aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
Diffstat
-rwxr-xr-xwqflask/base/webqtlCaseData.py4
-rwxr-xr-xwqflask/wqflask/show_trait/DataEditingPage.py77
-rw-r--r--wqflask/wqflask/templates/trait_data_and_analysis.html14
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">&nbsp;</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 %}
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 23:26:01 +0000