Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()
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 <carlfeberhard@gmail.com
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 the 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 <dtenenba@fhcrc.org
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 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/ > >>> >> >> > > >>> >> >> > > >>> >> > > >>> >> > > >>> > > >>> > > >> > >> > >
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/ >> >>> >> >> > >> >>> >> >> > >> >>> >> > >> >>> >> > >> >>> > >> >>> > >> >> >> >> >> > > >
On Wed, Jan 30, 2013 at 10:36 AM, Carl Eberhard <carlfeberhard@gmail.com> wrote:
Dan, Are you cloning from galaxy-central or galaxy-dist? Are you cloning from the tip or a specific revision?
I installed galaxy as recommended in the docs: hg clone https://bitbucket.org/galaxy/galaxy-dist/
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?
OK, now bizarrely I am having a slightly different problem, but AFAIK nothing has changed. I don't get that stack trace on startup and now I can upload pasted text, but I can't seem to upload files. I tried to upload a 3KB csv file called sample.csv and it shows up in history with the animated up arrow but the upload never finishes, and every 4 seconds the log shows: 127.0.0.1 - - [30/Jan/2013:11:10:09 -0700] "GET /api/histories/8237ee2988567c1c HTTP/1.1" 200 - "http://localhost:8080/history" "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" No error message in the log though. So I can at least get past my initial place where I was stuck, because the tools I am developing need only text files as input (which can be pasted). I'd still like to know why I can't upload files (from the Choose File button on the Upload File page). Thanks for your help, Dan
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 <carlfeberhard@gmail.com> 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 the 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 > > <dtenenba@fhcrc.org> > > 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 > >> >>> >> > 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/ > >> >>> >> >> > > >> >>> >> >> > > >> >>> >> > > >> >>> >> > > >> >>> > > >> >>> > > >> >> > >> >> > >> > > > > >
Well - as long as those errors don't happen again - it may well be progress. For the next step, can you: 1. open Galaxy in Chrome 2. Go to the settings menu (the button with three horizontal bars on the right side of the address bar). 3. Click the Tools submenu 4. Click the Javascript Console option 5. Try to upload your csv file again This will see if there are any client side errors that are happening during the upload process. It shouldn't take to long to see them if they're there. You may also want to post some of the server log information. Specifically, (around the time you start the failing upload) any lines you see that start with "galaxy.jobs" (e.g. "galaxy.jobs.manager", "galaxy.jobs.runners", etc.). C On Wed, Jan 30, 2013 at 2:13 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:
Dan, Are you cloning from galaxy-central or galaxy-dist? Are you cloning from
On Wed, Jan 30, 2013 at 10:36 AM, Carl Eberhard <carlfeberhard@gmail.com> wrote: the
tip or a specific revision?
I installed galaxy as recommended in the docs:
hg clone https://bitbucket.org/galaxy/galaxy-dist/
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?
OK, now bizarrely I am having a slightly different problem, but AFAIK nothing has changed. I don't get that stack trace on startup and now I can upload pasted text, but I can't seem to upload files. I tried to upload a 3KB csv file called sample.csv and it shows up in history with the animated up arrow but the upload never finishes, and every 4 seconds the log shows:
127.0.0.1 - - [30/Jan/2013:11:10:09 -0700] "GET /api/histories/8237ee2988567c1c HTTP/1.1" 200 - "http://localhost:8080/history" "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"
No error message in the log though.
So I can at least get past my initial place where I was stuck, because the tools I am developing need only text files as input (which can be pasted).
I'd still like to know why I can't upload files (from the Choose File button on the Upload File page).
Thanks for your help, Dan
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
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 <carlfeberhard@gmail.com> 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
> the > one > in Galaxy's eggs)? >
I don't think so. I never knowingly installed it and in a fresh
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 <
is python 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 >> > <dtenenba@fhcrc.org> >> > 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 >> >> >>> >> > 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/ >> >> >>> >> >> > >> >> >>> >> >> > >> >> >>> >> > >> >> >>> >> > >> >> >>> > >> >> >>> > >> >> >> >> >> >> >> >> > >> > >> > > >
On Wed, Jan 30, 2013 at 11:36 AM, Carl Eberhard <carlfeberhard@gmail.com> wrote:
Well - as long as those errors don't happen again - it may well be progress.
For the next step, can you: 1. open Galaxy in Chrome 2. Go to the settings menu (the button with three horizontal bars on the right side of the address bar). 3. Click the Tools submenu 4. Click the Javascript Console option 5. Try to upload your csv file again
This will see if there are any client side errors that are happening during the upload process. It shouldn't take to long to see them if they're there.
Nothing shows up in the javascript console.
You may also want to post some of the server log information. Specifically, (around the time you start the failing upload) any lines you see that start with "galaxy.jobs" (e.g. "galaxy.jobs.manager", "galaxy.jobs.runners", etc.).
I don't see any such lines, just this: 127.0.0.1 - - [30/Jan/2013:11:46:21 -0700] "POST /tool_runner/upload_async_create 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 - - [30/Jan/2013:11:46:21 -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 - - [30/Jan/2013:11:46:21 -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" 127.0.0.1 - - [30/Jan/2013:11:46:21 -0700] "GET /api/histories/8237ee2988567c1c HTTP/1.1" 200 - "http://localhost:8080/history" "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 - - [30/Jan/2013:11:46:25 -0700] "GET /api/histories/8237ee2988567c1c HTTP/1.1" 200 - "http://localhost:8080/history" "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 - - [30/Jan/2013:11:46:29 -0700] "GET /api/histories/8237ee2988567c1c HTTP/1.1" 200 - "http://localhost:8080/history" "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 - - [30/Jan/2013:11:46:33 -0700] "GET /api/histories/8237ee2988567c1c HTTP/1.1" 200 - "http://localhost:8080/history" "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 - - [30/Jan/2013:11:46:38 -0700] "GET /api/histories/8237ee2988567c1c HTTP/1.1" 200 - "http://localhost:8080/history" "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" And the last line repeats every 4 seconds (with timestamp updated). Dan
C
On Wed, Jan 30, 2013 at 2:13 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:
On Wed, Jan 30, 2013 at 10:36 AM, Carl Eberhard <carlfeberhard@gmail.com> wrote:
Dan, Are you cloning from galaxy-central or galaxy-dist? Are you cloning from the tip or a specific revision?
I installed galaxy as recommended in the docs:
hg clone https://bitbucket.org/galaxy/galaxy-dist/
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?
OK, now bizarrely I am having a slightly different problem, but AFAIK nothing has changed. I don't get that stack trace on startup and now I can upload pasted text, but I can't seem to upload files. I tried to upload a 3KB csv file called sample.csv and it shows up in history with the animated up arrow but the upload never finishes, and every 4 seconds the log shows:
127.0.0.1 - - [30/Jan/2013:11:10:09 -0700] "GET /api/histories/8237ee2988567c1c HTTP/1.1" 200 - "http://localhost:8080/history" "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"
No error message in the log though.
So I can at least get past my initial place where I was stuck, because the tools I am developing need only text files as input (which can be pasted).
I'd still like to know why I can't upload files (from the Choose File button on the Upload File page).
Thanks for your help, Dan
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 > <carlfeberhard@gmail.com> > 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 > > the > > 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 > >> > <dtenenba@fhcrc.org> > >> > 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 > >> >> >>> >> > 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/ > >> >> >>> >> >> > > >> >> >>> >> >> > > >> >> >>> >> > > >> >> >>> >> > > >> >> >>> > > >> >> >>> > > >> >> >> > >> >> >> > >> >> > > >> > > >> > > > > >
Ok - interesting! Can you send me the paster.log from a daemon session where you try an upload? Steps for that are: 1. from the directory of your galaxy installation: sh run.sh --daemon (you should see 'Entering daemon mode') 2. Wait a minute, then load localhost:8080 in your browser, login, and try an upload 3. When that fails, you can shut down: (from the galaxy installation again) sh run.sh --stop-daemon The file 'paster.log' should be in that same directory. Let me know if there are any problems, C
Here you go. I notice a couple of stack traces. Thanks! Dan On Thu, Jan 31, 2013 at 12:15 PM, Carl Eberhard <carlfeberhard@gmail.com> wrote:
Ok - interesting! Can you send me the paster.log from a daemon session where you try an upload?
Steps for that are: 1. from the directory of your galaxy installation: sh run.sh --daemon (you should see 'Entering daemon mode') 2. Wait a minute, then load localhost:8080 in your browser, login, and try an upload 3. When that fails, you can shut down: (from the galaxy installation again) sh run.sh --stop-daemon
The file 'paster.log' should be in that same directory.
Let me know if there are any problems, C
Hi Carl, On Thu, Jan 31, 2013 at 1:37 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:
Here you go. I notice a couple of stack traces. Thanks! Dan
I noticed that another user on the list seemed to have a similar problem and I saw that that problem was possibly addressed in a new commit. I updated to 8531:3299529e0fe8 and I still have the same problem, but perhaps different output. I tried logging in and the UI does not seem to recognize that I have logged in. Then I tried to upload a file and it failed, with a traceback in the console: 127.0.0.1 - - [04/Feb/2013:09:45:13 -0700] "GET /history HTTP/1.1" 200 - "http://localhost:8080/tool_runner/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.57 Safari/537.17" 127.0.0.1 - - [04/Feb/2013:09:45:12 -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/24.0.1312.57 Safari/537.17" ---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 49617) Traceback (most recent call last): File "/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 1053, in process_request_in_thread self.finish_request(request, client_address) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 323, in finish_request self.RequestHandlerClass(request, client_address, self) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 641, in __init__ self.finish() File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 694, in finish self.wfile.flush() File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/socket.py", line 303, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe ---------------------------------------- Then I started a daemon session in order to be able to send you the full output, but, although the upload still fails, I don't get this same traceback in the paster.log. I attach it anyway. Thanks, Dan
On Thu, Jan 31, 2013 at 12:15 PM, Carl Eberhard <carlfeberhard@gmail.com> wrote:
Ok - interesting! Can you send me the paster.log from a daemon session where you try an upload?
Steps for that are: 1. from the directory of your galaxy installation: sh run.sh --daemon (you should see 'Entering daemon mode') 2. Wait a minute, then load localhost:8080 in your browser, login, and try an upload 3. When that fails, you can shut down: (from the galaxy installation again) sh run.sh --stop-daemon
The file 'paster.log' should be in that same directory.
Let me know if there are any problems, C
Hello, Dan. I'm glad you updated. I noticed another error in your log: 127.0.0.1 - - [04/Feb/2013:09:50:43 -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/24.0.1312.57 Safari/537.17" Debug at: http://localhost:8080/_debug/view/1360000104 Two things - 1. Can you restart your daemon and make sure you're using a fresh history before the upload? 2. If you're upload fails this time, would you search your paster.log for something close to "Debug at: http://localhost:8080/_debug/view/"... and navigate there with your browser? It should show that error in more depth and allow you to post that here. Thanks for the help, C On Mon, Feb 4, 2013 at 12:55 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:
Hi Carl,
On Thu, Jan 31, 2013 at 1:37 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:
Here you go. I notice a couple of stack traces. Thanks! Dan
I noticed that another user on the list seemed to have a similar problem and I saw that that problem was possibly addressed in a new commit. I updated to 8531:3299529e0fe8 and I still have the same problem, but perhaps different output.
I tried logging in and the UI does not seem to recognize that I have logged in. Then I tried to upload a file and it failed, with a traceback in the console:
127.0.0.1 - - [04/Feb/2013:09:45:13 -0700] "GET /history HTTP/1.1" 200 - "http://localhost:8080/tool_runner/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.57 Safari/537.17" 127.0.0.1 - - [04/Feb/2013:09:45:12 -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/24.0.1312.57 Safari/537.17" ---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 49617) Traceback (most recent call last): File "/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 1053, in process_request_in_thread self.finish_request(request, client_address) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 323, in finish_request self.RequestHandlerClass(request, client_address, self) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 641, in __init__ self.finish() File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 694, in finish self.wfile.flush() File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/socket.py", line 303, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe ----------------------------------------
Then I started a daemon session in order to be able to send you the full output, but, although the upload still fails, I don't get this same traceback in the paster.log. I attach it anyway.
Thanks, Dan
Ok - interesting! Can you send me the paster.log from a daemon session where you try an upload?
Steps for that are: 1. from the directory of your galaxy installation: sh run.sh --daemon (you should see 'Entering daemon mode') 2. Wait a minute, then load localhost:8080 in your browser, login, and
On Thu, Jan 31, 2013 at 12:15 PM, Carl Eberhard <carlfeberhard@gmail.com> wrote: try
an upload 3. When that fails, you can shut down: (from the galaxy installation again) sh run.sh --stop-daemon
The file 'paster.log' should be in that same directory.
Let me know if there are any problems, C
Hi Carl, On Mon, Feb 4, 2013 at 10:22 AM, Carl Eberhard <carlfeberhard@gmail.com> wrote:
Hello, Dan. I'm glad you updated.
I noticed another error in your log: 127.0.0.1 - - [04/Feb/2013:09:50:43 -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/24.0.1312.57 Safari/537.17" Debug at: http://localhost:8080/_debug/view/1360000104
Two things -
1. Can you restart your daemon and make sure you're using a fresh history before the upload?
Not sure what you mean by this. I have no items in my history...
2. If you're upload fails this time, would you search your paster.log for something close to "Debug at: http://localhost:8080/_debug/view/"... and navigate there with your browser? It should show that error in more depth and allow you to post that here.
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' I did try and log in. The green panel that says I have logged in flashed past for a split second. I'm attaching the latest paster.log again as well. Thanks, Dan
Thanks for the help, C
On Mon, Feb 4, 2013 at 12:55 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:
Hi Carl,
On Thu, Jan 31, 2013 at 1:37 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:
Here you go. I notice a couple of stack traces. Thanks! Dan
I noticed that another user on the list seemed to have a similar problem and I saw that that problem was possibly addressed in a new commit. I updated to 8531:3299529e0fe8 and I still have the same problem, but perhaps different output.
I tried logging in and the UI does not seem to recognize that I have logged in. Then I tried to upload a file and it failed, with a traceback in the console:
127.0.0.1 - - [04/Feb/2013:09:45:13 -0700] "GET /history HTTP/1.1" 200 - "http://localhost:8080/tool_runner/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.57 Safari/537.17" 127.0.0.1 - - [04/Feb/2013:09:45:12 -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/24.0.1312.57 Safari/537.17" ---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 49617) Traceback (most recent call last): File "/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 1053, in process_request_in_thread self.finish_request(request, client_address) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 323, in finish_request self.RequestHandlerClass(request, client_address, self) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 641, in __init__ self.finish() File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 694, in finish self.wfile.flush() File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/socket.py", line 303, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe ----------------------------------------
Then I started a daemon session in order to be able to send you the full output, but, although the upload still fails, I don't get this same traceback in the paster.log. I attach it anyway.
Thanks, Dan
On Thu, Jan 31, 2013 at 12:15 PM, Carl Eberhard <carlfeberhard@gmail.com> wrote:
Ok - interesting! Can you send me the paster.log from a daemon session where you try an upload?
Steps for that are: 1. from the directory of your galaxy installation: sh run.sh --daemon (you should see 'Entering daemon mode') 2. Wait a minute, then load localhost:8080 in your browser, login, and try an upload 3. When that fails, you can shut down: (from the galaxy installation again) sh run.sh --stop-daemon
The file 'paster.log' should be in that same directory.
Let me know if there are any problems, C
Sorry about the miscommunication: when I mentioned 'make sure you're using a fresh history' I meant that you may want to go to the history options menu (the gear in the upper right of the history panel and click 'Create new'). It may be that previous datasets are causing some of the problems we're seeing (and you wouldn't see deleted datasets - even though they are still there - unless you checked the 'Include deleted datasets' from that same history options menu). Re: login: I believe there's a redirect in place that moves you past the older 'Return to the homepage' message automatically - I think you're good there (and logged in). Are you seeing the 'Logged in as <your email>' in the 'User' menu at the top? Re: the error: so it looks like this is back to square one (the original error). If this still happens after you've ensured you're using a new history - I'll keep digging. C On Mon, Feb 4, 2013 at 1:30 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:
Hi Carl,
On Mon, Feb 4, 2013 at 10:22 AM, Carl Eberhard <carlfeberhard@gmail.com> wrote:
Hello, Dan. I'm glad you updated.
I noticed another error in your log: 127.0.0.1 - - [04/Feb/2013:09:50:43 -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/24.0.1312.57 Safari/537.17" Debug at: http://localhost:8080/_debug/view/1360000104
Two things -
1. Can you restart your daemon and make sure you're using a fresh history before the upload?
Not sure what you mean by this. I have no items in my history...
2. If you're upload fails this time, would you search your paster.log for something close to "Debug at: http://localhost:8080/_debug/view/"... and navigate there with your browser? It should show that error in more depth and allow you to post that here.
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'
I did try and log in. The green panel that says I have logged in flashed past for a split second.
I'm attaching the latest paster.log again as well.
Thanks, Dan
Thanks for the help, C
On Mon, Feb 4, 2013 at 12:55 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:
Hi Carl,
On Thu, Jan 31, 2013 at 1:37 PM, Dan Tenenbaum <dtenenba@fhcrc.org>
wrote:
Here you go. I notice a couple of stack traces. Thanks! Dan
I noticed that another user on the list seemed to have a similar problem and I saw that that problem was possibly addressed in a new commit. I updated to 8531:3299529e0fe8 and I still have the same problem, but perhaps different output.
I tried logging in and the UI does not seem to recognize that I have logged in. Then I tried to upload a file and it failed, with a traceback in the console:
127.0.0.1 - - [04/Feb/2013:09:45:13 -0700] "GET /history HTTP/1.1" 200 - "http://localhost:8080/tool_runner/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.57 Safari/537.17" 127.0.0.1 - - [04/Feb/2013:09:45:12 -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/24.0.1312.57 Safari/537.17" ---------------------------------------- Exception happened during processing of request from ('127.0.0.1',
Traceback (most recent call last): File
"/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
line 1053, in process_request_in_thread self.finish_request(request, client_address) File
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py",
line 323, in finish_request self.RequestHandlerClass(request, client_address, self) File
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py",
line 641, in __init__ self.finish() File
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py",
line 694, in finish self.wfile.flush() File
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/socket.py",
line 303, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe ----------------------------------------
Then I started a daemon session in order to be able to send you the full output, but, although the upload still fails, I don't get this same traceback in the paster.log. I attach it anyway.
Thanks, Dan
On Thu, Jan 31, 2013 at 12:15 PM, Carl Eberhard <carlfeberhard@gmail.com> wrote:
Ok - interesting! Can you send me the paster.log from a daemon session where you try an upload?
Steps for that are: 1. from the directory of your galaxy installation: sh run.sh --daemon (you should see 'Entering daemon mode') 2. Wait a minute, then load localhost:8080 in your browser, login, and try an upload 3. When that fails, you can shut down: (from the galaxy installation again) sh run.sh --stop-daemon
The file 'paster.log' should be in that same directory.
Let me know if there are any problems, C
On Mon, Feb 4, 2013 at 10:45 AM, Carl Eberhard <carlfeberhard@gmail.com> wrote:
Sorry about the miscommunication: when I mentioned 'make sure you're using a fresh history' I meant that you may want to go to the history options menu (the gear in the upper right of the history panel and click 'Create new'). It may be that previous datasets are causing some of the problems we're seeing (and you wouldn't see deleted datasets - even though they are still there - unless you checked the 'Include deleted datasets' from that same history options menu).
OK, got it. Did that this time.
Re: login: I believe there's a redirect in place that moves you past the older 'Return to the homepage' message automatically - I think you're good there (and logged in). Are you seeing the 'Logged in as <your email>' in the 'User' menu at the top?
No. I think I'm not actually being logged in. All I see under the User menu is "Login" and "Register".
Re: the error: so it looks like this is back to square one (the original error). If this still happens after you've ensured you're using a new history - I'll keep digging.
Yes, it still happens...not sure if it is related to the login issue or not. Just for the sake of thouroughness I am attaching the latest paster.log which contains a url containing the following: 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
C
On Mon, Feb 4, 2013 at 1:30 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:
Hi Carl,
On Mon, Feb 4, 2013 at 10:22 AM, Carl Eberhard <carlfeberhard@gmail.com> wrote:
Hello, Dan. I'm glad you updated.
I noticed another error in your log: 127.0.0.1 - - [04/Feb/2013:09:50:43 -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/24.0.1312.57 Safari/537.17" Debug at: http://localhost:8080/_debug/view/1360000104
Two things -
1. Can you restart your daemon and make sure you're using a fresh history before the upload?
Not sure what you mean by this. I have no items in my history...
2. If you're upload fails this time, would you search your paster.log for something close to "Debug at: http://localhost:8080/_debug/view/"... and navigate there with your browser? It should show that error in more depth and allow you to post that here.
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'
I did try and log in. The green panel that says I have logged in flashed past for a split second.
I'm attaching the latest paster.log again as well.
Thanks, Dan
Thanks for the help, C
On Mon, Feb 4, 2013 at 12:55 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:
Hi Carl,
On Thu, Jan 31, 2013 at 1:37 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:
Here you go. I notice a couple of stack traces. Thanks! Dan
I noticed that another user on the list seemed to have a similar problem and I saw that that problem was possibly addressed in a new commit. I updated to 8531:3299529e0fe8 and I still have the same problem, but perhaps different output.
I tried logging in and the UI does not seem to recognize that I have logged in. Then I tried to upload a file and it failed, with a traceback in the console:
127.0.0.1 - - [04/Feb/2013:09:45:13 -0700] "GET /history HTTP/1.1" 200 - "http://localhost:8080/tool_runner/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.57 Safari/537.17" 127.0.0.1 - - [04/Feb/2013:09:45:12 -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/24.0.1312.57 Safari/537.17" ---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 49617) Traceback (most recent call last): File
"/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 1053, in process_request_in_thread self.finish_request(request, client_address) File
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 323, in finish_request self.RequestHandlerClass(request, client_address, self) File
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 641, in __init__ self.finish() File
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 694, in finish self.wfile.flush() File
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/socket.py", line 303, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe ----------------------------------------
Then I started a daemon session in order to be able to send you the full output, but, although the upload still fails, I don't get this same traceback in the paster.log. I attach it anyway.
Thanks, Dan
On Thu, Jan 31, 2013 at 12:15 PM, Carl Eberhard <carlfeberhard@gmail.com> wrote:
Ok - interesting! Can you send me the paster.log from a daemon session where you try an upload?
Steps for that are: 1. from the directory of your galaxy installation: sh run.sh --daemon (you should see 'Entering daemon mode') 2. Wait a minute, then load localhost:8080 in your browser, login, and try an upload 3. When that fails, you can shut down: (from the galaxy installation again) sh run.sh --stop-daemon
The file 'paster.log' should be in that same directory.
Let me know if there are any problems, C
On Mon, Feb 4, 2013 at 1:55 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:
Re: login: I believe there's a redirect in place that moves you past the older 'Return to the homepage' message automatically - I think you're good there (and logged in). Are you seeing the 'Logged in as <your email>' in the 'User' menu at the top?
No. I think I'm not actually being logged in. All I see under the User menu is "Login" and "Register".
I realize this is a long thread and my recommendation might not help much or was done it already. Sorry if that's the case. This behavior is something I have seen often with Chrome in particular and 99% of the time is related to an old cookie. Specially when I'm accessing a different galaxy instance from the same URL I accessed a previous one, something I see Dan did at the beginning of this thread. I recommend erasing any cookie related to galaxy and also trying with a different browser. Firefox seems to work particularly fine. Hope it helps, Carlos
On Mon, Feb 4, 2013 at 11:45 AM, Carlos Borroto <carlos.borroto@gmail.com> wrote:
On Mon, Feb 4, 2013 at 1:55 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:
Re: login: I believe there's a redirect in place that moves you past the older 'Return to the homepage' message automatically - I think you're good there (and logged in). Are you seeing the 'Logged in as <your email>' in the 'User' menu at the top?
No. I think I'm not actually being logged in. All I see under the User menu is "Login" and "Register".
I realize this is a long thread and my recommendation might not help much or was done it already. Sorry if that's the case.
This behavior is something I have seen often with Chrome in particular and 99% of the time is related to an old cookie. Specially when I'm accessing a different galaxy instance from the same URL I accessed a previous one, something I see Dan did at the beginning of this thread. I recommend erasing any cookie related to galaxy and also trying with a different browser. Firefox seems to work particularly fine.
Indeed, it works with Firefox. And it works with Chrome after I delete my cookies. Thanks very much! Dan
Hope it helps, Carlos
Thanks much, Carlos - I owe you a beer! On Mon, Feb 4, 2013 at 4:01 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:
On Mon, Feb 4, 2013 at 1:55 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:
Re: login: I believe there's a redirect in place that moves you past
On Mon, Feb 4, 2013 at 11:45 AM, Carlos Borroto <carlos.borroto@gmail.com> wrote: the
older 'Return to the homepage' message automatically - I think you're good there (and logged in). Are you seeing the 'Logged in as <your email>' in the 'User' menu at the top?
No. I think I'm not actually being logged in. All I see under the User menu is "Login" and "Register".
I realize this is a long thread and my recommendation might not help much or was done it already. Sorry if that's the case.
This behavior is something I have seen often with Chrome in particular and 99% of the time is related to an old cookie. Specially when I'm accessing a different galaxy instance from the same URL I accessed a previous one, something I see Dan did at the beginning of this thread. I recommend erasing any cookie related to galaxy and also trying with a different browser. Firefox seems to work particularly fine.
Indeed, it works with Firefox. And it works with Chrome after I delete my cookies.
Thanks very much! Dan
Hope it helps, Carlos
Just to be clear, Dan - this solved the login issue and not the upload issue (in which case I'd owe Carlos a six-pack), correct? C On Mon, Feb 4, 2013 at 4:04 PM, Carl Eberhard <carlfeberhard@gmail.com>wrote:
Thanks much, Carlos - I owe you a beer!
On Mon, Feb 4, 2013 at 4:01 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:
On Mon, Feb 4, 2013 at 1:55 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:
Re: login: I believe there's a redirect in place that moves you past
On Mon, Feb 4, 2013 at 11:45 AM, Carlos Borroto <carlos.borroto@gmail.com> wrote: the
older 'Return to the homepage' message automatically - I think you're good there (and logged in). Are you seeing the 'Logged in as <your email>' in the 'User' menu at the top?
No. I think I'm not actually being logged in. All I see under the User menu is "Login" and "Register".
I realize this is a long thread and my recommendation might not help much or was done it already. Sorry if that's the case.
This behavior is something I have seen often with Chrome in particular and 99% of the time is related to an old cookie. Specially when I'm accessing a different galaxy instance from the same URL I accessed a previous one, something I see Dan did at the beginning of this thread. I recommend erasing any cookie related to galaxy and also trying with a different browser. Firefox seems to work particularly fine.
Indeed, it works with Firefox. And it works with Chrome after I delete my cookies.
Thanks very much! Dan
Hope it helps, Carlos
On Mon, Feb 4, 2013 at 1:21 PM, Carl Eberhard <carlfeberhard@gmail.com> wrote:
Just to be clear, Dan - this solved the login issue and not the upload issue (in which case I'd owe Carlos a six-pack), correct?
Sorry...this solved both issues. Dan
C
On Mon, Feb 4, 2013 at 4:04 PM, Carl Eberhard <carlfeberhard@gmail.com> wrote:
Thanks much, Carlos - I owe you a beer!
On Mon, Feb 4, 2013 at 4:01 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:
On Mon, Feb 4, 2013 at 11:45 AM, Carlos Borroto <carlos.borroto@gmail.com> wrote:
On Mon, Feb 4, 2013 at 1:55 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:
Re: login: I believe there's a redirect in place that moves you past the older 'Return to the homepage' message automatically - I think you're good there (and logged in). Are you seeing the 'Logged in as <your email>' in the 'User' menu at the top?
No. I think I'm not actually being logged in. All I see under the User menu is "Login" and "Register".
I realize this is a long thread and my recommendation might not help much or was done it already. Sorry if that's the case.
This behavior is something I have seen often with Chrome in particular and 99% of the time is related to an old cookie. Specially when I'm accessing a different galaxy instance from the same URL I accessed a previous one, something I see Dan did at the beginning of this thread. I recommend erasing any cookie related to galaxy and also trying with a different browser. Firefox seems to work particularly fine.
Indeed, it works with Firefox. And it works with Chrome after I delete my cookies.
Thanks very much! Dan
Hope it helps, Carlos
On Mon, Feb 4, 2013 at 4:46 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:
On Mon, Feb 4, 2013 at 1:21 PM, Carl Eberhard <carlfeberhard@gmail.com> wrote:
Just to be clear, Dan - this solved the login issue and not the upload issue (in which case I'd owe Carlos a six-pack), correct?
Sorry...this solved both issues.
Great, glad it helped. Carl I like Sam Adams ;-).
Even better - thanks again, Carlos - and thanks for the help in tracking this down, Dan. On Mon, Feb 4, 2013 at 4:46 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:
On Mon, Feb 4, 2013 at 1:21 PM, Carl Eberhard <carlfeberhard@gmail.com> wrote:
Just to be clear, Dan - this solved the login issue and not the upload issue (in which case I'd owe Carlos a six-pack), correct?
Sorry...this solved both issues. Dan
C
On Mon, Feb 4, 2013 at 4:04 PM, Carl Eberhard <carlfeberhard@gmail.com> wrote:
Thanks much, Carlos - I owe you a beer!
On Mon, Feb 4, 2013 at 4:01 PM, Dan Tenenbaum <dtenenba@fhcrc.org>
On Mon, Feb 4, 2013 at 11:45 AM, Carlos Borroto <carlos.borroto@gmail.com> wrote:
On Mon, Feb 4, 2013 at 1:55 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:
> Re: login: I believe there's a redirect in place that moves you
> the > older 'Return to the homepage' message automatically - I think you're > good > there (and logged in). Are you seeing the 'Logged in as <your email>' > in the > 'User' menu at the top? >
No. I think I'm not actually being logged in. All I see under the User menu is "Login" and "Register".
I realize this is a long thread and my recommendation might not help much or was done it already. Sorry if that's the case.
This behavior is something I have seen often with Chrome in
and 99% of the time is related to an old cookie. Specially when I'm accessing a different galaxy instance from the same URL I accessed a previous one, something I see Dan did at the beginning of this
wrote: past particular thread.
I recommend erasing any cookie related to galaxy and also trying with a different browser. Firefox seems to work particularly fine.
Indeed, it works with Firefox. And it works with Chrome after I delete my cookies.
Thanks very much! Dan
Hope it helps, Carlos
participants (3)
-
Carl Eberhard -
Carlos Borroto -
Dan Tenenbaum