Re: [galaxy-dev] error on viewing workflow details via API
Glad you got it working, and thanks for the additional information. Now that I
know what's different about the non-working workflows I can probably recreate
and fix this on my end. Extracted workflows *should* function via the API.
-Dannon
On Jan 9, 2012, at 5:06 PM, Leon Mei wrote:
> Hi Dannon,
>
> Thanks for the hint. I got it working by removing "input dataset" step and
> adding it back in the workflow canvas. The previous workflow in question was
> purely extracted from history.
>
> So now I can check the details via API:
>
> ./display.py
> http://galaxy.nbic.nl/galaxy/api/workflows/e037fdb493429c2a
> Member Information
> --
> url: /galaxy/api/workflows/e037fdb493429c2a
> inputs: {'8648': {'value': '', 'label': 'Input Dataset'}}
> id: e037fdb493429c2a
> name: test
>
> I still don't understand why it is not working with an extracted workflow.
> But I can live with this work around.
>
> Cheers,
> Leon
>
>
> On Mon, Jan 9, 2012 at 3:18 PM, Dannon Baker wrote:
> Leon,
>
> I'm not seeing this behavior in any of my instances. I assume they work
> correctly through the standard galaxy interface, but is there anything
> special about the workflows in question? Is there perhaps a tool with no
> inputs in use?
>
> Thanks!
>
> -Dannon
>
>
>
>
> On Jan 6, 2012, at 11:59 AM, Leon Mei wrote:
>
> > Hi,
> >
> > I received an error when I was trying to view the details of existing
> > workflows through API.
> >
> > I can see 4 workflows owned by myself successfully. But viewing the details
> > of any workflow got me a 500 error.
> >
> > ./display.py http://galaxy.nbic.nl/galaxy/api/workflows
> > Collection Members
> > --
> > #1: /galaxy/api/workflows/e037fdb493429c2a
> > name: test
> > id: e037fdb493429c2a
> > #2: /galaxy/api/workflows/13120e62d0fbb985
> > name: imported: Partial Workflow for Student Project (1)
> > id: 13120e62d0fbb985
> > #3: /galaxy/api/workflows/c9468fdb6dc5c5f1
> > name: GAPSS SNP calling
> > id: c9468fdb6dc5c5f1
> > #4: /galaxy/api/workflows/3f5830403180d620
> > name: GAPPS CAGE
> > id: 3f5830403180d620
> >
> > 4 element(s) in collection
> >
> > ./display.py
> > http://galaxy.nbic.nl/galaxy/api/workflows/e037fdb493429c2a
> > HTTP Error 500: Internal Server Error
> > 500 Internal Server Error
> > The server has either erred or is incapable of performing
> > the requested operation.
> >
> > Here is the error message in paster.log:
> > /*
> > galaxy.web.framework ERROR 2012-01-06 17:46:53,349 Uncaught exception in
> > exposed API method:
> > Traceback (most recent call last):
> > File
> > "/opt/galaxy/prog/galaxy-2011-12-5/lib/galaxy/web/framework/__init__.py",
> > line 147, in decorator
> > return simplejson.dumps( func( self, trans, *args, **kwargs ) )
> > File "/opt/galaxy/prog/galaxy-2011-12-5/lib/galaxy/web/api/workflows.py",
> > line 68, in show
> > inputs[step.id] = {'label':step.tool_inputs['name'], 'value':""}
> > TypeError: 'NoneType' object is unsubscriptable
> > - - [06/Jan/2012:17:46:53 +0200] "GET
> > /galaxy/api/workflows/e037fdb493429c2a?key= HTTP/1.1" 500 - "-"
> > "Python-urllib/2.6"
> > */
> >
> > Any suggestion on how to solve this problem?
> >
> > Thanks,
> > Leon
> >
> > --
> > Hailiang (Leon) Mei
> > Netherlands Bioinformatics Center
> > BioAssist NGS Taskforce
> > - https://wiki.nbic.nl/index.php/Next_Generation_Sequencing
> > Skype: leon_meiMobile: +31 6 41709231
> > ___
> > 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/
>
>
>
>
> --
> Hailiang (Leon) Mei
> Netherlands Bioinformatics Center
> BioAssist NGS Taskforce
> - https://wiki.nbic.nl/index.php/Next_Generation_Sequencing
> Skype: leon_meiMobile: +31 6 41709231
___
Please keep all replies on the list by using "reply all"
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Re: [galaxy-dev] error on viewing workflow details via API
Hi Dannon,
Thanks for the hint. I got it working by removing "input dataset" step and
adding it back in the workflow canvas. The previous workflow in question
was purely extracted from history.
So now I can check the details via API:
./display.py
http://galaxy.nbic.nl/galaxy/api/workflows/e037fdb493429c2a
Member Information
--
url: /galaxy/api/workflows/e037fdb493429c2a
inputs: {'8648': {'value': '', 'label': 'Input Dataset'}}
id: e037fdb493429c2a
name: test
I still don't understand why it is not working with an extracted workflow.
But I can live with this work around.
Cheers,
Leon
On Mon, Jan 9, 2012 at 3:18 PM, Dannon Baker wrote:
> Leon,
>
> I'm not seeing this behavior in any of my instances. I assume they work
> correctly through the standard galaxy interface, but is there anything
> special about the workflows in question? Is there perhaps a tool with no
> inputs in use?
>
> Thanks!
>
> -Dannon
>
>
>
>
> On Jan 6, 2012, at 11:59 AM, Leon Mei wrote:
>
> > Hi,
> >
> > I received an error when I was trying to view the details of existing
> workflows through API.
> >
> > I can see 4 workflows owned by myself successfully. But viewing the
> details of any workflow got me a 500 error.
> >
> > ./display.py http://galaxy.nbic.nl/galaxy/api/workflows
> > Collection Members
> > --
> > #1: /galaxy/api/workflows/e037fdb493429c2a
> > name: test
> > id: e037fdb493429c2a
> > #2: /galaxy/api/workflows/13120e62d0fbb985
> > name: imported: Partial Workflow for Student Project (1)
> > id: 13120e62d0fbb985
> > #3: /galaxy/api/workflows/c9468fdb6dc5c5f1
> > name: GAPSS SNP calling
> > id: c9468fdb6dc5c5f1
> > #4: /galaxy/api/workflows/3f5830403180d620
> > name: GAPPS CAGE
> > id: 3f5830403180d620
> >
> > 4 element(s) in collection
> >
> > ./display.py
> http://galaxy.nbic.nl/galaxy/api/workflows/e037fdb493429c2a
> > HTTP Error 500: Internal Server Error
> > 500 Internal Server Error
> > The server has either erred or is incapable of performing
> > the requested operation.
> >
> > Here is the error message in paster.log:
> > /*
> > galaxy.web.framework ERROR 2012-01-06 17:46:53,349 Uncaught exception
> in exposed API method:
> > Traceback (most recent call last):
> > File
> "/opt/galaxy/prog/galaxy-2011-12-5/lib/galaxy/web/framework/__init__.py",
> line 147, in decorator
> > return simplejson.dumps( func( self, trans, *args, **kwargs ) )
> > File
> "/opt/galaxy/prog/galaxy-2011-12-5/lib/galaxy/web/api/workflows.py", line
> 68, in show
> > inputs[step.id] = {'label':step.tool_inputs['name'], 'value':""}
> > TypeError: 'NoneType' object is unsubscriptable
> > - - [06/Jan/2012:17:46:53 +0200] "GET
> /galaxy/api/workflows/e037fdb493429c2a?key= HTTP/1.1" 500 - "-"
> "Python-urllib/2.6"
> > */
> >
> > Any suggestion on how to solve this problem?
> >
> > Thanks,
> > Leon
> >
> > --
> > Hailiang (Leon) Mei
> > Netherlands Bioinformatics Center
> > BioAssist NGS Taskforce
> > - https://wiki.nbic.nl/index.php/Next_Generation_Sequencing
> > Skype: leon_meiMobile: +31 6 41709231
> > ___
> > 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/
>
>
--
Hailiang (Leon) Mei
Netherlands Bioinformatics Center
BioAssist NGS Taskforce
- https://wiki.nbic.nl/index.php/Next_Generation_Sequencing
Skype: leon_meiMobile: +31 6 41709231
___
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:
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Re: [galaxy-dev] error on viewing workflow details via API
Leon,
I'm not seeing this behavior in any of my instances. I assume they work
correctly through the standard galaxy interface, but is there anything special
about the workflows in question? Is there perhaps a tool with no inputs in use?
Thanks!
-Dannon
On Jan 6, 2012, at 11:59 AM, Leon Mei wrote:
> Hi,
>
> I received an error when I was trying to view the details of existing
> workflows through API.
>
> I can see 4 workflows owned by myself successfully. But viewing the details
> of any workflow got me a 500 error.
>
> ./display.py http://galaxy.nbic.nl/galaxy/api/workflows
> Collection Members
> --
> #1: /galaxy/api/workflows/e037fdb493429c2a
> name: test
> id: e037fdb493429c2a
> #2: /galaxy/api/workflows/13120e62d0fbb985
> name: imported: Partial Workflow for Student Project (1)
> id: 13120e62d0fbb985
> #3: /galaxy/api/workflows/c9468fdb6dc5c5f1
> name: GAPSS SNP calling
> id: c9468fdb6dc5c5f1
> #4: /galaxy/api/workflows/3f5830403180d620
> name: GAPPS CAGE
> id: 3f5830403180d620
>
> 4 element(s) in collection
>
> ./display.py
> http://galaxy.nbic.nl/galaxy/api/workflows/e037fdb493429c2a
> HTTP Error 500: Internal Server Error
> 500 Internal Server Error
> The server has either erred or is incapable of performing
> the requested operation.
>
> Here is the error message in paster.log:
> /*
> galaxy.web.framework ERROR 2012-01-06 17:46:53,349 Uncaught exception in
> exposed API method:
> Traceback (most recent call last):
> File
> "/opt/galaxy/prog/galaxy-2011-12-5/lib/galaxy/web/framework/__init__.py",
> line 147, in decorator
> return simplejson.dumps( func( self, trans, *args, **kwargs ) )
> File "/opt/galaxy/prog/galaxy-2011-12-5/lib/galaxy/web/api/workflows.py",
> line 68, in show
> inputs[step.id] = {'label':step.tool_inputs['name'], 'value':""}
> TypeError: 'NoneType' object is unsubscriptable
> - - [06/Jan/2012:17:46:53 +0200] "GET
> /galaxy/api/workflows/e037fdb493429c2a?key= HTTP/1.1" 500 - "-"
> "Python-urllib/2.6"
> */
>
> Any suggestion on how to solve this problem?
>
> Thanks,
> Leon
>
> --
> Hailiang (Leon) Mei
> Netherlands Bioinformatics Center
> BioAssist NGS Taskforce
> - https://wiki.nbic.nl/index.php/Next_Generation_Sequencing
> Skype: leon_meiMobile: +31 6 41709231
> ___
> 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/
___
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/
