Strange issue with datatypes in Galaxy version of last week

List overview All Threads
Download

newer

older

Assertion errors when starting...

Nginx + HTTPS

Lukasse, Pieter

25 Mar 2014 25 Mar '14

4:32 p.m.

Hi,

Apparently a new datatypes bug has been introduced in the Galaxy version of last week:

I have a tool that generates a csv file. Tool configuration is like this: <outputs> <data name="simOut" format="msclust.csv" label="${tool.name} on ${on_string} - SIM file"/>

The datatypes has this entry: <datatype extension="msclust.csv" type="galaxy.datatypes.tabular:Tabular" mimetype="text/csv" display_in_upload="true" subclass="true"/>

At first Galaxy output seems fine: [cid:image001.png@01CF4847.DE4A1A70]

But when I download the file, the downloaded file name will be : Galaxy40-[MsClust_on_data_1_-_SIM_file]-

When I go to "edit attributes" and just click "save", then upon downloading again, the file name is correct... Galaxy40-[MsClust_on_data_1_-_SIM_file].msclust.csv .

Anyone faced this issue?

Thanks and regards,

Pieter.

Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317481122; skype: pieter.lukasse.wur http://www.pri.wur.nl http://www.pri.wur.nl/

Attachments:

attachment.htm (text/html — 12.5 KB)
image001.png (image/png — 7.8 KB)

Show replies by date

Bossers, Alex

25 Mar 25 Mar

4:51 p.m.

Pieter, I just experienced the same with another generic tabular .tab file output. It broke the filename at dash without any extension. The file itself was ok, just the name. Alex

Van: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] Namens Lukasse, Pieter Verzonden: dinsdag 25 maart 2014 16:33 Aan: galaxy-dev@lists.bx.psu.edu Onderwerp: [galaxy-dev] Strange issue with datatypes in Galaxy version of last week

Hi,

Apparently a new datatypes bug has been introduced in the Galaxy version of last week:

I have a tool that generates a csv file. Tool configuration is like this: <outputs> <data name="simOut" format="msclust.csv" label="${tool.name} on ${on_string} - SIM file"/>

The datatypes has this entry: <datatype extension="msclust.csv" type="galaxy.datatypes.tabular:Tabular" mimetype="text/csv" display_in_upload="true" subclass="true"/>

At first Galaxy output seems fine: [cid:image001.png@01CF484A.88C64A30]

But when I download the file, the downloaded file name will be : Galaxy40-[MsClust_on_data_1_-_SIM_file]-

When I go to "edit attributes" and just click "save", then upon downloading again, the file name is correct... Galaxy40-[MsClust_on_data_1_-_SIM_file].msclust.csv .

Anyone faced this issue?

Thanks and regards,

Pieter.

Lukasse, Pieter

4 Apr 4 Apr

10:58 a.m.

Hi Alex, all

FYI - I've added the card to https://trello.com/c/ro8knsaa some time ago. Can you please vote for it?

Thanks,

Pieter.

From: Bossers, Alex Sent: dinsdag 25 maart 2014 16:52 To: Lukasse, Pieter Cc: galaxy-dev@lists.bx.psu.edu Subject: RE: [galaxy-dev] Strange issue with datatypes in Galaxy version of last week

Pieter, I just experienced the same with another generic tabular .tab file output. It broke the filename at dash without any extension. The file itself was ok, just the name. Alex

Van: galaxy-dev-bounces@lists.bx.psu.edumailto:galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] Namens Lukasse, Pieter Verzonden: dinsdag 25 maart 2014 16:33 Aan: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Onderwerp: [galaxy-dev] Strange issue with datatypes in Galaxy version of last week

Hi,

Apparently a new datatypes bug has been introduced in the Galaxy version of last week:

I have a tool that generates a csv file. Tool configuration is like this: <outputs> <data name="simOut" format="msclust.csv" label="${tool.name} on ${on_string} - SIM file"/>

The datatypes has this entry: <datatype extension="msclust.csv" type="galaxy.datatypes.tabular:Tabular" mimetype="text/csv" display_in_upload="true" subclass="true"/>

At first Galaxy output seems fine: [cid:image001.png@01CF4FF4.E1830B70]

But when I download the file, the downloaded file name will be : Galaxy40-[MsClust_on_data_1_-_SIM_file]-

When I go to "edit attributes" and just click "save", then upon downloading again, the file name is correct... Galaxy40-[MsClust_on_data_1_-_SIM_file].msclust.csv .

Anyone faced this issue?

Thanks and regards,

Pieter.

Lukasse, Pieter

19 Nov 19 Nov

1:49 p.m.

Hi,

This issue is appearing again, after the upgrade of our Galaxy on October the 23rd....anyone experiencing the same?

Thanks,

Pieter.

From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Lukasse, Pieter Sent: vrijdag 4 april 2014 10:59 To: Bossers, Alex; Kuijt, Eric Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Strange issue with datatypes in Galaxy version of last week

Hi Alex, all

FYI - I've added the card to https://trello.com/c/ro8knsaa some time ago. Can you please vote for it?

Thanks,

Pieter.

From: Bossers, Alex Sent: dinsdag 25 maart 2014 16:52 To: Lukasse, Pieter Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Subject: RE: [galaxy-dev] Strange issue with datatypes in Galaxy version of last week

Pieter, I just experienced the same with another generic tabular .tab file output. It broke the filename at dash without any extension. The file itself was ok, just the name. Alex

Hi,

Apparently a new datatypes bug has been introduced in the Galaxy version of last week:

I have a tool that generates a csv file. Tool configuration is like this: <outputs> <data name="simOut" format="msclust.csv" label="${tool.name} on ${on_string} - SIM file"/>

The datatypes has this entry: <datatype extension="msclust.csv" type="galaxy.datatypes.tabular:Tabular" mimetype="text/csv" display_in_upload="true" subclass="true"/>

At first Galaxy output seems fine: [cid:image001.png@01D003FF.9BD73320]

But when I download the file, the downloaded file name will be : Galaxy40-[MsClust_on_data_1_-_SIM_file]-

When I go to "edit attributes" and just click "save", then upon downloading again, the file name is correct... Galaxy40-[MsClust_on_data_1_-_SIM_file].msclust.csv .

Anyone faced this issue?

Thanks and regards,

Pieter.

John Chilton

3:52 p.m.

New subject: Strange issue with datatypes in Galaxy version of last week

I have created a ticket for this issue here (https://trello.com/c/jxqT0ndZ).

When the file is in the incorrect state (extension missing from the download) - if you close out your browser tab and reopen it in a new window and try to download the file does it still exhibit the problem (indicating a client-side problem instead of a server metadata/datatype issue)?

-John

On Wed, Nov 19, 2014 at 7:49 AM, Lukasse, Pieter pieter.lukasse@wur.nl wrote:

...

Hi,

This issue is appearing again, after the upgrade of our Galaxy on *October the 23rd*....anyone experiencing the same?

Thanks,

Pieter.

*From:* galaxy-dev-bounces@lists.bx.psu.edu [mailto: galaxy-dev-bounces@lists.bx.psu.edu] *On Behalf Of *Lukasse, Pieter *Sent:* vrijdag 4 april 2014 10:59 *To:* Bossers, Alex; Kuijt, Eric *Cc:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] Strange issue with datatypes in Galaxy version of last week

Hi Alex, all

FYI – I’ve added the card to https://trello.com/c/ro8knsaa some time ago. Can you please vote for it?

Thanks,

Pieter.

*From:* Bossers, Alex *Sent:* dinsdag 25 maart 2014 16:52 *To:* Lukasse, Pieter *Cc:* galaxy-dev@lists.bx.psu.edu *Subject:* RE: [galaxy-dev] Strange issue with datatypes in Galaxy version of last week

Pieter,

I just experienced the same with another generic tabular .tab file output. It broke the filename at dash without any extension.

The file itself was ok, just the name.

Alex

*Van:* galaxy-dev-bounces@lists.bx.psu.edu [ mailto:galaxy-dev-bounces@lists.bx.psu.edu galaxy-dev-bounces@lists.bx.psu.edu] *Namens *Lukasse, Pieter *Verzonden:* dinsdag 25 maart 2014 16:33 *Aan:* galaxy-dev@lists.bx.psu.edu *Onderwerp:* [galaxy-dev] Strange issue with datatypes in Galaxy version of last week

Hi,

Apparently a new datatypes bug has been introduced in the Galaxy version of last week:

I have a tool that generates a csv file. Tool configuration is like this:

<outputs>

<data name=*"simOut"* format=*"msclust.csv"* label=*"${tool.name http://tool.name} on ${on_string} - SIM file"*/>

The datatypes has this entry:

<datatype extension=*"msclust.csv"* type= *"galaxy.datatypes.tabular:Tabular"* mimetype=*"text/csv"* display_in_upload=*"true"* subclass=*"true"/*>

At first Galaxy output seems fine:

But when I download the file, the downloaded file name will be : Galaxy40-[MsClust_on_data_1_-_SIM_file]-

When I go to “edit attributes” and just click “save”, then upon downloading again, the file name is correct... Galaxy40-[MsClust_on_data_1_-_SIM_file].msclust.csv .

Anyone faced this issue?

Thanks and regards,

Pieter.

Pieter Lukasse

Wageningen UR, Plant Research International

Departments of Bioscience and Bioinformatics

Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands

+31-317481122; skype: pieter.lukasse.wur

http://www.pri.wur.nl

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/

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

Lukasse, Pieter

12 Dec 12 Dec

1:55 p.m.

New subject: Strange issue with datatypes in Galaxy version of last week

Hi John,

Sorry for the late reply. Thanks for making the new ticket.

Regarding your question: yes, the problem seems permanent and is only solved by editing the metadata of the history item (or at least opening the metadata and clicking “save”). I found no other trick to work around it.

Best regards,

Pieter.

From: John Chilton [mailto:jmchilton@gmail.com] Sent: woensdag 19 november 2014 15:53 To: Lukasse, Pieter Cc: Bossers, Alex; Kuijt, Eric; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Strange issue with datatypes in Galaxy version of last week

I have created a ticket for this issue here (https://trello.com/c/jxqT0ndZ).

-John

On Wed, Nov 19, 2014 at 7:49 AM, Lukasse, Pieter <pieter.lukasse@wur.nlmailto:pieter.lukasse@wur.nl> wrote: Hi,

This issue is appearing again, after the upgrade of our Galaxy on October the 23rd....anyone experiencing the same?

Thanks,

Pieter.

From: galaxy-dev-bounces@lists.bx.psu.edumailto:galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edumailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Lukasse, Pieter Sent: vrijdag 4 april 2014 10:59 To: Bossers, Alex; Kuijt, Eric Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Strange issue with datatypes in Galaxy version of last week

Hi Alex, all

FYI – I’ve added the card to https://trello.com/c/ro8knsaa some time ago. Can you please vote for it?

Thanks,

Pieter.

Pieter, I just experienced the same with another generic tabular .tab file output. It broke the filename at dash without any extension. The file itself was ok, just the name. Alex

Hi,

Apparently a new datatypes bug has been introduced in the Galaxy version of last week:

I have a tool that generates a csv file. Tool configuration is like this: <outputs> <data name="simOut" format="msclust.csv" label="${tool.name<http://tool.name>} on ${on_string} - SIM file"/>

The datatypes has this entry: <datatype extension="msclust.csv" type="galaxy.datatypes.tabular:Tabular" mimetype="text/csv" display_in_upload="true" subclass="true"/>

At first Galaxy output seems fine: [cid:image001.png@01D01613.3BD6B1A0]

But when I download the file, the downloaded file name will be : Galaxy40-[MsClust_on_data_1_-_SIM_file]-

When I go to “edit attributes” and just click “save”, then upon downloading again, the file name is correct... Galaxy40-[MsClust_on_data_1_-_SIM_file].msclust.csv .

Anyone faced this issue?

Thanks and regards,

Pieter.

Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317481122tel:%2B31-317481122; skype: pieter.lukasse.wur http://www.pri.wur.nl http://www.pri.wur.nl/

___________________________________________________________ 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/

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

3099

Age (days ago)

3361

Last active (days ago)

galaxy-dev@lists.galaxyproject.org

5 comments

3 participants

tags (0)

participants (3)

Bossers, Alex
John Chilton
Lukasse, Pieter