Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()
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/136104
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 dtene...@fhcrc.org wrote:
Hi Carl,
On Thu, Jan 31, 2013 at 1:37 PM, Dan Tenenbaum dtene...@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 carlfeberh...@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
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Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()
On Mon, Feb 4, 2013 at 1:55 PM, Dan Tenenbaum dtene...@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 ___ 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/
Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()
On Mon, Feb 4, 2013 at 11:45 AM, Carlos Borroto carlos.borr...@gmail.com wrote: On Mon, Feb 4, 2013 at 1:55 PM, Dan Tenenbaum dtene...@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 ___ 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/
Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()
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 carlfeberh...@gmail.comwrote: Thanks much, Carlos - I owe you a beer! On Mon, Feb 4, 2013 at 4:01 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: On Mon, Feb 4, 2013 at 11:45 AM, Carlos Borroto carlos.borr...@gmail.com wrote: On Mon, Feb 4, 2013 at 1:55 PM, Dan Tenenbaum dtene...@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 ___ 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/
Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()
On Mon, Feb 4, 2013 at 4:46 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: On Mon, Feb 4, 2013 at 1:21 PM, Carl Eberhard carlfeberh...@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 ;-). ___ 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/
Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()
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 dtene...@fhcrc.org wrote: On Mon, Feb 4, 2013 at 1:21 PM, Carl Eberhard carlfeberh...@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 carlfeberh...@gmail.com wrote: Thanks much, Carlos - I owe you a beer! On Mon, Feb 4, 2013 at 4:01 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: On Mon, Feb 4, 2013 at 11:45 AM, Carlos Borroto carlos.borr...@gmail.com wrote: On Mon, Feb 4, 2013 at 1:55 PM, Dan Tenenbaum dtene...@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 ___ 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/
Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()
Thanks much, Carlos - I owe you a beer! On Mon, Feb 4, 2013 at 4:01 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: On Mon, Feb 4, 2013 at 11:45 AM, Carlos Borroto carlos.borr...@gmail.com wrote: On Mon, Feb 4, 2013 at 1:55 PM, Dan Tenenbaum dtene...@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 ___ 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/
Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()
On Wed, Jan 30, 2013 at 10:36 AM, Carl Eberhard carlfeberh...@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 carlfeberh...@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 dtene...@fhcrc.org wrote: Hi Carl, On Tue, Jan 29, 2013 at 9:30 AM, Carl Eberhard carlfeberh...@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 dtene...@fhcrc.org wrote: On Mon, Jan 28, 2013 at 1:59 PM, Carl Eberhard carlfeberh...@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
Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()
On Wed, Jan 30, 2013 at 11:36 AM, Carl Eberhard carlfeberh...@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 dtene...@fhcrc.org wrote: On Wed, Jan 30, 2013 at 10:36 AM, Carl Eberhard carlfeberh...@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 carlfeberh...@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,
Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()
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?
On Thu, Jan 24, 2013 at 6:12 PM, Dan Tenenbaum dtene...@fhcrc.org wrote:
On Wed, Jan 23, 2013 at 3:19 PM, Carl Eberhard carlfeberh...@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 carlfeberh...@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 dtene...@fhcrc.org
wrote:
On Wed, Jan 23, 2013 at 2:42 PM, Carl Eberhard
carlfeberh...@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 dtene...@fhcrc.org
wrote:
On Wed, Jan 23, 2013 at 2:35 PM, Carl Eberhard
carlfeberh...@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
dtene...@fhcrc.org
wrote:
Hi Carl,
On Wed, Jan 23, 2013 at 2:14 PM, Carl Eberhard
carlfeberh...@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
Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()
On Mon, Jan 28, 2013 at 1:40 PM, Carl Eberhard carlfeberh...@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 dtene...@fhcrc.org wrote:
On Wed, Jan 23, 2013 at 3:19 PM, Carl Eberhard carlfeberh...@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 carlfeberh...@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 dtene...@fhcrc.org
wrote:
On Wed, Jan 23, 2013 at 2:42 PM, Carl Eberhard
carlfeberh...@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 dtene...@fhcrc.org
wrote:
On Wed, Jan 23, 2013 at 2:35 PM, Carl Eberhard
carlfeberh...@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
dtene...@fhcrc.org
wrote:
Hi Carl,
On Wed, Jan 23, 2013 at 2:14 PM, Carl Eberhard
carlfeberh...@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 )
)
Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()
If you go to your galaxy root in a terminal and then cd to eggs, what is
the version listed for SQLAlchemy?
Do you have SQLAlchemy installed already on that machine (apart from the
one in Galaxy's eggs)?
On Mon, Jan 28, 2013 at 4:50 PM, Dan Tenenbaum dtene...@fhcrc.org wrote:
On Mon, Jan 28, 2013 at 1:40 PM, Carl Eberhard carlfeberh...@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 dtene...@fhcrc.org
wrote:
On Wed, Jan 23, 2013 at 3:19 PM, Carl Eberhard carlfeberh...@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
carlfeberh...@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 dtene...@fhcrc.org
wrote:
On Wed, Jan 23, 2013 at 2:42 PM, Carl Eberhard
carlfeberh...@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
dtene...@fhcrc.org
wrote:
On Wed, Jan 23, 2013 at 2:35 PM, Carl Eberhard
carlfeberh...@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
dtene...@fhcrc.org
wrote:
Hi Carl,
On Wed, Jan 23, 2013 at 2:14 PM, Carl Eberhard
carlfeberh...@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
Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()
On Mon, Jan 28, 2013 at 1:59 PM, Carl Eberhard carlfeberh...@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 dtene...@fhcrc.org wrote:
On Mon, Jan 28, 2013 at 1:40 PM, Carl Eberhard carlfeberh...@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 dtene...@fhcrc.org
wrote:
On Wed, Jan 23, 2013 at 3:19 PM, Carl Eberhard
carlfeberh...@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
carlfeberh...@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 dtene...@fhcrc.org
wrote:
On Wed, Jan 23, 2013 at 2:42 PM, Carl Eberhard
carlfeberh...@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
dtene...@fhcrc.org
wrote:
On Wed, Jan 23, 2013 at 2:35 PM, Carl Eberhard
carlfeberh...@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
dtene...@fhcrc.org
wrote:
Hi Carl,
On Wed, Jan 23, 2013 at 2:14 PM, Carl Eberhard
carlfeberh...@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
