Dan, Are you cloning from galaxy-central or galaxy-dist? Are you cloning from the tip or a specific revision? When you see the Syntax error, does Galaxy continue to start up after and the upload error (AttributeError: 'NoneType' object has no attribute 'add') happens later? To make sure I'm understanding you correctly, you can find this error in the logs of both of your installations? Thanks, C On Tue, Jan 29, 2013 at 1:55 PM, Carl Eberhard <carlfeberhard@gmail.com>wrote:
galaxy.jobs.handler DEBUG 2013-01-29 09:43:52,107 Loaded job runner: galaxy.jobs.runners.local:LocalJobRunner galaxy.jobs.handler ERROR 2013-01-29 09:43:52,111 Job runner is not loadable: galaxy.jobs.runners.lwr Traceback (most recent call last): File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/handler.py", line 447, in _load_plugin module = __import__( module_name ) File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/runners/lwr.py", line 232 worker = threading.Thread( ( name="LwrJobRunner.thread-%d" % i ), target=self.run_next ) ^ SyntaxError: invalid syntax
It is significant - and not normal behavior. Good catch!
(You can disregard the 'Error: this request returned None from get_history()' message; it records the lack of a current history which is normal when you access those pages but haven't logged in yet)
On Tue, Jan 29, 2013 at 12:49 PM, Dan Tenenbaum <dtenenba@fhcrc.org>wrote:
Hi Carl,
On Tue, Jan 29, 2013 at 9:30 AM, Carl Eberhard <carlfeberhard@gmail.com> wrote:
Those are both fine then.
You've got us (temporarily) stumped - even the old timers here.
Can you give some rough information on your system - what OS you're using, what your network set up would be?
Thanks again for looking into this. It's Mac OS X 10.8.2 with Chrome 24.0.1312.56, though I have the same problems with Safari 6.0.2 (8536.26.17) and Firefox 17.0. Python 2.7.2.
Also - if it's not too problematic - can you do a fresh clone of Galaxy onto your system and see if that installation has the same problem?
I did this and it seems to have pretty much the same problem but a slightly different manifestation. Now I am now getting the error message "Error: this request returned None from get_history(): http://localhost:8080/" when I try and upload a file; instead, no error messages show up in the console, but the upload still fails. I do however get that error message when I try and log in as a user after registering that user.
Another thing I notice, in the output immediately after starting run.sh:
galaxy.jobs.handler DEBUG 2013-01-29 09:43:52,107 Loaded job runner: galaxy.jobs.runners.local:LocalJobRunner galaxy.jobs.handler ERROR 2013-01-29 09:43:52,111 Job runner is not loadable: galaxy.jobs.runners.lwr Traceback (most recent call last): File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/handler.py", line 447, in _load_plugin module = __import__( module_name ) File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/runners/lwr.py", line 232 worker = threading.Thread( ( name="LwrJobRunner.thread-%d" % i ), target=self.run_next ) ^ SyntaxError: invalid syntax
Maybe that is significant?
Switching back to my previous distribution I get the identical behavior...
Thanks, Dan
C
On Mon, Jan 28, 2013 at 5:03 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:
On Mon, Jan 28, 2013 at 1:59 PM, Carl Eberhard <
wrote:
If you go to your galaxy root in a terminal and then cd to eggs, what is the version listed for SQLAlchemy?
SQLAlchemy-0.5.6_dev_r6498-py2.7.egg
Do you have SQLAlchemy installed already on that machine (apart from
one in Galaxy's eggs)?
I don't think so. I never knowingly installed it and in a fresh python session, 'import sqlalchemy' returns an error that there is no such module.
Thanks, Dan
On Mon, Jan 28, 2013 at 4:50 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:
On Mon, Jan 28, 2013 at 1:40 PM, Carl Eberhard <carlfeberhard@gmail.com> wrote: > I was incorrect in stating that the changes in the next
galaxy-dist
> will > help in this case, unfortunately. From the stack trace you posted, > there > is > a deeper error with your instance that the client-side changes won't > help. > > Can you post the size, type, and name of the file you're trying to > upload? >
I can reproduce this by just typing "hello, world" into the "URL/Text:" box on the "Upload File" page. Any file of any type seems to trigger this problem.
Thanks, Dan
> > On Thu, Jan 24, 2013 at 6:12 PM, Dan Tenenbaum <
> wrote: >> >> On Wed, Jan 23, 2013 at 3:19 PM, Carl Eberhard >> <carlfeberhard@gmail.com> >> wrote: >> > Another thing you might try is to upload the file to our test >> > server: >> > https://test.g2.bx.psu.edu/ and see if that works. >> > >> >> Thanks, that does work. >> >> Setting up an FTP server on my local installation seems pretty >> complex. All I really want to do is work around this issue and fool >> Galaxy into thinking that I have uploaded a file using the >> uploader...since this is a local installation I can put a file >> anywhere on my system, I don't have to actually upload it, just >> place >> it in a directory. >> >> If there is no such workaround, I'll wait for the fix, I guess. >> Thanks >> very much for working on this! >> Dan >> >> >> > >> > On Wed, Jan 23, 2013 at 6:06 PM, Carl Eberhard >> > <carlfeberhard@gmail.com> >> > wrote: >> >> >> >> If this is happening consistently and a refresh on the history >> >> isn't >> >> doing >> >> anything, you might try ftp upload: >> >> http://wiki.galaxyproject.org/FTPUpload >> >> or if you have permissions or are an admin you can try uploading >> >> to >> >> a >> >> data >> >> library: >> >> >> >> >> >> http://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles >> >> >> >> >> >> >> >> On Wed, Jan 23, 2013 at 5:44 PM, Dan Tenenbaum >> >> <dtenenba@fhcrc.org> >> >> wrote: >> >>> >> >>> On Wed, Jan 23, 2013 at 2:42 PM, Carl Eberhard >> >>> <carlfeberhard@gmail.com> >> >>> wrote: >> >>> > What sort of database are you using on your local instance? >> >>> > >> >>> >> >>> The default (sqlite I guess). It's a completely vanilla >> >>> instance, I >> >>> have not touched the config files. >> >>> Dan >> >>> >> >>> >> >>> > >> >>> > On Wed, Jan 23, 2013 at 5:37 PM, Dan Tenenbaum >> >>> > <dtenenba@fhcrc.org> >> >>> > wrote: >> >>> >> >> >>> >> On Wed, Jan 23, 2013 at 2:35 PM, Carl Eberhard >> >>> >> <carlfeberhard@gmail.com> >> >>> >> wrote: >> >>> >> > Thanks, Dan. That helps and I'll start looking into
carlfeberhard@gmail.com> the dtenenba@fhcrc.org> this.
>> >>> >> > >> >>> >> > We will be pushing out a new galaxy-dist revision sometime >> >>> >> > this >> >>> >> > week >> >>> >> > if >> >>> >> > all >> >>> >> > goes well. This revision includes some code for the history >> >>> >> > panel >> >>> >> > that >> >>> >> > may >> >>> >> > help handle this situation a bit better. I'd recommend >> >>> >> > updating >> >>> >> > to >> >>> >> > that >> >>> >> > revision when it comes out. >> >>> >> > >> >>> >> >> >>> >> Thanks! Is there a workaround to upload a file or add it to >> >>> >> my >> >>> >> history >> >>> >> in the meantime? Command-line is ok. If there isn't one, >> >>> >> that's >> >>> >> ok >> >>> >> too.... >> >>> >> Dan >> >>> >> >> >>> >> >> >>> >> >> >>> >> > I'll let you know what I can find. >> >>> >> > Carl >> >>> >> > >> >>> >> > >> >>> >> > >> >>> >> > On Wed, Jan 23, 2013 at 5:18 PM, Dan Tenenbaum >> >>> >> > <dtenenba@fhcrc.org> >> >>> >> > wrote: >> >>> >> >> >> >>> >> >> Hi Carl, >> >>> >> >> >> >>> >> >> On Wed, Jan 23, 2013 at 2:14 PM, Carl Eberhard >> >>> >> >> <carlfeberhard@gmail.com> >> >>> >> >> wrote: >> >>> >> >> > Heya, Dan. >> >>> >> >> > >> >>> >> >> > Sorry for the trouble. >> >>> >> >> > When you get that error again look for a line like you >> >>> >> >> > have >> >>> >> >> > above: >> >>> >> >> > Debug at: http://localhost:8080/_debug/view/1358978130 >> >>> >> >> > >> >>> >> >> > If you open a new tab or window in your browser and go >> >>> >> >> > to >> >>> >> >> > the >> >>> >> >> > address >> >>> >> >> > ('http://localhost:8080/_debug ...'), you should see a >> >>> >> >> > more >> >>> >> >> > informative >> >>> >> >> > error message - complete with a list of function calls >> >>> >> >> > that >> >>> >> >> > led >> >>> >> >> > to >> >>> >> >> > the >> >>> >> >> > error >> >>> >> >> > (a stack trace). >> >>> >> >> > >> >>> >> >> > Can you post that stack trace when you see it? >> >>> >> >> > >> >>> >> >> >> >>> >> >> Thanks for the quick response. Here it is: >> >>> >> >> >> >>> >> >> URL: http://localhost:8080/tool_runner/upload_async_create >> >>> >> >> File >> >>> >> >> >> >>> >> >> >> >>> >> >> >> >>> >> >> >> >>> >> >> >> >>> >> >> '/Users/dtenenba/dev/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py', >> >>> >> >> line 364 in respond >> >>> >> >> app_iter = self.application(environ, >> >>> >> >> detect_start_response) >> >>> >> >> File >> >>> >> >> >> >>> >> >> >> >>> >> >> >> >>> >> >> >> >>> >> >> >> >>> >> >> '/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py', >> >>> >> >> line 98 in __call__ >> >>> >> >> environ, self.app) >> >>> >> >> File >> >>> >> >> >> >>> >> >> >> >>> >> >> >> >>> >> >> >> >>> >> >> >> >>> >> >> '/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py', >> >>> >> >> line 539 in intercept_output >> >>> >> >> app_iter = application(environ, >> >>> >> >> replacement_start_response) >> >>> >> >> File >> >>> >> >> >> >>> >> >> >> >>> >> >> >> >>> >> >> >> >>> >> >> >> >>> >> >> '/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', >> >>> >> >> line 80 in __call__ >> >>> >> >> return self.application(environ, start_response) >> >>> >> >> File >> >>> >> >> >> >>> >> >> >> >>> >> >> >> >>> >> >> >> >>> >> >> >> >>> >> >> '/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', >> >>> >> >> line 632 in __call__ >> >>> >> >> return self.application(environ, start_response) >> >>> >> >> File >> >>> >> >> >> >>> >> >> >> >>> >> >> >> >>> >> >> '/Users/dtenenba/dev/galaxy-dist/lib/galaxy/web/framework/base.py', >> >>> >> >> line 160 in __call__ >> >>> >> >> body = method( trans, **kwargs ) >> >>> >> >> File >> >>> >> >> >> >>> >> >> >> >>> >> >> >> >>> >> >> >> >>> >> >> '/Users/dtenenba/dev/galaxy-dist/lib/galaxy/web/framework/__init__.py', >> >>> >> >> line 73 in decorator >> >>> >> >> return simplejson.dumps( func( self, trans, *args, >> >>> >> >> **kwargs >> >>> >> >> ) >> >>> >> >> ) >> >>> >> >> File >> >>> >> >> >> >>> >> >> >> >>> >> >> >> >>> >> >> >> >>> >> >> >> >>> >> >> '/Users/dtenenba/dev/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py', >> >>> >> >> line 317 in upload_async_create >> >>> >> >> datasets.append( create_dataset( name ) ) >> >>> >> >> File >> >>> >> >> >> >>> >> >> >> >>> >> >> >> >>> >> >> >> >>> >> >> >> >>> >> >> '/Users/dtenenba/dev/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py', >> >>> >> >> line 287 in create_dataset >> >>> >> >> return upload_common.new_upload( trans, cntrller, ud, >> >>> >> >> library_bunch=library_bunch, >> >>> >> >> >> >>> >> >> state=trans.app.model.HistoryDatasetAssociation.states.UPLOAD >> >>> >> >> ) >> >>> >> >> File >> >>> >> >> >> >>> >> >> >> >>> >> >> >> >>> >> >> >> >>> >> >> >> >>> >> >> '/Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/actions/upload_common.py', >> >>> >> >> line 213 in new_upload >> >>> >> >> return new_history_upload( trans, uploaded_dataset, >> >>> >> >> state ) >> >>> >> >> File >> >>> >> >> >> >>> >> >> >> >>> >> >> >> >>> >> >> >> >>> >> >> >> >>> >> >> '/Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/actions/upload_common.py', >> >>> >> >> line 118 in new_history_upload >> >>> >> >> hda.state = state >> >>> >> >> File >> >>> >> >> >> >>> >> >> >> >>> >> >> '/Users/dtenenba/dev/galaxy-dist/lib/galaxy/model/__init__.py', >> >>> >> >> line 1048 in set_dataset_state >> >>> >> >> object_session( self ).add( self.dataset ) >> >>> >> >> AttributeError: 'NoneType' object has no attribute 'add' >> >>> >> >> >> >>> >> >> Dan >> >>> >> >> >> >>> >> >> >> >>> >> >> > We can take it from there and thanks, >> >>> >> >> > Carl >> >>> >> >> > >> >>> >> >> > >> >>> >> >> > On Wed, Jan 23, 2013 at 5:04 PM, Dan Tenenbaum >> >>> >> >> > <dtenenba@fhcrc.org> >> >>> >> >> > wrote: >> >>> >> >> >> >> >>> >> >> >> Hi, >> >>> >> >> >> >> >>> >> >> >> I installed galaxy completely from scratch: >> >>> >> >> >> >> >>> >> >> >> rm -rf galaxy-dist && hg clone >> >>> >> >> >> https://bitbucket.org/galaxy/galaxy-dist/ >> >>> >> >> >> >> >>> >> >> >> I'm not a mercurial expert but I think I have changeset >> >>> >> >> >> 8530:a4113cc1cb5e; at least that's the first entry in >> >>> >> >> >> "hg >> >>> >> >> >> log". >> >>> >> >> >> >> >>> >> >> >> Then started galaxy like this: >> >>> >> >> >> cd galaxy-dist >> >>> >> >> >> ./run.sh >> >>> >> >> >> >> >>> >> >> >> I went to http://localhost:8080 and tried to upload a >> >>> >> >> >> file. I >> >>> >> >> >> never >> >>> >> >> >> saw the file in my history, and this is what printed >> >>> >> >> >> out >> >>> >> >> >> in >> >>> >> >> >> the >> >>> >> >> >> console after I clicked "Execute" on the "Upload File" >> >>> >> >> >> page: >> >>> >> >> >> >> >>> >> >> >> galaxy.web.framework DEBUG 2013-01-23 13:56:11,573 >> >>> >> >> >> Error: >> >>> >> >> >> this >> >>> >> >> >> request >> >>> >> >> >> returned None from get_history(): >> >>> >> >> >> http://localhost:8080/tool_runner/upload_async_create >> >>> >> >> >> galaxy.web.framework DEBUG 2013-01-23 13:56:11,573 >> >>> >> >> >> Error: >> >>> >> >> >> this >> >>> >> >> >> request >> >>> >> >> >> returned None from get_history(): >> >>> >> >> >> http://localhost:8080/tool_runner/upload_async_create >> >>> >> >> >> galaxy.web.framework DEBUG 2013-01-23 13:56:11,573 >> >>> >> >> >> Error: >> >>> >> >> >> this >> >>> >> >> >> request >> >>> >> >> >> returned None from get_history(): >> >>> >> >> >> http://localhost:8080/tool_runner/upload_async_create >> >>> >> >> >> galaxy.web.framework DEBUG 2013-01-23 13:56:11,573 >> >>> >> >> >> Error: >> >>> >> >> >> this >> >>> >> >> >> request >> >>> >> >> >> returned None from get_history(): >> >>> >> >> >> http://localhost:8080/tool_runner/upload_async_create >> >>> >> >> >> galaxy.web.framework DEBUG 2013-01-23 13:56:11,573 >> >>> >> >> >> Error: >> >>> >> >> >> this >> >>> >> >> >> request >> >>> >> >> >> returned None from get_history(): >> >>> >> >> >> http://localhost:8080/tool_runner/upload_async_create >> >>> >> >> >> galaxy.web.framework DEBUG 2013-01-23 13:56:11,573 >> >>> >> >> >> Error: >> >>> >> >> >> this >> >>> >> >> >> request >> >>> >> >> >> returned None from get_history(): >> >>> >> >> >> http://localhost:8080/tool_runner/upload_async_create >> >>> >> >> >> galaxy.web.framework DEBUG 2013-01-23 13:56:11,573 >> >>> >> >> >> Error: >> >>> >> >> >> this >> >>> >> >> >> request >> >>> >> >> >> returned None from get_history(): >> >>> >> >> >> http://localhost:8080/tool_runner/upload_async_create >> >>> >> >> >> galaxy.web.framework DEBUG 2013-01-23 13:56:11,574 >> >>> >> >> >> Error: >> >>> >> >> >> this >> >>> >> >> >> request >> >>> >> >> >> returned None from get_history(): >> >>> >> >> >> http://localhost:8080/tool_runner/upload_async_create >> >>> >> >> >> galaxy.web.framework DEBUG 2013-01-23 13:56:11,574 >> >>> >> >> >> Error: >> >>> >> >> >> this >> >>> >> >> >> request >> >>> >> >> >> returned None from get_history(): >> >>> >> >> >> http://localhost:8080/tool_runner/upload_async_create >> >>> >> >> >> 127.0.0.1 - - [23/Jan/2013:13:56:11 -0700] "POST >> >>> >> >> >> /tool_runner/upload_async_create HTTP/1.1" 500 - >> >>> >> >> >> "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel >> >>> >> >> >> Mac >> >>> >> >> >> OS X >> >>> >> >> >> 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) >> >>> >> >> >> Chrome/24.0.1312.56 >> >>> >> >> >> Safari/537.17" >> >>> >> >> >> Debug at: http://localhost:8080/_debug/view/1358978130 >> >>> >> >> >> 127.0.0.1 - - [23/Jan/2013:13:56:11 -0700] "GET >> >>> >> >> >> /tool_runner/upload_async_message HTTP/1.1" 200 - >> >>> >> >> >> "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel >> >>> >> >> >> Mac >> >>> >> >> >> OS X >> >>> >> >> >> 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) >> >>> >> >> >> Chrome/24.0.1312.56 >> >>> >> >> >> Safari/537.17" >> >>> >> >> >> 127.0.0.1 - - [23/Jan/2013:13:56:11 -0700] "GET >> >>> >> >> >> /history >> >>> >> >> >> HTTP/1.1" >> >>> >> >> >> 200 >> >>> >> >> >> - >> >>> >> >> >> " http://localhost:8080/tool_runner/upload_async_message" >> >>> >> >> >> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) >> >>> >> >> >> AppleWebKit/537.17 >> >>> >> >> >> (KHTML, like Gecko) Chrome/24.0.1312.56 Safari/537.17" >> >>> >> >> >> >> >>> >> >> >> Hope someone can help. >> >>> >> >> >> Thanks, >> >>> >> >> >> Dan >> >>> >> >> >> >> >>> >> >> >> >> >>> >> >> >>
>> >>> >> >> >> Please keep all replies on the list by using "reply >> >>> >> >> >> all" >> >>> >> >> >> in your mail client. To manage your subscriptions to >> >>> >> >> >> this >> >>> >> >> >> and other Galaxy lists, please use the interface at: >> >>> >> >> >> >> >>> >> >> >> http://lists.bx.psu.edu/ >> >>> >> >> > >> >>> >> >> > >> >>> >> > >> >>> >> > >> >>> > >> >>> > >> >> >> >> >> > > >