diff options
| -rwxr-xr-x | wqflask/base/webqtlTrait.py | 16 | ||||
| -rwxr-xr-x | wqflask/utility/__init__.py | 14 | ||||
| -rw-r--r-- | wqflask/wqflask/__init__.py | 3 | ||||
| -rwxr-xr-x | wqflask/wqflask/show_trait/DataEditingPage.py | 192 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/trait_data_and_analysis.html | 4 |
5 files changed, 113 insertions, 116 deletions
diff --git a/wqflask/base/webqtlTrait.py b/wqflask/base/webqtlTrait.py index efbc1464..d6d537b7 100755 --- a/wqflask/base/webqtlTrait.py +++ b/wqflask/base/webqtlTrait.py @@ -359,14 +359,14 @@ class webqtlTrait: #else: # pass - def keys(self): - return self.__dict__.keys() - - def has_key(self, key): - return self.__dict__.has_key(key) - - def items(self): - return self.__dict__.items() + #def keys(self): + # return self.__dict__.keys() + # + #def has_key(self, key): + # return self.__dict__.has_key(key) + # + #def items(self): + # return self.__dict__.items() def retrieveInfo(self, QTL = None): assert self.db and self.cursor diff --git a/wqflask/utility/__init__.py b/wqflask/utility/__init__.py index 206d0d1c..d0e4a3fa 100755 --- a/wqflask/utility/__init__.py +++ b/wqflask/utility/__init__.py @@ -1,12 +1,12 @@ +from pprint import pformat as pf + + class Bunch(object): - """Make the configuration a little cleaner""" - def __init__(self, config_string = "", **kw): - if config_string: - td = yaml.load(config_string) - self.__dict__.update(td) - else: + """Like a dictionary but using object notation""" + def __init__(self, **kw): self.__dict__ = kw def __repr__(self): - return yaml.dump(self.__dict__, default_flow_style=False) + return pf(self.__dict__) + diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py index a7492e77..ff018fdc 100644 --- a/wqflask/wqflask/__init__.py +++ b/wqflask/wqflask/__init__.py @@ -3,6 +3,8 @@ from __future__ import absolute_import, division, print_function import sys print("sys.path is:", sys.path) +import jinja2 + from flask import Flask from utility import formatting @@ -14,6 +16,7 @@ app.config.from_object('cfg.default_settings') app.config.from_envvar('WQFLASK_SETTINGS') app.jinja_env.globals.update( + undefined = jinja2.StrictUndefined, numify = formatting.numify ) diff --git a/wqflask/wqflask/show_trait/DataEditingPage.py b/wqflask/wqflask/show_trait/DataEditingPage.py index e431fd76..24a37926 100755 --- a/wqflask/wqflask/show_trait/DataEditingPage.py +++ b/wqflask/wqflask/show_trait/DataEditingPage.py @@ -1466,43 +1466,23 @@ class DataEditingPage(templatePage): if fd.genotype.type == "riset": all_samples_ordered = fd.f1list + fd.samplelist else: - all_samples_ordered = fd.f1list + fd.parlist + fd.samplelist - - #ZS: Id values for this trait's extra attributes; - #used to create "Exclude" dropdown and query for attribute values and create - 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(this_trait.db.id),)) - - - - for this_attr_name in attribute_names: - # Todo: Needs testing still! - self.cursor.execute("""SELECT DISTINCT CaseAttributeXRef.Value - FROM CaseAttribute, CaseAttributeXRef - WHERE CaseAttribute.Name = %s AND - CaseAttributeXRef.CaseAttributeId = CaseAttribute.Id""", - (this_attr_name,)) - - distinct_values = self.cursor.fetchall() + all_samples_ordered = fd.parlist + fd.f1list + fd.samplelist this_trait_samples = set(this_trait.data.keys()) primary_sample_names = all_samples_ordered - print("primary_samplelist is:", pf(primary_sample_names)) + print("-*- primary_samplelist is:", pf(primary_sample_names)) primary_samples = SampleList(self.cursor, fd=fd, variance_data_page=variance_data_page, sample_names=primary_sample_names, this_trait=this_trait, - samples='primary', + sample_group_type='primary', header="%s Only" % (fd.RISet)) - + + print("primary_samples.attributes:", pf(primary_samples.attributes)) other_sample_names = [] for sample in this_trait.data.keys(): @@ -1515,15 +1495,15 @@ class DataEditingPage(templatePage): unappended_par_f1 = fd.f1list + fd.parlist par_f1_samples = ["_2nd_" + sample for sample in unappended_par_f1] - other_samples.sort() #Sort other samples - other_samples = par_f1_samples + other_samples + other_sample_names.sort() #Sort other samples + other_sample_names = par_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, - samples='other', + sample_group_type='other', header="Non-%s" % (fd.RISet)) self.sample_groups = (primary_samples, other_samples) @@ -1531,36 +1511,39 @@ class DataEditingPage(templatePage): self.sample_groups = (primary_samples,) #TODO: Figure out why this if statement is written this way - Zach - 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 - - - + #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 -class SampleList(list): +class SampleList(object): def __init__(self, cursor, fd, variance_data_page, sample_names, this_trait, - samples, + 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 = this_trait.data[sample_name] + 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) @@ -1569,37 +1552,37 @@ class SampleList(list): #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 fd.RISet == 'AXBXA' and sample_name in ('AXB18/19/20','AXB13/14','BXA8/17'): + 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("zyt - sampleNameOrig:", sampleNameOrig) + print(" type of sample:", type(sample)) - if samples == 'primary': + 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 two human datasets - Zach - if this_trait and this_trait.db and this_trait.db.type == 'ProbeSet': - self.get_extra_attribute_values(attribute_ids, this_trait, sample_name) - self.append(sample) - #table_body.append(table_row) + if self.this_trait and self.this_trait.db and self.this_trait.db.type == 'ProbeSet': + self.get_extra_attribute_values(sample_name) + self.sample_list.append(sample) self.do_outliers() #do_outliers(the_samples) - print("*the_samples are [%i]: %s" % (len(self), pf(self))) - for sample in self: + 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 if sample.value != None] + 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: + for sample in self.sample_list: if sample.value: if upper_bound and sample.value > upper_bound: sample.outlier = True @@ -1608,23 +1591,24 @@ class SampleList(list): 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(this_trait.db.id),)) + (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(): + print("radish: %s - %s" % (key, value)) self.attributes[key] = Bunch() self.attributes[key].name = value @@ -1633,64 +1617,65 @@ class SampleList(list): WHERE CaseAttribute.Name = %s AND CaseAttributeXRef.CaseAttributeId = CaseAttribute.Id''', (value,)) - self.attributes[key].distinct_values = self.cursor.fetchall() - - - 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 + self.attributes[key].distinct_values = [item[0] for item in self.cursor.fetchall()] + 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 - def get_extra_attribute_values(self): + def get_extra_attribute_values(self, sample_name): - if len(attribute_ids) > 0: + if len(self.attributes) > 0: #ZS: Get StrainId value for the next query - cursor.execute("""SELECT Strain.Id - FROM Strain, StrainXRef, InbredSetd - WHERE Strain.Name = '%s' and + 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'""" % (sampleName, fd.RISet)) + InbredSet.Name = %s""", (sample_name, self.fd.RISet)) - sample_id = cursor.fetchone()[0] + 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 attribute_ids: + for attribute_id in self.attributes.keys(): #ZS: Add extra case attribute values (if any) - cursor.execute("""SELECT Value + self.cursor.execute("""SELECT Value FROM CaseAttributeXRef WHERE ProbeSetFreezeId = '%s' AND StrainId = '%s' AND CaseAttributeId = '%s' - group by CaseAttributeXRef.CaseAttributeId""" % (this_trait.db.id, sample_id, str(attribute_id))) + group by CaseAttributeXRef.CaseAttributeId""" % (self.this_trait.db.id, sample_id, str(attribute_id))) - attributeValue = cursor.fetchone()[0] #Trait-specific attributes, if any + attributeValue = 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: @@ -1698,8 +1683,17 @@ class SampleList(list): 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)) + #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 + + +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 7cfb7916..6a5a4a80 100644 --- a/wqflask/wqflask/templates/trait_data_and_analysis.html +++ b/wqflask/wqflask/templates/trait_data_and_analysis.html @@ -1249,7 +1249,7 @@ <div style="float:left;width:50%;"> <h2>{{ sample_type.header }}</h2> - <div id="{{ sample_type.samples }}"> + <div id="{{ sample_type.sample_group_type }}"> <table class="not_tablesorter" {# Todo: Turn tablesorter back on #} id="{{ 'sortable%i' % (loop.index) }}" cellpadding="0" cellspacing="0"> @@ -1265,7 +1265,7 @@ <th class="fs13 fwb ff1 b1 cw cbrb" align="right" width="80">SE</th> </tr> - {% for sample in sample_type %} + {% for sample in sample_type.sample_list %} <tr class="{{ sample.class_outlier }} value_se" id="{{ sample.this_id }}"> <td class="fs13 b1 c222" align="right" width="45"> {{ loop.index }} |