diff options
Diffstat (limited to 'wqflask/base')
| -rwxr-xr-x | wqflask/base/data_set.py | 48 |
1 files changed, 20 insertions, 28 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index cf219fda..d5aae31d 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -43,6 +43,8 @@ from utility import webqtlUtil from utility.benchmark import Bench from wqflask.my_pylmm.pyLMM import chunks +from maintenance import get_group_samplelists + from MySQLdb import escape_string as escape from pprint import pformat as pf @@ -258,35 +260,25 @@ class DatasetGroup(object): if maternal and paternal: self.parlist = [maternal, paternal] - def get_sample_list(self): - genofilename = str(os.path.join(webqtlConfig.GENODIR, self.name + '.geno')) - genofile = open(genofilename, "r") - for line in genofile: - line = line.strip() - if line.startswith(("#", "@")): - continue - headline = line - break - headers = headline.split("\t") - if headers[3] == "Mb": - self.samplelist = headers[4:] - else: - self.samplelist = headers[3:] - - #if genotype_1.type == "group" and self.parlist: - # genotype_2 = genotype_1.add(Mat=self.parlist[0], Pat=self.parlist[1]) #, F1=_f1) - #else: - # genotype_2 = genotype_1 - #determine default genotype object - #if self.incparentsf1 and genotype_1.type != "intercross": - # genotype = genotype_2 - #else: - # self.incparentsf1 = 0 - # genotype = genotype_1 + def get_samplelist(self): + key = "samplelist:v4:" + self.name + print("key is:", key) + with Bench("Loading cache"): + result = Redis.get(key) - #self.samplelist = list(genotype.prgy) - + if result: + print("Sample List Cache hit!!!") + print("Before unjsonifying {}: {}".format(type(result), result)) + self.samplelist = json.loads(result) + print(" type: ", type(self.samplelist)) + print(" self.samplelist: ", self.samplelist) + else: + print("Cache not hit") + self.samplelist = get_group_samplelists.get_samplelist(self.name + ".geno") + print("after get_samplelist") + Redis.set(key, json.dumps(self.samplelist)) + Redis.expire(key, 60*5) def read_genotype_file(self): '''Read genotype from .geno file instead of database''' @@ -374,7 +366,7 @@ class DataSet(object): self.retrieve_other_names() self.group = DatasetGroup(self) # sets self.group and self.group_id and gets genotype - self.group.read_genotype_file() + self.group.get_samplelist() self.species = species.TheSpecies(self) |