diff options
| -rwxr-xr-x | wqflask/wqflask/show_trait/DataEditingPage.py | 171 | ||||
| -rw-r--r-- | wqflask/wqflask/show_trait/SampleList.py | 181 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/trait_data_and_analysis.html | 5 |
3 files changed, 187 insertions, 170 deletions
diff --git a/wqflask/wqflask/show_trait/DataEditingPage.py b/wqflask/wqflask/show_trait/DataEditingPage.py index 0f21a958..92d0feaf 100755 --- a/wqflask/wqflask/show_trait/DataEditingPage.py +++ b/wqflask/wqflask/show_trait/DataEditingPage.py @@ -5,12 +5,13 @@ import os import cPickle #import pyXLWriter as xl -import yaml +from collections import OrderedDict from htmlgen import HTMLgen2 as HT from base import webqtlConfig from base import webqtlCaseData +from wqflask.show_trait.SampleList import SampleList from utility import webqtlUtil, Plot, Bunch from base.webqtlTrait import webqtlTrait from dbFunction import webqtlDatabaseFunction @@ -1514,171 +1515,3 @@ class DataEditingPage(templatePage): # or (fd.f1list and this_trait.data.has_key(fd.f1list[1]))): # print("hjs") fd.allsamplelist = all_samples_ordered - -class SampleList(object): - def __init__(self, - cursor, - fd, - variance_data_page, - sample_names, - this_trait, - sample_group_type, - header): - - self.cursor = cursor - self.fd = fd - 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.calc_attributes() - - print("camera: attributes are:", pf(self.attributes)) - - for counter, sample_name in enumerate(sample_names, 1): - sample_name = sample_name.replace("_2nd_", "") - - #ZS - If there's no value for the sample/strain, create the sample object (so samples with no value are still displayed in the table) - try: - sample = self.this_trait.data[sample_name] - except KeyError: - print("No sample %s, let's create it now" % sample_name) - sample = webqtlCaseData.webqtlCaseData(sample_name) - - #sampleNameAdd = '' - #if fd.RISet == 'AXBXA' and sampleName in ('AXB18/19/20','AXB13/14','BXA8/17'): - # sampleNameAdd = HT.Href(url='/mouseCross.html#AXB/BXA', text=HT.Sup('#'), Class='fs12', target="_blank") - sample.extra_info = {} - if self.fd.RISet == 'AXBXA' and sample_name in ('AXB18/19/20','AXB13/14','BXA8/17'): - sample.extra_info['url'] = "/mouseCross.html#AXB/BXA" - sample.extra_info['css_class'] = "fs12" - - print(" type of sample:", type(sample)) - - if sample_group_type == 'primary': - sample.this_id = "Primary_" + str(counter) - else: - 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': - 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))) - for sample in self.sample_list: - print("apple:", type(sample), sample) - #return the_samples - - def __repr__(self): - return "<SampleList> --> %s" % (pf(self.__dict__)) - - def do_outliers(self): - values = [sample.value for sample in self.sample_list if sample.value != None] - upper_bound, lower_bound = Plot.find_outliers(values) - - for sample in self.sample_list: - if sample.value: - if upper_bound and sample.value > upper_bound: - sample.outlier = True - elif lower_bound and sample.value < lower_bound: - sample.outlier = True - else: - sample.outlier = False - - - def calc_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 - FROM CaseAttribute, CaseAttributeXRef - WHERE CaseAttributeXRef.ProbeSetFreezeId = %s AND - CaseAttribute.Id = CaseAttributeXRef.CaseAttributeId - group by CaseAttributeXRef.CaseAttributeId''', - (str(self.this_trait.db.id),)) - - - self.attributes = {} - for key, value in self.cursor.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,)) - - self.attributes[key].distinct_values = [item[0] for item in self.cursor.fetchall()] - self.attributes[key].distinct_values.sort(key=natural_sort_key) - - - # 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 this_attr_name in attribute_names: - # exclude_menu.append((this_attr_name.capitalize(), this_attr_name)) - # 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): - - 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)) - - sample_id = self.cursor.fetchone()[0] - - for attribute in self.attributes: - - #ZS: Add extra case attribute values (if any) - self.cursor.execute("""SELECT Value - FROM CaseAttributeXRef - 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 - - #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: - attribute_value = int(attribute_value) - except ValueError: - pass - - attribute_values[self.attributes[attribute].name] = attribute_value - - return attribute_values - - -def natural_sort_key(x): - """Get expected results when using as a key for sort - ints or strings are sorted properly""" - try: - x = int(x) - except ValueError: - pass - return x
\ No newline at end of file diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py new file mode 100644 index 00000000..62bc63c3 --- /dev/null +++ b/wqflask/wqflask/show_trait/SampleList.py @@ -0,0 +1,181 @@ +from __future__ import absolute_import, print_function, division + +from base import webqtlCaseData +from utility import webqtlUtil, Plot, Bunch +from base.webqtlTrait import webqtlTrait + +from pprint import pformat as pf + +class SampleList(object): + def __init__(self, + cursor, + fd, + variance_data_page, + sample_names, + this_trait, + sample_group_type, + header): + + self.cursor = cursor + self.fd = fd + 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.calc_attributes() + + print("camera: attributes are:", pf(self.attributes)) + + for counter, sample_name in enumerate(sample_names, 1): + sample_name = sample_name.replace("_2nd_", "") + + #ZS - If there's no value for the sample/strain, create the sample object (so samples with no value are still displayed in the table) + try: + sample = self.this_trait.data[sample_name] + except KeyError: + print("No sample %s, let's create it now" % sample_name) + sample = webqtlCaseData.webqtlCaseData(sample_name) + + #sampleNameAdd = '' + #if fd.RISet == 'AXBXA' and sampleName in ('AXB18/19/20','AXB13/14','BXA8/17'): + # sampleNameAdd = HT.Href(url='/mouseCross.html#AXB/BXA', text=HT.Sup('#'), Class='fs12', target="_blank") + sample.extra_info = {} + if self.fd.RISet == 'AXBXA' and sample_name in ('AXB18/19/20','AXB13/14','BXA8/17'): + sample.extra_info['url'] = "/mouseCross.html#AXB/BXA" + sample.extra_info['css_class'] = "fs12" + + print(" type of sample:", type(sample)) + + if sample_group_type == 'primary': + sample.this_id = "Primary_" + str(counter) + else: + 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': + 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))) + for sample in self.sample_list: + print("apple:", type(sample), sample) + #return the_samples + + def __repr__(self): + return "<SampleList> --> %s" % (pf(self.__dict__)) + + def do_outliers(self): + values = [sample.value for sample in self.sample_list if sample.value != None] + upper_bound, lower_bound = Plot.find_outliers(values) + + for sample in self.sample_list: + if sample.value: + if upper_bound and sample.value > upper_bound: + sample.outlier = True + elif lower_bound and sample.value < lower_bound: + sample.outlier = True + else: + sample.outlier = False + + + def calc_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 + FROM CaseAttribute, CaseAttributeXRef + WHERE CaseAttributeXRef.ProbeSetFreezeId = %s AND + CaseAttribute.Id = CaseAttributeXRef.CaseAttributeId + group by CaseAttributeXRef.CaseAttributeId''', + (str(self.this_trait.db.id),)) + + + self.attributes = {} + for key, value in self.cursor.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,)) + + self.attributes[key].distinct_values = [item[0] for item in self.cursor.fetchall()] + self.attributes[key].distinct_values.sort(key=natural_sort_key) + + + # 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 this_attr_name in attribute_names: + # exclude_menu.append((this_attr_name.capitalize(), this_attr_name)) + # 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): + + 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)) + + sample_id = self.cursor.fetchone()[0] + + for attribute in self.attributes: + + #ZS: Add extra case attribute values (if any) + self.cursor.execute("""SELECT Value + FROM CaseAttributeXRef + 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 + + #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: + attribute_value = int(attribute_value) + except ValueError: + pass + + attribute_values[self.attributes[attribute].name] = attribute_value + + return attribute_values + + def se_exists(self): + """Returns true if SE values exist for any samples, otherwise false""" + + return any(sample.variance for sample in self.sample_list) + + +def natural_sort_key(x): + """Get expected results when using as a key for sort - ints or strings are sorted properly""" + + try: + x = int(x) + except ValueError: + pass + return x
\ No newline at end of file diff --git a/wqflask/wqflask/templates/trait_data_and_analysis.html b/wqflask/wqflask/templates/trait_data_and_analysis.html index f227d780..7d0e671f 100644 --- a/wqflask/wqflask/templates/trait_data_and_analysis.html +++ b/wqflask/wqflask/templates/trait_data_and_analysis.html @@ -1259,10 +1259,11 @@ <th class="fs13 fwb ff1 b1 cw cbrb" align="right" width="100">Sample</th> <th class="fs13 fwb ff1 b1 cw cbrb" align="right" width="70">Value</th> - + {% if sample_type.se_exists() %} <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> + {% endif %} {% 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> @@ -1287,6 +1288,7 @@ style="text-align:right; background-color:#FFFFFF;"> </td> + {% if sample_type.se_exists() %} <td class="fs13 b1 c222" align="center" width="20"> ± </td> @@ -1297,6 +1299,7 @@ value="{{ sample.display_variance }}" size="8" maxlength="8" style="text-align:right"> </td> + {% endif %} {# Loop through each attribute type and input value #} {% for attribute in sample_type.attributes|sort() %} |