[PATCH 024/100] Sanitizing file handling

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