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-rw-r--r--wqflask/base/mrna_assay_tissue_data.py7
-rw-r--r--wqflask/base/species.py16
-rw-r--r--wqflask/base/trait.py18
-rw-r--r--wqflask/wqflask/do_search.py21
-rw-r--r--wqflask/wqflask/gsearch.py5
-rw-r--r--wqflask/wqflask/show_trait/show_trait.py3
-rw-r--r--wqflask/wqflask/update_search_results.py9
7 files changed, 45 insertions, 34 deletions
diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py
index 039f5d1f..5511af06 100644
--- a/wqflask/base/mrna_assay_tissue_data.py
+++ b/wqflask/base/mrna_assay_tissue_data.py
@@ -11,6 +11,9 @@ from MySQLdb import escape_string as escape
from pprint import pformat as pf
+from utility.logger import getLogger
+logger = getLogger(__name__ )
+
class MrnaAssayTissueData(object):
def __init__(self, gene_symbols=None):
@@ -54,7 +57,7 @@ class MrnaAssayTissueData(object):
as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol
and t.Mean = x.maxmean;
'''.format(in_clause)
-
+ logger.sql(query)
results = g.db.execute(query).fetchall()
lower_symbols = []
@@ -99,6 +102,7 @@ class MrnaAssayTissueData(object):
TissueProbeSetXRef.DataId = TissueProbeSetData.Id""".format(db_tools.create_in_clause(id_list))
print("TISSUE QUERY:", query)
+ logger.sql(query)
results = g.db.execute(query).fetchall()
for result in results:
@@ -157,4 +161,3 @@ class MrnaAssayTissueData(object):
#
# if len(tissue_data.gene_symbols):
# return get_symbol_values_pairs(tissue_data)
-
diff --git a/wqflask/base/species.py b/wqflask/base/species.py
index 79d867c8..ce763fc3 100644
--- a/wqflask/base/species.py
+++ b/wqflask/base/species.py
@@ -10,6 +10,9 @@ from utility import Bunch
from pprint import pformat as pf
+from utility.logger import getLogger
+logger = getLogger(__name__ )
+
class TheSpecies(object):
def __init__(self, dataset):
self.dataset = dataset
@@ -48,16 +51,17 @@ class Chromosomes(object):
self.dataset = dataset
self.chromosomes = collections.OrderedDict()
- results = g.db.execute("""
+
+ query = """
Select
Chr_Length.Name, Chr_Length.OrderId, Length from Chr_Length, InbredSet
where
Chr_Length.SpeciesId = InbredSet.SpeciesId AND
- InbredSet.Name = %s
+ InbredSet.Name = '%s'
Order by OrderId
- """, self.dataset.group.name).fetchall()
- #print("group: ", self.dataset.group.name)
- #print("bike:", results)
+ """ % self.dataset.group.name
+ logger.sql(query)
+ results = g.db.execute(query).fetchall()
for item in results:
self.chromosomes[item.OrderId] = IndChromosome(item.Name, item.Length)
@@ -120,4 +124,4 @@ class Chromosomes(object):
# Testing
#if __name__ == '__main__':
-# foo = dict(bar=dict(length)) \ No newline at end of file
+# foo = dict(bar=dict(length))
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 3dc4ddda..4d4d1a42 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -20,6 +20,9 @@ from pprint import pformat as pf
from flask import Flask, g, request
+from utility.logger import getLogger
+logger = getLogger(__name__ )
+
def print_mem(stage=""):
mem = resource.getrusage(resource.RUSAGE_SELF).ru_maxrss
print("{}: {}".format(stage, mem/1024))
@@ -259,6 +262,7 @@ class GeneralTrait(object):
PublishFreeze.Id = %s
""" % (self.name, self.dataset.id)
+ logger.sql(query)
trait_info = g.db.execute(query).fetchone()
@@ -278,6 +282,7 @@ class GeneralTrait(object):
""" % (escape(display_fields_string),
escape(self.dataset.name),
escape(str(self.name)))
+ logger.sql(query)
trait_info = g.db.execute(query).fetchone()
#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.
@@ -295,9 +300,11 @@ class GeneralTrait(object):
""" % (escape(display_fields_string),
escape(self.dataset.name),
escape(self.name))
+ logger.sql(query)
trait_info = g.db.execute(query).fetchone()
else: #Temp type
query = """SELECT %s FROM %s WHERE Name = %s"""
+ logger.sql(query)
trait_info = g.db.execute(query,
(string.join(self.dataset.display_fields,','),
self.dataset.type, self.name)).fetchone()
@@ -368,6 +375,7 @@ class GeneralTrait(object):
InbredSet.SpeciesId = Species.Id AND
Species.TaxonomyId = Homologene.TaxonomyId
""" % (escape(str(self.geneid)), escape(self.dataset.group.name))
+ logger.sql(query)
result = g.db.execute(query).fetchone()
#else:
# result = None
@@ -429,6 +437,7 @@ class GeneralTrait(object):
ProbeSet.Name = "{}" AND
ProbeSetXRef.ProbeSetFreezeId ={}
""".format(self.name, self.dataset.id)
+ logger.sql(query)
trait_qtl = g.db.execute(query).fetchone()
if trait_qtl:
self.locus, self.lrs, self.pvalue, self.mean, self.additive= trait_qtl
@@ -439,6 +448,7 @@ class GeneralTrait(object):
Geno.Name = '{}' and
Geno.SpeciesId = Species.Id
""".format(self.dataset.group.species, self.locus)
+ logger.sql(query)
result = g.db.execute(query).fetchone()
if result:
self.locus_chr = result[0]
@@ -452,7 +462,7 @@ class GeneralTrait(object):
if self.dataset.type == 'Publish':
- trait_qtl = g.db.execute("""
+ query = """
SELECT
PublishXRef.Locus, PublishXRef.LRS, PublishXRef.additive
FROM
@@ -461,7 +471,9 @@ class GeneralTrait(object):
PublishXRef.Id = %s AND
PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
PublishFreeze.Id =%s
- """, (self.name, self.dataset.id)).fetchone()
+ """ % (self.name, self.dataset.id)
+ logger.sql(query)
+ trait_qtl = g.db.execute(query).fetchone()
if trait_qtl:
self.locus, self.lrs, self.additive = trait_qtl
if self.locus:
@@ -471,6 +483,7 @@ class GeneralTrait(object):
Geno.Name = '{}' and
Geno.SpeciesId = Species.Id
""".format(self.dataset.group.species, self.locus)
+ logger.sql(query)
result = g.db.execute(query).fetchone()
if result:
self.locus_chr = result[0]
@@ -730,4 +743,3 @@ def get_sample_data():
# jsonable_sample_data[sample] = trait_ob.data[sample].value
#
#return jsonable_sample_data
-
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index ff64b518..ad3eab79 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -38,7 +38,7 @@ class DoSearch(object):
def execute(self, query):
"""Executes query and returns results"""
query = self.normalize_spaces(query)
- logger.debug("execute:", pf(query))
+ logger.sql(query)
results = g.db.execute(query, no_parameters=True).fetchall()
return results
@@ -108,8 +108,6 @@ class QuickMrnaAssaySearch(DoSearch):
AGAINST ('%s' IN BOOLEAN MODE))
""" % (escape(self.search_term[0]))
- logger.debug("final query is:", pf(query))
-
return self.execute(query)
@@ -175,9 +173,6 @@ class MrnaAssaySearch(DoSearch):
""" % (escape(from_clause),
where_clause,
escape(str(self.dataset.id))))
-
- #logger.debug("query is:", pf(query))
-
return query
def run_combined(self, from_clause = '', where_clause = ''):
@@ -198,8 +193,6 @@ class MrnaAssaySearch(DoSearch):
where_clause,
escape(str(self.dataset.id))))
- logger.debug("final query is:", pf(query))
-
return self.execute(query)
def run(self):
@@ -209,8 +202,6 @@ class MrnaAssaySearch(DoSearch):
where_clause = self.get_where_clause()
query = self.base_query + "WHERE " + where_clause + "ORDER BY ProbeSet.symbol ASC"
- #logger.debug("final query is:", pf(query))
-
return self.execute(query)
@@ -290,8 +281,6 @@ class PhenotypeSearch(DoSearch):
escape(str(self.dataset.group.id)),
escape(str(self.dataset.id))))
- logger.debug("query is:", pf(query))
-
return query
def run_combined(self, from_clause, where_clause):
@@ -313,9 +302,6 @@ class PhenotypeSearch(DoSearch):
escape(str(self.dataset.group.id)),
escape(str(self.dataset.id))))
- logger.debug("final query is:", pf(query))
-
-
return self.execute(query)
def run(self):
@@ -364,8 +350,6 @@ class QuickPhenotypeSearch(PhenotypeSearch):
PublishXRef.InbredSetId = InbredSet.Id and
InbredSet.SpeciesId = Species.Id""" % where_clause)
- logger.debug("query is:", pf(query))
-
return query
def run(self):
@@ -432,8 +416,6 @@ class GenotypeSearch(DoSearch):
and GenoFreeze.Id = %s"""% (where_clause,
escape(str(self.dataset.id))))
- logger.debug("query is:", pf(query))
-
return query
def run(self):
@@ -931,6 +913,7 @@ class PvalueSearch(MrnaAssaySearch):
self.query = self.compile_final_query(where_clause = self.where_clause)
+ logger.sql(self.query)
return self.execute(self.query)
class AuthorSearch(PhenotypeSearch):
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index 5072f931..64d638b2 100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -7,6 +7,9 @@ from db import webqtlDatabaseFunction
from utility.benchmark import Bench
+from utility.logger import getLogger
+logger = getLogger(__name__)
+
class GSearch(object):
def __init__(self, kw):
@@ -42,6 +45,7 @@ class GSearch(object):
LIMIT 6000
""" % (self.terms)
with Bench("Running query"):
+ logger.sql(sql)
re = g.db.execute(sql).fetchall()
self.trait_list = []
with Bench("Creating trait objects"):
@@ -84,6 +88,7 @@ class GSearch(object):
ORDER BY Species.`Name`, InbredSet.`Name`, PublishXRef.`Id`
LIMIT 6000
""" % (self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms)
+ logger.sql(sql)
re = g.db.execute(sql).fetchall()
self.trait_list = []
with Bench("Creating trait objects"):
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 7c961091..5340301a 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -406,6 +406,7 @@ class ShowTrait(object):
ProbeSet.Name = '{}' AND
Probe.ProbeSetId = ProbeSet.Id order by Probe.SerialOrder""".format(this_trait.dataset.name, this_trait.name)
+ logger.sql(query)
seqs = g.db.execute(query).fetchall()
for seqt in seqs:
@@ -450,6 +451,7 @@ class ShowTrait(object):
FROM Probe, ProbeSet
WHERE ProbeSet.Name = '%s' AND Probe.ProbeSetId = ProbeSet.Id""" % (this_trait.name)
#query database for number of probes associated with trait; if count > 0, set probe tool button and text
+ logger.sql(query)
probeResult = g.db.execute(query).fetchone()
if probeResult[0] > 0:
self.show_probes = "True"
@@ -1250,6 +1252,7 @@ def get_nearest_marker(this_trait, this_db):
ORDER BY ABS( Geno.Mb - {}) LIMIT 1""".format(this_chr, this_db.group.name+"Geno", this_mb)
logger.debug("query:", query)
+ logger.sql(query)
result = g.db.execute(query).fetchall()
logger.debug("result:", result)
diff --git a/wqflask/wqflask/update_search_results.py b/wqflask/wqflask/update_search_results.py
index 7681e7fb..68bea9d6 100644
--- a/wqflask/wqflask/update_search_results.py
+++ b/wqflask/wqflask/update_search_results.py
@@ -9,6 +9,9 @@ from db import webqtlDatabaseFunction
from utility.benchmark import Bench
+from utility.logger import getLogger
+logger = getLogger(__name__)
+
class GSearch(object):
def __init__(self, kw):
@@ -45,6 +48,7 @@ class GSearch(object):
LIMIT 6000
""" % (self.terms)
with Bench("Running query"):
+ logger.sql(sql)
re = g.db.execute(sql).fetchall()
self.trait_list = []
with Bench("Creating trait objects"):
@@ -87,6 +91,7 @@ class GSearch(object):
ORDER BY Species.`Name`, InbredSet.`Name`, PublishXRef.`Id`
LIMIT 6000
""" % (self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms)
+ logger.sql(sql)
re = g.db.execute(sql).fetchall()
self.trait_list = []
with Bench("Creating trait objects"):
@@ -123,7 +128,3 @@ class GSearch(object):
json_results = json.dumps(json_dict)
return json_results
-
-
-
-
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-19 19:47:28 +0000