AttributeError: 'module' object has no attribute 'FakeSocket'
Hi all, today I updated my test server to the newest galaxy-central version. However, when I start it, I get the following error: Traceback (most recent call last): File "./scripts/paster.py", line 34, in <module> command.run() File "/galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 84, in run invoke(command, command_name, options, args[1:]) File "/galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 123, in invoke exit_code = runner.run(args) File "/galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 218, in run result = self.command() File "/galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py", line 276, in command relative_to=base, global_conf=vars) File "/galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py", line 313, in loadapp **kw) File "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 224, in loadobj global_conf=global_conf) File "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 248, in loadcontext global_conf=global_conf) File "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 278, in _loadconfig return loader.get_context(object_type, name, global_conf) File "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 413, in get_context section) File "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 458, in _context_from_explicit value = import_string(found_expr) File "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 18, in import_string return pkg_resources.EntryPoint.parse("x="+s).load(False) File "/galaxy/galaxy_test/lib/pkg_resources.py", line 1954, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File "/galaxy/galaxy_test/lib/galaxy/web/buildapp.py", line 19, in <module> from galaxy import config, jobs, util, tools File "/galaxy/galaxy_test/lib/galaxy/tools/__init__.py", line 33, in <module> from galaxy.util.shed_util import * File "/galaxy/galaxy_test/lib/galaxy/util/shed_util.py", line 14, in <module> from mercurial import ui, commands File "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/commands.py", line 12, in <module> import hg, scmutil, util, revlog, extensions, copies, error, bookmarks File "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/hg.py", line 12, in <module> import localrepo, bundlerepo, httprepo, sshrepo, statichttprepo, bookmarks File "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/httprepo.py", line 11, in <module> import changegroup, statichttprepo, error, httpconnection, url, util, wireproto File "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/statichttprepo.py", line 11, in <module> import changelog, byterange, url, error File "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/url.py", line 13, in <module> import httpconnection as httpconnectionmod File "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/httpconnection.py", line 16, in <module> from mercurial import httpclient File "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/httpclient/__init__.py", line 48, in <module> import socketutil File "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/httpclient/socketutil.py", line 82, in <module> class FakeSocket(httplib.FakeSocket): AttributeError: 'module' object has no attribute 'FakeSocket' Any help appreciated. Thanks. Sarah
On Tue, May 22, 2012 at 3:30 PM, Sarah Diehl <diehl@immunbio.mpg.de> wrote:
Hi all,
today I updated my test server to the newest galaxy-central version. However, when I start it, I get the following error:
Traceback (most recent call last): File "./scripts/paster.py", line 34, in <module> command.run() File "/galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 84, in run invoke(command, command_name, options, args[1:]) File "/galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 123, in invoke exit_code = runner.run(args) File "/galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 218, in run result = self.command() File "/galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py", line 276, in command relative_to=base, global_conf=vars) File "/galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py", line 313, in loadapp **kw) File "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 224, in loadobj global_conf=global_conf) File "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 248, in loadcontext global_conf=global_conf) File "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 278, in _loadconfig return loader.get_context(object_type, name, global_conf) File "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 413, in get_context section) File "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 458, in _context_from_explicit value = import_string(found_expr) File "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 18, in import_string return pkg_resources.EntryPoint.parse("x="+s).load(False) File "/galaxy/galaxy_test/lib/pkg_resources.py", line 1954, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File "/galaxy/galaxy_test/lib/galaxy/web/buildapp.py", line 19, in <module> from galaxy import config, jobs, util, tools File "/galaxy/galaxy_test/lib/galaxy/tools/__init__.py", line 33, in <module> from galaxy.util.shed_util import * File "/galaxy/galaxy_test/lib/galaxy/util/shed_util.py", line 14, in <module> from mercurial import ui, commands File "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/commands.py", line 12, in <module> import hg, scmutil, util, revlog, extensions, copies, error, bookmarks File "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/hg.py", line 12, in <module> import localrepo, bundlerepo, httprepo, sshrepo, statichttprepo, bookmarks File "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/httprepo.py", line 11, in <module> import changegroup, statichttprepo, error, httpconnection, url, util, wireproto File "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/statichttprepo.py", line 11, in <module> import changelog, byterange, url, error File "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/url.py", line 13, in <module> import httpconnection as httpconnectionmod File "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/httpconnection.py", line 16, in <module> from mercurial import httpclient File "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/httpclient/__init__.py", line 48, in <module> import socketutil File "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/httpclient/socketutil.py", line 82, in <module> class FakeSocket(httplib.FakeSocket): AttributeError: 'module' object has no attribute 'FakeSocket'
Any help appreciated. Thanks. Sarah
I had this happen to me last month, https://twitter.com/#!/pjacock/statuses/194797125375234053 Quote: Just recompiled #Python 2.6 ... missing ssl libraries last time finally bit me with import error doing 'from httplib import FakeSocket' Basically (outside Galaxy), using the same Python that Galaxy uses, try 'from httplib import FakeSocket' - if you get an ImportError that explains why Galaxy breaks. In my case this was a locally compiled Python (since we are using CentOS where the system Python is too old), and we'd compiled it without the SSL libraries. Until relatively recently this didn't mater for using Galaxy - now it does. Peter
Thanks Peter! It's very likely that I have the exact same problem, because I also have CentOS and needed to compile Python. On 05/22/2012 05:04 PM, Peter Cock wrote:
On Tue, May 22, 2012 at 3:30 PM, Sarah Diehl<diehl@immunbio.mpg.de> wrote:
Hi all,
today I updated my test server to the newest galaxy-central version. However, when I start it, I get the following error:
Traceback (most recent call last): File "./scripts/paster.py", line 34, in<module> command.run() File "/galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 84, in run invoke(command, command_name, options, args[1:]) File "/galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 123, in invoke exit_code = runner.run(args) File "/galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 218, in run result = self.command() File "/galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py", line 276, in command relative_to=base, global_conf=vars) File "/galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py", line 313, in loadapp **kw) File "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 224, in loadobj global_conf=global_conf) File "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 248, in loadcontext global_conf=global_conf) File "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 278, in _loadconfig return loader.get_context(object_type, name, global_conf) File "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 413, in get_context section) File "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 458, in _context_from_explicit value = import_string(found_expr) File "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 18, in import_string return pkg_resources.EntryPoint.parse("x="+s).load(False) File "/galaxy/galaxy_test/lib/pkg_resources.py", line 1954, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File "/galaxy/galaxy_test/lib/galaxy/web/buildapp.py", line 19, in<module> from galaxy import config, jobs, util, tools File "/galaxy/galaxy_test/lib/galaxy/tools/__init__.py", line 33, in <module> from galaxy.util.shed_util import * File "/galaxy/galaxy_test/lib/galaxy/util/shed_util.py", line 14, in <module> from mercurial import ui, commands File "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/commands.py", line 12, in<module> import hg, scmutil, util, revlog, extensions, copies, error, bookmarks File "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/hg.py", line 12, in<module> import localrepo, bundlerepo, httprepo, sshrepo, statichttprepo, bookmarks File "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/httprepo.py", line 11, in<module> import changegroup, statichttprepo, error, httpconnection, url, util, wireproto File "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/statichttprepo.py", line 11, in<module> import changelog, byterange, url, error File "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/url.py", line 13, in<module> import httpconnection as httpconnectionmod File "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/httpconnection.py", line 16, in<module> from mercurial import httpclient File "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/httpclient/__init__.py", line 48, in<module> import socketutil File "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/httpclient/socketutil.py", line 82, in<module> class FakeSocket(httplib.FakeSocket): AttributeError: 'module' object has no attribute 'FakeSocket'
Any help appreciated. Thanks. Sarah I had this happen to me last month, https://twitter.com/#!/pjacock/statuses/194797125375234053
Quote: Just recompiled #Python 2.6 ... missing ssl libraries last time finally bit me with import error doing 'from httplib import FakeSocket'
Basically (outside Galaxy), using the same Python that Galaxy uses, try 'from httplib import FakeSocket' - if you get an ImportError that explains why Galaxy breaks.
In my case this was a locally compiled Python (since we are using CentOS where the system Python is too old), and we'd compiled it without the SSL libraries. Until relatively recently this didn't mater for using Galaxy - now it does.
Peter
On Tue, May 22, 2012 at 4:14 PM, Sarah Diehl <diehl@immunbio.mpg.de> wrote:
Thanks Peter! It's very likely that I have the exact same problem, because I also have CentOS and needed to compile Python.
In that case make sure you've done this: sudo yum install openssl openssl-dev and then repeat the Python 2.6 configure, make, make test, make install. Peter P.S. We also wanted this: sudo yum install bzip2 bzip2-devel At the end of the configure output you get told what Python modules are disabled due to missing libraries - check this list for any other potential problems later on.
On May 22, 2012, at 11:18 AM, Peter Cock wrote:
On Tue, May 22, 2012 at 4:14 PM, Sarah Diehl <diehl@immunbio.mpg.de> wrote:
Thanks Peter! It's very likely that I have the exact same problem, because I also have CentOS and needed to compile Python.
In that case make sure you've done this:
sudo yum install openssl openssl-dev
and then repeat the Python 2.6 configure, make, make test, make install.
Peter
P.S. We also wanted this:
sudo yum install bzip2 bzip2-devel
At the end of the configure output you get told what Python modules are disabled due to missing libraries - check this list for any other potential problems later on.
Hi Peter, Thanks for pointing this out, this information is useful and I've added it to "Step 0" at http://getgalaxy.org/ --nate
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participants (3)
-
Nate Coraor -
Peter Cock -
Sarah Diehl