Merge pull request #4559 from mvdbeek/use_bzip2file

Allow working with pbzip2 compressed files

lib/galaxy/datatypes/sniff.py

@@ -3,7 +3,6 @@
 """
 from __future__ import absolute_import
 
-import bz2
 import codecs
 import gzip
 import logging
@@ -30,6 +29,11 @@
     is_gzip
 )
 
+if sys.version_info < (3, 3):
+    import bz2file as bz2
+else:
+    import bz2
+
 log = logging.getLogger(__name__)
 
 

lib/galaxy/dependencies/pinned-requirements.txt

@@ -13,6 +13,7 @@ uWSGI==2.0.15
 #python_lzo==1.8
 
 # pure Python packages
+bz2file==0.98; python_version < '3.3'
 Paste==2.0.2
 PasteDeploy==1.5.2
 docutils==0.12
@@ -77,4 +78,4 @@ ecdsa==0.13
 pysam==0.8.4+gx5
 
 # GenomeSpace dependencies
-python-genomespaceclient==0.1.8
+python-genomespaceclient==0.1.8

lib/galaxy/dependencies/requirements.txt

@@ -13,6 +13,7 @@ pycrypto
 #python_lzo
 
 # pure Python packages
+bz2file; python_version < '3.3'
 Paste
 PasteDeploy
 docutils

lib/galaxy/util/checkers.py

@@ -1,13 +1,18 @@
-import bz2
 import gzip
 import re
+import sys
 import zipfile
 
 from six import StringIO
 
 from galaxy import util
 from galaxy.util.image_util import image_type
 
+if sys.version_info < (3, 3):
+    import bz2file as bz2
+else:
+    import bz2
+
 HTML_CHECK_LINES = 100
 
 

lib/galaxy/util/compression_utils.py

@@ -1,12 +1,17 @@
-import bz2
 import gzip
+import sys
 import zipfile
 
 from .checkers import (
     is_bz2,
     is_gzip
 )
 
+if sys.version_info < (3, 3):
+    import bz2file as bz2
+else:
+    import bz2
+
 
 def get_fileobj(filename, mode="r", gzip_only=False, bz2_only=False, zip_only=False):
     """

lib/tool_shed/util/commit_util.py

@@ -1,9 +1,9 @@
-import bz2
 import gzip
 import json
 import logging
 import os
 import shutil
+import sys
 import tempfile
 from collections import namedtuple
 
@@ -14,6 +14,11 @@
 from tool_shed.tools import data_table_manager
 from tool_shed.util import basic_util, hg_util, shed_util_common as suc
 
+if sys.version_info < (3, 3):
+    import bz2file as bz2
+else:
+    import bz2
+
 log = logging.getLogger(__name__)
 
 UNDESIRABLE_DIRS = ['.hg', '.svn', '.git', '.cvs']

tools/data_source/upload.py

@@ -25,12 +25,12 @@
 from galaxy.util.image_util import get_image_ext
 
 
-try:
+if sys.version_info < (3, 3):
+    import bz2file as bz2
+else:
     import bz2
-except:
-    bz2 = None
 
-assert sys.version_info[:2] >= (2, 4)
+assert sys.version_info[:2] >= (2, 7)
 
 
 def stop_err(msg, ret=1):
@@ -165,7 +165,7 @@ def add_file(dataset, registry, json_file, output_path):
                     os.chmod(dataset.path, 0o644)
                 dataset.name = dataset.name.rstrip('.gz')
                 data_type = 'gzip'
-            if not data_type and bz2 is not None:
+            if not data_type:
                 # See if we have a bz2 file, much like gzip
                 is_bzipped, is_valid = check_bz2(dataset.path, check_content)
                 if is_bzipped and not is_valid: