Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()

2013-02-04 Thread Carl Eberhard
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
 
 

___
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()

2013-02-04 Thread Carl Eberhard
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 dtene...@fhcrc.org wrote:

 Hi Carl,

 On Mon, Feb 4, 2013 at 10:22 AM, Carl Eberhard carlfeberh...@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/136104
 
  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 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
  - 

Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()

2013-02-04 Thread Carlos Borroto
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()

2013-02-04 Thread Dan Tenenbaum
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()

2013-02-04 Thread Carl Eberhard
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()

2013-02-04 Thread Dan Tenenbaum
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()

2013-02-04 Thread Carlos Borroto
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()

2013-02-04 Thread Carl Eberhard
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()

2013-02-04 Thread Carl Eberhard
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()

2013-01-31 Thread Carl Eberhard
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
___
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()

2013-01-30 Thread Dan Tenenbaum
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()

2013-01-30 Thread Dan Tenenbaum
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()

2013-01-28 Thread Carl Eberhard
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()

2013-01-28 Thread Dan Tenenbaum
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()

2013-01-28 Thread Carl Eberhard
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()

2013-01-28 Thread Dan Tenenbaum
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

Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()

2013-01-24 Thread Dan Tenenbaum
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
  
  
   '/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
   

Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()

2013-01-23 Thread Dan Tenenbaum
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 
'/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 dtene...@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) 

Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()

2013-01-23 Thread Carl Eberhard
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.

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
 '/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 dtene...@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
  

Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()

2013-01-23 Thread Dan Tenenbaum
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
 '/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 dtene...@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 

Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()

2013-01-23 Thread Carl Eberhard
What sort of database are you using on your local instance?


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
 
 '/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 dtene...@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():
   

Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()

2013-01-23 Thread Dan Tenenbaum
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
 
  '/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 dtene...@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 

Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()

2013-01-23 Thread Carl Eberhard
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
  
  
 '/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 dtene...@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 

Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()

2013-01-23 Thread Carl Eberhard
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.


On Wed, Jan 23, 2013 at 6:06 PM, Carl Eberhard carlfeberh...@gmail.comwrote:

 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
  
  
 '/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 
 dtene...@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