diff options
Diffstat (limited to 'wqflask')
| -rwxr-xr-x | wqflask/base/webqtlCaseData.py | 2 | ||||
| -rwxr-xr-x | wqflask/base/webqtlDataset.py | 4 | ||||
| -rwxr-xr-x | wqflask/base/webqtlFormData.py | 9 | ||||
| -rwxr-xr-x | wqflask/base/webqtlTrait.py | 4 | ||||
| -rwxr-xr-x | wqflask/wqflask/show_trait/DataEditingPage.py | 261 | ||||
| -rw-r--r-- | wqflask/wqflask/show_trait/show_trait_page.py | 64 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/trait_data_and_analysis.html | 11 |
7 files changed, 96 insertions, 259 deletions
diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py index 25665c55..c805a95c 100755 --- a/wqflask/base/webqtlCaseData.py +++ b/wqflask/base/webqtlCaseData.py @@ -40,7 +40,7 @@ class webqtlCaseData(object): self.outlier = None # Not set to True/False until later def __repr__(self): - str = "" + str = "<webqtlCaseData> " if self.value != None: str += "value=%2.3f" % self.value if self.variance != None: diff --git a/wqflask/base/webqtlDataset.py b/wqflask/base/webqtlDataset.py index f8491bb1..4f98e90c 100755 --- a/wqflask/base/webqtlDataset.py +++ b/wqflask/base/webqtlDataset.py @@ -32,8 +32,8 @@ import webqtlConfig class webqtlDataset: """ - Database class defines a database in webqtl, can be either Microarray, - Published phenotype, genotype, or user input database(temp) + Dataset class defines a dataset in webqtl, can be either Microarray, + Published phenotype, genotype, or user input dataset(temp) """ def __init__(self, dbName, cursor=None): diff --git a/wqflask/base/webqtlFormData.py b/wqflask/base/webqtlFormData.py index eb1ebd5e..63263895 100755 --- a/wqflask/base/webqtlFormData.py +++ b/wqflask/base/webqtlFormData.py @@ -46,9 +46,9 @@ from utility import webqtlUtil class webqtlFormData: 'Represents data from a WebQTL form page, needed to generate the next page' - attrs = ('formID','RISet','genotype','samplelist','allsamplelist', - 'suggestive','significance','submitID','identification', 'enablevariance', - 'nperm','nboot','email','incparentsf1','genotype_1','genotype_2','traitInfo') + attrs = ('formID','RISet','genotype','samplelist','allsamplelist', 'display_variance' + 'suggestive','significance','submitID','identification', 'enablevariance', + 'nperm','nboot','email','incparentsf1','genotype_1','genotype_2','traitInfo') #XZ: Attention! All attribute values must be picklable! @@ -61,6 +61,9 @@ class webqtlFormData: print("in webqtlFormData start_vars are:", pf(start_vars)) for item in webqtlFormData.attrs: self.__dict__[item] = None + + #ZS: This is only used in DataEditingPage.py (as far as I know) + self.varianceDispName = None for item in start_vars: self.__dict__[item] = start_vars[item] diff --git a/wqflask/base/webqtlTrait.py b/wqflask/base/webqtlTrait.py index 4d642ffe..efbc1464 100755 --- a/wqflask/base/webqtlTrait.py +++ b/wqflask/base/webqtlTrait.py @@ -157,8 +157,8 @@ class webqtlTrait: #def __str__(self): # #return "%s %s" % (self.getName(), self.riset) # return self.getName() - __str__ = getName - __repr__ = __str__ + #__str__ = getName + #__repr__ = __str__ def exportData(self, samplelist, type="val"): """ diff --git a/wqflask/wqflask/show_trait/DataEditingPage.py b/wqflask/wqflask/show_trait/DataEditingPage.py index 83dbfe03..d186889b 100755 --- a/wqflask/wqflask/show_trait/DataEditingPage.py +++ b/wqflask/wqflask/show_trait/DataEditingPage.py @@ -1,7 +1,5 @@ from __future__ import absolute_import, print_function, division -print("Google") - import string import os import cPickle @@ -22,26 +20,17 @@ from basicStatistics import BasicStatisticsFunctions from pprint import pformat as pf -######################################### -# DataEditingPage -######################################### class DataEditingPage(templatePage): def __init__(self, fd, this_trait=None): templatePage.__init__(self, fd) - - #self.dict['title'] = 'Data Editing' - #TD_LR = HT.TD(valign="top",width="100%",bgcolor="#fafafa") - - if not self.openMysql(): - return + assert self.openMysql(), "No datbase!" + if not fd.genotype: fd.readData(incf1=1) - ############################# # determine data editing page format - ############################# variance_data_page = 0 if fd.formID == 'varianceChoice': variance_data_page = 1 @@ -54,33 +43,6 @@ class DataEditingPage(templatePage): else: fmID='dataEditing' - ############################# - ## titles, etc. - ############################# - - #titleTop = HT.Div() - # - #title1 = HT.Paragraph(" Details and Links", style="border-radius: 5px;", Id="title1", Class="sectionheader") - #title1Body = HT.Paragraph(Id="sectionbody1") - # - #if fd.enablevariance and not variance_data_page: - # title2 = HT.Paragraph(" Submit Variance", style="border-radius: 5px;", Id="title2", Class="sectionheader") - #else: - # title2 = HT.Paragraph(" Basic Statistics", style="border-radius: 5px;", Id="title2", Class="sectionheader") - #title2Body = HT.Paragraph(Id="sectionbody2") - # - #title3 = HT.Paragraph(" Calculate Correlations", style="border-radius: 5px;", Id="title3", Class="sectionheader") - #title3Body = HT.Paragraph(Id="sectionbody3") - # - #title4 = HT.Paragraph(" Mapping Tools", style="border-radius: 5px;", Id="title4", Class="sectionheader") - #title4Body = HT.Paragraph(Id="sectionbody4") - # - #title5 = HT.Paragraph(" Review and Edit Data", style="border-radius: 5px;", Id="title5", Class="sectionheader") - #title5Body = HT.Paragraph(Id="sectionbody5") - - ############################# - ## Hidden field - ############################# # Some fields, like method, are defaulted to None; otherwise in IE the field can't be changed using jquery hddn = OrderedDict( @@ -134,41 +96,23 @@ class DataEditingPage(templatePage): if this_trait.cellid: hddn['cellid'] = this_trait.cellid else: - self.cursor.execute("SELECT h2 from ProbeSetXRef WHERE DataId = %d" % this_trait.mysqlid) + self.cursor.execute("SELECT h2 from ProbeSetXRef WHERE DataId = %d" % + this_trait.mysqlid) heritability = self.cursor.fetchone() hddn['heritability'] = heritability hddn['attribute_names'] = "" - hddn['mappingMethodId'] = webqtlDatabaseFunction.getMappingMethod (cursor=self.cursor, groupName=fd.RISet) - - ############################# - ## Display Trait Information - ############################# - - #headSpan = self.dispHeader(fd,this_trait) #Draw header - # - #titleTop.append(headSpan) + hddn['mappingMethodId'] = webqtlDatabaseFunction.getMappingMethod (cursor=self.cursor, + groupName=fd.RISet) if fd.identification: hddn['identification'] = fd.identification - else: hddn['identification'] = "Un-named trait" #If no identification, set identification to un-named self.dispTraitInformation(fd, "", hddn, this_trait) #Display trait information + function buttons - ############################# - ## Generate form and buttons - ############################# - - #mainForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), - # name='dataInput', submit=HT.Input(type='hidden')) - - #next=HT.Input(type='submit', name='submit',value='Next',Class="button") - #reset=HT.Input(type='Reset',name='',value=' Reset ',Class="button") - #correlationMenus = [] - if this_trait == None: this_trait = webqtlTrait(data=fd.allTraitData, db=None) @@ -182,105 +126,29 @@ class DataEditingPage(templatePage): # # We'll get this part working later # print("Calling dispBasicStatistics") # self.dispBasicStatistics(fd, this_trait) - + self.build_correlation_tools(fd, this_trait) - - # self.dispMappingTools(fd, title4Body, this_trait) - ############################# - ## Trait Value Table - ############################# - # + self.make_sample_lists(fd, variance_data_page, this_trait) - # + if fd.allsamplelist: hddn['allsamplelist'] = string.join(fd.allsamplelist, ' ') - # We put isSE into hddn if fd.varianceDispName != 'Variance': hddn['isSE'] = "yes" - #for key in hddn.keys(): - # mainForm.append(HT.Input(name=key, value=hddn[key], type='hidden')) - # - #if fd.enablevariance and not variance_data_page: - # #pre dataediting page, need to submit variance - # mainForm.append(titleTop, title1,title1Body,title2,title2Body,title3,title3Body,title4,title4Body,title5,title5Body) - #else: - # mainForm.append(titleTop, title1,title1Body,title2,title2Body,title3,title3Body,title4,title4Body,title5,title5Body) - #TD_LR.append(HT.Paragraph(mainForm)) - #self.dict['body'] = str(TD_LR) - - # We'll need access to this_trait and hddn uin the Jinja2 Template, so we put it inside self + # We'll need access to this_trait and hddn in the Jinja2 Template, so we put it inside self self.this_trait = this_trait self.hddn = hddn - #self.basic_table = {} - #self.basic_table['rows'] = yaml.load(""" - # - N of Samples - # - Mean - # - Median - # - Standard Error (SE) - # - Standard Deviation (SD) - # - Minimum - # - Maximum - # - Range (log2) - # - Range (fold) - # - Interquartile Range - # """) - - #self.sample_groups = [] - #self.sample_groups.append(dict(label=fd.RISet + " Only", - # value="primary_only")) - #self.sample_groups.append(dict(label="Non-"+fd.RISet, - # value="other_only")) - #self.sample_groups.append(dict(label="All Cases", - # value="all_cases")) - - self.sample_groups = OrderedDict() - self.sample_groups['primary_only'] = fd.RISet + " Only" - self.sample_groups['other_only'] = "Non-" + fd.RISet - self.sample_groups['all_cases'] = "All Cases" - self.js_data = dict(sample_groups = self.sample_groups) - - - #self.basic_table['columns'] = yaml.load(""" - # - - # n: All Cases - # t: all - # - - # n: BXD Only - # t: primary - # - - # n: Non-BXD Only - # t: other - # """) - - #print(pf(self.basic_table)) - - ########################################## - ## Function to display header - ########################################## - def dispHeader(self, fd, this_trait): - headSpan = HT.Div(style="font-size:14px;") - - #If trait, use trait name; otherwise, use identification value - if this_trait: - if this_trait.cellid: - headSpan.append(HT.Strong('Trait Data and Analysis ', style='font-size:16px;'),' for Probe ID ', this_trait.cellid) - else: - headSpan.append(HT.Strong('Trait Data and Analysis ', style='font-size:16px;'),' for Record ID ', this_trait.name) - else: - if fd.identification: - headSpan.append(HT.Strong('Trait ID ', style='font-size:16px;'),fd.identification) - else: - headSpan.append(HT.Strong('Un-named Trait', style='font-size:16px;')) + self.sample_group_types = OrderedDict() + self.sample_group_types['primary_only'] = fd.RISet + " Only" + self.sample_group_types['other_only'] = "Non-" + fd.RISet + self.sample_group_types['all_cases'] = "All Cases" + self.js_data = dict(sample_groups = self.sample_group_types) - return headSpan - ########################################## - ## Function to display trait infos - ########################################## def dispTraitInformation(self, fd, title1Body, hddn, this_trait): _Species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet) @@ -884,9 +752,6 @@ class DataEditingPage(templatePage): pass - ########################################## - ## Function to display analysis tools - ########################################## def dispBasicStatistics(self, fd, this_trait): #XZ, June 22, 2011: The definition and usage of primary_samples, other_samples, specialStrains, all_samples are not clear and hard to understand. But since they are only used in this function for draw graph purpose, they will not hurt the business logic outside. As of June 21, 2011, this function seems work fine, so no hurry to clean up. These parameters and code in this function should be cleaned along with fd.f1list, fd.parlist, fd.samplelist later. @@ -1029,7 +894,6 @@ class DataEditingPage(templatePage): vals_set = [vals] - #stats_script = HT.Script(language="Javascript") #script needed for tabs self.stats_data = [] for i, vals in enumerate(vals_set): if i == 0 and len(vals) < 4: @@ -1628,7 +1492,8 @@ class DataEditingPage(templatePage): 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 - other_samplesExist = this_trait_samples - set(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 @@ -1636,15 +1501,16 @@ class DataEditingPage(templatePage): print("primary_samplelist is:", pf(primary_samplelist)) - primary_samples = self.create_sample_objects(fd=fd, + primary_samples = SampleList(self.cursor, + fd=fd, variance_data_page=variance_data_page, samplelist=primary_samplelist, #mainForm=mainForm, this_trait=this_trait, - other_samplesExist=other_samplesExist, attribute_ids=attribute_ids, attribute_names=attribute_names, - samples='primary') + samples='primary', + header="%s Only" % (fd.RISet)) other_samples = [] @@ -1661,14 +1527,16 @@ class DataEditingPage(templatePage): other_samples.sort() #Sort other samples other_samples = par_f1_samples + other_samples - other_samples = self.create_sample_objects(fd=fd, + 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') + samples='other', + header="Non-%s" % (fd.RISet)) #TODO: Figure out why this if statement is written this way - Zach @@ -1678,16 +1546,28 @@ class DataEditingPage(templatePage): 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.primary_samples = dict(header = "%s Only" % (fd.RISet), + # samples = primary_samples,) + # + #self.other_samples = dict(header = "Non-%s" % (fd.RISet), + # samples = other_samples,) - - def create_sample_objects(self, fd, variance_data_page, samplelist, this_trait, - other_samplesExist=None, attribute_ids=None, - attribute_names=None, samples='primary'): + self.sample_groups = (primary_samples, other_samples) + + +class SampleList(list): + def __init__(self, + cursor, + fd, + variance_data_page, + samplelist, + this_trait, + attribute_ids, + attribute_names, + samples, + header): + + self.header = header if attribute_ids == None: attribute_ids = [] @@ -1717,7 +1597,7 @@ class DataEditingPage(templatePage): #upperBound, lowerBound = Plot.findOutliers(vals) # ZS: Values greater than upperBound or less than lowerBound are considered outliers. - the_samples = [] + #the_samples = [] for counter, sampleNameOrig in enumerate(samplelist, 1): sampleName = sampleNameOrig.replace("_2nd_", "") @@ -1731,7 +1611,7 @@ class DataEditingPage(templatePage): print("No sample %s, let's create it now" % sampleName) sample = webqtlCaseData.webqtlCaseData(sampleName) print("zyt - sampleNameOrig:", sampleNameOrig) - + print(" type of sample:", type(sample)) if samples == 'primary': sample.this_id = "Primary_" + str(counter) @@ -1743,27 +1623,27 @@ class DataEditingPage(templatePage): if len(attribute_ids) > 0: #ZS: Get StrainId value for the next query - self.cursor.execute("""SELECT Strain.Id - FROM Strain, StrainXRef, InbredSet + 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 = self.cursor.fetchone()[0] + 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) - self.cursor.execute("""SELECT Value + 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 = self.cursor.fetchone()[0] #Trait-specific attributes, if any + 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: @@ -1776,23 +1656,26 @@ class DataEditingPage(templatePage): attr_className = str(attributeValue) + " " + className table_row.append(HT.TD(attr_container, align='right', Class=attr_className)) attr_counter += 1 - the_samples.append(sample) + self.append(sample) #table_body.append(table_row) - do_outliers(the_samples) - print("*the_samples are [%i]: %s" % (len(the_samples), pf(the_samples))) - return the_samples + self.do_outliers() + #do_outliers(the_samples) + print("*the_samples are [%i]: %s" % (len(self), pf(self))) + for sample in self: + print("apple:", type(sample), sample) + #return the_samples -def do_outliers(sample_objects): - values = [sample.value for sample in sample_objects if sample.value != None] - upper_bound, lower_bound = Plot.find_outliers(values) - - for sample in sample_objects: - 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 do_outliers(self): + values = [sample.value for sample in self if sample.value != None] + upper_bound, lower_bound = Plot.find_outliers(values) + + for sample in self: + 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 diff --git a/wqflask/wqflask/show_trait/show_trait_page.py b/wqflask/wqflask/show_trait/show_trait_page.py index 858f16ea..cf056d35 100644 --- a/wqflask/wqflask/show_trait/show_trait_page.py +++ b/wqflask/wqflask/show_trait/show_trait_page.py @@ -41,39 +41,24 @@ from DataEditingPage import DataEditingPage class ShowTraitPage(DataEditingPage): def __init__(self, fd, traitInfos = None): - - #templatePage.__init__(self, fd) self.fd = fd - if not self.openMysql(): - return + # This sets self.cursor + assert self.openMysql(), "No database" - #TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee') - print("j2") # When is traitInfos used? if traitInfos: - print("j2.2") database, ProbeSetID, CellID = traitInfos else: - print("j2.3") print("fd is:", fd) database = fd['database'] ProbeSetID = fd['ProbeSetID'] - print("j2.4") + CellID = fd.get('CellID') - print("j2.6") + - # We're no longer wrapping this in an exception. If we fail, let's fail hard - # Log it and fix it - #try: - print("j3") thisTrait = webqtlTrait(db=database, name=ProbeSetID, cellid=CellID, cursor=self.cursor) - #except: - # heading = "Trait Data and Analysis Form" - # detail = ["The trait isn't available currently."] - # self.error(heading=heading,detail=detail,error="Error") - # return - print("j4") + if thisTrait.db.type == "ProbeSet": self.cursor.execute('''SELECT Id, Name, FullName, confidentiality, AuthorisedUsers @@ -120,10 +105,7 @@ class ShowTraitPage(DataEditingPage): try it again tomorrow.' % webqtlConfig.DAILYMAXIMUM] self.error(heading=heading,detail=detail) return - else: - pass - else: - pass + if thisTrait.db.type != 'ProbeSet' and thisTrait.cellid: heading = "Retrieve Data" @@ -131,26 +113,6 @@ class ShowTraitPage(DataEditingPage): self.error(heading=heading,detail=detail) return - #XZ: Aug 23, 2010: I commented out this block because this feature is not used anymore - # check if animal information are available - """ - self.cursor.execute(''' - SELECT - SampleXRef.ProbeFreezeId - FROM - SampleXRef, ProbeSetFreeze - WHERE - SampleXRef.ProbeFreezeId = ProbeSetFreeze.ProbeFreezeId AND - ProbeSetFreeze.Name = "%s" - ''' % thisTrait.db.name) - - sampleId = self.cursor.fetchall() - if sampleId: - thisTrait.strainInfo = 1 - else: - thisTrait.strainInfo = None - """ - ##identification, etc. fd.identification = '%s : %s' % (thisTrait.db.shortname,ProbeSetID) thisTrait.returnURL = webqtlConfig.CGIDIR + webqtlConfig.SCRIPTFILE + '?FormID=showDatabase&database=%s\ @@ -160,19 +122,12 @@ class ShowTraitPage(DataEditingPage): fd.identification = '%s/%s'%(fd.identification, CellID) thisTrait.returnURL = '%s&CellID=%s' % (thisTrait.returnURL, CellID) - #retrieve trait information - #try: thisTrait.retrieveInfo() thisTrait.retrieveData() self.updMysql() self.cursor.execute("insert into AccessLog(accesstime,ip_address) values(Now(),%s)", user_ip) self.openMysql() - #except Exception as why: - # print("Got an exception:", why) - # heading = "Retrieve Data" - # detail = ["The information you requested is not avaiable at this time."] - # self.error(heading=heading, detail=detail) - # return + ##read genotype file fd.RISet = thisTrait.riset @@ -180,10 +135,7 @@ class ShowTraitPage(DataEditingPage): #if webqtlUtil.ListNotNull(map(lambda x:x.var, thisTrait.data.values())): if any([x.variance for x in thisTrait.data.values()]): - fd.displayVariance = 1 - fd.varianceDispName = 'SE' + fd.display_variance = True fd.formID = 'varianceChoice' - #self.dict['body']= thisTrait DataEditingPage.__init__(self, fd, thisTrait) - #self.dict['title'] = '%s: Display Trait' % fd.identification diff --git a/wqflask/wqflask/templates/trait_data_and_analysis.html b/wqflask/wqflask/templates/trait_data_and_analysis.html index 6ae91c6d..7cfb7916 100644 --- a/wqflask/wqflask/templates/trait_data_and_analysis.html +++ b/wqflask/wqflask/templates/trait_data_and_analysis.html @@ -243,7 +243,7 @@ <p id="sectionbody2"></p>Include: <select name="corr_samples_group" size="1"> - {% for group, pretty_group in sample_groups.items() %} + {% for group, pretty_group in sample_group_types.items() %} <option value="{{ group }}"> {{ pretty_group }} </option> @@ -751,7 +751,7 @@ <td><span class="ffl fwb fs12">Samples:</span></td> <td> <select name="corr_samples_group" size="1"> - {% for group, pretty_group in sample_groups.items() %} + {% for group, pretty_group in sample_group_types.items() %} <option value="{{ group }}"> {{ pretty_group }} </option> @@ -1245,12 +1245,11 @@ </div><br> <div style="width:80%;margin:0;padding:0;border:none;"> - {% for sample_type in (primary_samples, other_samples) %} - + {% for sample_type in sample_groups %} <div style="float:left;width:50%;"> <h2>{{ sample_type.header }}</h2> - <div id="{{ sample_type.samples[0]['this_id'].lower().partition('_')[0] }}"> {# Slightly tortuous, but best way to get the id we need #} + <div id="{{ sample_type.samples }}"> <table class="not_tablesorter" {# Todo: Turn tablesorter back on #} id="{{ 'sortable%i' % (loop.index) }}" cellpadding="0" cellspacing="0"> @@ -1266,7 +1265,7 @@ <th class="fs13 fwb ff1 b1 cw cbrb" align="right" width="80">SE</th> </tr> - {% for sample in sample_type.samples %} + {% for sample in sample_type %} <tr class="{{ sample.class_outlier }} value_se" id="{{ sample.this_id }}"> <td class="fs13 b1 c222" align="right" width="45"> {{ loop.index }} |