diff options
| -rw-r--r-- | wqflask/wqflask/do_search.py | 137 | ||||
| -rw-r--r-- | wqflask/wqflask/search_results.py | 8 | ||||
| -rwxr-xr-x | wqflask/wqflask/show_trait/show_trait.py | 126 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/search_result_page.html | 1 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 3 |
5 files changed, 193 insertions, 82 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index 11411b26..17078802 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -74,6 +74,14 @@ class ProbeSetSearch(DoSearch): ProbeSet.name_num as TNAME_NUM FROM ProbeSetXRef, ProbeSet """ + header_fields = ['', + 'Record ID', + 'Symbol', + 'Description', + 'Location', + 'Mean', + 'Max LRS', + 'Max LRS Location'] def compile_final_query(self, from_clause = '', where_clause = ''): """Generates the final query string""" @@ -188,36 +196,49 @@ class GenotypeSearch(DoSearch): search_fields = ('Name', 'Chr') - def get_where_clause(self): - """Generate clause for WHERE portion of query""" + def get_fields_clause(self): + """Generate clause for part of the WHERE portion of query""" # This adds a clause to the query that matches the search term # against each field in search_fields (above) - where_clause = [] + fields_clause = [] + + if "'" not in self.search_term: + self.search_term = "[[:<:]]" + self.search_term + "[[:>:]]" + for field in self.search_fields: - where_clause.append('''%s REGEXP "%s"''' % ("%s.%s" % (self.dataset.type, field), - self.escape(self.search_term))) - print("where_clause is:", pf(where_clause)) - where_clause = "(%s)" % ' OR '.join(where_clause) + fields_clause.append('''%s REGEXP "%s"''' % ("%s.%s" % self.mescape(self.dataset.type, + field, + self.search_term))) + print("hello ;where_clause is:", pf(fields_clause)) + fields_clause = "(%s)" % ' OR '.join(fields_clause) - return where_clause + return fields_clause - def run(self): - """Generates and runs a simple search of a genotype dataset""" - #Todo: Zach will figure out exactly what both these lines mean - #and comment here - if "'" not in self.search_term: - search_term = "[[:<:]]" + self.search_term + "[[:>:]]" + def compile_final_query(self, from_clause = '', where_clause = ''): + """Generates the final query string""" + + from_clause = self.normalize_spaces(from_clause) query = (self.base_query + """WHERE %s and Geno.Id = GenoXRef.GenoId and GenoXRef.GenoFreezeId = GenoFreeze.Id and - GenoFreeze.Id = %s"""% ( - self.get_where_clause(), - self.escape(self.dataset.id))) + GenoFreeze.Id = %s"""% (where_clause, + self.escape(self.dataset.id))) - return self.execute(query) + print("query is:", pf(query)) + + return query + + def run(self): + """Generates and runs a simple search of a genotype dataset""" + #Todo: Zach will figure out exactly what both these lines mean + #and comment here + + self.query = self.compile_final_query(where_clause = self.get_fields_clause()) + + return self.execute(self.query) class RifSearch(ProbeSetSearch): """Searches for traits with a Gene RIF entry including the search term.""" @@ -497,9 +518,84 @@ class RangeSearch(ProbeSetSearch): self.query = self.compile_final_query(where_clause = self.where_clause) - return self.execute(self.query) + return self.execute(self.query) + +class PositionSearch(DoSearch): + """Searches for genes/markers located within a specified range on a specified chromosome""" + + for search_key in ('POSITION', 'POS', 'MB'): + DoSearch.search_types[search_key] = "PositionSearch" + + def setup(self): + self.search_term = [float(value) for value in self.search_term] + self.chr, self.mb_min, self.mb_max = self.search_term[:3] + self.where_clause = """ %s.Chr = '%s' and + %s.Mb > %s and + %s.Mb < %s """ % self.mescape(self.dataset.type, + self.chr, + self.dataset.type, + min(self.mb_min, self.mb_max), + self.dataset.type, + max(self.mb_min, self.mb_max)) + + def real_run(self): + + self.query = self.compile_final_query(where_clause = self.where_clause) + + return self.execute(self.query) + +class MrnaPositionSearch(ProbeSetSearch, PositionSearch): + """Searches for genes located within a specified range on a specified chromosome""" + + def run(self): + + self.setup() + self.query = self.compile_final_query(where_clause = self.where_clause) + + return self.execute(self.query) + +class GenotypePositionSearch(GenotypeSearch, PositionSearch): + """Searches for genes located within a specified range on a specified chromosome""" + + def run(self): + + self.setup() + self.query = self.compile_final_query(where_clause = self.where_clause) + + return self.execute(self.query) + +class PvalueSearch(ProbeSetSearch): + """Searches for traits with a permutationed p-value between low and high""" + + def run(self): + + self.search_term = [float(value) for value in self.search_term] + + if self.search_operator == "=": + assert isinstance(self.search_term, (list, tuple)) + self.pvalue_min, self.pvalue_max = self.search_term[:2] + self.where_clause = """ %sXRef.pValue > %s and %sXRef.pValue < %s + """ % self.mescape( + self.dataset.type, + min(self.pvalue_min, self.pvalue_max), + self.dataset.type, + max(self.pvalue_min, self.pvalue_max)) + else: + # Deal with >, <, >=, and <= + self.where_clause = """ %sXRef.pValue %s %s + """ % self.mescape( + self.dataset.type, + self.search_operator, + self.search_term[0]) + + print("where_clause is:", pf(self.where_clause)) + + self.query = self.compile_final_query(where_clause = self.where_clause) + + return self.execute(self.query) + if __name__ == "__main__": ### Usually this will be used as a library, but call it from the command line for testing ### And it runs the code below @@ -538,7 +634,8 @@ if __name__ == "__main__": ProbeSetXRef.ProbeSetFreezeId = 112""") #print(pf(cursor.fetchall())) - results = ProbeSetSearch("shh", None, dataset, cursor, db_conn).run() + #results = ProbeSetSearch("shh", None, dataset, cursor, db_conn).run() + results = PvalueSearch(['0.005'], '<', dataset, cursor, db_conn).run() #results = RifSearch("diabetes", dataset, cursor, db_conn).run() #results = WikiSearch("nicotine", dataset, cursor, db_conn).run() #results = CisLrsSearch(['99'], '>', dataset, cursor, db_conn).run() # cisLRS > 99 diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index 63e0153d..c7bbdaf2 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -143,14 +143,16 @@ class SearchResultPage(templatePage): search_ob = do_search.DoSearch.get_search(search_type) search_class = getattr(do_search, search_ob) - self.results.extend(search_class(search_term, + the_search = search_class(search_term, search_operator, self.dataset, self.cursor, - self.db_conn).run()) - + self.db_conn) + self.results.extend(the_search.run()) print("in the search results are:", self.results) + self.header_fields = the_search.header_fields + #ZS: This should be handled in the parser def encregexp(self,str): diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index db2636bc..e8ad0b1d 100755 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -34,15 +34,22 @@ class ShowTrait(templatePage): def __init__(self, fd): self.fd = fd + print("red1 fd.group:", fd.group) templatePage.__init__(self, fd) + + print("red2 fd.group:", fd.group) assert self.openMysql(), "No database!" - + + print("red3 fd.group:", fd.group) this_trait = self.get_this_trait() - + + print("red4 fd.group:", fd.group) ##read genotype file fd.group = this_trait.group - fd.readGenotype() - + + print("[red5] fd.group is:", fd.group) + fd.readGenotype() + if not fd.genotype: fd.readData(incf1=1) @@ -107,8 +114,8 @@ class ShowTrait(templatePage): except: hddn['normalPlotTitle'] = str(this_trait.name) hddn['fromDataEditingPage'] = 1 - if this_trait.db and this_trait.db.type and this_trait.db.type == 'ProbeSet': - hddn['trait_type'] = this_trait.db.type + if this_trait.dataset and this_trait.dataset.type and this_trait.dataset.type == 'ProbeSet': + hddn['trait_type'] = this_trait.dataset.type if this_trait.cellid: hddn['cellid'] = this_trait.cellid else: @@ -130,7 +137,7 @@ class ShowTrait(templatePage): self.dispTraitInformation(fd, "", hddn, this_trait) #Display trait information + function buttons if this_trait == None: - this_trait = webqtlTrait(data=fd.allTraitData, db=None) + this_trait = webqtlTrait(data=fd.allTraitData, dataset=None) ## Variance submit page only #if fd.enablevariance and not variance_data_page: @@ -147,7 +154,7 @@ class ShowTrait(templatePage): self.make_sample_lists(fd, variance_data_page, this_trait) - + if fd.allsamplelist: hddn['allsamplelist'] = string.join(fd.allsamplelist, ' ') @@ -178,12 +185,12 @@ class ShowTrait(templatePage): #else: dataset = self.fd['dataset'] trait_id = self.fd['trait_id'] - cell_id = self.fd.get('CellID') + cell_id = self.fd.get('CellID') + + this_trait = webqtlTrait(self.db_conn, dataset=dataset, name=trait_id, cellid=cell_id) - this_trait = webqtlTrait(self.db_conn, db=dataset, name=trait_id, cellid=cell_id) - ##identification, etc. - self.fd.identification = '%s : %s' % (this_trait.db.shortname, trait_id) + self.fd.identification = '%s : %s' % (this_trait.dataset.shortname, trait_id) this_trait.returnURL = webqtlConfig.CGIDIR + webqtlConfig.SCRIPTFILE + '?FormID=showDatabase&database=%s\ &ProbeSetID=%s&group=%s&parentsf1=on' %(dataset, trait_id, self.fd['group']) @@ -191,10 +198,13 @@ class ShowTrait(templatePage): self.fd.identification = '%s/%s'%(self.fd.identification, cell_id) this_trait.returnURL = '%s&CellID=%s' % (this_trait.returnURL, cell_id) + print("yellow1:", self.group) this_trait.retrieveInfo() + print("yellow2:", self.group) this_trait.retrieveData() + print("yellow3:", self.group) return this_trait - + def dispTraitInformation(self, fd, title1Body, hddn, this_trait): @@ -225,13 +235,13 @@ class ShowTrait(templatePage): if webqtlConfig.USERDICT[self.privilege] >= webqtlConfig.USERDICT['user']: - if this_trait==None or this_trait.db.type=='Temp': + if this_trait==None or this_trait.dataset.type=='Temp': updateButton = HT.Href(url="#redirect", onClick="dataEditingFunc(document.getElementsByName('dataInput')[0],'addPublish');") updateButton_img = HT.Image("/images/edit_icon.jpg", name="addnew", alt="Add To Publish", title="Add To Publish", style="border:none;") updateButton.append(updateButton_img) updateText = "Edit" - elif this_trait.db.type != 'Temp': - if this_trait.db.type == 'Publish' and this_trait.confidential: #XZ: confidential phenotype trait + elif this_trait.dataset.type != 'Temp': + if this_trait.dataset.type == 'Publish' and this_trait.confidential: #XZ: confidential phenotype trait if webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=self.privilege, userName=self.userName, authorized_users=this_trait.authorized_users): updateButton = HT.Href(url="#redirect", onClick="dataEditingFunc(document.getElementsByName('dataInput')[0],'updateRecord');") updateButton_img = HT.Image("/images/edit_icon.jpg", name="update", alt="Edit", title="Edit", style="border:none;") @@ -261,7 +271,7 @@ class ShowTrait(templatePage): # Microarray database information to display - if this_trait and this_trait.db and this_trait.db.type == 'ProbeSet': #before, this line was only reached if this_trait != 0, but now we need to check + if this_trait and this_trait.dataset and this_trait.dataset.type == 'ProbeSet': #before, this line was only reached if this_trait != 0, but now we need to check try: hddn['GeneId'] = int(string.strip(this_trait.geneid)) except: @@ -297,7 +307,7 @@ class ShowTrait(templatePage): geneWikiText = 'GeneWiki' #XZ: display similar traits in other selected datasets - if this_trait and this_trait.db and this_trait.db.type=="ProbeSet" and this_trait.symbol: + if this_trait and this_trait.dataset and this_trait.dataset.type=="ProbeSet" and this_trait.symbol: if _Species in ("mouse", "rat", "human"): similarUrl = "%s?cmd=sch&gene=%s&alias=1&species=%s" % (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), this_trait.symbol, _Species) similarButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % similarUrl) @@ -331,7 +341,7 @@ class ShowTrait(templatePage): ProbeSetXRef.ProbeSetId = ProbeSet.Id AND ProbeSetFreeze.Name = '%s' AND ProbeSet.Name = '%s' AND - Probe.ProbeSetId = ProbeSet.Id order by Probe.SerialOrder""" % (this_trait.db.name, this_trait.name) ) + Probe.ProbeSetId = ProbeSet.Id order by Probe.SerialOrder""" % (this_trait.dataset.name, this_trait.name) ) seqs = self.cursor.fetchall() if not seqs: raise ValueError @@ -350,7 +360,7 @@ class ShowTrait(templatePage): ProbeSetXRef.ProbeSetId = ProbeSet.Id AND ProbeSetFreeze.Name = '%s' AND ProbeSet.Name = '%s' AND - Probe.ProbeSetId = ProbeSet.Id order by Probe.SerialOrder""" % (this_trait.db.name, this_trait.name) ) + Probe.ProbeSetId = ProbeSet.Id order by Probe.SerialOrder""" % (this_trait.dataset.name, this_trait.name) ) seqs = self.cursor.fetchall() for seqt in seqs: @@ -393,7 +403,7 @@ class ShowTrait(templatePage): pass #Display probe information (if any) - if this_trait.db.name.find('Liver') >= 0 and this_trait.db.name.find('F2') < 0: + if this_trait.dataset.name.find('Liver') >= 0 and this_trait.dataset.name.find('F2') < 0: pass else: #query database for number of probes associated with trait; if count > 0, set probe tool button and text @@ -404,7 +414,7 @@ class ShowTrait(templatePage): probeResult = self.cursor.fetchone() if probeResult[0] > 0: probeurl = "%s?FormID=showProbeInfo&database=%s&ProbeSetID=%s&CellID=%s&group=%s&incparentsf1=ON" \ - % (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), this_trait.db, this_trait.name, this_trait.cellid, fd.group) + % (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), this_trait.dataset, this_trait.name, this_trait.cellid, fd.group) probeButton = HT.Href(url="#", onClick="javascript:openNewWin('%s'); return false;" % probeurl) probeButton_img = HT.Image("/images/probe_icon.jpg", name="probe", alt=" Check sequence of probes ", title=" Check sequence of probes ", style="border:none;") #probeButton.append(probeButton_img) @@ -443,7 +453,7 @@ class ShowTrait(templatePage): # select ProbeFreeze.Name from ProbeFreeze, ProbeSetFreeze # where # ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND - # ProbeSetFreeze.Id = %d""" % this_trait.db.id) + # ProbeSetFreeze.Id = %d""" % this_trait.dataset.id) # probeDBName = self.cursor.fetchone()[0] # tbl.append(HT.TR( # HT.TD('Database: ', Class="fs13 fwb", valign="top", nowrap="on"), @@ -454,7 +464,7 @@ class ShowTrait(templatePage): #tbl.append(HT.TR( # HT.TD('Database: ', Class="fs13 fwb", valign="top", nowrap="on"), # HT.TD(width=10, valign="top"), - # HT.TD(HT.Href(text=this_trait.db.fullname, url = webqtlConfig.INFOPAGEHREF % this_trait.db.name, + # HT.TD(HT.Href(text=this_trait.dataset.fullname, url = webqtlConfig.INFOPAGEHREF % this_trait.dataset.name, # target='_blank', Class="fs13 fwn non_bold"), valign="top") # )) #pass @@ -635,7 +645,7 @@ class ShowTrait(templatePage): #Info2Disp.append(linkTable) #title1Body.append(tbl, HT.BR(), menuTable) - elif this_trait and this_trait.db and this_trait.db.type =='Publish': #Check if trait is phenotype + elif this_trait and this_trait.dataset and this_trait.dataset.type =='Publish': #Check if trait is phenotype if this_trait.confidential: pass @@ -723,7 +733,7 @@ class ShowTrait(templatePage): #title1Body.append(tbl, HT.BR(), menuTable) - elif this_trait and this_trait.db and this_trait.db.type == 'Geno': #Check if trait is genotype + elif this_trait and this_trait.dataset and this_trait.dataset.type == 'Geno': #Check if trait is genotype GenoInfo = HT.Paragraph() if this_trait.chr and this_trait.mb: @@ -775,7 +785,7 @@ class ShowTrait(templatePage): #title1Body.append(tbl, HT.BR(), menuTable) - elif (this_trait == None or this_trait.db.type == 'Temp'): #if temporary trait (user-submitted trait or PCA trait) + elif (this_trait == None or this_trait.dataset.type == 'Temp'): #if temporary trait (user-submitted trait or PCA trait) #TempInfo = HT.Paragraph() if this_trait != None: @@ -888,13 +898,13 @@ class ShowTrait(templatePage): # continue vals1.append(thisValFull) - - + + #vals1 = [[sampleNameOrig.replace("_2nd_", ""), # this_trait.data[sampleName].val, # this_trait.data[sampleName].var] # for sampleNameOrig in all_samples]] - # + # #Using just the group sample for sampleNameOrig in primary_samples: @@ -971,11 +981,11 @@ class ShowTrait(templatePage): # #statsTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") - if this_trait.db: + if this_trait.dataset: if this_trait.cellid: - self.stats_data.append(BasicStatisticsFunctions.basicStatsTable(vals=vals, trait_type=this_trait.db.type, cellid=this_trait.cellid)) + self.stats_data.append(BasicStatisticsFunctions.basicStatsTable(vals=vals, trait_type=this_trait.dataset.type, cellid=this_trait.cellid)) else: - self.stats_data.append(BasicStatisticsFunctions.basicStatsTable(vals=vals, trait_type=this_trait.db.type)) + self.stats_data.append(BasicStatisticsFunctions.basicStatsTable(vals=vals, trait_type=this_trait.dataset.type)) else: self.stats_data.append(BasicStatisticsFunctions.basicStatsTable(vals=vals)) @@ -1005,7 +1015,7 @@ class ShowTrait(templatePage): #normalplot_container.append(normalplot) #normalplot_div.append(normalplot_container) #stats_container.append(normalplot_div) - + #boxplot_div = HT.Div(id="statstabs-2") #boxplot_container = HT.Paragraph() #boxplot = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") @@ -1014,8 +1024,8 @@ class ShowTrait(templatePage): #boxplot_container.append(boxplot) #boxplot_div.append(boxplot_container) #stats_container.append(boxplot_div) - - + + #barName_div = HT.Div(id="statstabs-3") #barName_container = HT.Paragraph() #barName = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") @@ -1033,17 +1043,17 @@ class ShowTrait(templatePage): #barRank_container.append(barRank) #barRank_div.append(barRank_container) #stats_container.append(barRank_div) - + # stats_cell.append(stats_container) # #stats_script.append(stats_script_text) # #submitTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%", Class="target2") #stats_row.append(stats_cell) - + #submitTable.append(stats_row) #submitTable.append(stats_script) - + #title2Body.append(submitTable) @@ -1052,7 +1062,7 @@ class ShowTrait(templatePage): #species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, group=fd.group) this_group = fd.group - + # We're checking a string here! assert isinstance(this_group, basestring), "We need a string type thing here" if this_group[:3] == 'BXD': @@ -1072,17 +1082,17 @@ class ShowTrait(templatePage): dataset_menu = [] print("[tape4] webqtlConfig.PUBLICTHRESH:", webqtlConfig.PUBLICTHRESH) print("[tape4] type webqtlConfig.PUBLICTHRESH:", type(webqtlConfig.PUBLICTHRESH)) - self.cursor.execute('''SELECT PublishFreeze.FullName,PublishFreeze.Name FROM - PublishFreeze,InbredSet WHERE PublishFreeze.InbredSetId = InbredSet.Id - and InbredSet.Name = %s and PublishFreeze.public > %s''', + self.cursor.execute('''SELECT PublishFreeze.FullName,PublishFreeze.Name FROM + PublishFreeze,InbredSet WHERE PublishFreeze.InbredSetId = InbredSet.Id + and InbredSet.Name = %s and PublishFreeze.public > %s''', (this_group, webqtlConfig.PUBLICTHRESH)) for item in self.cursor.fetchall(): dataset_menu.append(dict(tissue=None, datasets=[item])) self.cursor.execute('''SELECT GenoFreeze.FullName,GenoFreeze.Name FROM GenoFreeze, - InbredSet WHERE GenoFreeze.InbredSetId = InbredSet.Id and InbredSet.Name = - %s and GenoFreeze.public > %s''', + InbredSet WHERE GenoFreeze.InbredSetId = InbredSet.Id and InbredSet.Name = + %s and GenoFreeze.public > %s''', (this_group, webqtlConfig.PUBLICTHRESH)) for item in self.cursor.fetchall(): dataset_menu.append(dict(tissue=None, @@ -1109,19 +1119,19 @@ class ShowTrait(templatePage): datasets=dataset_sub_menu)) # ("**heading**", tissue_name)) #dataset_menu.append(dataset_sub_menu) - + dataset_menu_selected = None if len(dataset_menu): - if this_trait and this_trait.db: - dataset_menu_selected = this_trait.db.name + if this_trait and this_trait.dataset: + dataset_menu_selected = this_trait.dataset.name #criteriaText = HT.Span("Return:", Class="ffl fwb fs12") #criteriaMenu1 = HT.Select(name='criteria1', selected='500', onMouseOver="if (NS4 || IE4) activateEl('criterias', event);") - + return_results_menu = (100, 200, 500, 1000, 2000, 5000, 10000, 15000, 20000) return_results_menu_selected = 500 - + #criteriaMenu1.append(('top 100','100')) #criteriaMenu1.append(('top 200','200')) #criteriaMenu1.append(('top 500','500')) @@ -1159,7 +1169,7 @@ class ShowTrait(templatePage): #corr_row = HT.TR() #corr_container = HT.Div(id="corr_tabs", Class="ui-tabs") # - #if (this_trait.db != None and this_trait.db.type =='ProbeSet'): + #if (this_trait.dataset != None and this_trait.dataset.type =='ProbeSet'): # corr_tab_list = [HT.Href(text='Sample r', url="#corrtabs-1"), # HT.Href(text='Literature r', url="#corrtabs-2"), # HT.Href(text='Tissue r', url="#corrtabs-3")] @@ -1210,8 +1220,8 @@ class ShowTrait(templatePage): #literature_container.append(literatureTable) #literature_div.append(literature_container) # - #if this_trait.db != None: - # if (this_trait.db.type =='ProbeSet'): + #if this_trait.dataset != None: + # if (this_trait.dataset.type =='ProbeSet'): # corr_container.append(literature_div) # #tissue_div = HT.Div(id="corrtabs-3") @@ -1235,8 +1245,8 @@ class ShowTrait(templatePage): # #tissue_container.append(tissueTable) #tissue_div.append(tissue_container) - #if this_trait.db != None: - # if (this_trait.db.type =='ProbeSet'): + #if this_trait.dataset != None: + # if (this_trait.dataset.type =='ProbeSet'): # corr_container.append(tissue_div) # #corr_row.append(HT.TD(corr_container)) @@ -1538,7 +1548,7 @@ class ShowTrait(templatePage): if other_sample_names: par_f1_samples = fd.parlist + fd.f1list - + other_sample_names.sort() #Sort other samples other_sample_names = par_f1_samples + other_sample_names @@ -1549,13 +1559,13 @@ class ShowTrait(templatePage): this_trait=this_trait, sample_group_type='other', header="Non-%s" % (fd.group)) - + 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_sample_names 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 diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index 54cdd42b..35ff4e8e 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -39,6 +39,7 @@ {% for header in header_fields %} <th>{{header}}</th> {% endfor %} + </tr> </thead> <tbody> diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index fb93af53..cdc3379f 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -67,7 +67,7 @@ def search_page(): #print("trait_list is:", pf(the_search.__dict__['trait_list'][0].__dict__)) #for trait in the_search.trait_list: # print(" -", trait.description_display) - + return render_template("search_result_page.html", **the_search.__dict__) @@ -87,6 +87,7 @@ def whats_new_page(): def show_trait_page(): # Here it's currently too complicated not to use an fd that is a webqtlFormData fd = webqtlFormData.webqtlFormData(request.args) + print("stp y1:", pf(vars(fd))) template_vars = show_trait.ShowTrait(fd) template_vars.js_data = json.dumps(template_vars.js_data, default=json_default_handler, |