diff options
| -rw-r--r-- | misc/notes.txt | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/do_search.py | 140 | ||||
| -rw-r--r-- | wqflask/wqflask/search_results.py | 306 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/base.html | 13 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/index_page.html | 8 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/search_result_page.html | 27 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait.html | 32 |
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(); $("#stats_tabs2").tabs();}); - - // - --> - </script> <table cellpadding="0" cellspacing="0" border="0" class="display" id="stats_dyn"></table> @@ -669,13 +661,7 @@ <p class="sectionheader" id="title4" style="border-radius: 5px;"> Mapping Tools</p> - <p id="sectionbody4"></p><script language="Javascript" type="text/javascript"> - <!-- - - //$(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;"> 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 %} |