set up an asynchronous data source in galaxy

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set up an asynchronous data source in galaxy

Galaxy Development List Archive mailing list
Hi,

I'm trying to set up an asynchronous data source in galaxy.
I follow the examples that Helena provide here :
https://github.com/erasche/galaxy-data_source-examples/tree/master/flask

It's a success for synchronous modE.
But when I test the asynchronous mode, it fails.

from what I understand, the file in history (that would contains the data) is not well created.
The example creates a link like this one :
https://galaxydev.biogemma.fr:4430/export/?gx_url=https%3A%2F%2Fgalaxydev.biogemma.fr%2Fasync%2Fds_test_async


When I click on the link, no file is created in my history.
The error in the log is :  
  File "lib/galaxy/webapps/galaxy/controllers/async.py", line 150, in index
    open(data.file_name, 'wb').close()  # create the file
IOError: [Errno 2] No such file or directory: ''

The filename is missing, so I have no new file in my history waiting for the asynchronous process to fill it.

I've described the error here (with complete log messages) :
https://github.com/erasche/galaxy-data_source-examples/issues/6

Can anybody reproduce this? Is this an issue? or a misconfiguration from my side?

thank you.

Fred
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Re: set up an asynchronous data source in galaxy

Galaxy Development List Archive mailing list
Hi,

I've tried with branch release_19.05 and dev (fetch yesterday from git)

Fred

-----Message d'origine-----
De : SAPET, Frederic via galaxy-dev <[hidden email]>
Envoyé : lundi 19 août 2019 17:19
À : Galaxy-dev <[hidden email]>
Objet : [galaxy-dev] set up an asynchronous data source in galaxy

Hi,

I'm trying to set up an asynchronous data source in galaxy.
I follow the examples that Helena provide here :
https://github.com/erasche/galaxy-data_source-examples/tree/master/flask

It's a success for synchronous modE.
But when I test the asynchronous mode, it fails.

from what I understand, the file in history (that would contains the data) is not well created.
The example creates a link like this one :
https://galaxydev.biogemma.fr:4430/export/?gx_url=https%3A%2F%2Fgalaxydev.biogemma.fr%2Fasync%2Fds_test_async


When I click on the link, no file is created in my history.
The error in the log is :  
  File "lib/galaxy/webapps/galaxy/controllers/async.py", line 150, in index
    open(data.file_name, 'wb').close()  # create the file
IOError: [Errno 2] No such file or directory: ''

The filename is missing, so I have no new file in my history waiting for the asynchronous process to fill it.

I've described the error here (with complete log messages) :
https://github.com/erasche/galaxy-data_source-examples/issues/6

Can anybody reproduce this? Is this an issue? or a misconfiguration from my side?

thank you.

Fred
___________________________________________________________
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:
  %(web_page_url)s

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/
___________________________________________________________
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: set up an asynchronous data source in galaxy

Galaxy Development List Archive mailing list
It was a bug:
https://github.com/galaxyproject/galaxy/pull/8515

I still have the issue related to authentication. Indeed when the async server need to contact my galaxy server (and sent STATUS=OK) it faces the authentication. And everything is redirected to /root/login...

Fred

-----Message d'origine-----
De : SAPET, Frederic
Envoyé : mardi 20 août 2019 09:28
À : Galaxy-dev <[hidden email]>
Objet : RE: set up an asynchronous data source in galaxy

Hi,

I've tried with branch release_19.05 and dev (fetch yesterday from git)

Fred

-----Message d'origine-----
De : SAPET, Frederic via galaxy-dev <[hidden email]>
Envoyé : lundi 19 août 2019 17:19
À : Galaxy-dev <[hidden email]>
Objet : [galaxy-dev] set up an asynchronous data source in galaxy

Hi,

I'm trying to set up an asynchronous data source in galaxy.
I follow the examples that Helena provide here :
https://github.com/erasche/galaxy-data_source-examples/tree/master/flask

It's a success for synchronous modE.
But when I test the asynchronous mode, it fails.

from what I understand, the file in history (that would contains the data) is not well created.
The example creates a link like this one :
https://galaxydev.biogemma.fr:4430/export/?gx_url=https%3A%2F%2Fgalaxydev.biogemma.fr%2Fasync%2Fds_test_async


When I click on the link, no file is created in my history.
The error in the log is :  
  File "lib/galaxy/webapps/galaxy/controllers/async.py", line 150, in index
    open(data.file_name, 'wb').close()  # create the file
IOError: [Errno 2] No such file or directory: ''

The filename is missing, so I have no new file in my history waiting for the asynchronous process to fill it.

I've described the error here (with complete log messages) :
https://github.com/erasche/galaxy-data_source-examples/issues/6

Can anybody reproduce this? Is this an issue? or a misconfiguration from my side?

thank you.

Fred
___________________________________________________________
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:
  %(web_page_url)s

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/
___________________________________________________________
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:
  %(web_page_url)s

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/