From b8fa8728b7afebbada49f29b85fa5db40e137e1b Mon Sep 17 00:00:00 2001
From: Zachary Sloan
Date: Fri, 30 Nov 2012 16:19:30 -0600
Subject: Finished pValue search Got headers working in search page
---
wqflask/wqflask/do_search.py | 137 ++++++++++++++++++----
wqflask/wqflask/search_results.py | 8 +-
wqflask/wqflask/show_trait/show_trait.py | 126 +++++++++++---------
wqflask/wqflask/templates/search_result_page.html | 1 +
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 %}
| {{header}} |
{% endfor %}
+
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,
--
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