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-rwxr-xr-xwqflask/base/data_set.py34
-rwxr-xr-xwqflask/base/webqtlTrait.py15
-rw-r--r--wqflask/wqflask/do_search.py101
-rw-r--r--wqflask/wqflask/search_results.py2
4 files changed, 103 insertions, 49 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 34e5eaa1..cd9e810e 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -90,9 +90,7 @@ class DataSet(object):
def get_group(self):
- assert self.cursor
- self.cursor.execute(self.query)
- self.group, self.group_id = self.cursor.fetchone()
+ self.group, self.group_id = g.db.execute(self.query).fetchone()
if self.group == 'BXD300':
self.group = "BXD"
#return group
@@ -107,7 +105,7 @@ class DataSet(object):
"""
- query_args = tuple(self.db_conn.escape_string(x) for x in (
+ query_args = tuple(escape(x) for x in (
(self.type + "Freeze"),
str(webqtlConfig.PUBLICTHRESH),
self.name,
@@ -115,18 +113,22 @@ class DataSet(object):
self.name))
print("query_args are:", query_args)
- query = '''
- SELECT
- Id, Name, FullName, ShortName
- FROM
- %s
- WHERE
- public > %s AND
- (Name = "%s" OR FullName = "%s" OR ShortName = "%s")
- ''' % (query_args)
+ print("""
+ SELECT Id, Name, FullName, ShortName
+ FROM %s
+ WHERE public > %s AND
+ (Name = '%s' OR FullName = '%s' OR ShortName = '%s')
+ """ % (query_args))
+
+ self.id, self.name, self.fullname, self.shortname = g.db.execute("""
+ SELECT Id, Name, FullName, ShortName
+ FROM %s
+ WHERE public > %s AND
+ (Name = '%s' OR FullName = '%s' OR ShortName = '%s')
+ """ % (query_args)).fetchone()
- self.cursor.execute(query)
- self.id, self.name, self.fullname, self.shortname = self.cursor.fetchone()
+ #self.cursor.execute(query)
+ #self.id, self.name, self.fullname, self.shortname = self.cursor.fetchone()
#def genHTML(self, Class='c0dd'):
@@ -185,7 +187,7 @@ class PhenotypeDataSet(DataSet):
WHERE
PublishFreeze.InbredSetId = InbredSet.Id AND
PublishFreeze.Name = "%s"
- ''' % self.db_conn.escape_string(self.name)
+ ''' % escape(self.name)
def check_confidentiality(self):
# (Urgently?) Need to write this
diff --git a/wqflask/base/webqtlTrait.py b/wqflask/base/webqtlTrait.py
index 1dceba08..9763e441 100755
--- a/wqflask/base/webqtlTrait.py
+++ b/wqflask/base/webqtlTrait.py
@@ -30,9 +30,9 @@ class webqtlTrait:
self.cellid = kw.get('cellid', None)
self.identification = kw.get('identification', 'un-named trait')
self.group = kw.get('group', None)
- self.haveinfo = kw.get(haveinfo, False)
- self.sequence = kw.get(sequence, None) # Blat sequence, available for ProbeSet
- self.data = kw.get(data, {})
+ self.haveinfo = kw.get('haveinfo', False)
+ self.sequence = kw.get('sequence', None) # Blat sequence, available for ProbeSet
+ self.data = kw.get('data', {})
if kw.get('fullname'):
name2 = value.split("::")
@@ -381,7 +381,7 @@ class webqtlTrait:
# return self.__dict__.items()
def retrieveInfo(self, QTL = None):
- assert self.dataset and self.cursor
+ assert self.dataset
if self.dataset.type == 'Publish':
#self.dataset.DisField = ['Name','PubMed_ID','Phenotype','Abbreviation','Authors','Title',\
# 'Abstract', 'Journal','Volume','Pages','Month','Year','Sequence',\
@@ -434,10 +434,11 @@ class webqtlTrait:
Geno.Name = '%s'
""" % (display_fields_string, self.dataset.name, self.name)
else: #Temp type
- query = 'SELECT %s FROM %s WHERE Name = "%s"' % \
- (string.join(self.dataset.display_fields,','), self.dataset.type, self.name)
-
+ traitInfo = g.db.execute("""SELECT %s FROM %s WHERE Name = '%s'
+ """, (string.join(self.dataset.display_fields,','),
+ self.dataset.type, self.name)).fetchone()
+
self.cursor.execute(query)
traitInfo = self.cursor.fetchone()
if traitInfo:
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index bae3df08..802cbea5 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -3,6 +3,9 @@
from __future__ import print_function, division
+from flask import Flask, g
+
+from MySQLdb import escape_string as escape
from pprint import pformat as pf
import sys
@@ -34,13 +37,13 @@ class DoSearch(object):
"""Executes query and returns results"""
query = self.normalize_spaces(query)
print("in do_search query is:", pf(query))
- self.cursor.execute(query)
+ g.db.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))
+ return escape(str(stringy))
def mescape(self, *items):
"""Multiple escape"""
@@ -153,7 +156,7 @@ class PhenotypeSearch(DoSearch):
'Max LRS',
'Max LRS Location']
- def get_where_clause(self):
+ def get_fields_clause(self):
"""Generate clause for WHERE portion of query"""
#Todo: Zach will figure out exactly what both these lines mean
@@ -163,15 +166,17 @@ class PhenotypeSearch(DoSearch):
# This adds a clause to the query that matches the search term
# against each field in the search_fields tuple
- where_clause = []
+ fields_clause = []
for field in self.search_fields:
- where_clause.append('''%s REGEXP "%s"''' % (field, search_term))
- where_clause = "(%s)" % ' OR '.join(where_clause)
+ fields_clause.append('''%s REGEXP "%s"''' % (field, search_term))
+ fields_clause = "(%s)" % ' OR '.join(fields_clause)
- return where_clause
+ return fields_clause
- def run(self):
- """Generates and runs a simple search of a phenotype dataset"""
+ def compile_final_query(self, from_clause = '', where_clause = ''):
+ """Generates the final query string"""
+
+ from_clause = self.normalize_spaces(from_clause)
#Get group information for dataset
self.dataset.get_group()
@@ -182,12 +187,42 @@ class PhenotypeSearch(DoSearch):
PublishXRef.PhenotypeId = Phenotype.Id and
PublishXRef.PublicationId = Publication.Id and
PublishFreeze.Id = %s""" % (
- self.get_where_clause(),
+ self.get_fields_clause(),
self.escape(self.dataset.group_id),
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 phenotype dataset"""
+
+ self.query = self.compile_final_query(where_clause = self.get_fields_clause())
+
+# self.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 WHERE (Phenotype.Post_publication_description
+#REGEXP "[[:<:]]brain[[:>:]]" OR Phenotype.Pre_publication_description REGEXP "[[:<:]]brain[[:>:]]"
+#OR Phenotype.Pre_publication_abbreviation REGEXP "[[:<:]]brain[[:>:]]"
+#OR Phenotype.Post_publication_abbreviation REGEXP "[[:<:]]brain[[:>:]]"
+#OR Phenotype.Lab_code REGEXP "[[:<:]]brain[[:>:]]"
+#OR Publication.PubMed_ID REGEXP "[[:<:]]brain[[:>:]]"
+#OR Publication.Abstract REGEXP "[[:<:]]brain[[:>:]]"
+#OR Publication.Title REGEXP "[[:<:]]brain[[:>:]]"
+#OR Publication.Authors REGEXP "[[:<:]]brain[[:>:]]"
+#OR PublishXRef.Id REGEXP "[[:<:]]brain[[:>:]]")
+#and PublishXRef.InbredSetId = 1
+#and PublishXRef.PhenotypeId = Phenotype.Id
+#and PublishXRef.PublicationId = Publication.Id
+#and PublishFreeze.Id = 1;"""
+
+
+ results = g.db.execute(self.query, no_parameters=True).fetchall()
+ print("in [df] run results are:", results)
+ return results
class GenotypeSearch(DoSearch):
"""A search within a genotype dataset"""
@@ -606,6 +641,22 @@ class PvalueSearch(ProbeSetSearch):
return self.execute(self.query)
+class AuthorSearch(PhenotypeSearch):
+ """Searches for phenotype traits with specified author(s)"""
+
+ DoSearch.search_types["NAME"] = "AuthorSearch"
+
+ def run(self):
+
+ self.search_term = [float(value) for value in self.search_term]
+
+ self.where_clause = """ Publication.Authors LIKE %s and
+ """ % (self.escape(self.search_term[0]))
+
+ self.query = self.compile_final_query(where_clause = self.where_clause)
+
+ return self.execute(self.query)
+
if __name__ == "__main__":
@@ -630,20 +681,20 @@ if __name__ == "__main__":
dataset_name = "HC_M2_0606_P"
dataset = create_dataset(db_conn, dataset_name)
- cursor.execute("""
- SELECT 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, Geno
- WHERE ProbeSetXRef.LRS > 99.0 and
- ABS(ProbeSet.Mb-Geno.Mb) < 5 and
- ProbeSetXRef.Locus = Geno.name and
- Geno.SpeciesId = 1 and
- ProbeSet.Chr = Geno.Chr and
- ProbeSet.Id = ProbeSetXRef.ProbeSetId and
- ProbeSetXRef.ProbeSetFreezeId = 112""")
+ #cursor.execute("""
+ # SELECT 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, Geno
+ # WHERE ProbeSetXRef.LRS > 99.0 and
+ # ABS(ProbeSet.Mb-Geno.Mb) < 5 and
+ # ProbeSetXRef.Locus = Geno.name and
+ # Geno.SpeciesId = 1 and
+ # ProbeSet.Chr = Geno.Chr and
+ # ProbeSet.Id = ProbeSetXRef.ProbeSetId and
+ # ProbeSetXRef.ProbeSetFreezeId = 112""")
#print(pf(cursor.fetchall()))
#results = ProbeSetSearch("shh", None, dataset, cursor, db_conn).run()
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 04b14e8f..52f628f6 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -113,7 +113,7 @@ class SearchResultPage(templatePage):
print("foo locals are:", locals())
trait_id = result[0]
- this_trait = webqtlTrait(self.db_conn, dataset=self.dataset, name=trait_id)
+ this_trait = webqtlTrait(dataset=self.dataset, name=trait_id)
this_trait.retrieveInfo(QTL=True)
self.trait_list.append(this_trait)