From aaaf0d55318deb64a0fb844dab007ccf40e387c4 Mon Sep 17 00:00:00 2001
From: Aroon Chande <git@atc.io>
Date: Tue, 5 Mar 2019 07:56:45 -0500
Subject: [PATCH] Escape the species name to be safe

---
 setup.cfg     |  2 +-
 setup.py      | 59 ++++++++++++++++++++++++++++-----------------------
 stringMLST.py |  7 ++----
 3 files changed, 36 insertions(+), 32 deletions(-)

diff --git a/setup.cfg b/setup.cfg
index 5aef279..b88034e 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,2 +1,2 @@
 [metadata]
-description-file = README.rst
+description-file = README.md
diff --git a/setup.py b/setup.py
index ef3ecfb..e88193b 100644
--- a/setup.py
+++ b/setup.py
@@ -1,26 +1,33 @@
-#!/usr/bin/env python
-try:
-  import os
-  from setuptools import setup, find_packages
-except ImportError:
-  from distutils.core import setup
-from os import path
-here = path.abspath(path.dirname(__file__))
-long_description="Fast k-mer based tool for alignment and assembly-free multi locus sequence typing (MLST) directly from genome sequencing reads."
-
-setup(
-  name = 'stringMLST',
-  scripts = ['stringMLST.py'], 
-  version = '0.5.2',
-  description = 'Fast k-mer based tool for alignment and assembly-free multi locus sequence typing (MLST) directly from genome sequencing reads.',
-  long_description=long_description,
-  author = 'Jordan Lab',
-  author_email = 'pypi@atc.io',
-  url = 'https://github.com/jordanlab/stringMLST',
-  keywords = ['MLST', 'kmer', "NGS", "stringMSLT"], 
-  classifiers = [
-      'Programming Language :: Python :: 2.7',
-      'Programming Language :: Python :: 3.5',
-  ],
-  install_requires=['lxml','pyfaidx'],
-)
+#!/usr/bin/env python
+try:
+  import os
+  from setuptools import setup, find_packages
+except ImportError:
+  from distutils.core import setup
+from os import path
+here = path.abspath(path.dirname(__file__))
+try:
+  with open("README.md", "r") as fh:
+      long_description = fh.read()
+  except:
+    pass
+  else:
+    long_description = 'Fast k-mer based tool for alignment and assembly-free multi locus sequence typing (MLST) directly from genome sequencing reads.'
+
+setup(
+  name = 'stringMLST',
+  scripts = ['stringMLST.py'],
+  version = '0.6',
+  description = 'Fast k-mer based tool for alignment and assembly-free multi locus sequence typing (MLST) directly from genome sequencing reads.',
+  long_description=long_description,
+  long_description_content_type="text/markdown",
+  author = 'Jordan Lab',
+  author_email = 'pypi@atc.io',
+  url = 'https://github.com/jordanlab/stringMLST',
+  keywords = ['MLST', 'kmer', "NGS", "stringMSLT"],
+  classifiers = [
+      'Programming Language :: Python :: 2.7',
+      'Programming Language :: Python :: 3.5',
+  ],
+  install_requires=['lxml','pyfaidx'],
+)
diff --git a/stringMLST.py b/stringMLST.py
index 22f2e60..3ddba0e 100755
--- a/stringMLST.py
+++ b/stringMLST.py
@@ -15,7 +15,7 @@
 except ImportError:
     from urllib import urlopen, urlretrieve
 import argparse
-version = """ stringMLST v0.5.2 (updated : January, 7 2018) """
+version = """ stringMLST v0.6 (updated : March, 5 2019) """
 """
 
 stringMLST free for academic users and requires permission before any commercial
@@ -259,13 +259,11 @@
 def get_links(xmlData, savePath, speciesName):
     lociList = {}
     for species in xmlData:
-        if re.search(speciesName, species.text, re.IGNORECASE):
+        if re.search(re.escape(speciesName), species.text, re.IGNORECASE, ):
             for mlst in species:
                 for database in mlst:
                     for child in database:
-                        print(child.text)
                         if child.tag == "profiles":
-                            print(child[1].text)
                             profileURL = child[1].text
                         if child.tag == "loci":
                             for locus in child:
@@ -1545,7 +1543,6 @@ def checkParams(buildDB, predict, config, k, listMode, list, batch, dir, fastq1,
             else:
                 filePrefix = dbPrefix
         config = filePrefix + "_config.txt"
-        print("Get URLs")
         profileURL, loci = get_links(dbRoot, filePrefix, species)
         get_files(filePrefix, loci, profileURL, species)