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authorPjotr Prins2016-04-20 08:46:23 +0000
committerPjotr Prins2016-04-20 08:46:23 +0000
commit4b80bbfe261e8d0587a637b35416834e027f0999 (patch)
treea67fa988cad9f8c0a3e77b49a3fc6db34b56e40e /wqflask
parentaf7d0bca229f3ebaa80a16d1ce3a2bf1a8abd5df (diff)
downloadgenenetwork2-4b80bbfe261e8d0587a637b35416834e027f0999.tar.gz
[PATCH 024/100] Sanitizing file handling
Diffstat (limited to 'wqflask')
-rwxr-xr-xwqflask/base/data_set.py29
-rw-r--r--wqflask/utility/tools.py20
-rwxr-xr-xwqflask/wqflask/show_trait/show_trait.py11
3 files changed, 29 insertions, 31 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 0e5a3ac1..c6f34143 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -44,12 +44,15 @@ from dbFunction import webqtlDatabaseFunction
from utility import webqtlUtil
from utility.benchmark import Bench
from utility import chunks
+from utility.tools import flat_files
from maintenance import get_group_samplelists
from MySQLdb import escape_string as escape
from pprint import pformat as pf
+MAPPING_PATH = flat_files("mapping")
+
# Used by create_database to instantiate objects
# Each subclass will add to this
DS_NAME_MAP = {}
@@ -404,15 +407,11 @@ class DatasetGroup(object):
else:
#print("Cache not hit")
- from utility.tools import plink_command
- PLINK_RUN = plink_command()
-
geno_file_path = webqtlConfig.GENODIR+self.name+".geno"
- plink_file_path = PLINK_PATH+"/"+self.name+".fam"
- # @FIXME PJOTR/ZACH: .fam files should go into FLATFILES
- if os.path.isfile(plink_file_path):
- self.samplelist = get_group_samplelists.get_samplelist("plink", plink_file_path)
+ mapping_file_path = MAPPING_PATH+"/"+self.name+".fam"
+ if os.path.isfile(mapping_file_path):
+ self.samplelist = get_group_samplelists.get_samplelist("plink", mapping_file_path)
elif os.path.isfile(geno_file_path):
self.samplelist = get_group_samplelists.get_samplelist("geno", geno_file_path)
else:
@@ -441,18 +440,10 @@ class DatasetGroup(object):
# reaper barfs on unicode filenames, so here we ensure it's a string
full_filename = str(os.path.join(webqtlConfig.GENODIR, self.name + '.geno'))
- if os.path.isfile(full_filename):
- #print("Reading file: ", full_filename)
- genotype_1.read(full_filename)
- #print("File read")
- else:
- try:
- full_filename = str(os.path.join(webqtlConfig.TMPDIR, self.name + '.geno'))
- #print("Reading file")
- genotype_1.read(full_filename)
- #print("File read")
- except IOError:
- print("File doesn't exist!")
+ if not os.path.isfile(full_filename):
+ raise SystemError("File "+full_filename+" does not exist")
+ print("Reading file: ", full_filename)
+ genotype_1.read(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)
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index c3c9b292..44bbb1b0 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -52,17 +52,27 @@ def get_setting(command_id,guess=None):
raise Exception(command_id+' path unknown or faulty (update settings.py?). '+command_id+' should point to the path')
return command
+def valid_bin(bin):
+ if os.path.islink(bin) or os.path.isfile(bin):
+ return bin
+ return None
+
+def valid_path(dir):
+ if os.path.isdir(dir):
+ return dir
+ return None
+
def pylmm_command(guess=None):
- return get_setting("PYLMM_RUN",guess)
+ return valid_bin(get_setting("PYLMM_RUN",guess))
def gemma_command(guess=None):
- return get_setting("GEMMA_RUN",guess)
+ return valid_bin(get_setting("GEMMA_RUN",guess))
def plink_command(guess=None):
- return get_setting("PLINK_RUN",guess)
+ return valid_bin(get_setting("PLINK_RUN",guess))
def flat_files(subdir=None):
base = get_setting("GENENETWORK_FILES")
if subdir:
- return base+"/"+subdir
- return base
+ return valid_path(base+"/"+subdir)
+ return valid_path(base)
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 458e48da..35f7fe5f 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -16,8 +16,6 @@ from base import webqtlConfig
from base import webqtlCaseData
from wqflask.show_trait.SampleList import SampleList
from utility import webqtlUtil, Plot, Bunch, helper_functions
-# from utility.tools import plink_command
-from utility.tools import flat_files
from base.trait import GeneralTrait
from base import data_set
from dbFunction import webqtlDatabaseFunction
@@ -25,7 +23,8 @@ from basicStatistics import BasicStatisticsFunctions
from pprint import pformat as pf
-MAPPING_FILES = flat_files("mapping")
+from utility.tools import flat_files
+MAPPING_PATH = flat_files("mapping")
###############################################
#
@@ -34,8 +33,6 @@ MAPPING_FILES = flat_files("mapping")
#
##############################################
-
-
class ShowTrait(object):
def __init__(self, kw):
@@ -162,8 +159,8 @@ class ShowTrait(object):
def get_mapping_methods(self):
'''Only display mapping methods when the dataset group's genotype file exists'''
def check_plink_gemma():
- if (os.path.isfile(MAPPYING_FILES+"/"+self.dataset.group.name+".bed") and
- os.path.isfile(MAPPING_FILES+"/"+self.dataset.group.name+".map")):
+ if (os.path.isfile(MAPPYING_PATH+"/"+self.dataset.group.name+".bed") and
+ os.path.isfile(MAPPING_PATH+"/"+self.dataset.group.name+".map")):
return True
else:
return False