From 290971ca7a28eb579dc2d40c9653b9e160253634 Mon Sep 17 00:00:00 2001
From: E Rasche <hxr@hx42.org>
Date: Mon, 18 Sep 2017 10:32:49 +0200
Subject: [PATCH] more review comments

---
 cron/build_chrom_db.py                       |  2 +-
 cron/parse_builds.py                         |  1 +
 lib/galaxy/datatypes/text.py                 |  2 +-
 lib/galaxy/jobs/transfer_manager.py          |  2 +-
 scripts/data_libraries/build_lucene_index.py |  1 +
 scripts/edam_mapping.py                      |  1 +
 scripts/microbes/harvest_bacteria.py         |  2 +-
 scripts/tool_shed/api/export.py              | 21 ++++++--------------
 8 files changed, 13 insertions(+), 19 deletions(-)

diff --git a/cron/build_chrom_db.py b/cron/build_chrom_db.py
index d3cba98b8dc..4775897548f 100644
--- a/cron/build_chrom_db.py
+++ b/cron/build_chrom_db.py
@@ -15,9 +15,9 @@ from __future__ import print_function
 
 import fileinput
 import os
-import requests
 import sys
 
+import requests
 from six.moves.urllib.parse import urlencode
 
 import parse_builds
diff --git a/cron/parse_builds.py b/cron/parse_builds.py
index 2e4149fce57..243440a331b 100644
--- a/cron/parse_builds.py
+++ b/cron/parse_builds.py
@@ -11,6 +11,7 @@ import xml.etree.ElementTree as ElementTree
 
 import requests
 
+
 def getbuilds(url):
     try:
         text = requests.get(url).text
diff --git a/lib/galaxy/datatypes/text.py b/lib/galaxy/datatypes/text.py
index 3b72e3d48b0..12235e566c4 100644
--- a/lib/galaxy/datatypes/text.py
+++ b/lib/galaxy/datatypes/text.py
@@ -155,7 +155,7 @@ class Ipynb(Json):
                 ofilename = '%s.html' % ofilename
             except subprocess.CalledProcessError:
                 ofilename = dataset.file_name
-                log.exception('Command "%s" failed. Could not convert the Jupyter Notebook to HTML, defaulting to plain text.', map(shlex_quote, cmd))
+                log.exception('Command "%s" failed. Could not convert the Jupyter Notebook to HTML, defaulting to plain text.', ' '.join(map(shlex_quote, cmd)))
             return open(ofilename)
 
     def set_meta(self, dataset, **kwd):
diff --git a/lib/galaxy/jobs/transfer_manager.py b/lib/galaxy/jobs/transfer_manager.py
index 6bca709af3b..8e06024832c 100644
--- a/lib/galaxy/jobs/transfer_manager.py
+++ b/lib/galaxy/jobs/transfer_manager.py
@@ -70,7 +70,7 @@ class TransferManager(object):
             # The transfer script should daemonize fairly quickly - if this is
             # not the case, this process will need to be moved to a
             # non-blocking method.
-            cmd = self.command.append(tj.id)
+            cmd = self.command + [tj.id]
             log.debug('Transfer command is: %s', ' '.join(map(shlex_quote, cmd)))
             p = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
             p.wait()
diff --git a/scripts/data_libraries/build_lucene_index.py b/scripts/data_libraries/build_lucene_index.py
index 710747068be..b3f787e8b02 100644
--- a/scripts/data_libraries/build_lucene_index.py
+++ b/scripts/data_libraries/build_lucene_index.py
@@ -14,6 +14,7 @@ import csv
 import os
 import sys
 import urllib
+
 import requests
 
 sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, 'lib')))
diff --git a/scripts/edam_mapping.py b/scripts/edam_mapping.py
index 7e70c5467cd..bb5e495aa46 100644
--- a/scripts/edam_mapping.py
+++ b/scripts/edam_mapping.py
@@ -17,6 +17,7 @@ from __future__ import print_function
 import os
 import sys
 import requests
+
 from xml import etree
 
 sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))
diff --git a/scripts/microbes/harvest_bacteria.py b/scripts/microbes/harvest_bacteria.py
index 175ce70cb0d..3226dec78ce 100644
--- a/scripts/microbes/harvest_bacteria.py
+++ b/scripts/microbes/harvest_bacteria.py
@@ -8,9 +8,9 @@ import os
 import sys
 import time
 from ftplib import FTP
-import requests
 from urllib import urlretrieve
 
+import requests
 from BeautifulSoup import BeautifulSoup
 from util import get_bed_from_genbank, get_bed_from_glimmer3, get_bed_from_GeneMarkHMM, get_bed_from_GeneMark
 
diff --git a/scripts/tool_shed/api/export.py b/scripts/tool_shed/api/export.py
index 68005de0746..6a5d030c6a0 100644
--- a/scripts/tool_shed/api/export.py
+++ b/scripts/tool_shed/api/export.py
@@ -11,6 +11,7 @@ import argparse
 import os
 import sys
 import tempfile
+
 import requests
 
 sys.path.insert(1, os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, os.pardir, 'lib'))
@@ -98,21 +99,11 @@ def main(options):
             download_url = export_dict['download_url']
             download_dir = os.path.abspath(options.download_dir)
             file_path = os.path.join(download_dir, repositories_archive_filename)
-            src = None
-            dst = None
-            try:
-                src = requests.get(download_url, stream=True)
-                with open(file_path, 'wb') as handle:
-                    for chunk in src.iter_content(chunk_size=CHUNK_SIZE):
-                        if chunk:
-                            handle.write(chunk)
-            except:
-                raise
-            finally:
-                if src:
-                    src.close()
-                if dst:
-                    dst.close()
+            src = requests.get(download_url, stream=True)
+            with open(file_path, 'wb') as dst:
+                for chunk in src.iter_content(chunk_size=CHUNK_SIZE):
+                    if chunk:
+                        dst.write(chunk)
             print "Successfully exported revision ", options.changeset_revision, " of repository ", options.name, " owned by ", options.owner
             print "to location ", file_path
     else: