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(a)bx.psu.edu&gt;: > 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 >

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

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.

--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(a)gmail.com&gt;: >> >> 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(a)bx.psu.edu&gt;: >>> >>> 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 >>>