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authorzsloan2017-02-06 20:01:03 +0000
committerzsloan2017-02-06 20:01:03 +0000
commitf2e3407585862581b82680e8521b1e4d944f558a (patch)
treed18789ed1c375bb5b36d2f067534b5b92def89d6 /wqflask/base
parente63c4014e7bc34b440707be19af3779b72102fdb (diff)
downloadgenenetwork2-f2e3407585862581b82680e8521b1e4d944f558a.tar.gz
Fixed appearance of several tables (search, mapping results, sample data)
Temporarily removed second sample table for CFW traits Fixed location of global search bar to work with wider screens
Diffstat (limited to 'wqflask/base')
-rw-r--r--wqflask/base/data_set.py143
1 files changed, 80 insertions, 63 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 94b38e13..30c8e996 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -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):
"""