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-rw-r--r--[-rwxr-xr-x]wqflask/base/data_set.py74
1 files changed, 3 insertions, 71 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index e37a838f..379e5906 100755..100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -509,6 +509,7 @@ class DataSet(object):
self.shortname = None
self.fullname = None
self.type = None
+ self.data_scale = None #ZS: For example log2
self.setup()
@@ -569,8 +570,8 @@ class DataSet(object):
self.name,
self.name))
- self.id, self.name, self.fullname, self.shortname, self.tissue = g.db.execute("""
- SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName, ProbeSetFreeze.ShortName, Tissue.Name
+ self.id, self.name, self.fullname, self.shortname, self.data_scale, self.tissue = g.db.execute("""
+ 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
@@ -1035,75 +1036,6 @@ class MrnaAssayDataSet(DataSet):
#print("After retrieve_sample_data")
return trait_data
- #def get_trait_data(self):
- # self.samplelist = self.group.samplelist + self.group.parlist + self.group.f1list
- # query = """
- # SELECT Strain.Name, Strain.Id FROM Strain, Species
- # WHERE Strain.Name IN {}
- # and Strain.SpeciesId=Species.Id
- # and Species.name = '{}'
- # """.format(create_in_clause(self.samplelist), *mescape(self.group.species))
- # results = dict(g.db.execute(query).fetchall())
- # sample_ids = [results[item] for item in self.samplelist]
- #
- # # MySQL limits the number of tables that can be used in a join to 61,
- # # so we break the sample ids into smaller chunks
- # # Postgres doesn't have that limit, so we can get rid of this after we transition
- # chunk_size = 50
- # number_chunks = int(math.ceil(len(sample_ids) / chunk_size))
- # trait_sample_data = []
- # for sample_ids_step in chunks.divide_into_chunks(sample_ids, number_chunks):
- #
- # #XZ, 09/24/2008: build one temporary table that only contains the records associated with the input GeneId
- # #tempTable = None
- # #if GeneId and db.type == "ProbeSet":
- # # if method == "3":
- # # tempTable = self.getTempLiteratureTable(species=species,
- # # input_species_geneid=GeneId,
- # # returnNumber=returnNumber)
- # #
- # # if method == "4" or method == "5":
- # # tempTable = self.getTempTissueCorrTable(primaryTraitSymbol=GeneSymbol,
- # # TissueProbeSetFreezeId=tissueProbeSetFreezeId,
- # # method=method,
- # # returnNumber=returnNumber)
- #
- # temp = ['T%s.value' % item for item in sample_ids_step]
- # query = "SELECT {}.Name,".format(escape(self.type))
- # data_start_pos = 1
- # query += string.join(temp, ', ')
- # query += ' FROM ({}, {}XRef, {}Freeze) '.format(*mescape(self.type,
- # self.type,
- # self.type))
- #
- # for item in sample_ids_step:
- # query += """
- # left join {}Data as T{} on T{}.Id = {}XRef.DataId
- # and T{}.StrainId={}\n
- # """.format(*mescape(self.type, item, item, self.type, item, item))
- #
- # query += """
- # WHERE {}XRef.{}FreezeId = {}Freeze.Id
- # and {}Freeze.Name = '{}'
- # and {}.Id = {}XRef.{}Id
- # order by {}.Id
- # """.format(*mescape(self.type, self.type, self.type, self.type,
- # self.name, self.type, self.type, self.type, self.type))
- # results = g.db.execute(query).fetchall()
- # trait_sample_data.append(results)
- #
- # trait_count = len(trait_sample_data[0])
- # self.trait_data = collections.defaultdict(list)
- #
- # # put all of the separate data together into a dictionary where the keys are
- # # trait names and values are lists of sample values
- # for trait_counter in range(trait_count):
- # trait_name = trait_sample_data[0][trait_counter][0]
- # for chunk_counter in range(int(number_chunks)):
- # self.trait_data[trait_name] += (
- # trait_sample_data[chunk_counter][trait_counter][data_start_pos:])
-
-
def get_trait_info(self, trait_list=None, species=''):
# Note: setting trait_list to [] is probably not a great idea.