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-rw-r--r--wqflask/base/data_set.py349
1 files changed, 137 insertions, 212 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 54dd3c4b..ebf3f021 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -26,10 +26,10 @@ import collections
import codecs
import json
+import requests
import gzip
import cPickle as pickle
import itertools
-from operator import itemgetter
from redis import Redis
Redis = Redis()
@@ -44,8 +44,11 @@ from db import webqtlDatabaseFunction
from utility import webqtlUtil
from utility.benchmark import Bench
from utility import chunks
+from utility import gen_geno_ob
from utility.tools import locate, locate_ignore_error, flat_files
+from wqflask.api import gen_menu
+
from maintenance import get_group_samplelists
from MySQLdb import escape_string as escape
@@ -61,18 +64,21 @@ logger = getLogger(__name__ )
# Each subclass will add to this
DS_NAME_MAP = {}
-def create_dataset(dataset_name, dataset_type = None, get_samplelist = True):
+def create_dataset(dataset_name, rebuild=True, dataset_type = None, get_samplelist = True, group_name = None):
if not dataset_type:
dataset_type = Dataset_Getter(dataset_name)
logger.debug("dataset_type", dataset_type)
dataset_ob = DS_NAME_MAP[dataset_type]
dataset_class = globals()[dataset_ob]
- return dataset_class(dataset_name, get_samplelist)
+ if dataset_type == "Temp":
+ return dataset_class(dataset_name, get_samplelist, group_name)
+ else:
+ return dataset_class(dataset_name, get_samplelist)
class Dataset_Types(object):
- def __init__(self):
+ def __init__(self, rebuild=False):
"""Create a dictionary of samples where the value is set to Geno,
Publish or ProbeSet. E.g.
@@ -88,8 +94,10 @@ Publish or ProbeSet. E.g.
"""
self.datasets = {}
- if USE_GN_SERVER:
- data = menu_main()
+ if rebuild: #ZS: May make this the only option
+ data = json.loads(requests.get("http://gn2.genenetwork.org/api/v_pre1/gen_dropdown").content)
+ logger.debug("THE DATA:", data)
+ #data = gen_menu.gen_dropdown_json()
else:
file_name = "wqflask/static/new/javascript/dataset_menu_structure.json"
with open(file_name, 'r') as fh:
@@ -107,8 +115,9 @@ Publish or ProbeSet. E.g.
else:
new_type = "ProbeSet"
self.datasets[short_dataset_name] = new_type
+
# Set LOG_LEVEL_DEBUG=5 to see the following:
- logger.debugf(5,"datasets",self.datasets)
+ logger.debugf(5, "datasets",self.datasets)
def __call__(self, name):
return self.datasets[name]
@@ -166,20 +175,31 @@ def mescape(*items):
class Markers(object):
"""Todo: Build in cacheing so it saves us reading the same file more than once"""
def __init__(self, name):
- json_data_fh = open(locate(name + '.json','genotype/json'))
- try:
- markers = json.load(json_data_fh)
- except:
- markers = []
+ json_data_fh = open(locate(name + ".json",'genotype/json'))
+
+ markers = []
+ with open("%s/%s_snps.txt" % (flat_files('genotype/bimbam'), name), 'r') as bimbam_fh:
+ if len(bimbam_fh.readline().split(", ")) > 2:
+ delimiter = ", "
+ elif len(bimbam_fh.readline().split(",")) > 2:
+ delimiter = ","
+ elif len(bimbam_fh.readline().split("\t")) > 2:
+ delimiter = "\t"
+ else:
+ delimiter = " "
+ for line in bimbam_fh:
+ marker = {}
+ marker['name'] = line.split(delimiter)[0].rstrip()
+ marker['Mb'] = float(line.split(delimiter)[1].rstrip())/1000000
+ marker['chr'] = line.split(delimiter)[2].rstrip()
+ markers.append(marker)
for marker in markers:
- if (marker['chr'] != "X") and (marker['chr'] != "Y"):
+ if (marker['chr'] != "X") and (marker['chr'] != "Y") and (marker['chr'] != "M"):
marker['chr'] = int(marker['chr'])
marker['Mb'] = float(marker['Mb'])
self.markers = markers
- #logger.debug("self.markers:", self.markers)
-
def add_pvalues(self, p_values):
logger.debug("length of self.markers:", len(self.markers))
@@ -261,10 +281,12 @@ class DatasetGroup(object):
has multiple datasets associated with it.
"""
- def __init__(self, dataset):
+ def __init__(self, dataset, name=None):
"""This sets self.group and self.group_id"""
- #logger.debug("DATASET NAME2:", dataset.name)
- self.name, self.id, self.genetic_type = fetchone(dataset.query_for_group)
+ if name == None:
+ self.name, self.id, self.genetic_type = fetchone(dataset.query_for_group)
+ else:
+ self.name, self.id, self.genetic_type = fetchone("SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType FROM InbredSet where Name='%s'" % name)
if self.name == 'BXD300':
self.name = "BXD"
@@ -272,7 +294,6 @@ class DatasetGroup(object):
self.parlist = None
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)
@@ -282,55 +303,39 @@ class DatasetGroup(object):
self._datasets = None
self.genofile = None
- def get_accession_id(self):
- results = g.db.execute("""select InfoFiles.GN_AccesionId from InfoFiles, PublishFreeze, InbredSet where
- InbredSet.Name = %s and
- PublishFreeze.InbredSetId = InbredSet.Id and
- InfoFiles.InfoPageName = PublishFreeze.Name and
- PublishFreeze.public > 0 and
- PublishFreeze.confidentiality < 1 order by
- PublishFreeze.CreateTime desc""", (self.name)).fetchone()
-
- if results != None:
- return str(results[0])
- 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"]
+ mapping_names = ["GEMMA", "QTLReaper", "R/qtl"]
elif mapping_id == "2":
mapping_names = ["GEMMA"]
+ elif mapping_id == "3":
+ mapping_names = ["R/qtl"]
elif mapping_id == "4":
- mapping_names = ["PLINK"]
+ mapping_names = ["GEMMA", "PLINK"]
else:
mapping_names = []
return mapping_id, mapping_names
- def get_specified_markers(self, markers = []):
- self.markers = HumanMarkers(self.name, markers)
-
def get_markers(self):
- logger.debug("self.species is:", self.species)
-
def check_plink_gemma():
if flat_file_exists("mapping"):
MAPPING_PATH = flat_files("mapping")+"/"
- if (os.path.isfile(MAPPING_PATH+self.name+".bed") and
- (os.path.isfile(MAPPING_PATH+self.name+".map") or
- os.path.isfile(MAPPING_PATH+self.name+".bim"))):
+ if os.path.isfile(MAPPING_PATH+self.name+".bed"):
return True
return False
if check_plink_gemma():
marker_class = HumanMarkers
else:
- marker_class = Markers
+ marker_class = Markers
- self.markers = marker_class(self.name)
+ if self.genofile:
+ self.markers = marker_class(self.genofile[:-5])
+ else:
+ self.markers = marker_class(self.name)
def get_f1_parent_strains(self):
try:
@@ -344,30 +349,32 @@ class DatasetGroup(object):
if maternal and paternal:
self.parlist = [maternal, paternal]
+ def get_genofiles(self):
+ jsonfile = "%s/%s.json" % (webqtlConfig.GENODIR, self.name)
+ try:
+ f = open(jsonfile)
+ except:
+ return None
+ jsondata = json.load(f)
+ return jsondata['genofile']
+
def get_samplelist(self):
result = None
- key = "samplelist:v2:" + self.name
+ key = "samplelist:v3:" + self.name
if USE_REDIS:
result = Redis.get(key)
if result is not None:
- #logger.debug("Sample List Cache hit!!!")
- #logger.debug("Before unjsonifying {}: {}".format(type(result), result))
self.samplelist = json.loads(result)
- #logger.debug(" type: ", type(self.samplelist))
- #logger.debug(" self.samplelist: ", self.samplelist)
else:
logger.debug("Cache not hit")
genotype_fn = locate_ignore_error(self.name+".geno",'genotype')
- mapping_fn = locate_ignore_error(self.name+".fam",'mapping')
- if mapping_fn:
- self.samplelist = get_group_samplelists.get_samplelist("plink", mapping_fn)
- elif genotype_fn:
+ if genotype_fn:
self.samplelist = get_group_samplelists.get_samplelist("geno", genotype_fn)
else:
self.samplelist = None
- logger.debug("Sample list: ",self.samplelist)
+
if USE_REDIS:
Redis.set(key, json.dumps(self.samplelist))
Redis.expire(key, 60*5)
@@ -378,19 +385,27 @@ class DatasetGroup(object):
[result.extend(l) for l in lists if l]
return result
- def read_genotype_file(self):
+ def read_genotype_file(self, use_reaper=False):
'''Read genotype from .geno file instead of database'''
#genotype_1 is Dataset Object without parents and f1
#genotype_2 is Dataset Object with parents and f1 (not for intercross)
- genotype_1 = reaper.Dataset()
+ #genotype_1 = reaper.Dataset()
# reaper barfs on unicode filenames, so here we ensure it's a string
if self.genofile:
- full_filename = str(locate(self.genofile, 'genotype'))
+ if "RData" in self.genofile: #ZS: This is a temporary fix; I need to change the way the JSON files that point to multiple genotype files are structured to point to other file types like RData
+ full_filename = str(locate(self.genofile.split(".")[0] + ".geno", 'genotype'))
+ else:
+ full_filename = str(locate(self.genofile, 'genotype'))
else:
full_filename = str(locate(self.name + '.geno', 'genotype'))
- genotype_1.read(full_filename)
+
+ if use_reaper:
+ genotype_1 = reaper.Dataset()
+ genotype_1.read(full_filename)
+ else:
+ genotype_1 = gen_geno_ob.genotype(full_filename)
if genotype_1.type == "group" and self.parlist:
genotype_2 = genotype_1.add(Mat=self.parlist[0], Pat=self.parlist[1]) #, F1=_f1)
@@ -419,13 +434,16 @@ def datasets(group_name, this_group = None):
FROM PublishFreeze,InbredSet
WHERE PublishFreeze.InbredSetId = InbredSet.Id
and InbredSet.Name = '%s'
- and PublishFreeze.public > %s)
+ and PublishFreeze.public > %s
+ and PublishFreeze.confidentiality < 1
+ ORDER BY PublishFreeze.Id ASC)
UNION
(SELECT '#GenoFreeze',GenoFreeze.FullName,GenoFreeze.Name
FROM GenoFreeze, InbredSet
WHERE GenoFreeze.InbredSetId = InbredSet.Id
and InbredSet.Name = '%s'
- and GenoFreeze.public > %s)
+ and GenoFreeze.public > %s
+ and GenoFreeze.confidentiality < 1)
UNION
(SELECT Tissue.Name, ProbeSetFreeze.FullName,ProbeSetFreeze.Name
FROM ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue
@@ -434,27 +452,34 @@ def datasets(group_name, this_group = None):
and ProbeFreeze.InbredSetId = InbredSet.Id
and InbredSet.Name like %s
and ProbeSetFreeze.public > %s
- ORDER BY Tissue.Name, ProbeSetFreeze.CreateTime desc, ProbeSetFreeze.AvgId)
+ and ProbeSetFreeze.confidentiality < 1
+ ORDER BY Tissue.Name, ProbeSetFreeze.OrderList DESC)
''' % (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:
+ sorted_results = sorted(the_results, key=lambda kv: kv[0])
+
+ pheno_inserted = False #ZS: This is kind of awkward, but need to ensure Phenotypes show up before Genotypes in dropdown
+ geno_inserted = False
+ for dataset_item in sorted_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)]))
+ if tissue_name == '#PublishFreeze' and (dataset_short == group_name + 'Publish'):
+ dataset_menu.insert(0, dict(tissue=None, datasets=[(dataset, dataset_short)]))
+ pheno_inserted = True
+ elif pheno_inserted and tissue_name == '#GenoFreeze':
+ dataset_menu.insert(1, dict(tissue=None, datasets=[(dataset, dataset_short)]))
+ geno_inserted = True
+ else:
+ 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:
@@ -481,7 +506,7 @@ class DataSet(object):
"""
- def __init__(self, name, get_samplelist = True):
+ def __init__(self, name, get_samplelist = True, group_name = None):
assert name, "Need a name"
self.name = name
@@ -493,11 +518,13 @@ class DataSet(object):
self.setup()
- self.check_confidentiality()
-
- self.retrieve_other_names()
-
- self.group = DatasetGroup(self) # sets self.group and self.group_id and gets genotype
+ if self.type == "Temp": #Need to supply group name as input if temp trait
+ self.group = DatasetGroup(self, name=group_name) # sets self.group and self.group_id and gets genotype
+ else:
+ self.check_confidentiality()
+ self.retrieve_other_names()
+ self.group = DatasetGroup(self) # sets self.group and self.group_id and gets genotype
+ self.accession_id = self.get_accession_id()
if get_samplelist == True:
self.group.get_samplelist()
self.species = species.TheSpecies(self)
@@ -512,6 +539,31 @@ class DataSet(object):
def riset():
Weve_Renamed_This_As_Group
+ def get_accession_id(self):
+ if self.type == "Publish":
+ results = g.db.execute("""select InfoFiles.GN_AccesionId from InfoFiles, PublishFreeze, InbredSet where
+ InbredSet.Name = %s and
+ PublishFreeze.InbredSetId = InbredSet.Id and
+ InfoFiles.InfoPageName = PublishFreeze.Name and
+ PublishFreeze.public > 0 and
+ PublishFreeze.confidentiality < 1 order by
+ PublishFreeze.CreateTime desc""", (self.group.name)).fetchone()
+ elif self.type == "Geno":
+ results = g.db.execute("""select InfoFiles.GN_AccesionId from InfoFiles, GenoFreeze, InbredSet where
+ InbredSet.Name = %s and
+ GenoFreeze.InbredSetId = InbredSet.Id and
+ InfoFiles.InfoPageName = GenoFreeze.ShortName and
+ GenoFreeze.public > 0 and
+ GenoFreeze.confidentiality < 1 order by
+ GenoFreeze.CreateTime desc""", (self.group.name)).fetchone()
+ else:
+ results = None
+
+ if results != None:
+ return str(results[0])
+ else:
+ return "None"
+
def retrieve_other_names(self):
"""This method fetches the the dataset names in search_result.
@@ -658,6 +710,7 @@ class PhenotypeDataSet(DataSet):
'Phenotype.Pre_publication_description',
'Phenotype.Pre_publication_abbreviation',
'Phenotype.Post_publication_abbreviation',
+ 'PublishXRef.mean',
'Phenotype.Lab_code',
'Publication.PubMed_ID',
'Publication.Abstract',
@@ -666,13 +719,14 @@ class PhenotypeDataSet(DataSet):
'PublishXRef.Id']
# Figure out what display_fields is
- self.display_fields = ['name',
+ self.display_fields = ['name', 'group_code',
'pubmed_id',
'pre_publication_description',
'post_publication_description',
'original_description',
'pre_publication_abbreviation',
'post_publication_abbreviation',
+ 'mean',
'lab_code',
'submitter', 'owner',
'authorized_users',
@@ -708,20 +762,6 @@ class PhenotypeDataSet(DataSet):
# (Urgently?) Need to write this
pass
- def get_trait_list(self):
- query = """
- select PublishXRef.Id
- from PublishXRef, PublishFreeze
- 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:
- trait_data[trait[0]] = self.retrieve_sample_data(trait[0])
- return trait_data
-
def get_trait_info(self, trait_list, species = ''):
for this_trait in trait_list:
@@ -735,7 +775,7 @@ class PhenotypeDataSet(DataSet):
#of the post-publication description
if this_trait.confidential:
this_trait.description_display = ""
- continue # for now
+ continue # for now, because no authorization features
if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(
privilege=self.privilege,
@@ -759,9 +799,7 @@ class PhenotypeDataSet(DataSet):
#LRS and its location
this_trait.LRS_score_repr = "N/A"
- this_trait.LRS_score_value = 0
this_trait.LRS_location_repr = "N/A"
- this_trait.LRS_location_value = 1000000
if this_trait.lrs:
query = """
@@ -778,17 +816,7 @@ class PhenotypeDataSet(DataSet):
LRS_Chr = result[0]
LRS_Mb = result[1]
- #XZ: LRS_location_value is used for sorting
- try:
- LRS_location_value = int(LRS_Chr)*1000 + float(LRS_Mb)
- except:
- if LRS_Chr.upper() == 'X':
- LRS_location_value = 20*1000 + float(LRS_Mb)
- else:
- LRS_location_value = ord(str(LRS_chr).upper()[0])*1000 + float(LRS_Mb)
-
this_trait.LRS_score_repr = LRS_score_repr = '%3.1f' % this_trait.lrs
- this_trait.LRS_score_value = LRS_score_value = this_trait.lrs
this_trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (LRS_Chr, float(LRS_Mb))
def retrieve_sample_data(self, trait):
@@ -850,45 +878,18 @@ class GenotypeDataSet(DataSet):
def check_confidentiality(self):
return geno_mrna_confidentiality(self)
- def get_trait_list(self):
- query = """
- select Geno.Name
- from Geno, GenoXRef
- 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:
- trait_data[trait[0]] = self.retrieve_sample_data(trait[0])
- return trait_data
-
def get_trait_info(self, trait_list, species=None):
for this_trait in trait_list:
if not this_trait.haveinfo:
this_trait.retrieveInfo()
- #XZ: trait_location_value is used for sorting
- trait_location_repr = 'N/A'
- trait_location_value = 1000000
-
if this_trait.chr and this_trait.mb:
- try:
- trait_location_value = int(this_trait.chr)*1000 + this_trait.mb
- except:
- if this_trait.chr.upper() == 'X':
- trait_location_value = 20*1000 + this_trait.mb
- else:
- trait_location_value = ord(str(this_trait.chr).upper()[0])*1000 + this_trait.mb
-
this_trait.location_repr = 'Chr%s: %.6f' % (this_trait.chr, float(this_trait.mb) )
- this_trait.location_value = trait_location_value
def retrieve_sample_data(self, trait):
query = """
SELECT
- Strain.Name, GenoData.value, GenoSE.error, GenoData.Id, Sample.Name2
+ Strain.Name, GenoData.value, GenoSE.error, GenoData.Id, Strain.Name2
FROM
(GenoData, GenoFreeze, Strain, Geno, GenoXRef)
left join GenoSE on
@@ -940,6 +941,7 @@ class MrnaAssayDataSet(DataSet):
'blatseq', 'targetseq',
'chipid', 'comments',
'strand_probe', 'strand_gene',
+ 'proteinid', 'uniprotid',
'probe_set_target_region',
'probe_set_specificity',
'probe_set_blat_score',
@@ -978,20 +980,6 @@ class MrnaAssayDataSet(DataSet):
def check_confidentiality(self):
return geno_mrna_confidentiality(self)
- def get_trait_list_1(self):
- query = """
- select ProbeSet.Name
- from ProbeSet, ProbeSetXRef
- 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:
- trait_data[trait[0]] = self.retrieve_sample_data(trait[0])
- return trait_data
-
def get_trait_info(self, trait_list=None, species=''):
# Note: setting trait_list to [] is probably not a great idea.
@@ -1023,27 +1011,8 @@ class MrnaAssayDataSet(DataSet):
# Save it for the jinja2 template
this_trait.description_display = description_display
- #XZ: trait_location_value is used for sorting
- trait_location_repr = 'N/A'
- trait_location_value = 1000000
-
if this_trait.chr and this_trait.mb:
- #Checks if the chromosome number can be cast to an int (i.e. isn't "X" or "Y")
- #This is so we can convert the location to a number used for sorting
- trait_location_value = self.convert_location_to_value(this_trait.chr, this_trait.mb)
- #try:
- # trait_location_value = int(this_trait.chr)*1000 + this_trait.mb
- #except ValueError:
- # if this_trait.chr.upper() == 'X':
- # trait_location_value = 20*1000 + this_trait.mb
- # else:
- # trait_location_value = (ord(str(this_trait.chr).upper()[0])*1000 +
- # this_trait.mb)
-
- #ZS: Put this in function currently called "convert_location_to_value"
- this_trait.location_repr = 'Chr%s: %.6f' % (this_trait.chr,
- float(this_trait.mb))
- this_trait.location_value = trait_location_value
+ this_trait.location_repr = 'Chr%s: %.6f' % (this_trait.chr, float(this_trait.mb))
#Get mean expression value
query = (
@@ -1065,9 +1034,7 @@ class MrnaAssayDataSet(DataSet):
#LRS and its location
this_trait.LRS_score_repr = 'N/A'
- this_trait.LRS_score_value = 0
this_trait.LRS_location_repr = 'N/A'
- this_trait.LRS_location_value = 1000000
#Max LRS and its Locus location
if this_trait.lrs and this_trait.locus:
@@ -1082,40 +1049,10 @@ class MrnaAssayDataSet(DataSet):
if result:
lrs_chr, lrs_mb = result
- #XZ: LRS_location_value is used for sorting
- lrs_location_value = self.convert_location_to_value(lrs_chr, lrs_mb)
this_trait.LRS_score_repr = '%3.1f' % this_trait.lrs
- this_trait.LRS_score_value = this_trait.lrs
this_trait.LRS_location_repr = 'Chr%s: %.6f' % (lrs_chr, float(lrs_mb))
-
- def convert_location_to_value(self, chromosome, mb):
- try:
- location_value = int(chromosome)*1000 + float(mb)
- except ValueError:
- if chromosome.upper() == 'X':
- location_value = 20*1000 + float(mb)
- else:
- location_value = (ord(str(chromosome).upper()[0])*1000 +
- float(mb))
-
- return location_value
-
- def get_sequence(self):
- query = """
- SELECT
- ProbeSet.BlatSeq
- FROM
- ProbeSet, ProbeSetFreeze, ProbeSetXRef
- WHERE
- ProbeSet.Id=ProbeSetXRef.ProbeSetId and
- ProbeSetFreeze.Id = ProbeSetXRef.ProbSetFreezeId and
- 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]
+ return trait_list
def retrieve_sample_data(self, trait):
query = """
@@ -1139,7 +1076,6 @@ class MrnaAssayDataSet(DataSet):
#logger.debug("RETRIEVED RESULTS HERE:", results)
return results
-
def retrieve_genes(self, column_name):
query = """
select ProbeSet.Name, ProbeSet.%s
@@ -1156,6 +1092,8 @@ class MrnaAssayDataSet(DataSet):
class TempDataSet(DataSet):
'''Temporary user-generated data set'''
+ DS_NAME_MAP['Temp'] = 'TempDataSet'
+
def setup(self):
self.search_fields = ['name',
'description']
@@ -1191,19 +1129,6 @@ class TempDataSet(DataSet):
desc = self.handle_pca(desc)
return desc
- def get_group(self):
- query = """
- SELECT
- InbredSet.Name, InbredSet.Id
- FROM
- InbredSet, Temp
- WHERE
- Temp.InbredSetId = InbredSet.Id AND
- Temp.Name = "%s"
- """ % self.name
- logger.sql(query)
- self.group, self.group_id = g.db.execute(query).fetchone()
-
def retrieve_sample_data(self, trait):
query = """
SELECT