2008/9/15 Nate Coraor <nate@bx.psu.edu>:

Hi James,

Is this to say that it resolved your problem in the message below (importing simplejson)?

Yes. I think this is a MacPorts issue. If python -S doesn't get you python, it's their problem, right?

The reason for -ES: site or PYTHONPATH installed dependencies often conflict with those dependencies provided with Galaxy. Since setuptools doesn't currently offer a method to continue trying the search path when adding dependencies, conflicting versions in the path almost always cause problems.

For example, if you had Cheetah 2.x in your PYTHONPATH or site-installed and it happened to be found before ours, loading would fail, since setuptools would see the wrong version and never continue down the path to find the correct version.

The joys of setuptools! Thanks for taking the time to help. Now I have it up and running I hope to integrate some tools. I love the work you have done with the workflow interface. cheers, James

--nate

James Casbon wrote:

...

The problem is this:

_hashlib.so and zlib.so live in site-packages because macports bundles them separately. Since you do python -S these cannot be seen. The quick fix was to copy these files from site-packages into the python dir, which I will probably forget about when I upgrade ;)

This raises the question of why you are being so protective over your python path? Presumbaly this was discussed before.

thanks, James

2008/9/15 James Casbon <casbon@gmail.com>:

...

Hi Nate,

Your fix works for the scramble fine, but not for the run.sh which now fails. On removing the -ES from run.sh, I get an error importing simplejson (see below). simplejson.egg is in the eggs/py2.5-noplatform dir so I dont' see why it doesn't pick this up if it manages to pick up WebHelpers.

Traceback (most recent call last): File "./scripts/paster.py", line 26, in <module> command.run() File "/Users/james/Src/galaxy_dist/eggs/py2.5-noplatform/PasteScript-1.3.6-py2.5.egg/paste/script/command.py", line 78, in run File "/Users/james/Src/galaxy_dist/eggs/py2.5-noplatform/PasteScript-1.3.6-py2.5.egg/paste/script/command.py", line 117, in invoke File "/Users/james/Src/galaxy_dist/eggs/py2.5-noplatform/PasteScript-1.3.6-py2.5.egg/paste/script/command.py", line 212, in run File "/Users/james/Src/galaxy_dist/eggs/py2.5-noplatform/PasteScript-1.3.6-py2.5.egg/paste/script/serve.py", line 227, in command File "/Users/james/Src/galaxy_dist/eggs/py2.5-noplatform/PasteScript-1.3.6-py2.5.egg/paste/script/serve.py", line 250, in loadapp File "/Users/james/Src/galaxy_dist/eggs/py2.5-noplatform/PasteDeploy-1.3.1-py2.5.egg/paste/deploy/loadwsgi.py", line 193, in loadapp File "/Users/james/Src/galaxy_dist/eggs/py2.5-noplatform/PasteDeploy-1.3.1-py2.5.egg/paste/deploy/loadwsgi.py", line 213, in loadobj File "/Users/james/Src/galaxy_dist/eggs/py2.5-noplatform/PasteDeploy-1.3.1-py2.5.egg/paste/deploy/loadwsgi.py", line 237, in loadcontext File "/Users/james/Src/galaxy_dist/eggs/py2.5-noplatform/PasteDeploy-1.3.1-py2.5.egg/paste/deploy/loadwsgi.py", line 267, in _loadconfig File "/Users/james/Src/galaxy_dist/eggs/py2.5-noplatform/PasteDeploy-1.3.1-py2.5.egg/paste/deploy/loadwsgi.py", line 397, in get_context File "/Users/james/Src/galaxy_dist/eggs/py2.5-noplatform/PasteDeploy-1.3.1-py2.5.egg/paste/deploy/loadwsgi.py", line 439, in _context_from_explicit File "/Users/james/Src/galaxy_dist/eggs/py2.5-noplatform/PasteDeploy-1.3.1-py2.5.egg/paste/deploy/loadwsgi.py", line 18, in import_string File "/Users/james/Src/galaxy_dist/lib/pkg_resources.py", line 1912, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File "/Users/james/Src/galaxy_dist/lib/galaxy/web/__init__.py", line 5, in <module> from framework import expose, json, require_login, url_for, error, form, FormBuilder File "/Users/james/Src/galaxy_dist/lib/galaxy/web/framework/__init__.py", line 17, in <module> import webhelpers File "/Users/james/Src/galaxy_dist/eggs/py2.5-noplatform/WebHelpers-0.2-py2.5.egg/webhelpers/__init__.py", line 1, in <module> File "/Users/james/Src/galaxy_dist/eggs/py2.5-noplatform/WebHelpers-0.2-py2.5.egg/webhelpers/rails/__init__.py", line 7, in <module> File "/Users/james/Src/galaxy_dist/eggs/py2.5-noplatform/WebHelpers-0.2-py2.5.egg/webhelpers/rails/scriptaculous.py", line 16, in <module> ImportError: No module named simplejson

2008/9/12 Nate Coraor <nate@bx.psu.edu>:

...

James Casbon wrote:

...

Here is the traceback. If you read hashlib, it tries to import _hashlib and if that fails and so it tries to get _md5. The MacPorts python should have _hashlib but not _md5 (as below). _hashlib cannot be found with the path for some reason.

Traceback (most recent call last): File "scramble.py", line 11, in <module> use_setuptools( download_delay=8, to_dir=scramble_lib ) File

"/Users/james/Src/galaxy_dist/scripts/scramble/build/py2.5-macosx-10.3-i386-ucs2/Cheetah/ez_setup.py", line 91, in use_setuptools return do_download() File

"/Users/james/Src/galaxy_dist/scripts/scramble/build/py2.5-macosx-10.3-i386-ucs2/Cheetah/ez_setup.py", line 85, in do_download egg = download_setuptools(version, download_base, to_dir, download_delay) File

"/Users/james/Src/galaxy_dist/scripts/scramble/build/py2.5-macosx-10.3-i386-ucs2/Cheetah/ez_setup.py", line 120, in download_setuptools import urllib2, shutil File

"/opt/local/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/urllib2.py", line 91, in <module> import hashlib File

"/opt/local/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/hashlib.py", line 133, in <module> md5 = __get_builtin_constructor('md5') File

"/opt/local/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/hashlib.py", line 60, in __get_builtin_constructor import _md5 ImportError: No module named _md5

Okay, what's happening here is that in the egg's source directory, scramble creates a script which it then executes in a clean environment using python -ES. Since your hashlib/md5 isn't part of the base install, you'll need to remove the -ES from line 132 of lib/galaxy/eggs/__init__.py:

cmd = "%s -ES %s" % ( self.python, "scramble.py" )

becomes:

cmd = "%s %s" % ( self.python, "scramble.py" )

Try this out and let me know if it works.

--nate