Merge pull request #772 from jessicamizzi/existerror

Start of issue 718, file not existing clean up

ChangeLog

@@ -1,3 +1,9 @@
+2015-03-16  Jessica Mizzi  <mizzijes@msu.edu>
+
+    * khmer/kfile.py: Added file not existing error for system exit
+    * tests/{test_scripts,test_functions}.py: Added tests for
+    check_file_status for file existence and force option
+
 2015-03-15  Kevin Murray  <spam@kdmurray.id.au>  &  Titus Brown  <titus@idyll.org>
 
    * tests/test_counting_hash.py: Skip get_raw_tables test if python doesn't

khmer/kfile.py

@@ -19,10 +19,22 @@ def check_file_status(file_path, force):
     AND if the file is NOT a fifo/block/named pipe then a warning is printed
     and sys.exit(1) is called
     """
+    mode = None
 
     if file_path is '-':
         return
-    mode = os.stat(file_path).st_mode
+    try:
+        mode = os.stat(file_path).st_mode
+    except OSError:
+        print >>sys.stderr, "ERROR: Input file %s does not exist" % \
+                            file_path
+
+        if not force:
+            print >>sys.stderr, "Exiting"
+            sys.exit(1)
+        else:
+            return
+
     # block devices will be nonzero
     if S_ISBLK(mode) or S_ISFIFO(mode):
         return

tests/test_functions.py

@@ -11,6 +11,7 @@
 import collections
 from khmer.utils import (check_is_pair, broken_paired_reader, check_is_left,
                          check_is_right)
+from khmer.kfile import check_file_status
 
 
 def test_forward_hash():
@@ -115,6 +116,24 @@ def test_extract_hashbits_info():
             print >>sys.stderr, '...failed to remove {fn}'.format(fn)
 
 
+def test_check_file_status_kfile():
+    fn = utils.get_temp_filename('thisfiledoesnotexist')
+    check_file_status_exited = False
+    try:
+        check_file_status(fn, False)
+    except SystemExit:
+        check_file_status_exited = True
+    assert check_file_status_exited
+
+
+def test_check_file_status_kfile_force():
+    fn = utils.get_temp_filename('thisfiledoesnotexist')
+    try:
+        check_file_status(fn, True)
+    except OSError as e:
+        assert False
+
+
 FakeFQRead = collections.namedtuple('Read', ['name', 'quality', 'sequence'])
 FakeFastaRead = collections.namedtuple('Read', ['name', 'sequence'])
 

tests/test_scripts.py

@@ -2814,3 +2814,15 @@ def test_roundtrip_casava_format_2():
     r = open(infile).read()
     r2 = open(outfile).read()
     assert r == r2, (r, r2)
+
+
+def test_existance_failure():
+    expected_output = 'ERROR: Input file'
+
+    args = [utils.get_temp_filename('thisfiledoesnotexistatall')]
+
+    status, out, err = utils.runscript(
+        'extract-paired-reads.py', args, fail_ok=True)
+    assert status == 1
+
+    assert expected_output in err