diff options
Diffstat (limited to 'wqflask/base/data_set/datasetgroup.py')
| -rw-r--r-- | wqflask/base/data_set/datasetgroup.py | 22 |
1 files changed, 13 insertions, 9 deletions
diff --git a/wqflask/base/data_set/datasetgroup.py b/wqflask/base/data_set/datasetgroup.py index 72577f38..90c59a1e 100644 --- a/wqflask/base/data_set/datasetgroup.py +++ b/wqflask/base/data_set/datasetgroup.py @@ -3,6 +3,7 @@ import os import json +from flask import current_app as app from base import webqtlConfig from .markers import Markers, HumanMarkers @@ -11,11 +12,11 @@ from utility import gen_geno_ob from db import webqtlDatabaseFunction from maintenance import get_group_samplelists from wqflask.database import database_connection -from utility.tools import ( +from utility.configuration import ( locate, - USE_REDIS, flat_files, flat_file_exists, + get_setting_bool, locate_ignore_error) class DatasetGroup: @@ -87,8 +88,8 @@ class DatasetGroup: def get_markers(self): def check_plink_gemma(): - if flat_file_exists("mapping"): - MAPPING_PATH = flat_files("mapping") + "/" + if flat_file_exists(app, "mapping"): + MAPPING_PATH = flat_files(app, "mapping") + "/" if os.path.isfile(MAPPING_PATH + self.name + ".bed"): return True return False @@ -117,6 +118,7 @@ class DatasetGroup: def get_study_samplelists(self): study_sample_file = locate_ignore_error( + app, self.name + ".json", 'study_sample_lists') try: f = open(study_sample_file) @@ -137,13 +139,15 @@ class DatasetGroup: def get_samplelist(self, redis_conn): result = None key = "samplelist:v3:" + self.name + USE_REDIS = get_setting_bool(app, "USE_REDIS") if USE_REDIS: result = redis_conn.get(key) if result is not None: self.samplelist = json.loads(result) else: - genotype_fn = locate_ignore_error(self.name + ".geno", 'genotype') + genotype_fn = locate_ignore_error( + app, self.name + ".geno", 'genotype') if genotype_fn: self.samplelist = get_group_samplelists.get_samplelist( "geno", genotype_fn) @@ -168,12 +172,12 @@ class DatasetGroup: # reaper barfs on unicode filenames, so here we ensure it's a string if self.genofile: 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')) + full_filename = str(locate( + app, self.genofile.split(".")[0] + ".geno", 'genotype')) else: - full_filename = str(locate(self.genofile, 'genotype')) + full_filename = str(locate(app, self.genofile, 'genotype')) else: - full_filename = str(locate(self.name + '.geno', 'genotype')) + full_filename = str(locate(app, self.name + '.geno', 'genotype')) genotype_1 = gen_geno_ob.genotype(full_filename) if genotype_1.type == "group" and self.parlist: |