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-rw-r--r--[-rwxr-xr-x]wqflask/base/__init__.py0
-rw-r--r--[-rwxr-xr-x]wqflask/base/anon_collection.py0
-rw-r--r--wqflask/base/data_set.py204
-rw-r--r--wqflask/base/mrna_assay_tissue_data.py8
-rw-r--r--[-rwxr-xr-x]wqflask/base/species.py16
-rw-r--r--[-rwxr-xr-x]wqflask/base/template.py0
-rw-r--r--wqflask/base/trait.py32
-rw-r--r--[-rwxr-xr-x]wqflask/base/trait_collection.py0
-rw-r--r--[-rwxr-xr-x]wqflask/base/webqtlCaseData.py8
-rw-r--r--[-rwxr-xr-x]wqflask/base/webqtlFormData.py0
10 files changed, 165 insertions, 103 deletions
diff --git a/wqflask/base/__init__.py b/wqflask/base/__init__.py
index e69de29b..e69de29b 100755..100644
--- a/wqflask/base/__init__.py
+++ b/wqflask/base/__init__.py
diff --git a/wqflask/base/anon_collection.py b/wqflask/base/anon_collection.py
index 8ee73296..8ee73296 100755..100644
--- a/wqflask/base/anon_collection.py
+++ b/wqflask/base/anon_collection.py
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 4953e728..c70738f7 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -40,7 +40,7 @@ import reaper
from base import webqtlConfig
from base import species
-from dbFunction import webqtlDatabaseFunction
+from db import webqtlDatabaseFunction
from utility import webqtlUtil
from utility.benchmark import Bench
from utility import chunks
@@ -50,6 +50,12 @@ from maintenance import get_group_samplelists
from MySQLdb import escape_string as escape
from pprint import pformat as pf
+from db.gn_server import menu_main
+from db.call import fetchall,fetchone,fetch1
+
+from utility.tools import USE_GN_SERVER, USE_REDIS
+from utility.logger import getLogger
+logger = getLogger(__name__ )
# Used by create_database to instantiate objects
# Each subclass will add to this
@@ -58,8 +64,7 @@ DS_NAME_MAP = {}
def create_dataset(dataset_name, dataset_type = None, get_samplelist = True):
if not dataset_type:
dataset_type = Dataset_Getter(dataset_name)
-
- print("dataset_type is:", dataset_type)
+ logger.debug("dataset_type", dataset_type)
dataset_ob = DS_NAME_MAP[dataset_type]
dataset_class = globals()[dataset_ob]
@@ -68,12 +73,28 @@ def create_dataset(dataset_name, dataset_type = None, get_samplelist = True):
class Dataset_Types(object):
def __init__(self):
+ """Create a dictionary of samples where the value is set to Geno,
+Publish or ProbeSet. E.g.
+
+ {'AD-cases-controls-MyersGeno': 'Geno',
+ 'AD-cases-controls-MyersPublish': 'Publish',
+ 'AKXDGeno': 'Geno',
+ 'AXBXAGeno': 'Geno',
+ 'AXBXAPublish': 'Publish',
+ 'Aging-Brain-UCIPublish': 'Publish',
+ 'All Phenotypes': 'Publish',
+ 'B139_K_1206_M': 'ProbeSet',
+ 'B139_K_1206_R': 'ProbeSet' ...
+
+ """
self.datasets = {}
- file_name = "wqflask/static/new/javascript/dataset_menu_structure.json"
- with open(file_name, 'r') as fh:
- data = json.load(fh)
+ if USE_GN_SERVER:
+ data = menu_main()
+ else:
+ file_name = "wqflask/static/new/javascript/dataset_menu_structure.json"
+ with open(file_name, 'r') as fh:
+ data = json.load(fh)
- print("*" * 70)
for species in data['datasets']:
for group in data['datasets'][species]:
for dataset_type in data['datasets'][species][group]:
@@ -85,7 +106,8 @@ class Dataset_Types(object):
new_type = "Geno"
else:
new_type = "ProbeSet"
- self.datasets[short_dataset_name] = new_type
+ self.datasets[short_dataset_name] = new_type
+ logger.info("datasets",self.datasets)
def __call__(self, name):
return self.datasets[name]
@@ -94,14 +116,15 @@ class Dataset_Types(object):
Dataset_Getter = Dataset_Types()
def create_datasets_list():
- key = "all_datasets"
- result = Redis.get(key)
+ if USE_REDIS:
+ key = "all_datasets"
+ result = Redis.get(key)
- if result:
- print("Cache hit!!!")
- datasets = pickle.loads(result)
+ if result:
+ logger.debug("Redis cache hit")
+ datasets = pickle.loads(result)
- else:
+ if result is None:
datasets = list()
with Bench("Creating DataSets object"):
type_dict = {'Publish': 'PublishFreeze',
@@ -110,15 +133,17 @@ def create_datasets_list():
for dataset_type in type_dict:
query = "SELECT Name FROM {}".format(type_dict[dataset_type])
- for result in g.db.execute(query).fetchall():
- #The query at the beginning of this function isn't necessary here, but still would
- #rather just reuse it
- #print("type: {}\tname: {}".format(dataset_type, result.Name))
+ for result in fetchall(query):
+ #The query at the beginning of this function isn't
+ #necessary here, but still would rather just reuse
+ #it logger.debug("type: {}\tname:
+ #{}".format(dataset_type, result.Name))
dataset = create_dataset(result.Name, dataset_type)
datasets.append(dataset)
- Redis.set(key, pickle.dumps(datasets, pickle.HIGHEST_PROTOCOL))
- Redis.expire(key, 60*60)
+ if USE_REDIS:
+ Redis.set(key, pickle.dumps(datasets, pickle.HIGHEST_PROTOCOL))
+ Redis.expire(key, 60*60)
return datasets
@@ -133,7 +158,7 @@ def create_in_clause(items):
def mescape(*items):
"""Multiple escape"""
escaped = [escape(str(item)) for item in items]
- #print("escaped is:", escaped)
+ #logger.debug("escaped is:", escaped)
return escaped
@@ -152,12 +177,12 @@ class Markers(object):
marker['Mb'] = float(marker['Mb'])
self.markers = markers
- #print("self.markers:", self.markers)
+ #logger.debug("self.markers:", self.markers)
def add_pvalues(self, p_values):
- print("length of self.markers:", len(self.markers))
- print("length of p_values:", len(p_values))
+ logger.debug("length of self.markers:", len(self.markers))
+ logger.debug("length of p_values:", len(p_values))
if type(p_values) is list:
# THIS IS only needed for the case when we are limiting the number of p-values calculated
@@ -178,10 +203,10 @@ class Markers(object):
elif type(p_values) is dict:
filtered_markers = []
for marker in self.markers:
- #print("marker[name]", marker['name'])
- #print("p_values:", p_values)
+ #logger.debug("marker[name]", marker['name'])
+ #logger.debug("p_values:", p_values)
if marker['name'] in p_values:
- #print("marker {} IS in p_values".format(i))
+ #logger.debug("marker {} IS in p_values".format(i))
marker['p_value'] = p_values[marker['name']]
if math.isnan(marker['p_value']) or (marker['p_value'] <= 0):
marker['lod_score'] = 0
@@ -192,7 +217,7 @@ class Markers(object):
marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61
filtered_markers.append(marker)
#else:
- #print("marker {} NOT in p_values".format(i))
+ #logger.debug("marker {} NOT in p_values".format(i))
#self.markers.remove(marker)
#del self.markers[i]
self.markers = filtered_markers
@@ -204,7 +229,7 @@ class HumanMarkers(Markers):
self.markers = []
for line in marker_data_fh:
splat = line.strip().split()
- #print("splat:", splat)
+ #logger.debug("splat:", splat)
if len(specified_markers) > 0:
if splat[1] in specified_markers:
marker = {}
@@ -220,7 +245,7 @@ class HumanMarkers(Markers):
marker['Mb'] = float(splat[3]) / 1000000
self.markers.append(marker)
- #print("markers is: ", pf(self.markers))
+ #logger.debug("markers is: ", pf(self.markers))
def add_pvalues(self, p_values):
@@ -237,15 +262,15 @@ class DatasetGroup(object):
"""
def __init__(self, dataset):
"""This sets self.group and self.group_id"""
- #print("DATASET NAME2:", dataset.name)
- self.name, self.id = g.db.execute(dataset.query_for_group).fetchone()
+ #logger.debug("DATASET NAME2:", dataset.name)
+ self.name, self.id = fetchone(dataset.query_for_group)
if self.name == 'BXD300':
self.name = "BXD"
self.f1list = None
self.parlist = None
self.get_f1_parent_strains()
- #print("parents/f1s: {}:{}".format(self.parlist, self.f1list))
+ #logger.debug("parents/f1s: {}:{}".format(self.parlist, self.f1list))
self.species = webqtlDatabaseFunction.retrieve_species(self.name)
@@ -257,7 +282,7 @@ class DatasetGroup(object):
self.markers = HumanMarkers(self.name, markers)
def get_markers(self):
- #print("self.species is:", self.species)
+ #logger.debug("self.species is:", self.species)
if self.species == "human":
marker_class = HumanMarkers
else:
@@ -267,21 +292,21 @@ class DatasetGroup(object):
def datasets(self):
key = "group_dataset_menu:v2:" + self.name
- print("key is2:", key)
+ logger.debug("key is2:", key)
dataset_menu = []
- print("[tape4] webqtlConfig.PUBLICTHRESH:", webqtlConfig.PUBLICTHRESH)
- print("[tape4] type webqtlConfig.PUBLICTHRESH:", type(webqtlConfig.PUBLICTHRESH))
- results = g.db.execute('''
+ logger.debug("[tape4] webqtlConfig.PUBLICTHRESH:", webqtlConfig.PUBLICTHRESH)
+ logger.debug("[tape4] type webqtlConfig.PUBLICTHRESH:", type(webqtlConfig.PUBLICTHRESH))
+ the_results = fetchall('''
(SELECT '#PublishFreeze',PublishFreeze.FullName,PublishFreeze.Name
FROM PublishFreeze,InbredSet
WHERE PublishFreeze.InbredSetId = InbredSet.Id
- and InbredSet.Name = %s
+ and InbredSet.Name = '%s'
and PublishFreeze.public > %s)
UNION
(SELECT '#GenoFreeze',GenoFreeze.FullName,GenoFreeze.Name
FROM GenoFreeze, InbredSet
WHERE GenoFreeze.InbredSetId = InbredSet.Id
- and InbredSet.Name = %s
+ and InbredSet.Name = '%s'
and GenoFreeze.public > %s)
UNION
(SELECT Tissue.Name, ProbeSetFreeze.FullName,ProbeSetFreeze.Name
@@ -292,11 +317,9 @@ class DatasetGroup(object):
and InbredSet.Name like %s
and ProbeSetFreeze.public > %s
ORDER BY Tissue.Name, ProbeSetFreeze.CreateTime desc, ProbeSetFreeze.AvgId)
- ''', (self.name, webqtlConfig.PUBLICTHRESH,
+ ''' % (self.name, webqtlConfig.PUBLICTHRESH,
self.name, webqtlConfig.PUBLICTHRESH,
- "%" + self.name + "%", webqtlConfig.PUBLICTHRESH))
-
- the_results = results.fetchall()
+ "'" + self.name + "'", webqtlConfig.PUBLICTHRESH))
#for tissue_name, dataset in itertools.groupby(the_results, itemgetter(0)):
for dataset_item in the_results:
@@ -317,14 +340,15 @@ class DatasetGroup(object):
break
if tissue_already_exists:
- #print("dataset_menu:", dataset_menu[i]['datasets'])
+ #logger.debug("dataset_menu:", dataset_menu[i]['datasets'])
dataset_menu[i]['datasets'].append((dataset, dataset_short))
else:
dataset_menu.append(dict(tissue=tissue_name,
datasets=[(dataset, dataset_short)]))
- Redis.set(key, pickle.dumps(dataset_menu, pickle.HIGHEST_PROTOCOL))
- Redis.expire(key, 60*5)
+ if USE_REDIS:
+ Redis.set(key, pickle.dumps(dataset_menu, pickle.HIGHEST_PROTOCOL))
+ Redis.expire(key, 60*5)
self._datasets = dataset_menu
return self._datasets
@@ -342,19 +366,19 @@ class DatasetGroup(object):
self.parlist = [maternal, paternal]
def get_samplelist(self):
+ result = None
key = "samplelist:v2:" + self.name
- #print("key is:", key)
- #with Bench("Loading cache"):
- result = Redis.get(key)
+ if USE_REDIS:
+ result = Redis.get(key)
- if result:
- #print("Sample List Cache hit!!!")
- #print("Before unjsonifying {}: {}".format(type(result), result))
+ if result is not None:
+ #logger.debug("Sample List Cache hit!!!")
+ #logger.debug("Before unjsonifying {}: {}".format(type(result), result))
self.samplelist = json.loads(result)
- #print(" type: ", type(self.samplelist))
- #print(" self.samplelist: ", self.samplelist)
+ #logger.debug(" type: ", type(self.samplelist))
+ #logger.debug(" self.samplelist: ", self.samplelist)
else:
- print("Cache not hit")
+ logger.debug("Cache not hit")
genotype_fn = locate_ignore_error(self.name+".geno",'genotype')
mapping_fn = locate_ignore_error(self.name+".fam",'mapping')
@@ -364,9 +388,10 @@ class DatasetGroup(object):
self.samplelist = get_group_samplelists.get_samplelist("geno", genotype_fn)
else:
self.samplelist = None
- print("Sample list: ",self.samplelist)
- Redis.set(key, json.dumps(self.samplelist))
- Redis.expire(key, 60*5)
+ logger.debug("Sample list: ",self.samplelist)
+ if USE_REDIS:
+ Redis.set(key, json.dumps(self.samplelist))
+ Redis.expire(key, 60*5)
def all_samples_ordered(self):
result = []
@@ -457,14 +482,14 @@ class DataSet(object):
self.name,
self.name))
- self.id, self.name, self.fullname, self.shortname, self.data_scale, self.tissue = g.db.execute("""
+ self.id, self.name, self.fullname, self.shortname, self.data_scale, self.tissue = fetchone("""
SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName, ProbeSetFreeze.ShortName, ProbeSetFreeze.DataScale, Tissue.Name
FROM ProbeSetFreeze, ProbeFreeze, Tissue
WHERE ProbeSetFreeze.public > %s AND
ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND
ProbeFreeze.TissueId = Tissue.Id AND
(ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFreeze.ShortName = '%s')
- """ % (query_args)).fetchone()
+ """ % (query_args))
else:
query_args = tuple(escape(x) for x in (
(self.type + "Freeze"),
@@ -474,15 +499,15 @@ class DataSet(object):
self.name))
self.tissue = "N/A"
- self.id, self.name, self.fullname, self.shortname = g.db.execute("""
+ self.id, self.name, self.fullname, self.shortname = fetchone("""
SELECT Id, Name, FullName, ShortName
FROM %s
WHERE public > %s AND
(Name = '%s' OR FullName = '%s' OR ShortName = '%s')
- """ % (query_args)).fetchone()
+ """ % (query_args))
except TypeError:
- print("Dataset {} is not yet available in GeneNetwork.".format(self.name))
+ logger.debug("Dataset {} is not yet available in GeneNetwork.".format(self.name))
pass
def get_trait_data(self, sample_list=None):
@@ -501,6 +526,7 @@ class DataSet(object):
and Strain.SpeciesId=Species.Id
and Species.name = '{}'
""".format(create_in_clause(self.samplelist), *mescape(self.group.species))
+ logger.sql(query)
results = dict(g.db.execute(query).fetchall())
sample_ids = [results[item] for item in self.samplelist]
@@ -549,10 +575,11 @@ class DataSet(object):
""".format(*mescape(self.type, self.type, self.type, self.type,
self.name, dataset_type, self.type, self.type, dataset_type))
- #print("trait data query: ", query)
+ #logger.debug("trait data query: ", query)
+ logger.sql(query)
results = g.db.execute(query).fetchall()
- #print("query results:", results)
+ #logger.debug("query results:", results)
trait_sample_data.append(results)
trait_count = len(trait_sample_data[0])
@@ -571,7 +598,7 @@ class PhenotypeDataSet(DataSet):
def setup(self):
- #print("IS A PHENOTYPEDATASET")
+ #logger.debug("IS A PHENOTYPEDATASET")
# Fields in the database table
self.search_fields = ['Phenotype.Post_publication_description',
@@ -635,6 +662,7 @@ class PhenotypeDataSet(DataSet):
where PublishFreeze.InbredSetId=PublishXRef.InbredSetId
and PublishFreeze.Id = {}
""".format(escape(str(self.id)))
+ logger.sql(query)
results = g.db.execute(query).fetchall()
trait_data = {}
for trait in results:
@@ -683,12 +711,14 @@ class PhenotypeDataSet(DataSet):
this_trait.LRS_location_value = 1000000
if this_trait.lrs:
- result = g.db.execute("""
+ query = """
select Geno.Chr, Geno.Mb from Geno, Species
where Species.Name = %s and
Geno.Name = %s and
Geno.SpeciesId = Species.Id
- """, (species, this_trait.locus)).fetchone()
+ """ % (species, this_trait.locus)
+ logger.sql(query)
+ result = g.db.execute(query).fetchone()
if result:
if result[0] and result[1]:
@@ -726,6 +756,7 @@ class PhenotypeDataSet(DataSet):
Order BY
Strain.Name
"""
+ logger.sql(query)
results = g.db.execute(query, (trait, self.id)).fetchall()
return results
@@ -773,6 +804,7 @@ class GenotypeDataSet(DataSet):
where GenoXRef.GenoId = Geno.Id
and GenoFreezeId = {}
""".format(escape(str(self.id)))
+ logger.sql(query)
results = g.db.execute(query).fetchall()
trait_data = {}
for trait in results:
@@ -817,6 +849,7 @@ class GenotypeDataSet(DataSet):
Order BY
Strain.Name
"""
+ logger.sql(query)
results = g.db.execute(query,
(webqtlDatabaseFunction.retrieve_species_id(self.group.name),
trait, self.name)).fetchall()
@@ -899,6 +932,7 @@ class MrnaAssayDataSet(DataSet):
where ProbeSetXRef.ProbeSetId = ProbeSet.Id
and ProbeSetFreezeId = {}
""".format(escape(str(self.id)))
+ logger.sql(query)
results = g.db.execute(query).fetchall()
trait_data = {}
for trait in results:
@@ -967,8 +1001,8 @@ class MrnaAssayDataSet(DataSet):
""" % (escape(str(this_trait.dataset.id)),
escape(this_trait.name)))
- #print("query is:", pf(query))
-
+ #logger.debug("query is:", pf(query))
+ logger.sql(query)
result = g.db.execute(query).fetchone()
mean = result[0] if result else 0
@@ -990,6 +1024,7 @@ class MrnaAssayDataSet(DataSet):
Geno.Name = '{}' and
Geno.SpeciesId = Species.Id
""".format(species, this_trait.locus)
+ logger.sql(query)
result = g.db.execute(query).fetchone()
if result:
@@ -1025,6 +1060,7 @@ class MrnaAssayDataSet(DataSet):
ProbeSet.Name = %s
ProbeSetFreeze.Name = %s
""" % (escape(self.name), escape(self.dataset.name))
+ logger.sql(query)
results = g.db.execute(query).fetchone()
return results[0]
@@ -1045,8 +1081,9 @@ class MrnaAssayDataSet(DataSet):
Order BY
Strain.Name
""" % (escape(trait), escape(self.name))
+ logger.sql(query)
results = g.db.execute(query).fetchall()
- #print("RETRIEVED RESULTS HERE:", results)
+ #logger.debug("RETRIEVED RESULTS HERE:", results)
return results
@@ -1057,6 +1094,7 @@ class MrnaAssayDataSet(DataSet):
where ProbeSetXRef.ProbeSetFreezeId = %s and
ProbeSetXRef.ProbeSetId=ProbeSet.Id;
""" % (column_name, escape(str(self.id)))
+ logger.sql(query)
results = g.db.execute(query).fetchall()
return dict(results)
@@ -1093,13 +1131,15 @@ class TempDataSet(DataSet):
return desc
def get_desc(self):
- g.db.execute('SELECT description FROM Temp WHERE Name=%s', self.name)
+ query = 'SELECT description FROM Temp WHERE Name=%s' % self.name
+ logger.sql(query)
+ g.db.execute(query)
desc = g.db.fetchone()[0]
desc = self.handle_pca(desc)
return desc
def get_group(self):
- self.cursor.execute("""
+ query = """
SELECT
InbredSet.Name, InbredSet.Id
FROM
@@ -1107,9 +1147,9 @@ class TempDataSet(DataSet):
WHERE
Temp.InbredSetId = InbredSet.Id AND
Temp.Name = "%s"
- """, self.name)
- self.group, self.group_id = self.cursor.fetchone()
- #return self.group
+ """ % self.name
+ logger.sql(query)
+ self.group, self.group_id = g.db.execute(query).fetchone()
def retrieve_sample_data(self, trait):
query = """
@@ -1125,17 +1165,18 @@ class TempDataSet(DataSet):
Strain.Name
""" % escape(trait.name)
+ logger.sql(query)
results = g.db.execute(query).fetchall()
def geno_mrna_confidentiality(ob):
dataset_table = ob.type + "Freeze"
- #print("dataset_table [%s]: %s" % (type(dataset_table), dataset_table))
+ #logger.debug("dataset_table [%s]: %s" % (type(dataset_table), dataset_table))
query = '''SELECT Id, Name, FullName, confidentiality,
- AuthorisedUsers FROM %s WHERE Name = %%s''' % (dataset_table)
-
- result = g.db.execute(query, ob.name)
+ AuthorisedUsers FROM %s WHERE Name = "%s"''' % (dataset_table,ob.name)
+ logger.sql(query)
+ result = g.db.execute(query)
(dataset_id,
name,
@@ -1145,4 +1186,3 @@ def geno_mrna_confidentiality(ob):
if confidential:
return True
-
diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py
index 1f1be1e5..e99ef7b5 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 = []
@@ -97,7 +100,7 @@ class MrnaAssayTissueData(object):
WHERE TissueProbeSetData.Id IN {} and
TissueProbeSetXRef.DataId = TissueProbeSetData.Id""".format(db_tools.create_in_clause(id_list))
- print("TISSUE QUERY:", query)
+ logger.sql('tissue query',query)
results = g.db.execute(query).fetchall()
for result in results:
@@ -156,4 +159,3 @@ 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 100755..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/template.py b/wqflask/base/template.py
index aa8f90dc..aa8f90dc 100755..100644
--- a/wqflask/base/template.py
+++ b/wqflask/base/template.py
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 4bce25ac..9566c192 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -9,7 +9,7 @@ from htmlgen import HTMLgen2 as HT
from base import webqtlConfig
from base.webqtlCaseData import webqtlCaseData
from base.data_set import create_dataset
-from dbFunction import webqtlDatabaseFunction
+from db import webqtlDatabaseFunction
from utility import webqtlUtil
from wqflask import app
@@ -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))
@@ -253,6 +256,7 @@ class GeneralTrait(object):
PublishFreeze.Id = %s
""" % (self.name, self.dataset.id)
+ logger.sql(query)
trait_info = g.db.execute(query).fetchone()
@@ -272,6 +276,7 @@ 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.
@@ -289,9 +294,11 @@ 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()
@@ -362,6 +369,7 @@ 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
@@ -423,6 +431,7 @@ 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
@@ -433,6 +442,7 @@ 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]
@@ -446,7 +456,7 @@ class GeneralTrait(object):
if self.dataset.type == 'Publish':
- trait_qtl = g.db.execute("""
+ query = """
SELECT
PublishXRef.Locus, PublishXRef.LRS, PublishXRef.additive
FROM
@@ -455,7 +465,9 @@ 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:
@@ -465,6 +477,7 @@ 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]
@@ -651,12 +664,12 @@ class GeneralTrait(object):
"""
if self.cellid:
- self.cursor.execute("""
- select ProbeFreeze.Name from ProbeFreeze, ProbeSetFreeze
- where
- ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND
- ProbeSetFreeze.Id = %d""" % thisTrait.dataset.id)
- probeDBName = self.cursor.fetchone()[0]
+ query = """ select ProbeFreeze.Name from ProbeFreeze, ProbeSetFreeze where
+ ProbeFreeze.Id =
+ ProbeSetFreeze.ProbeFreezeId AND
+ ProbeSetFreeze.Id = %d""" % thisTrait.dataset.id
+ logger.sql(query)
+ probeDBName = g.db.execute(query).fetchone()[0]
return dict(name = probeDBName,
url = None)
else:
@@ -724,4 +737,3 @@ def get_sample_data():
# jsonable_sample_data[sample] = trait_ob.data[sample].value
#
#return jsonable_sample_data
-
diff --git a/wqflask/base/trait_collection.py b/wqflask/base/trait_collection.py
index d388a3af..d388a3af 100755..100644
--- a/wqflask/base/trait_collection.py
+++ b/wqflask/base/trait_collection.py
diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py
index 411b0d24..c80fcb65 100755..100644
--- a/wqflask/base/webqtlCaseData.py
+++ b/wqflask/base/webqtlCaseData.py
@@ -24,7 +24,12 @@
#
# Last updated by GeneNetwork Core Team 2010/10/20
-print("Mr. Mojo Risin 2")
+from utility.logger import getLogger
+logger = getLogger(__name__)
+
+import utility.tools
+
+utility.tools.show_settings()
class webqtlCaseData(object):
"""one case data in one trait"""
@@ -70,4 +75,3 @@ class webqtlCaseData(object):
return "%2.3f" % self.variance
else:
return "x"
-
diff --git a/wqflask/base/webqtlFormData.py b/wqflask/base/webqtlFormData.py
index 10251756..10251756 100755..100644
--- a/wqflask/base/webqtlFormData.py
+++ b/wqflask/base/webqtlFormData.py
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 05:28:04 +0000