tabular data display

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tabular data display

Matthias Bernt
Dear list,

I'm struggling with tabular data in Galaxy. Attached is a tab separated
file that is generated by MetaProSIP (an updated - not yet committed --
version).

The problem is that it is not shown as table in Galaxy (dev) at all.
Also the peek preview is odd, some values of the header and data are
omitted.

Is this a bug in Galaxy, or of the data in the table?

Cheers,
Matthias
--

-------------------------------------------
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
[hidden email], www.ufz.de

Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
-------------------------------------------

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
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Re: tabular data display

Dannon Baker-2
I'm not familiar with MetaProSIP, but how many columns *should* be in the output?  Galaxy automatically displays tabular data with more than 50 columns in the 'raw' view you're seeing here, instead of using a table.  The last bit of data in particular, when looking at the sample, is a ton of `0` columns.  Is that correct?

One more possible issue is that this is sniffed as a `scidx` file, for me, though that's unrelated to the display problem here.

-Dannon

On Fri, Jun 1, 2018 at 9:03 AM Matthias Bernt <[hidden email]> wrote:
Dear list,

I'm struggling with tabular data in Galaxy. Attached is a tab separated
file that is generated by MetaProSIP (an updated - not yet committed --
version).

The problem is that it is not shown as table in Galaxy (dev) at all.
Also the peek preview is odd, some values of the header and data are
omitted.

Is this a bug in Galaxy, or of the data in the table?

Cheers,
Matthias
--

-------------------------------------------
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
[hidden email], www.ufz.de

Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
-------------------------------------------
___________________________________________________________
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:
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Re: tabular data display

Matthias Bernt
Dear Dannon,

its 59 columns :( the last columns are only sometimes 0.

Is there a performance issue when rendering html tables with a larger
number of columns?

What would be the Galaxy way to handle data with a larger number of
columns?

I agree that the scidx problem is unrelated. Might be worth to open an
issue?

Best,
Matthias

On 01.06.2018 15:44, Dannon Baker wrote:

> I'm not familiar with MetaProSIP, but how many columns *should* be in
> the output?  Galaxy automatically displays tabular data with more than
> 50 columns in the 'raw' view you're seeing here, instead of using a
> table.  The last bit of data in particular, when looking at the sample,
> is a ton of `0` columns.  Is that correct?
>
> One more possible issue is that this is sniffed as a `scidx` file, for
> me, though that's unrelated to the display problem here.
>
> -Dannon
>
> On Fri, Jun 1, 2018 at 9:03 AM Matthias Bernt <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Dear list,
>
>     I'm struggling with tabular data in Galaxy. Attached is a tab separated
>     file that is generated by MetaProSIP (an updated - not yet committed --
>     version).
>
>     The problem is that it is not shown as table in Galaxy (dev) at all.
>     Also the peek preview is odd, some values of the header and data are
>     omitted.
>
>     Is this a bug in Galaxy, or of the data in the table?
>
>     Cheers,
>     Matthias
>     --
>
>     -------------------------------------------
>     Matthias Bernt
>     Bioinformatics Service
>     Molekulare Systembiologie (MOLSYB)
>     Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
>     Helmholtz Centre for Environmental Research GmbH - UFZ
>     Permoserstraße 15, 04318 Leipzig, Germany
>     Phone +49 341 235 482296,
>     [hidden email] <mailto:[hidden email]>, www.ufz.de <http://www.ufz.de>
>
>     Sitz der Gesellschaft/Registered Office: Leipzig
>     Registergericht/Registration Office: Amtsgericht Leipzig
>     Handelsregister Nr./Trade Register Nr.: B 4703
>     Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
>     MinDirig Wilfried Kraus
>     Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
>     Prof. Dr. Dr. h.c. Georg Teutsch
>     Administrative Geschäftsführerin/ Administrative Managing Director:
>     Prof. Dr. Heike Graßmann
>     -------------------------------------------
>     ___________________________________________________________
>     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/
>

--

-------------------------------------------
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
[hidden email], www.ufz.de

Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
-------------------------------------------
___________________________________________________________
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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Re: tabular data display

Dannon Baker-2
Yeah, it was intentional to avoid browser crashes years ago with very large tables.  50 was somewhat arbitrarily chosen, at the time.  We could make this configurable for galaxy instances and/or increase it outright.  Here's the logic in question, if you wanted to tinker with it:
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/tabular.py#L90

On Fri, Jun 1, 2018 at 10:04 AM Matthias Bernt <[hidden email]> wrote:
Dear Dannon,

its 59 columns :( the last columns are only sometimes 0.

Is there a performance issue when rendering html tables with a larger
number of columns?

What would be the Galaxy way to handle data with a larger number of
columns?

I agree that the scidx problem is unrelated. Might be worth to open an
issue?

Best,
Matthias

On 01.06.2018 15:44, Dannon Baker wrote:
> I'm not familiar with MetaProSIP, but how many columns *should* be in
> the output?  Galaxy automatically displays tabular data with more than
> 50 columns in the 'raw' view you're seeing here, instead of using a
> table.  The last bit of data in particular, when looking at the sample,
> is a ton of `0` columns.  Is that correct?
>
> One more possible issue is that this is sniffed as a `scidx` file, for
> me, though that's unrelated to the display problem here.
>
> -Dannon
>
> On Fri, Jun 1, 2018 at 9:03 AM Matthias Bernt <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Dear list,
>
>     I'm struggling with tabular data in Galaxy. Attached is a tab separated
>     file that is generated by MetaProSIP (an updated - not yet committed --
>     version).
>
>     The problem is that it is not shown as table in Galaxy (dev) at all.
>     Also the peek preview is odd, some values of the header and data are
>     omitted.
>
>     Is this a bug in Galaxy, or of the data in the table?
>
>     Cheers,
>     Matthias
>     --
>
>     -------------------------------------------
>     Matthias Bernt
>     Bioinformatics Service
>     Molekulare Systembiologie (MOLSYB)
>     Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
>     Helmholtz Centre for Environmental Research GmbH - UFZ
>     Permoserstraße 15, 04318 Leipzig, Germany
>     Phone +49 341 235 482296,
>     [hidden email] <mailto:[hidden email]>, www.ufz.de <http://www.ufz.de>
>
>     Sitz der Gesellschaft/Registered Office: Leipzig
>     Registergericht/Registration Office: Amtsgericht Leipzig
>     Handelsregister Nr./Trade Register Nr.: B 4703
>     Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
>     MinDirig Wilfried Kraus
>     Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
>     Prof. Dr. Dr. h.c. Georg Teutsch
>     Administrative Geschäftsführerin/ Administrative Managing Director:
>     Prof. Dr. Heike Graßmann
>     -------------------------------------------
>     ___________________________________________________________
>     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/
>

--

-------------------------------------------
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
[hidden email], www.ufz.de

Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
-------------------------------------------

___________________________________________________________
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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Re: tabular data display

Matthias Bernt
Dear Dannon,

I will talk to our users first and see if filtering columns is
applicable for this 'monster'. IMHO 50 columns are not nice to look at
anyway, but some sort of filtering or aggregate statistics should be
applied anyway.

Cheers,
Matthias

On 01.06.2018 16:14, Dannon Baker wrote:

> Yeah, it was intentional to avoid browser crashes years ago with very
> large tables.  50 was somewhat arbitrarily chosen, at the time.  We
> could make this configurable for galaxy instances and/or increase it
> outright.  Here's the logic in question, if you wanted to tinker with it:
> https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/tabular.py#L90
>
> On Fri, Jun 1, 2018 at 10:04 AM Matthias Bernt <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Dear Dannon,
>
>     its 59 columns :( the last columns are only sometimes 0.
>
>     Is there a performance issue when rendering html tables with a larger
>     number of columns?
>
>     What would be the Galaxy way to handle data with a larger number of
>     columns?
>
>     I agree that the scidx problem is unrelated. Might be worth to open an
>     issue?
>
>     Best,
>     Matthias
>
>     On 01.06.2018 15:44, Dannon Baker wrote:
>      > I'm not familiar with MetaProSIP, but how many columns *should*
>     be in
>      > the output?  Galaxy automatically displays tabular data with more
>     than
>      > 50 columns in the 'raw' view you're seeing here, instead of using a
>      > table.  The last bit of data in particular, when looking at the
>     sample,
>      > is a ton of `0` columns.  Is that correct?
>      >
>      > One more possible issue is that this is sniffed as a `scidx`
>     file, for
>      > me, though that's unrelated to the display problem here.
>      >
>      > -Dannon
>      >
>      > On Fri, Jun 1, 2018 at 9:03 AM Matthias Bernt <[hidden email]
>     <mailto:[hidden email]>
>      > <mailto:[hidden email] <mailto:[hidden email]>>> wrote:
>      >
>      >     Dear list,
>      >
>      >     I'm struggling with tabular data in Galaxy. Attached is a tab
>     separated
>      >     file that is generated by MetaProSIP (an updated - not yet
>     committed --
>      >     version).
>      >
>      >     The problem is that it is not shown as table in Galaxy (dev)
>     at all.
>      >     Also the peek preview is odd, some values of the header and
>     data are
>      >     omitted.
>      >
>      >     Is this a bug in Galaxy, or of the data in the table?
>      >
>      >     Cheers,
>      >     Matthias
>      >     --
>      >
>      >     -------------------------------------------
>      >     Matthias Bernt
>      >     Bioinformatics Service
>      >     Molekulare Systembiologie (MOLSYB)
>      >     Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
>      >     Helmholtz Centre for Environmental Research GmbH - UFZ
>      >     Permoserstraße 15, 04318 Leipzig, Germany
>      >     Phone +49 341 235 482296,
>      > [hidden email] <mailto:[hidden email]> <mailto:[hidden email]
>     <mailto:[hidden email]>>, www.ufz.de <http://www.ufz.de>
>     <http://www.ufz.de>
>      >
>      >     Sitz der Gesellschaft/Registered Office: Leipzig
>      >     Registergericht/Registration Office: Amtsgericht Leipzig
>      >     Handelsregister Nr./Trade Register Nr.: B 4703
>      >     Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
>      >     MinDirig Wilfried Kraus
>      >     Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
>      >     Prof. Dr. Dr. h.c. Georg Teutsch
>      >     Administrative Geschäftsführerin/ Administrative Managing
>     Director:
>      >     Prof. Dr. Heike Graßmann
>      >     -------------------------------------------
>      >     ___________________________________________________________
>      >     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/
>      >
>
>     --
>
>     -------------------------------------------
>     Matthias Bernt
>     Bioinformatics Service
>     Molekulare Systembiologie (MOLSYB)
>     Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
>     Helmholtz Centre for Environmental Research GmbH - UFZ
>     Permoserstraße 15, 04318 Leipzig, Germany
>     Phone +49 341 235 482296,
>     [hidden email] <mailto:[hidden email]>, www.ufz.de <http://www.ufz.de>
>
>     Sitz der Gesellschaft/Registered Office: Leipzig
>     Registergericht/Registration Office: Amtsgericht Leipzig
>     Handelsregister Nr./Trade Register Nr.: B 4703
>     Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
>     MinDirig Wilfried Kraus
>     Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
>     Prof. Dr. Dr. h.c. Georg Teutsch
>     Administrative Geschäftsführerin/ Administrative Managing Director:
>     Prof. Dr. Heike Graßmann
>     -------------------------------------------
>

--

-------------------------------------------
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
[hidden email], www.ufz.de

Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
-------------------------------------------
___________________________________________________________
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/