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-rw-r--r--misc/notes.txt2
-rw-r--r--wqflask/wqflask/do_search.py140
-rw-r--r--wqflask/wqflask/search_results.py306
-rw-r--r--wqflask/wqflask/templates/base.html13
-rw-r--r--wqflask/wqflask/templates/index_page.html8
-rw-r--r--wqflask/wqflask/templates/search_result_page.html27
-rw-r--r--wqflask/wqflask/templates/show_trait.html32
7 files changed, 281 insertions, 247 deletions
diff --git a/misc/notes.txt b/misc/notes.txt
index e7b94087..b3678a04 100644
--- a/misc/notes.txt
+++ b/misc/notes.txt
@@ -41,7 +41,7 @@ Go to /tmp and tail -f flask_gn_log
Coffeescript Stuff:
coffee -c (filename)
-coffee -c -w (to watch for changes and recompile)
+coffee -c -w . (to watch for changes and recompile in current directory; the "." is for current directory)
coffee --help (for information about setting options)
===========================================
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index cfa73334..19c6fa74 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -7,31 +7,35 @@ from pprint import pformat as pf
class DoSearch(object):
+ """Parent class containing parameters/functions used for all searches"""
+
def __init__(self, search_term, dataset, cursor, db_conn):
self.search_term = search_term
self.dataset = dataset
self.db_conn = db_conn
self.cursor = cursor
-
+
def execute(self, query):
+ """Executes query and returns results"""
query = self.normalize_spaces(query)
- print("query is:", pf(query))
+ print("in do_search query is:", pf(query))
self.cursor.execute(query)
results = self.cursor.fetchall()
return results
-
+
def escape(self, stringy):
"""Shorter name than self.db_conn.escape_string"""
return self.db_conn.escape_string(str(stringy))
-
+
def normalize_spaces(self, stringy):
- """Strips out newlines extra spaces and replaces them with just spaces"""
+ """Strips out newlines extra spaces and replaces them with just spaces"""
step_one = " ".join(stringy.split())
return step_one
-
-
+
class ProbeSetSearch(DoSearch):
+ """A search within an mRNA expression dataset"""
+
base_query = """SELECT ProbeSet.Name as TNAME,
0 as thistable,
ProbeSetXRef.Mean as TMEAN,
@@ -42,9 +46,11 @@ class ProbeSetSearch(DoSearch):
ProbeSet.Symbol as TSYMBOL,
ProbeSet.name_num as TNAME_NUM
FROM ProbeSetXRef, ProbeSet """
-
+
def run(self):
+ """Generates and runs a simple search of an mRNA expression dataset"""
+ print("Running ProbeSetSearch")
query = (self.base_query +
"""WHERE (MATCH (ProbeSet.Name,
ProbeSet.description,
@@ -57,18 +63,22 @@ class ProbeSetSearch(DoSearch):
and ProbeSet.Id = ProbeSetXRef.ProbeSetId
and ProbeSetXRef.ProbeSetFreezeId = %s
""" % (self.escape(self.search_term),
- self.escape(dataset.id)))
-
+ self.escape(self.dataset.id)))
+
+ print("final query is:", pf(query))
+
return self.execute(query)
class PhenotypeSearch(DoSearch):
+ """A search within a phenotype dataset"""
+
base_query = """SELECT PublishXRef.Id,
PublishFreeze.createtime as thistable,
Publication.PubMed_ID as Publication_PubMed_ID,
Phenotype.Post_publication_description as Phenotype_Name
FROM Phenotype, PublishFreeze, Publication, PublishXRef """
-
+
search_fields = ('Phenotype.Post_publication_description',
'Phenotype.Pre_publication_description',
'Phenotype.Pre_publication_abbreviation',
@@ -78,65 +88,108 @@ class PhenotypeSearch(DoSearch):
'Publication.Abstract',
'Publication.Title',
'Publication.Authors',
- 'PublishXRef.Id')
-
- def run(self):
+ 'PublishXRef.Id')
+
+ def get_where_clause(self):
+ """Generate clause for WHERE portion of query"""
+
#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 + "[[:>:]]"
+ # This adds a clause to the query that matches the search term
+ # against each field in the search_fields tuple
where_clause = []
for field in self.search_fields:
where_clause.append('''%s REGEXP "%s"''' % (field, search_term))
-
where_clause = "(%s)" % ' OR '.join(where_clause)
+ return where_clause
+
+ def run(self):
+ """Generates and runs a simple search of a phenotype dataset"""
+
#Get group information for dataset
self.dataset.get_group()
-
- print("before query where clause is:", where_clause)
-
+
query = (self.base_query +
"""WHERE %s and
PublishXRef.InbredSetId = %s and
PublishXRef.PhenotypeId = Phenotype.Id and
PublishXRef.PublicationId = Publication.Id and
PublishFreeze.Id = %s""" % (
- where_clause,
+ self.get_where_clause(),
self.escape(self.dataset.group_id),
self.escape(self.dataset.id)))
+ return self.execute(query)
+class GenotypeSearch(DoSearch):
+ """A search within a genotype dataset"""
+
+ base_query = """SELECT Geno.Name,
+ GenoFreeze.createtime as thistable,
+ Geno.Name as Geno_Name,
+ Geno.Source2 as Geno_Source2,
+ Geno.chr_num as Geno_chr_num,
+ Geno.Mb as Geno_Mb
+ FROM GenoXRef, GenoFreeze, Geno """
+
+ search_fields = ('Name', 'Chr')
+
+ def get_where_clause(self):
+ """Generate clause for 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 = []
+ for field in self.search_fields:
+ where_clause.append('''%s REGEXP "%s"''' % ("%s.%s" % (self.dataset.type, field),
+ self.search_term))
+ where_clause = "(%s)" % ' OR '.join(where_clause)
+
+ return where_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 + "[[:>:]]"
+
+ 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)))
+
return self.execute(query)
-
-class GenotypeSearch(DoSearch):
- def __init__(self):
- pass
-
class GoSearch(ProbeSetSearch):
- """searches for synapse-associated genes listed in the Gene Ontology."""
-
+ """Searches for synapse-associated genes listed in the Gene Ontology."""
+
def run(self):
field = 'GOterm.acc'
go_id = 'GO:' + ('0000000'+self.search_term)[-7:]
-
+
statements = ("""%s.symbol=GOgene_product.symbol and
GOassociation.gene_product_id=GOgene_product.id and
GOterm.id=GOassociation.term_id""" % (
self.db_conn.escape_string(self.dataset.type)))
-
+
clause_item = " %s = '%s' and %s " % (field, go_id, statements)
-
+
+ #
gene_ontology_from_table = """ , db_GeneOntology.term as GOterm,
db_GeneOntology.association as GOassociation,
db_GeneOntology.gene_product as GOgene_product """
-
+
gene_ontology_from_table = self.normalize_spaces(gene_ontology_from_table)
- #gene_ontology_from_table = " ".join(gene_ontology_from_table.splitlines())
-
+
query = (self.base_query +
"""%s
WHERE %s
@@ -145,36 +198,37 @@ class GoSearch(ProbeSetSearch):
""" % (self.db_conn.escape_string(gene_ontology_from_table),
clause_item,
self.db_conn.escape_string(str(self.dataset.id))))
-
+
return self.execute(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
+
import MySQLdb
import sys
sys.path.append("/home/zas1024/gene/wqflask")
print("Path is:", sys.path)
-
-
+
+
from base import webqtlConfig
from base.webqtlDataset import webqtlDataset
from base.templatePage import templatePage
from utility import webqtlUtil
from dbFunction import webqtlDatabaseFunction
-
+
db_conn = MySQLdb.Connect(db=webqtlConfig.DB_NAME,
host=webqtlConfig.MYSQL_SERVER,
user=webqtlConfig.DB_USER,
passwd=webqtlConfig.DB_PASSWD)
cursor = db_conn.cursor()
-
+
dataset_name = "HC_M2_0606_P"
dataset = webqtlDataset(dataset_name, cursor)
-
- #results = ProbeSetSearch("salt", dataset, cursor, db_conn).run()
+
+ results = ProbeSetSearch("salt", dataset, cursor, db_conn).run()
#results = PhenotypeSearch("brain", dataset, cursor, db_conn).run()
-
- results = GoSearch("0045202", dataset, cursor, db_conn).run()
+ #results = GenotypeSearch("rs13475699", dataset, cursor, db_conn).run()
+ #results = GoSearch("0045202", dataset, cursor, db_conn).run()
print("results are:", pf(results)) \ No newline at end of file
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 02d2bef2..51204ddf 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -33,14 +33,12 @@ from base.webqtlDataset import webqtlDataset
from base.webqtlTrait import webqtlTrait
from base.templatePage import templatePage
from wqflask import parser
+from wqflask import do_search
from utility import webqtlUtil
from dbFunction import webqtlDatabaseFunction
from utility import formatting
-import sys
-
-
#from base.JinjaPage import JinjaEnv, JinjaPage
@@ -194,7 +192,7 @@ class SearchResultPage(templatePage):
self.search_fields = ['Name','Chr']
- self.do_search()
+ self.search()
self.gen_search_result()
###########################################
@@ -635,167 +633,167 @@ class SearchResultPage(templatePage):
return 0
- def do_search(self):
+ def search(self):
print("fd.search_terms:", self.fd['search_terms'])
self.search_terms = parser.parse(self.fd['search_terms'])
print("After parsing:", self.search_terms)
-
-
- #print("ORkeyword is:", pf(self.ORkeyword))
- #self.ANDkeyword2 = parser.parse(self.ANDkeyword)
- #self.ORkeyword2 = parser.parse(self.ORkeyword)
- #print("ORkeyword2 is:", pf(parser.parse(self.ORkeyword)))
-
- #self.ANDkeyword2 = re.sub(self._1mPattern, '', self.ANDkeyword)
- #self.ANDkeyword2 = re.sub(self._2mPattern, '', self.ANDkeyword2)
- #self.ANDkeyword2 = re.sub(self._3mPattern, '', self.ANDkeyword2)
- #self.ANDkeyword2 = re.sub(self._5mPattern, '', self.ANDkeyword2)
- ###remove remain parethesis, could be input with syntax error
- #self.ANDkeyword2 = re.sub(re.compile('\s*\([\s\S]*\)'), '', self.ANDkeyword2)
- #self.ANDkeyword2 = self.encregexp(self.ANDkeyword2)
-
- #self.ORkeyword2 = re.sub(self._1mPattern, '', self.ORkeyword)
- #self.ORkeyword2 = re.sub(self._2mPattern, '', self.ORkeyword2)
- #self.ORkeyword2 = re.sub(self._3mPattern, '', self.ORkeyword2)
- #self.ORkeyword2 = re.sub(self._5mPattern, '', self.ORkeyword2)
- ###remove remain parethesis, could be input with syntax error
- #self.ORkeyword2 = re.sub(re.compile('\s*\([\s\S]*\)'), '', self.ORkeyword2)
- #self.ORkeyword2 = self.encregexp(self.ORkeyword2)
self.results = []
- for item in self.search_terms:
- search_term = item['search_term']
- # self.nkeywords += 1
- # #ZS: If there are both AND and OR keywords, just use the OR keywords
- # if k >=len(self.ORkeyword2):
- # query = self.ANDQuery
- # DescriptionText = self.ANDDescriptionText
- # clausejoin = ' OR '
- # fulltext = ANDFulltext
- # else:
- # query = self.ORQuery
- # DescriptionText = self.ORDescriptionText
- # clausejoin = ' OR '
- # fulltext = ORFulltext
-
- print("item is:", pf(search_term))
-
-
-# clause_item = (
-#""" MATCH (ProbeSet.Name,
+ for a_search in self.search_terms:
+ print("[kodak] item is:", pf(a_search))
+ search_term = None
+ search_type = None
+ if "search_term" in a_search:
+ search_term = a_search['search_term']
+ elif key in a_search:
+ search_type = a_search['key']
+
+
+ if search_term:
+ if self.dataset.type == "ProbeSet":
+ search_ob = "ProbeSetSearch"
+ elif self.dataset.type == "Publish":
+ search_ob = "PhenotypeSearch"
+ elif self.dataset.type == "Geno":
+ search_ob = "GenotypeSearch"
+ else:
+ SearchTermNeedsToBeDefined # Cause an error on purpose
+ search_class = getattr(do_search, search_ob)
+ results = search_class(search_term,
+ self.dataset,
+ self.cursor,
+ self.db_conn).run()
+
+ print("in the search results are:", results)
+#
+#
+## clause_item = (
+##""" MATCH (ProbeSet.Name,
+## ProbeSet.description,
+## ProbeSet.symbol,
+## alias,
+## GenbankId,
+## UniGeneId,
+## Probe_Target_Description)
+## AGAINST ('%s' IN BOOLEAN MODE) """ % self.db_conn.escape_string(search_term))
+# if self.dataset.type == "ProbeSet":
+#
+# query = (
+#"""SELECT distinct 0,
+# ProbeSet.Name as TNAME,
+# 0 as thistable,
+# ProbeSetXRef.Mean as TMEAN,
+# ProbeSetXRef.LRS as TLRS,
+# ProbeSetXRef.PVALUE as TPVALUE,
+# ProbeSet.Chr_num as TCHR_NUM,
+# ProbeSet.Mb as TMB,
+# ProbeSet.Symbol as TSYMBOL,
+# ProbeSet.name_num as TNAME_NUM
+# FROM ProbeSetXRef, ProbeSet
+# WHERE (MATCH (ProbeSet.Name,
# ProbeSet.description,
# ProbeSet.symbol,
# alias,
# GenbankId,
# UniGeneId,
# Probe_Target_Description)
-# AGAINST ('%s' IN BOOLEAN MODE) """ % self.db_conn.escape_string(search_term))
- if self.dataset.type == "ProbeSet":
-
- query = (
-"""SELECT distinct 0, ProbeSet.Name as TNAME, 0 as thistable,
- ProbeSetXRef.Mean as TMEAN,
- ProbeSetXRef.LRS as TLRS,
- ProbeSetXRef.PVALUE as TPVALUE,
- ProbeSet.Chr_num as TCHR_NUM,
- ProbeSet.Mb as TMB,
- ProbeSet.Symbol as TSYMBOL,
- ProbeSet.name_num as TNAME_NUM
- FROM ProbeSetXRef, ProbeSet
- WHERE (MATCH (ProbeSet.Name,
- ProbeSet.description,
- ProbeSet.symbol,
- alias,
- GenbankId,
- UniGeneId,
- Probe_Target_Description)
- AGAINST ('%s' IN BOOLEAN MODE))
- and ProbeSet.Id = ProbeSetXRef.ProbeSetId
- and ProbeSetXRef.ProbeSetFreezeId = %s
- """ % (self.db_conn.escape_string(search_term),
- self.db_conn.escape_string(str(self.dataset.id))))
-
- elif self.dataset.type == "Publish":
- include_geno = ""
- if search_term.find("Geno.name") >= 0:
- include_geno = " Geno, "
-
- query = (
-"""SELECT 0, PublishXRef.Id, PublishFreeze.createtime as thistable,
- Publication.PubMed_ID as Publication_PubMed_ID,
- Phenotype.Post_publication_description as Phenotype_Name
- FROM %s PublishFreeze, Publication, PublishXRef, Phenotype
- WHERE (MATCH (ProbeSet.Name,
- ProbeSet.description,
- ProbeSet.symbol,
- alias,
- GenbankId,
- UniGeneId,
- Probe_Target_Description)
- AGAINST ('%s' IN BOOLEAN MODE)) and
- PublishXRef.InbredSetId = %s and
- PublishXRef.PhenotypeId = Phenotype.Id and
- PublishXRef.PublicationId = Publication.Id and
- PublishFreeze.Id = %s
- """ % (include_geno,
- self.db_conn.escape_string(search_term),
- self.db_conn.escape_string(str(self.dataset.group_id)),
- self.db_conn.escape_string(str(self.dataset.id))))
-
- elif self.dataset.type == "Geno":
- query = (
-"""SELECT 0, Geno.Name, GenoFreeze.createtime as thistable,
- Geno.Name as Geno_Name,
- Geno.Source2 as Geno_Source2,
- Geno.chr_num as Geno_chr_num,
- Geno.Mb as Geno_Mb
- FROM GenoXRef, GenoFreeze, Geno
- WHERE (MATCH (ProbeSet.Name,
- ProbeSet.description,
- ProbeSet.symbol,
- alias,
- GenbankId,
- UniGeneId,
- Probe_Target_Description)
- AGAINST ('%s' IN BOOLEAN MODE)) and
- and Geno.Id = GenoXRef.GenoId and
- GenoXRef.GenoFreezeId = GenoFreeze.Id and
- GenoFreeze.Id = %d
- """% (self.db_conn.escape_string(search_term),
- self.db_conn.escape_string(str(self.dataset.id))))
-
-
- self.cursor.execute(query)
- self.results.append(self.cursor.fetchall())
-
- print("self.results is:", pf(self.results))
-
-
-
-
- #if self.dataset.type == "ProbeSet" and search_term.find('.') < 0 and search_term.find('\'') < 0:
- # full_text.append(search_term)
- #else:
- # if self.matchwhole and search_term.find("'") < 0:
- # search_term = "[[:<:]]"+ search_term+"[[:>:]]"
- # clause2 = []
- # for field in self.search_fields:
- # if self.dataset.type == "Publish":
- # clause2.append("%s REGEXP \"%s\"" % (field,search_term))
- # else:
- # clause2.append("%s REGEXP \"%s\"" % ("%s.%s" % (self.dataset.type,field),search_term))
- # clause_item = "(%s)" % string.join(clause2, clausejoin)
- # query.append(" (%s) " % clause_item)
- #if ANDFulltext:
- # clauseItem = """ MATCH (ProbeSet.Name,ProbeSet.description,ProbeSet.symbol,
- # alias,GenbankId, UniGeneId, Probe_Target_Description)
- # AGAINST ('+%s' IN BOOLEAN MODE) """ % string.join(ANDFulltext, " +")
- # self.ANDQuery.append(" (%s) " % clauseItem)
- #if ORFulltext:
- #clauseItem = """ MATCH (ProbeSet.Name,ProbeSet.description,ProbeSet.symbol,alias,
- #GenbankId, UniGeneId, Probe_Target_Description) AGAINST ('%s' IN BOOLEAN MODE)
- #""" % string.join(full_text, " ")
- #self.query.append(" (%s) " % clauseItem)
+# AGAINST ('%s' IN BOOLEAN MODE))
+# and ProbeSet.Id = ProbeSetXRef.ProbeSetId
+# and ProbeSetXRef.ProbeSetFreezeId = %s
+# """ % (self.db_conn.escape_string(search_term),
+# self.db_conn.escape_string(str(self.dataset.id))))
+#
+# elif self.dataset.type == "Publish":
+# include_geno = ""
+# if search_term.find("Geno.name") >= 0:
+# include_geno = " Geno, "
+#
+# if self.matchwhole and item.find("'") < 0:
+# item = "[[:<:]]"+ item+"[[:>:]]"
+# clause2 = []
+# for field in self.searchField:
+# if self.dbType == "Publish":
+# clause2.append("%s REGEXP \"%s\"" % (field,item))
+# else:
+# clause2.append("%s REGEXP \"%s\"" % ("%s.%s" % (self.dbType,field),item))
+#
+#
+# query = (
+#"""SELECT 0, PublishXRef.Id, PublishFreeze.createtime as thistable,
+# Publication.PubMed_ID as Publication_PubMed_ID,
+# Phenotype.Post_publication_description as Phenotype_Name
+# FROM %s PublishFreeze, Publication, PublishXRef, Phenotype
+# WHERE (MATCH (ProbeSet.Name,
+# ProbeSet.description,
+# ProbeSet.symbol,
+# alias,
+# GenbankId,
+# UniGeneId,
+# Probe_Target_Description)
+# AGAINST ('%s' IN BOOLEAN MODE)) and
+# PublishXRef.InbredSetId = %s and
+# PublishXRef.PhenotypeId = Phenotype.Id and
+# PublishXRef.PublicationId = Publication.Id and
+# PublishFreeze.Id = %s
+# """ % (include_geno,
+# self.db_conn.escape_string(search_term),
+# self.db_conn.escape_string(str(self.dataset.group_id)),
+# self.db_conn.escape_string(str(self.dataset.id))))
+#
+# elif self.dataset.type == "Geno":
+# query = (
+#"""SELECT 0, Geno.Name, GenoFreeze.createtime as thistable,
+# Geno.Name as Geno_Name,
+# Geno.Source2 as Geno_Source2,
+# Geno.chr_num as Geno_chr_num,
+# Geno.Mb as Geno_Mb
+# FROM GenoXRef, GenoFreeze, Geno
+# WHERE (MATCH (ProbeSet.Name,
+# ProbeSet.description,
+# ProbeSet.symbol,
+# alias,
+# GenbankId,
+# UniGeneId,
+# Probe_Target_Description)
+# AGAINST ('%s' IN BOOLEAN MODE)) and
+# and Geno.Id = GenoXRef.GenoId and
+# GenoXRef.GenoFreezeId = GenoFreeze.Id and
+# GenoFreeze.Id = %d
+# """% (self.db_conn.escape_string(search_term),
+# self.db_conn.escape_string(str(self.dataset.id))))
+#
+#
+# self.cursor.execute(query)
+# self.results.append(self.cursor.fetchall())
+#
+# print("self.results is:", pf(self.results))
+#
+#
+#
+#
+# #if self.dataset.type == "ProbeSet" and search_term.find('.') < 0 and search_term.find('\'') < 0:
+# # full_text.append(search_term)
+# #else:
+# # if self.matchwhole and search_term.find("'") < 0:
+# # search_term = "[[:<:]]"+ search_term+"[[:>:]]"
+# # clause2 = []
+# # for field in self.search_fields:
+# # if self.dataset.type == "Publish":
+# # clause2.append("%s REGEXP \"%s\"" % (field,search_term))
+# # else:
+# # clause2.append("%s REGEXP \"%s\"" % ("%s.%s" % (self.dataset.type,field),search_term))
+# # clause_item = "(%s)" % string.join(clause2, clausejoin)
+# # query.append(" (%s) " % clause_item)
+# #if ANDFulltext:
+# # clauseItem = """ MATCH (ProbeSet.Name,ProbeSet.description,ProbeSet.symbol,
+# # alias,GenbankId, UniGeneId, Probe_Target_Description)
+# # AGAINST ('+%s' IN BOOLEAN MODE) """ % string.join(ANDFulltext, " +")
+# # self.ANDQuery.append(" (%s) " % clauseItem)
+# #if ORFulltext:
+# #clauseItem = """ MATCH (ProbeSet.Name,ProbeSet.description,ProbeSet.symbol,alias,
+# #GenbankId, UniGeneId, Probe_Target_Description) AGAINST ('%s' IN BOOLEAN MODE)
+# #""" % string.join(full_text, " ")
+# #self.query.append(" (%s) " % clauseItem)
def encregexp(self,str):
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 385512e3..b54d3424 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -1,7 +1,7 @@
<!DOCTYPE HTML>
<html lang="en">
<html xmlns="http://www.w3.org/1999/xhtml">
-
+
<head>
<meta charset="utf-8">
<title>GeneNetwork</title>
@@ -67,9 +67,9 @@
</div>
</div>
</div>
-
+
{% block content %}{% endblock %}
-
+
<!-- Footer
================================================== -->
<footer class="footer">
@@ -146,11 +146,10 @@
}
})
</script>
- <!--<SCRIPT SRC="/javascript/webqtl.js"></SCRIPT>-->
- <!--<script src="/static/new/javascript/dataset_menu_structure.json"></script>-->
- <!--<script src="/static/new/javascript/dataset_select_items.js"></script>-->
<script src="/static/new/js_external/jquery.cookie.js"></script>
<script type="text/javascript" src="/static/new/js_external/json2.js"></script>
- <script src="/static/new/javascript/dataset_select_menu.js"></script>
+ <script src="http://ajax.googleapis.com/ajax/libs/jqueryui/1.8.12/jquery-ui.min.js" type="text/javascript"></script>
+ {% block js %}
+ {% endblock %}
</body>
</html>
diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html
index 2d7ba44c..a113bc15 100644
--- a/wqflask/wqflask/templates/index_page.html
+++ b/wqflask/wqflask/templates/index_page.html
@@ -1,6 +1,6 @@
{% extends "base.html" %}
{% block title %}GeneNetwork{% endblock %}
-{% block content %}
+{% block content %}
<!-- Start of body -->
@@ -275,4 +275,8 @@
</div>
</div>
-{%endblock%} \ No newline at end of file
+{%endblock%}
+
+{% block js %}
+ <script src="/static/new/javascript/dataset_select_menu.js"></script>
+{% endblock %}
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index abf2dba7..65182e1f 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -15,9 +15,9 @@
<div class="page-header">
<h1>Your Search</h1>
</div>
-
+
<p>We searched <a href="/dbdoc/{{dataset.fullname}}">{{ dataset.fullname }}</a><//>
-
+
<p>To find all records that match:</p>
<ul>
{% if search_terms %}
@@ -28,10 +28,10 @@
</li>
{% endif %}
</ul>
-
+
<p>To study a record, click on its ID below.<br />
Check records below and click Add button to add to selection.</p>
-
+
<div class="bs-docs-example">
<table class="table table-hover">
<thead>
@@ -40,7 +40,7 @@
<th>{{header}}</th>
{% endfor %}
</thead>
-
+
<tbody>
{% for this_trait in trait_list %}
<TR id="{{ this_trait }}">
@@ -56,12 +56,7 @@
{{ this_trait.name.upper() }}
</a>
</TD>
- <TD>
- <A HREF=
- "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids={{this_trait.geneid}}" TARGET="_blank">
- {{ this_trait.symbol }}
- </A>
- </TD>
+ <TD>{{ this_trait.symbol }}</TD>
<TD>{{ this_trait.description_display }}</TD>
<TD>{{ this_trait.trait_location_repr }}</TD>
<TD>{{ this_trait.mean }}</TD>
@@ -70,20 +65,20 @@
</TR>
{% endfor %}
</tbody>
-
+
</table>
-
+
<br />
-
+
<button class="btn"><i class="icon-ok"></i> Select</button>
<button class="btn"><i class="icon-remove"></i> Deselect</button>
<button class="btn"><i class="icon-resize-vertical"></i> Invert</button>
<button class="btn"><i class="icon-plus-sign"></i> Add</button>
<button class="btn btn-primary pull-right"><i class="icon-download icon-white"></i> Download Table</button>
</div>
-
+
</div>
-
+
<!-- End of body -->
{% endblock %}
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index d7b81562..79f6e78e 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -106,14 +106,6 @@
<br>
<input type="button" name="Default_Name" class="btn update" value=" Update Figures "><br>
<br>
- <script language="Javascript" type="text/javascript">
- <!--
-
- //$(function() { $("#stats_tabs0").tabs(); $("#stats_tabs1").tabs(); $("#stats_tabs2").tabs();});
-
- //
- -->
- </script>
<table cellpadding="0" cellspacing="0" border="0" class="display" id="stats_dyn"></table>
@@ -669,13 +661,7 @@
<p class="sectionheader" id="title4" style="border-radius: 5px;">&nbsp;&nbsp;Mapping Tools</p>
- <p id="sectionbody4"></p><script language="Javascript" type="text/javascript">
- <!--
-
- //$(function() { $("#mapping_tabs").tabs(); });
-
- //-->
- </script>
+ <p id="sectionbody4"></p>
<table class="target2" cellpadding="0" cellspacing="0" width="100%">
<tr>
@@ -1055,7 +1041,7 @@
<p class="sectionheader" id="title5" style="border-radius: 5px;">&nbsp;&nbsp;Review and Edit Data</p>
- <table id="stats_table" class="one-column-emphasis" />
+ <table id="stats_table" class="table table-striped table-bordered" />
<p id="sectionbody5"></p>
@@ -1230,6 +1216,12 @@
</td>
</tr>
</div>
+
+ <!-- End of body -->
+
+{% endblock %}
+
+{% block js %}
<script>
js_data = {{ js_data | safe }}
</script>
@@ -1240,13 +1232,5 @@
<script type="text/javascript" src="/static/new/javascript/stats.js"></script>
<script type="text/javascript" src="/static/new/javascript/show_trait.js"></script>
- <script type="text/javascript" src="/static/new/js_external/json2.js"></script>
<script type="text/javascript" src="/static/new/javascript/validation.js"></script>
-
-
- <!-- End of body -->
-
-
-
-
{% endblock %}