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-rw-r--r--wqflask/base/data_set.py151
1 files changed, 84 insertions, 67 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 41c5d8ba..54dd3c4b 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -264,7 +264,7 @@ class DatasetGroup(object):
def __init__(self, dataset):
"""This sets self.group and self.group_id"""
#logger.debug("DATASET NAME2:", dataset.name)
- self.name, self.id = fetchone(dataset.query_for_group)
+ self.name, self.id, self.genetic_type = fetchone(dataset.query_for_group)
if self.name == 'BXD300':
self.name = "BXD"
@@ -273,6 +273,7 @@ class DatasetGroup(object):
self.get_f1_parent_strains()
self.accession_id = self.get_accession_id()
+ self.mapping_id, self.mapping_names = self.get_mapping_methods()
self.species = webqtlDatabaseFunction.retrieve_species(self.name)
@@ -295,6 +296,20 @@ class DatasetGroup(object):
else:
return "None"
+ def get_mapping_methods(self):
+
+ mapping_id = g.db.execute("select MappingMethodId from InbredSet where Name= '%s'" % self.name).fetchone()[0]
+ if mapping_id == "1":
+ mapping_names = ["QTLReaper", "PYLMM", "R/qtl"]
+ elif mapping_id == "2":
+ mapping_names = ["GEMMA"]
+ elif mapping_id == "4":
+ mapping_names = ["PLINK"]
+ else:
+ mapping_names = []
+
+ return mapping_id, mapping_names
+
def get_specified_markers(self, markers = []):
self.markers = HumanMarkers(self.name, markers)
@@ -317,69 +332,6 @@ class DatasetGroup(object):
self.markers = marker_class(self.name)
- def datasets(self):
- key = "group_dataset_menu:v2:" + self.name
- logger.debug("key is2:", key)
- dataset_menu = []
- 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 PublishFreeze.public > %s)
- UNION
- (SELECT '#GenoFreeze',GenoFreeze.FullName,GenoFreeze.Name
- FROM GenoFreeze, InbredSet
- WHERE GenoFreeze.InbredSetId = InbredSet.Id
- and InbredSet.Name = '%s'
- and GenoFreeze.public > %s)
- UNION
- (SELECT Tissue.Name, ProbeSetFreeze.FullName,ProbeSetFreeze.Name
- FROM ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue
- WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id
- and ProbeFreeze.TissueId = Tissue.Id
- and ProbeFreeze.InbredSetId = InbredSet.Id
- 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))
-
- #for tissue_name, dataset in itertools.groupby(the_results, itemgetter(0)):
- for dataset_item in the_results:
- tissue_name = dataset_item[0]
- dataset = dataset_item[1]
- dataset_short = dataset_item[2]
- if tissue_name in ['#PublishFreeze', '#GenoFreeze']:
- dataset_menu.append(dict(tissue=None, datasets=[(dataset, dataset_short)]))
- else:
- dataset_sub_menu = [item[1:] for item in dataset]
-
- tissue_already_exists = False
- tissue_position = None
- for i, tissue_dict in enumerate(dataset_menu):
- if tissue_dict['tissue'] == tissue_name:
- tissue_already_exists = True
- tissue_position = i
- break
-
- if tissue_already_exists:
- #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)]))
-
- 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
-
def get_f1_parent_strains(self):
try:
# NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py;
@@ -456,6 +408,71 @@ class DatasetGroup(object):
return genotype
+def datasets(group_name, this_group = None):
+ key = "group_dataset_menu:v2:" + group_name
+ logger.debug("key is2:", key)
+ dataset_menu = []
+ 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 PublishFreeze.public > %s)
+ UNION
+ (SELECT '#GenoFreeze',GenoFreeze.FullName,GenoFreeze.Name
+ FROM GenoFreeze, InbredSet
+ WHERE GenoFreeze.InbredSetId = InbredSet.Id
+ and InbredSet.Name = '%s'
+ and GenoFreeze.public > %s)
+ UNION
+ (SELECT Tissue.Name, ProbeSetFreeze.FullName,ProbeSetFreeze.Name
+ FROM ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue
+ WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id
+ and ProbeFreeze.TissueId = Tissue.Id
+ and ProbeFreeze.InbredSetId = InbredSet.Id
+ and InbredSet.Name like %s
+ and ProbeSetFreeze.public > %s
+ ORDER BY Tissue.Name, ProbeSetFreeze.CreateTime desc, ProbeSetFreeze.AvgId)
+ ''' % (group_name, webqtlConfig.PUBLICTHRESH,
+ group_name, webqtlConfig.PUBLICTHRESH,
+ "'" + group_name + "'", webqtlConfig.PUBLICTHRESH))
+
+ #for tissue_name, dataset in itertools.groupby(the_results, itemgetter(0)):
+ for dataset_item in the_results:
+ tissue_name = dataset_item[0]
+ dataset = dataset_item[1]
+ dataset_short = dataset_item[2]
+ if tissue_name in ['#PublishFreeze', '#GenoFreeze']:
+ dataset_menu.append(dict(tissue=None, datasets=[(dataset, dataset_short)]))
+ else:
+ dataset_sub_menu = [item[1:] for item in dataset]
+
+ tissue_already_exists = False
+ tissue_position = None
+ for i, tissue_dict in enumerate(dataset_menu):
+ if tissue_dict['tissue'] == tissue_name:
+ tissue_already_exists = True
+ tissue_position = i
+ break
+
+ if tissue_already_exists:
+ #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)]))
+
+ if USE_REDIS:
+ Redis.set(key, pickle.dumps(dataset_menu, pickle.HIGHEST_PROTOCOL))
+ Redis.expire(key, 60*5)
+
+ if this_group != None:
+ this_group._datasets = dataset_menu
+ return this_group._datasets
+ else:
+ return dataset_menu
class DataSet(object):
"""
@@ -679,7 +696,7 @@ class PhenotypeDataSet(DataSet):
self.query_for_group = '''
SELECT
- InbredSet.Name, InbredSet.Id
+ InbredSet.Name, InbredSet.Id, InbredSet.GeneticType
FROM
InbredSet, PublishFreeze
WHERE
@@ -822,7 +839,7 @@ class GenotypeDataSet(DataSet):
self.query_for_group = '''
SELECT
- InbredSet.Name, InbredSet.Id
+ InbredSet.Name, InbredSet.Id, InbredSet.GeneticType
FROM
InbredSet, GenoFreeze
WHERE
@@ -948,7 +965,7 @@ class MrnaAssayDataSet(DataSet):
self.query_for_group = '''
SELECT
- InbredSet.Name, InbredSet.Id
+ InbredSet.Name, InbredSet.Id, InbredSet.GeneticType
FROM
InbredSet, ProbeSetFreeze, ProbeFreeze
WHERE
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 18:32:04 +0000