Fix unclosed file descriptors returned by mkstemp

lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py

@@ -34,7 +34,8 @@ def timenow():
 def pruneLD(plinktasks=[], cd='./', vclbase=[]):
     """
     """
-    fplog, plog = tempfile.mkstemp()
+    fd, plog = tempfile.mkstemp()
+    os.close(fd)
     alog = []
     alog.append('## Rgenetics: http://rgenetics.org Galaxy Tools rgQC.py Plink pruneLD runner\n')
     for task in plinktasks:  # each is a list

lib/galaxy/datatypes/sniff.py

@@ -51,6 +51,7 @@ def stream_url_to_file(path, file_sources=None):
     if file_sources and file_sources.looks_like_uri(path):
         file_source_path = file_sources.get_file_source_path(path)
         _, temp_name = tempfile.mkstemp(prefix=prefix)
+        os.close(_)
         file_source_path.file_source.realize_to(file_source_path.path, temp_name)
         return temp_name
     else:

lib/galaxy/datatypes/util/maf_utilities.py

@@ -357,9 +357,8 @@ def build_maf_index(maf_file, species=None):
     indexes, found_species, species_chromosomes, blocks = build_maf_index_species_chromosomes(maf_file, species)
     if indexes is not None:
         fd, index_filename = tempfile.mkstemp()
-        out = os.fdopen(fd, 'w')
-        indexes.write(out)
-        out.close()
+        with os.fdopen(fd, 'w') as out:
+            indexes.write(out)
         return (bx.align.maf.Indexed(maf_file, index_filename=index_filename, keep_open=True, parse_e_rows=False), index_filename)
     return (None, None)
 

lib/tool_shed/webapp/controllers/upload.py

@@ -80,6 +80,7 @@ class UploadController(BaseUIController):
                     uploaded_file = None
                 if valid_url:
                     fd, uploaded_file_name = tempfile.mkstemp()
+                    os.close(fd)
                     uploaded_file = open(uploaded_file_name, 'wb')
                     for chunk in stream.iter_content(chunk_size=util.CHUNK_SIZE):
                         if chunk:

tools/extract/liftOver_wrapper.py

@@ -25,15 +25,13 @@ def safe_bed_file(infile):
     https://lists.soe.ucsc.edu/pipermail/genome/2007-May/013561.html
     """
     fix_pat = re.compile("^(track|browser)")
-    (fd, fname) = tempfile.mkstemp()
-    in_handle = open(infile)
-    out_handle = open(fname, "w")
-    for line in in_handle:
-        if fix_pat.match(line):
-            line = "#" + line
-        out_handle.write(line)
-    in_handle.close()
-    out_handle.close()
+    fd, fname = tempfile.mkstemp()
+    os.close(fd)
+    with open(infile) as in_handle, open(fname, 'w') as out_handle:
+        for line in in_handle:
+            if fix_pat.match(line):
+                line = "#" + line
+            out_handle.write(line)
     return fname