Merge pull request #2075 from jmchilton/conda_download_fixes

Fix deps.command.download_command on Mac OS X.

lib/galaxy/tools/deps/commands.py

@@ -1,16 +1,21 @@
+"""Generic I/O and shell processing code used by Galaxy tool dependencies."""
 import os
 import subprocess
 import sys as _sys
+
 from galaxy.util import which
 
+STDOUT_INDICATOR = "-"
+
 
 def redirecting_io(sys=_sys):
+    """Predicate to determine if we are redicting I/O in process."""
     assert sys is not None
-    # We are redirecting standard out and standard error.
     return not hasattr(sys.stdout, "fileno")
 
 
 def redirect_aware_commmunicate(p, sys=_sys):
+    """Variant of process.communicate that works with in process I/O redirection."""
     assert sys is not None
     out, err = p.communicate()
     if redirecting_io(sys=sys):
@@ -24,6 +29,7 @@ def redirect_aware_commmunicate(p, sys=_sys):
 
 
 def shell(cmds, env=None, **kwds):
+    """Run shell commands with `shell_process` and wait."""
     sys = kwds.get("sys", _sys)
     assert sys is not None
     p = shell_process(cmds, env, **kwds)
@@ -36,6 +42,11 @@ def shell(cmds, env=None, **kwds):
 
 
 def shell_process(cmds, env=None, **kwds):
+    """A high-level method wrapping subprocess.Popen.
+
+    Handles details such as environment extension and in process I/O
+    redirection.
+    """
     sys = kwds.get("sys", _sys)
     popen_kwds = dict(
         shell=True,
@@ -55,10 +66,14 @@ def shell_process(cmds, env=None, **kwds):
 
 
 def execute(cmds):
-    return __wait(cmds, shell=False)
+    """Execute commands and throw an exception on a non-zero exit.
+
+    Return the standard output if the commands are successful
+    """
+    return _wait(cmds, shell=False)
 
 
-def __wait(cmds, **popen_kwds):
+def _wait(cmds, **popen_kwds):
     p = subprocess.Popen(cmds, **popen_kwds)
     stdout, stderr = p.communicate()
     if p.returncode != 0:
@@ -66,19 +81,34 @@ def __wait(cmds, **popen_kwds):
     return stdout
 
 
-def download_command(url, quote_url=False):
+def download_command(url, to=STDOUT_INDICATOR, quote_url=False):
+    """Build a command line to download a URL.
+
+    By default the URL will be downloaded to standard output but a specific
+    file can be specified with the `to` argument.
+    """
     if quote_url:
         url = "'%s'" % url
+        if to != STDOUT_INDICATOR:
+            to = "'%s'" % to
     if which("wget"):
-        download_cmd = ["wget", "-q", "--recursive", "-O" "-", url]
+        download_cmd = ["wget", "-q"]
+        if to == STDOUT_INDICATOR:
+            download_cmd += ["-O" , STDOUT_INDICATOR, url]
+        else:
+            download_cmd += ["--recursive", "-O" , to, url]
     else:
         download_cmd = ["curl", "-L", url]
+        if to != STDOUT_INDICATOR:
+            download_cmd += ["-o", to]
     return download_cmd
 
 
 class CommandLineException(Exception):
+    """An exception indicating a non-zero command-line exit."""
 
     def __init__(self, command, stdout, stderr):
+        """Construct a CommandLineException from command and standard I/O."""
         self.command = command
         self.stdout = stdout
         self.stderr = stderr
@@ -92,6 +122,7 @@ class CommandLineException(Exception):
                         ) % (command, stderr, stdout)
 
     def __str__(self):
+        """Return a verbose error message indicating the command problem."""
         return self.message
 
 

lib/galaxy/tools/deps/conda_util.py

@@ -260,10 +260,9 @@ def hash_conda_packages(conda_packages, conda_target=None):
 # these commands as Python
 def install_conda(conda_context=None):
     conda_context = _ensure_conda_context(conda_context)
-    download_cmd = " ".join(commands.download_command(conda_link(), quote_url=True))
     f, script_path = tempfile.mkstemp(suffix=".bash", prefix="conda_install")
     os.close(f)
-    download_cmd = "%s >> '%s'" % (download_cmd, script_path)
+    download_cmd = " ".join(commands.download_command(conda_link(), to=script_path, quote_url=True))
     install_cmd = "bash '%s' -b -p '%s'" % (script_path, conda_context.conda_prefix)
     full_command = "%s; %s" % (download_cmd, install_cmd)
     try:

test/unit/tools/test_conda_resolution.py

@@ -1,12 +1,8 @@
 import os
 import shutil
-from sys import version_info
 from tempfile import mkdtemp
 
-if version_info < (2, 7):
-    import unittest2 as unittest
-else:
-    import unittest as unittest
+import unittest as unittest
 
 from galaxy.tools.deps import DependencyManager
 from galaxy.tools.deps.resolvers.conda import CondaDependencyResolver