diff options
| -rwxr-xr-x | wqflask/utility/__init__.py | 12 | ||||
| -rwxr-xr-x | wqflask/wqflask/show_trait/DataEditingPage.py | 264 |
2 files changed, 156 insertions, 120 deletions
diff --git a/wqflask/utility/__init__.py b/wqflask/utility/__init__.py index e69de29b..206d0d1c 100755 --- a/wqflask/utility/__init__.py +++ b/wqflask/utility/__init__.py @@ -0,0 +1,12 @@ +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: + self.__dict__ = kw + + def __repr__(self): + return yaml.dump(self.__dict__, default_flow_style=False) + diff --git a/wqflask/wqflask/show_trait/DataEditingPage.py b/wqflask/wqflask/show_trait/DataEditingPage.py index d186889b..e431fd76 100755 --- a/wqflask/wqflask/show_trait/DataEditingPage.py +++ b/wqflask/wqflask/show_trait/DataEditingPage.py @@ -12,7 +12,7 @@ from htmlgen import HTMLgen2 as HT from base import webqtlConfig from base import webqtlCaseData -from utility import webqtlUtil, Plot +from utility import webqtlUtil, Plot, Bunch from base.webqtlTrait import webqtlTrait from dbFunction import webqtlDatabaseFunction from base.templatePage import templatePage @@ -1467,9 +1467,6 @@ class DataEditingPage(templatePage): all_samples_ordered = fd.f1list + fd.samplelist else: all_samples_ordered = fd.f1list + fd.parlist + fd.samplelist - - attribute_ids = [] - attribute_names = [] #ZS: Id values for this trait's extra attributes; #used to create "Exclude" dropdown and query for attribute values and create @@ -1479,6 +1476,8 @@ class DataEditingPage(templatePage): CaseAttribute.Id = CaseAttributeXRef.CaseAttributeId group by CaseAttributeXRef.CaseAttributeId""", (str(this_trait.db.id),)) + + for this_attr_name in attribute_names: # Todo: Needs testing still! @@ -1491,36 +1490,28 @@ class DataEditingPage(templatePage): distinct_values = self.cursor.fetchall() this_trait_samples = set(this_trait.data.keys()) - #ZS - Checks if there are any samples in this_trait_samples that aren't in all_samples_ordered - #Will need to be used in the future to determine whether to create one or two tables are created (probably) - #other_samples_exist = this_trait_samples - set(all_samples_ordered) - #mainForm = None # Just trying to get things working + primary_sample_names = all_samples_ordered - primary_samplelist = all_samples_ordered - - print("primary_samplelist is:", pf(primary_samplelist)) + print("primary_samplelist is:", pf(primary_sample_names)) primary_samples = SampleList(self.cursor, - fd=fd, - variance_data_page=variance_data_page, - samplelist=primary_samplelist, - #mainForm=mainForm, - this_trait=this_trait, - attribute_ids=attribute_ids, - attribute_names=attribute_names, - samples='primary', - header="%s Only" % (fd.RISet)) - - - other_samples = [] + fd=fd, + variance_data_page=variance_data_page, + sample_names=primary_sample_names, + this_trait=this_trait, + samples='primary', + header="%s Only" % (fd.RISet)) + + + other_sample_names = [] for sample in this_trait.data.keys(): print("hjk - sample is:", sample) if sample not in all_samples_ordered: all_samples_ordered.append(sample) - other_samples.append(sample) + other_sample_names.append(sample) - if other_samples: + if other_sample_names: unappended_par_f1 = fd.f1list + fd.parlist par_f1_samples = ["_2nd_" + sample for sample in unappended_par_f1] @@ -1528,31 +1519,24 @@ class DataEditingPage(templatePage): other_samples = par_f1_samples + other_samples other_samples = SampleList(self.cursor, - fd=fd, - variance_data_page=variance_data_page, - samplelist=other_samples, - #mainForm=mainForm, - this_trait=this_trait, - attribute_ids=attribute_ids, - attribute_names=attribute_names, - samples='other', - header="Non-%s" % (fd.RISet)) - + fd=fd, + variance_data_page=variance_data_page, + sample_names=other_sample_names, + this_trait=this_trait, + samples='other', + header="Non-%s" % (fd.RISet)) + + self.sample_groups = (primary_samples, other_samples) + else: + self.sample_groups = (primary_samples,) #TODO: Figure out why this if statement is written this way - Zach - if (other_samples or (fd.f1list and this_trait.data.has_key(fd.f1list[0])) + 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.primary_samples = dict(header = "%s Only" % (fd.RISet), - # samples = primary_samples,) - # - #self.other_samples = dict(header = "Non-%s" % (fd.RISet), - # samples = other_samples,) - self.sample_groups = (primary_samples, other_samples) + class SampleList(list): @@ -1560,56 +1544,35 @@ class SampleList(list): cursor, fd, variance_data_page, - samplelist, + sample_names, this_trait, - attribute_ids, - attribute_names, samples, header): self.header = header - - if attribute_ids == None: - attribute_ids = [] - - if attribute_names == None: - attribute_names = [] - - #XZ, Aug 23, 2010: I commented the code related to the display of animal case - #sampleInfo = this_trait.has_key('sampleInfo') and this_trait.sampleInfo - print("in create_sample_objects") - #table_body = [] - ################### Only used to find upperBound and lowerBound - #vals = [] - #for sampleNameOrig in samplelist: - # sampleName = sampleNameOrig.replace("_2nd_", "") - # print("pen: %s - %s" % (sampleNameOrig, sampleName)) - # try: - # thisval = this_trait.data[sampleName].value - # thisvar = this_trait.data[sampleName].variance - # thisValFull = [sampleName, thisval, thisvar] - # - # vals.append(thisValFull) - # except KeyError: - # print("**x** Skipping:", sampleName) - # - #upperBound, lowerBound = Plot.findOutliers(vals) # ZS: Values greater than upperBound or less than lowerBound are considered outliers. - + + + self.calc_attributes() - #the_samples = [] + for counter, sample_name in enumerate(sample_names, 1): + sample_name = sample_name.replace("_2nd_", "") - for counter, sampleNameOrig in enumerate(samplelist, 1): - sampleName = sampleNameOrig.replace("_2nd_", "") - 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") - + #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[sampleName] + sample = this_trait.data[sample_name] except KeyError: - print("No sample %s, let's create it now" % sampleName) - sample = webqtlCaseData.webqtlCaseData(sampleName) + 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 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)) @@ -1620,42 +1583,7 @@ class SampleList(list): #### 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': - if len(attribute_ids) > 0: - - #ZS: Get StrainId value for the next query - cursor.execute("""SELECT Strain.Id - FROM Strain, StrainXRef, InbredSetd - WHERE Strain.Name = '%s' and - StrainXRef.StrainId = Strain.Id and - InbredSet.Id = StrainXRef.InbredSetId and - InbredSet.Name = '%s'""" % (sampleName, fd.RISet)) - - sample_id = 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: - - #ZS: Add extra case attribute values (if any) - 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))) - - attributeValue = 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: - attributeValue = int(attributeValue) - except: - 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 + self.get_extra_attribute_values(attribute_ids, this_trait, sample_name) self.append(sample) #table_body.append(table_row) @@ -1679,3 +1607,99 @@ class SampleList(list): 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(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(): + 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 = 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 + + + def get_extra_attribute_values(self): + + if len(attribute_ids) > 0: + + #ZS: Get StrainId value for the next query + cursor.execute("""SELECT Strain.Id + FROM Strain, StrainXRef, InbredSetd + WHERE Strain.Name = '%s' and + StrainXRef.StrainId = Strain.Id and + InbredSet.Id = StrainXRef.InbredSetId and + InbredSet.Name = '%s'""" % (sampleName, fd.RISet)) + + sample_id = 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: + + #ZS: Add extra case attribute values (if any) + 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))) + + attributeValue = 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: + attributeValue = int(attributeValue) + 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 |