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-rw-r--r--misc/new_variable_names.txt1
-rwxr-xr-xwqflask/base/data_set.py9
-rwxr-xr-xwqflask/base/webqtlTrait.py46
-rw-r--r--wqflask/wqflask/correlation/CorrelationPage.py2
-rw-r--r--wqflask/wqflask/correlation/correlationFunction.py2
-rw-r--r--wqflask/wqflask/do_search.py10
-rw-r--r--wqflask/wqflask/search_results.py4
-rw-r--r--wqflask/wqflask/show_trait/SampleList.py2
-rwxr-xr-xwqflask/wqflask/show_trait/show_trait.py2
9 files changed, 38 insertions, 40 deletions
diff --git a/misc/new_variable_names.txt b/misc/new_variable_names.txt
index 2b10c07e..c11c160e 100644
--- a/misc/new_variable_names.txt
+++ b/misc/new_variable_names.txt
@@ -3,3 +3,4 @@ webqtlDataset.py -> data_set.py
webqtlDataset (class object) -> DataSet
database/db -> dataset/data_set
DataEditingPage -> show_trait.py/show_trait.html
+webqtlTrait -> GeneralTrait \ No newline at end of file
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 7833f5c1..70b33014 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -272,7 +272,7 @@ class GenotypeDataSet(DataSet):
WHERE
GenoFreeze.InbredSetId = InbredSet.Id AND
GenoFreeze.Name = "%s"
- ''' % self.db_conn.escape_string(self.name)
+ ''' % escape(self.name)
def check_confidentiality(self):
return geno_mrna_confidentiality(self)
@@ -425,13 +425,12 @@ class MrnaAssayDataSet(DataSet):
where ProbeSetXRef.ProbeSetFreezeId = %s and
ProbeSet.Id = ProbeSetXRef.ProbeSetId and
ProbeSet.Name = '%s'
- """ % (self.db_conn.escape_string(str(this_trait.dataset.id)),
- self.db_conn.escape_string(this_trait.name)))
+ """ % (escape(str(this_trait.dataset.id)),
+ escape(this_trait.name)))
print("query is:", pf(query))
- self.cursor.execute(query)
- result = self.cursor.fetchone()
+ result = g.db.execute(query).fetchone()
if result:
if result[0]:
diff --git a/wqflask/base/webqtlTrait.py b/wqflask/base/webqtlTrait.py
index dec5fa00..5367b41f 100755
--- a/wqflask/base/webqtlTrait.py
+++ b/wqflask/base/webqtlTrait.py
@@ -10,6 +10,7 @@ from data_set import create_dataset
from dbFunction import webqtlDatabaseFunction
from utility import webqtlUtil
+from MySQLdb import escape_string as escape
from pprint import pformat as pf
from flask import Flask, g
@@ -40,9 +41,7 @@ class GeneralTrait:
self.dataset, self.name, self.cellid = name2
#if self.dataset and isinstance(self.dataset, basestring):
- self.dataset = create_dataset(self.dataset)
-
-
+ self.dataset = create_dataset(self.dataset.name)
print("self.dataset is:", self.dataset, type(self.dataset))
#if self.dataset:
@@ -367,7 +366,7 @@ class GeneralTrait:
def retrieve_info(self, QTL=False):
assert self.dataset, "Dataset doesn't exist"
if self.dataset.type == 'Publish':
- traitInfo = g.db.execute("""
+ query = """
SELECT
PublishXRef.Id, Publication.PubMed_ID,
Phenotype.Pre_publication_description, Phenotype.Post_publication_description, Phenotype.Original_description,
@@ -384,47 +383,46 @@ class GeneralTrait:
Phenotype.Id = PublishXRef.PhenotypeId AND
Publication.Id = PublishXRef.PublicationId AND
PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
- PublishFreeze.Id =%s
- """, (self.name, self.dataset.id)).fetchone()
+ PublishFreeze.Id = %s
+ """ % (self.name, self.dataset.id)
+ traitInfo = g.db.execute(query).fetchone()
#XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name
#XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms.
elif self.dataset.type == 'ProbeSet':
- display_fields_string = ',ProbeSet.'.join(self.dataset.display_fields)
+ display_fields_string = ', ProbeSet.'.join(self.dataset.display_fields)
display_fields_string = 'ProbeSet.' + display_fields_string
- traitInfo = g.db.execute("""
+ query = """
SELECT %s
FROM ProbeSet, ProbeSetFreeze, ProbeSetXRef
WHERE
ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
- ProbeSetFreeze.Name = %s AND
- ProbeSet.Name = %s
- """, (display_fields_string, self.dataset.name, self.name)).fetchone()
+ ProbeSetFreeze.Name = '%s' AND
+ ProbeSet.Name = '%s'
+ """ % (display_fields_string, self.dataset.name, self.name)
+ traitInfo = g.db.execute(query).fetchone()
+ print("traitInfo is: ", pf(traitInfo))
#XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name
# to avoid the problem of same marker name from different species.
elif self.dataset.type == 'Geno':
display_fields_string = string.join(self.dataset.display_fields,',Geno.')
display_fields_string = 'Geno.' + display_fields_string
- traitInfo = g.db.execute("""
+ query = """
SELECT %s
FROM Geno, GenoFreeze, GenoXRef
WHERE
GenoXRef.GenoFreezeId = GenoFreeze.Id AND
GenoXRef.GenoId = Geno.Id AND
- GenoFreeze.Name = %s AND
- Geno.Name = %s
- """, (display_fields_string, self.dataset.name, self.name)).fetchone()
+ GenoFreeze.Name = '%s' AND
+ Geno.Name = '%s'
+ """ % (display_fields_string, self.dataset.name, self.name)
+ traitInfo = g.db.execute(query).fetchone()
+ print("traitInfo is: ", pf(traitInfo))
else: #Temp type
- traitInfo = g.db.execute("""SELECT %s FROM %s WHERE Name = %s
- """, (string.join(self.dataset.display_fields,','),
- self.dataset.type, self.name)).fetchone()
-
- query = """SELECT %s FROM %s WHERE Name = %s
+ query = """SELECT %s FROM %s WHERE Name = %s
""" % (string.join(self.dataset.display_fields,','),
- self.dataset.type, self.name)
-
- print("query is:", pf(query))
- print("traitInfo is: ", pf(traitInfo))
+ self.dataset.type, self.name)
+ traitInfo = g.db.execute(query).fetchone()
#self.cursor.execute(query)
diff --git a/wqflask/wqflask/correlation/CorrelationPage.py b/wqflask/wqflask/correlation/CorrelationPage.py
index 8af30d1e..f1dd96ef 100644
--- a/wqflask/wqflask/correlation/CorrelationPage.py
+++ b/wqflask/wqflask/correlation/CorrelationPage.py
@@ -46,7 +46,7 @@ import reaper
from base import webqtlConfig
from utility.THCell import THCell
from utility.TDCell import TDCell
-from base.webqtlTrait import webqtlTrait
+from base.webqtlTrait import GeneralTrait
from base.data_set import create_dataset
from base.templatePage import templatePage
from utility import webqtlUtil
diff --git a/wqflask/wqflask/correlation/correlationFunction.py b/wqflask/wqflask/correlation/correlationFunction.py
index 4d62a468..8638cb1e 100644
--- a/wqflask/wqflask/correlation/correlationFunction.py
+++ b/wqflask/wqflask/correlation/correlationFunction.py
@@ -31,7 +31,7 @@ import pp
import string
from utility import webqtlUtil
-from base.webqtlTrait import webqtlTrait
+from base.webqtlTrait import GeneralTrait
from dbFunction import webqtlDatabaseFunction
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index 2094ed14..4301fb50 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -35,7 +35,7 @@ class DoSearch(object):
"""Executes query and returns results"""
query = self.normalize_spaces(query)
print("in do_search query is:", pf(query))
- results = g.db.execute(query).fetchall()
+ results = g.db.execute(query, no_parameters=True).fetchall()
#results = self.cursor.fetchall()
return results
@@ -167,7 +167,7 @@ class PhenotypeSearch(DoSearch):
fields_clause = []
for field in self.search_fields:
fields_clause.append('''%s REGEXP "%s"''' % (field, search_term))
- fields_clause = "(%s)" % ' OR '.join(fields_clause)
+ fields_clause = "(%s) and " % ' OR '.join(fields_clause)
return fields_clause
@@ -198,7 +198,7 @@ class PhenotypeSearch(DoSearch):
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())
+ query = self.compile_final_query(where_clause = self.get_fields_clause())
# self.query = """SELECT PublishXRef.Id,
#PublishFreeze.createtime as thistable,
@@ -220,7 +220,7 @@ class PhenotypeSearch(DoSearch):
#and PublishFreeze.Id = 1;"""
- results = g.db.execute(self.query, no_parameters=True).fetchall()
+ results = self.execute(query)
print("in [df] run results are:", results)
return results
@@ -272,7 +272,7 @@ class GenotypeSearch(DoSearch):
Geno.Id = GenoXRef.GenoId and
GenoXRef.GenoFreezeId = GenoFreeze.Id and
GenoFreeze.Id = %s"""% (where_clause,
- escape(self.dataset.id)))
+ escape(str(self.dataset.id))))
print("query is:", pf(query))
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index efa1c5cc..cd478110 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -30,7 +30,7 @@ from base import webqtlConfig
from utility.THCell import THCell
from utility.TDCell import TDCell
from base.data_set import create_dataset
-from base.webqtlTrait import webqtlTrait
+from base.webqtlTrait import GeneralTrait
from base.templatePage import templatePage
from wqflask import parser
from wqflask import do_search
@@ -113,7 +113,7 @@ class SearchResultPage(templatePage):
print("foo locals are:", locals())
trait_id = result[0]
- this_trait = webqtlTrait(dataset=self.dataset, name=trait_id)
+ this_trait = GeneralTrait(dataset=self.dataset, name=trait_id)
this_trait.retrieve_info(QTL=True)
self.trait_list.append(this_trait)
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index df0dc61e..25877521 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -2,7 +2,7 @@ from __future__ import absolute_import, print_function, division
from base import webqtlCaseData
from utility import webqtlUtil, Plot, Bunch
-from base.webqtlTrait import webqtlTrait
+from base.webqtlTrait import GeneralTrait
from pprint import pformat as pf
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 7060f2ea..aef9219f 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -13,7 +13,7 @@ from base import webqtlConfig
from base import webqtlCaseData
from wqflask.show_trait.SampleList import SampleList
from utility import webqtlUtil, Plot, Bunch
-from base.webqtlTrait import webqtlTrait
+from base.webqtlTrait import GeneralTrait
from dbFunction import webqtlDatabaseFunction
from base.templatePage import templatePage
from basicStatistics import BasicStatisticsFunctions
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 22:19:59 +0000