xr-x | wqflask/wqflask/show_trait/DataEditingPage.py | 77 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/trait_data_and_analysis.html | 14 |
3 files changed, 46 insertions, 49 deletions
diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py index c805a95c..6352a083 100755 --- a/wqflask/base/webqtlCaseData.py +++ b/wqflask/base/webqtlCaseData.py @@ -36,6 +36,7 @@ class webqtlCaseData(object): self.value = value # Trait Value self.variance = variance # Trait Variance self.num_cases = num_cases # Number of individuals/cases + self.extra_attributes = None self.this_id = None # Set a sane default (can't be just "id" cause that's a reserved word) self.outlier = None # Not set to True/False until later @@ -70,5 +71,4 @@ class webqtlCaseData(object): return "%2.3f" % self.variance else: return "x" - - + diff --git a/wqflask/wqflask/show_trait/DataEditingPage.py b/wqflask/wqflask/show_trait/DataEditingPage.py index 24a37926..0f21a958 100755 --- a/wqflask/wqflask/show_trait/DataEditingPage.py +++ b/wqflask/wqflask/show_trait/DataEditingPage.py @@ -3,7 +3,6 @@ from __future__ import absolute_import, print_function, division import string import os import cPickle -from collections import OrderedDict #import pyXLWriter as xl import yaml @@ -1563,11 +1562,14 @@ class SampleList(object): else: sample.this_id = "Other_" + str(counter) - #### For extra attribute columns; currently only used by two human datasets - Zach + #### 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': - self.get_extra_attribute_values(sample_name) + sample.extra_attributes = self.get_extra_attribute_values(sample_name) + print("sample.extra_attributes is", pf(sample.extra_attributes)) self.sample_list.append(sample) + print("self.attributes is", pf(self.attributes)) + self.do_outliers() #do_outliers(the_samples) print("*the_samples are [%i]: %s" % (len(self.sample_list), pf(self.sample_list))) @@ -1603,8 +1605,6 @@ class SampleList(object): group by CaseAttributeXRef.CaseAttributeId''', (str(self.this_trait.db.id),)) - #self.attributes = {key, value in self.cursor.fetchall()} - #self.attributes = OrderedDict(self.attributes.iteritems()) self.attributes = {} for key, value in self.cursor.fetchall(): @@ -1621,51 +1621,36 @@ class SampleList(object): self.attributes[key].distinct_values.sort(key=natural_sort_key) - #try: - # # exclude_menu = HT.Select(name="exclude_menu") # dropdown_menus = [] #ZS: list of dropdown menus with the distinct values of each attribute (contained in DIVs so the style parameter can be edited and they can be hidden) - # - # for attribute in self.cursor.fetchall(): - # attribute_ids.append(attribute[0]) - # attribute_names.append(attribute[1]) # for this_attr_name in attribute_names: # exclude_menu.append((this_attr_name.capitalize(), this_attr_name)) - # self.cursor.execute("""SELECT DISTINCT CaseAttributeXRef.Value - # FROM CaseAttribute, CaseAttributeXRef - # WHERE CaseAttribute.Name = '%s' AND - # CaseAttributeXRef.CaseAttributeId = CaseAttribute.Id""" % (this_attr_name)) - # try: - # distinct_values = self.cursor.fetchall() - # attr_value_menu_div = HT.Div(style="display:none;", Class="attribute_values") #container used to show/hide dropdown menus - # attr_value_menu = HT.Select(name=this_attr_name) - # attr_value_menu.append(("None", "show_all")) - # for value in distinct_values: - # attr_value_menu.append((str(value[0]), value[0])) - # attr_value_menu_div.append(attr_value_menu) - # dropdown_menus.append(attr_value_menu_div) - # except: - # pass - #except: - # pass + # attr_value_menu_div = HT.Div(style="display:none;", Class="attribute_values") #container used to show/hide dropdown menus + # attr_value_menu = HT.Select(name=this_attr_name) + # attr_value_menu.append(("None", "show_all")) + # for value in distinct_values: + # attr_value_menu.append((str(value[0]), value[0])) + # attr_value_menu_div.append(attr_value_menu) + # dropdown_menus.append(attr_value_menu_div) def get_extra_attribute_values(self, sample_name): - if len(self.attributes) > 0: + attribute_values = {} + + if self.attributes: #ZS: Get StrainId value for the next query self.cursor.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.fd.RISet)) + 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.fd.RISet)) sample_id = self.cursor.fetchone()[0] - attr_counter = 1 # This is needed so the javascript can know which attribute type to associate this value with for the exported excel sheet (each attribute type being a column). - for attribute_id in self.attributes.keys(): + for attribute in self.attributes: #ZS: Add extra case attribute values (if any) self.cursor.execute("""SELECT Value @@ -1673,21 +1658,21 @@ class SampleList(object): WHERE ProbeSetFreezeId = '%s' AND StrainId = '%s' AND CaseAttributeId = '%s' - group by CaseAttributeXRef.CaseAttributeId""" % (self.this_trait.db.id, sample_id, str(attribute_id))) + group by CaseAttributeXRef.CaseAttributeId""" % ( + self.this_trait.db.id, sample_id, str(attribute))) - attributeValue = self.cursor.fetchone()[0] #Trait-specific attributes, if any + attribute_value = self.cursor.fetchone()[0] #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) + #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) try: - attributeValue = int(attributeValue) + attribute_value = int(attribute_value) except ValueError: pass - - #span_Id = samples+"_attribute"+str(attr_counter)+"_sample"+str(i+1) - #attr_container = HT.Span(attributeValue, Id=span_Id) - #attr_className = str(attributeValue) + " " + className - #table_row.append(HT.TD(attr_container, align='right', Class=attr_className)) - attr_counter += 1 + + attribute_values[self.attributes[attribute].name] = attribute_value + + return attribute_values def natural_sort_key(x): diff --git a/wqflask/wqflask/templates/trait_data_and_analysis.html b/wqflask/wqflask/templates/trait_data_and_analysis.html index 6a5a4a80..f227d780 100644 --- a/wqflask/wqflask/templates/trait_data_and_analysis.html +++ b/wqflask/wqflask/templates/trait_data_and_analysis.html @@ -1263,6 +1263,10 @@ <th class="fs13 fwb ff1 b1 cw cbrb" width="20"> </th> <th class="fs13 fwb ff1 b1 cw cbrb" align="right" width="80">SE</th> + + {% for attribute in sample_type.attributes|sort() %} + <th class="fs13 fwb ff1 b1 cw cbrb" align="right" width="60">{{ sample_type.attributes[attribute].name }}</th> + {% endfor %} </tr> {% for sample in sample_type.sample_list %} @@ -1291,7 +1295,15 @@ <td class="fs13 b1 c222" align="right" width="80"> <input type="text" name=""{{ 'V' + sample.name}}" class="fs13 b1 c222 valueField edit_sample_se" value="{{ sample.display_variance }}" - size="8" maxlength="8" style="text-align:right"></td> + size="8" maxlength="8" style="text-align:right"> + </td> + + {# Loop through each attribute type and input value #} + {% for attribute in sample_type.attributes|sort() %} + <td class="fd13 b1 c222" align="right" width="80"> + {{ sample.extra_attributes[sample_type.attributes[attribute].name] }} + </td> + {% endfor %} </tr> {% endfor %} |