Get Data and 'xlsx'

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D K
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Get Data and 'xlsx'

D K
It looks like uploading 'xlsx' data through 'Get Data' is not working. When I try this on my local Galaxy (v18.05) and on usegalaxy.org it gets automatically converted to 'BLAST xml' when using Automatic Detection. If I select 'xlsx' during uploading I get the error message ( Warning: The file 'Type' was set to 'xlsx' but the file does not appear to be of that type  )
Does anyone have any suggestions?

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Re: Get Data and 'xlsx'

Peter Cock
That sounds very strange - could you share the test file (ideally publicly, but at least by private email)? Modern MS files do use XML but I don't understand how it would be recognised as BLAST XML...

It may also be useful to see your Galaxy data types configuration file.

Peter

On Wed, 10 Oct 2018 at 01:39, D K <[hidden email]> wrote:
It looks like uploading 'xlsx' data through 'Get Data' is not working. When I try this on my local Galaxy (v18.05) and on usegalaxy.org it gets automatically converted to 'BLAST xml' when using Automatic Detection. If I select 'xlsx' during uploading I get the error message ( Warning: The file 'Type' was set to 'xlsx' but the file does not appear to be of that type  )
Does anyone have any suggestions?
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D K
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Re: Get Data and 'xlsx'

D K
Sure, I've attached a sample xlsx file and my datatypes_conf.xml file

Thanks!

On Tue, Oct 9, 2018 at 11:52 PM Peter Cock <[hidden email]> wrote:
That sounds very strange - could you share the test file (ideally publicly, but at least by private email)? Modern MS files do use XML but I don't understand how it would be recognised as BLAST XML...

It may also be useful to see your Galaxy data types configuration file.

Peter

On Wed, 10 Oct 2018 at 01:39, D K <[hidden email]> wrote:
It looks like uploading 'xlsx' data through 'Get Data' is not working. When I try this on my local Galaxy (v18.05) and on usegalaxy.org it gets automatically converted to 'BLAST xml' when using Automatic Detection. If I select 'xlsx' during uploading I get the error message ( Warning: The file 'Type' was set to 'xlsx' but the file does not appear to be of that type  )
Does anyone have any suggestions?
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datatypes_conf.xml (98K) Download Attachment
Book1.xlsx (10K) Download Attachment
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Re: Get Data and 'xlsx'

Martin Čech
Hi all,

I can confirm this file is sniffed as `format: blastxml` on usegalaxy.org, which is surely wrong.

I created an issue for it here: https://github.com/galaxyproject/galaxy/issues/6849 

M.



On Wed, Oct 10, 2018 at 2:11 PM D K <[hidden email]> wrote:
Sure, I've attached a sample xlsx file and my datatypes_conf.xml file

Thanks!

On Tue, Oct 9, 2018 at 11:52 PM Peter Cock <[hidden email]> wrote:
That sounds very strange - could you share the test file (ideally publicly, but at least by private email)? Modern MS files do use XML but I don't understand how it would be recognised as BLAST XML...

It may also be useful to see your Galaxy data types configuration file.

Peter

On Wed, 10 Oct 2018 at 01:39, D K <[hidden email]> wrote:
It looks like uploading 'xlsx' data through 'Get Data' is not working. When I try this on my local Galaxy (v18.05) and on usegalaxy.org it gets automatically converted to 'BLAST xml' when using Automatic Detection. If I select 'xlsx' during uploading I get the error message ( Warning: The file 'Type' was set to 'xlsx' but the file does not appear to be of that type  )
Does anyone have any suggestions?
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Re: Get Data and 'xlsx'

Peter Cock
Thanks Martin, and D K,

I've commented on https://github.com/galaxyproject/galaxy/issues/6849
but am puzzled as to what might be going on here. The BLAST XML
sniffer code (which I wrote) is deliberately very selective with the intent
of avoid any false positives.

I would try it locally (thank you for sharing the test file), but right now
it looks like a recent cluster change has disrupted our local Galaxy
instance.

Peter
On Wed, Oct 10, 2018 at 7:20 PM Martin Čech <[hidden email]> wrote:

>
> Hi all,
>
> I can confirm this file is sniffed as `format: blastxml` on usegalaxy.org, which is surely wrong.
>
> I created an issue for it here: https://github.com/galaxyproject/galaxy/issues/6849
>
> M.
>
>
>
> On Wed, Oct 10, 2018 at 2:11 PM D K <[hidden email]> wrote:
>>
>> Sure, I've attached a sample xlsx file and my datatypes_conf.xml file
>>
>> Thanks!
>>
>> On Tue, Oct 9, 2018 at 11:52 PM Peter Cock <[hidden email]> wrote:
>>>
>>> That sounds very strange - could you share the test file (ideally publicly, but at least by private email)? Modern MS files do use XML but I don't understand how it would be recognised as BLAST XML...
>>>
>>> It may also be useful to see your Galaxy data types configuration file.
>>>
>>> Peter
>>>
>>>
>>> On Wed, 10 Oct 2018 at 01:39, D K <[hidden email]> wrote:
>>>>
>>>> It looks like uploading 'xlsx' data through 'Get Data' is not working. When I try this on my local Galaxy (v18.05) and on usegalaxy.org it gets automatically converted to 'BLAST xml' when using Automatic Detection. If I select 'xlsx' during uploading I get the error message ( Warning: The file 'Type' was set to 'xlsx' but the file does not appear to be of that type  )
>>>> Does anyone have any suggestions?
>>>> ___________________________________________________________
>>>> 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:
>>>>   https://lists.galaxyproject.org/
>>>>
>>>> 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:
>>   https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/
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