Re: [galaxy-dev] customize the Upload File tool form (version 1.1.4)

[Christophe Antoniewski]

Hi,

This is a quick follow up about the instructions given by Aysam and Martin,
which may help others (including me ;-).

Indeed I upgraded our galaxy-dist to the last commit and the /client
directory showed up.
To get the instructions working I had to install as root some grunt related
packages, otherwise it failed:
including
$ sudo apt-get install software-properties-common
$ sudo apt-get install python-software-properties
$ sudo apt-get update
$ sudo npm -g install grunt
$ sudo npm install -g grunt-cli
Then I had the "grunt watch" working and could make the changes - *opening
another shell session* (I say this because it is not evident for those who
are not familiar with grunt).

Yet the changes still do not show up in the browser.
My guess is that the galaxy configuration model has changed too, with the
creation of a config directory. I suppose that the use of the /client
directory is specified in the new galaxy.ini file which replaces
universe_wsgi.ini in / .

More generally, I did not see instructions on how to move from the old .ini
file*sss* at / to the new configuration model using the /config directory
without crashing the production instance. Is it available somewhere in the
wiki or in a discussion ?

Chris


Christophe Antoniewski

Drosophila Genetics and Epigenetics
Institut de Biologie Paris Seine

9, Quai St Bernard, Boîte courrier 24
75252 Paris Cedex 05

Tel +33 1 44 27 34 39
Fax +33 1 44 27 34 45
Mobile +33 6 68 60 51 50
christophe.antoniew...@upmc.fr

http://drosophile.org



2014-11-12 16:11 GMT+01:00 Aysam Guerler :

> Hi Christophe,
>
> In order to apply the changes scripts have to be packed properly. Please
> follow these steps:
>
> 1. Go to the client/ directory and type 'npm install'
> 2. Now type 'grunt watch'. This will start a listener which captures code
> changes and repacks scripts automatically
> 3. Finally, make your changes to the code files in
> client/galaxy/scripts/mvc/upload and reload your browser
>
> Let me know if that works for you or if you have any other questions.
>
> Thanks,
> Sam
>
>
>
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Re: [galaxy-dev] customize the Upload File tool form (version 1.1.4)

[Christophe Antoniewski]

Ok I just noticed the new client directory in Bitbucket and the
accompanying trello cards.
Make things more understandable...

Thanks

Chris

Christophe Antoniewski

Drosophila Genetics and Epigenetics
Institut de Biologie Paris Seine

9, Quai St Bernard, Boîte courrier 24
75252 Paris Cedex 05

Tel +33 1 44 27 34 39
Fax +33 1 44 27 34 45
Mobile +33 6 68 60 51 50
christophe.antoniew...@upmc.fr

http://drosophile.org



2014-11-12 19:23 GMT+01:00 Martin Čech :

> corrrect: /client is a directory within Galaxy root - it contains all the
> javascripts
>
> The build (grunt) process takes the /client directory and copies the
> scripts to /static/scripts directory within Galaxy root (and packs them and
> stuff) from where the files are served to the browser.
> If you want to make JS changes, make them in /client and propagate it via
> grunt.
>
> Make sure you have up to date version of Galaxy since the grunt building
> was added fairly recently.
>
> note: /scripts directory within Galaxy root has a different purpose, those
> are python scripts (API and stuff)
>
> M.
>
> On Wed, Nov 12, 2014 at 1:16 PM, Christophe Antoniewski <
> christophe.antoniew...@snv.jussieu.fr> wrote:
>
>> Aysam and Martin,
>>
>> Thanks for your help. I am not familiar with JS development.
>>
>> To make "client" crystal clear :
>>
>> /client stands for the home directory where Galaxy-dist is installed ?
>> and client/galaxy/scripts/mvc/upload stands for
>> ~/galaxy-dist/scripts/mvc/upload (assuming that the galaxy code is
>> installed in galaxy-dis) ?
>>
>> right ?
>>
>> Chris
>>
>> Christophe Antoniewski
>>
>> Drosophila Genetics and Epigenetics
>> Institut de Biologie Paris Seine
>> 
>> 9, Quai St Bernard, Boîte courrier 24
>> 75252 Paris Cedex 05
>>
>> Tel +33 1 44 27 34 39
>> Fax +33 1 44 27 34 45
>> Mobile +33 6 68 60 51 50
>> christophe.antoniew...@upmc.fr
>>
>> http://drosophile.org
>>
>>
>>
>> 2014-11-12 16:42 GMT+01:00 Martin Čech :
>>
>>> I updated our wiki with this new build information.
>>> https://wiki.galaxyproject.org/Develop/JSA
>>>
>>> M.
>>>
>>> On Wed, Nov 12, 2014 at 10:11 AM, Aysam Guerler >> > wrote:
>>>
 Hi Christophe,

 In order to apply the changes scripts have to be packed properly.
 Please follow these steps:

 1. Go to the client/ directory and type 'npm install'
 2. Now type 'grunt watch'. This will start a listener which captures
 code changes and repacks scripts automatically
 3. Finally, make your changes to the code files in
 client/galaxy/scripts/mvc/upload and reload your browser

 Let me know if that works for you or if you have any other questions.

 Thanks,
 Sam

 On Wed, Nov 12, 2014 at 4:47 AM, Christophe Antoniewski <
 christophe.antoniew...@snv.jussieu.fr> wrote:

> Hi,
>
> As we have arranged an sftp upload system through ftp port for our
> Galaxy instance, we would need to customize the Upload File tool form, so
> that a few more line explain how-to-do in the FTP section of the form, in
> addition to the "This Galaxy server allows you to upload files via FTP. To
> upload some files, log in to the FTP server at 127.0.0.1 using your Galaxy
> credentials (email address and password)."
>
> I dug into
> /home/galaxy/galaxy-dist/static/scripts/mvc/upload/upload-ftp.js
> and
> /home/galaxy/galaxy-dist/static/scripts/packed/mvc/upload/upload-ftp.js
>
> but the changes I tried into these files do not show up in the tool
> form.
>
> If someone can indicate the right way to intercept this content and
> enrich it as mentioned above,  I would be grateful !
>
> Cheers
>
> Chris
>
> Christophe Antoniewski
>
> Drosophila Genetics and Epigenetics
> Institut de Biologie Paris Seine
> 
> 9, Quai St Bernard, Boîte courrier 24
> 75252 Paris Cedex 05
>
> Tel +33 1 44 27 34 39
> Fax +33 1 44 27 34 45
> Mobile +33 6 68 60 51 50
> christophe.antoniew...@upmc.fr
>
> http://drosophile.org
>
>
>
> ___
> 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/
>


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 Please keep all replies on the list by using "reply all"
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Re: [galaxy-dev] customize the Upload File tool form (version 1.1.4)

[Martin Čech]

corrrect: /client is a directory within Galaxy root - it contains all the
javascripts

The build (grunt) process takes the /client directory and copies the
scripts to /static/scripts directory within Galaxy root (and packs them and
stuff) from where the files are served to the browser.
If you want to make JS changes, make them in /client and propagate it via
grunt.

Make sure you have up to date version of Galaxy since the grunt building
was added fairly recently.

note: /scripts directory within Galaxy root has a different purpose, those
are python scripts (API and stuff)

M.

On Wed, Nov 12, 2014 at 1:16 PM, Christophe Antoniewski <
christophe.antoniew...@snv.jussieu.fr> wrote:

> Aysam and Martin,
>
> Thanks for your help. I am not familiar with JS development.
>
> To make "client" crystal clear :
>
> /client stands for the home directory where Galaxy-dist is installed ?
> and client/galaxy/scripts/mvc/upload stands for
> ~/galaxy-dist/scripts/mvc/upload (assuming that the galaxy code is
> installed in galaxy-dis) ?
>
> right ?
>
> Chris
>
> Christophe Antoniewski
>
> Drosophila Genetics and Epigenetics
> Institut de Biologie Paris Seine
> 
> 9, Quai St Bernard, Boîte courrier 24
> 75252 Paris Cedex 05
>
> Tel +33 1 44 27 34 39
> Fax +33 1 44 27 34 45
> Mobile +33 6 68 60 51 50
> christophe.antoniew...@upmc.fr
>
> http://drosophile.org
>
>
>
> 2014-11-12 16:42 GMT+01:00 Martin Čech :
>
>> I updated our wiki with this new build information.
>> https://wiki.galaxyproject.org/Develop/JSA
>>
>> M.
>>
>> On Wed, Nov 12, 2014 at 10:11 AM, Aysam Guerler 
>> wrote:
>>
>>> Hi Christophe,
>>>
>>> In order to apply the changes scripts have to be packed properly. Please
>>> follow these steps:
>>>
>>> 1. Go to the client/ directory and type 'npm install'
>>> 2. Now type 'grunt watch'. This will start a listener which captures
>>> code changes and repacks scripts automatically
>>> 3. Finally, make your changes to the code files in
>>> client/galaxy/scripts/mvc/upload and reload your browser
>>>
>>> Let me know if that works for you or if you have any other questions.
>>>
>>> Thanks,
>>> Sam
>>>
>>> On Wed, Nov 12, 2014 at 4:47 AM, Christophe Antoniewski <
>>> christophe.antoniew...@snv.jussieu.fr> wrote:
>>>
 Hi,

 As we have arranged an sftp upload system through ftp port for our
 Galaxy instance, we would need to customize the Upload File tool form, so
 that a few more line explain how-to-do in the FTP section of the form, in
 addition to the "This Galaxy server allows you to upload files via FTP. To
 upload some files, log in to the FTP server at 127.0.0.1 using your Galaxy
 credentials (email address and password)."

 I dug into
 /home/galaxy/galaxy-dist/static/scripts/mvc/upload/upload-ftp.js
 and
 /home/galaxy/galaxy-dist/static/scripts/packed/mvc/upload/upload-ftp.js

 but the changes I tried into these files do not show up in the tool
 form.

 If someone can indicate the right way to intercept this content and
 enrich it as mentioned above,  I would be grateful !

 Cheers

 Chris

 Christophe Antoniewski

 Drosophila Genetics and Epigenetics
 Institut de Biologie Paris Seine
 
 9, Quai St Bernard, Boîte courrier 24
 75252 Paris Cedex 05

 Tel +33 1 44 27 34 39
 Fax +33 1 44 27 34 45
 Mobile +33 6 68 60 51 50
 christophe.antoniew...@upmc.fr

 http://drosophile.org



 ___
 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/

>>>
>>>
>>> ___
>>> 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/
>>>
>>
>>
>
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Re: [galaxy-dev] customize the Upload File tool form (version 1.1.4)

[Christophe Antoniewski]

Aysam and Martin,

Thanks for your help. I am not familiar with JS development.

To make "client" crystal clear :

/client stands for the home directory where Galaxy-dist is installed ?
and client/galaxy/scripts/mvc/upload stands for
~/galaxy-dist/scripts/mvc/upload (assuming that the galaxy code is
installed in galaxy-dis) ?

right ?

Chris

Christophe Antoniewski

Drosophila Genetics and Epigenetics
Institut de Biologie Paris Seine

9, Quai St Bernard, Boîte courrier 24
75252 Paris Cedex 05

Tel +33 1 44 27 34 39
Fax +33 1 44 27 34 45
Mobile +33 6 68 60 51 50
christophe.antoniew...@upmc.fr

http://drosophile.org



2014-11-12 16:42 GMT+01:00 Martin Čech :

> I updated our wiki with this new build information.
> https://wiki.galaxyproject.org/Develop/JSA
>
> M.
>
> On Wed, Nov 12, 2014 at 10:11 AM, Aysam Guerler 
> wrote:
>
>> Hi Christophe,
>>
>> In order to apply the changes scripts have to be packed properly. Please
>> follow these steps:
>>
>> 1. Go to the client/ directory and type 'npm install'
>> 2. Now type 'grunt watch'. This will start a listener which captures code
>> changes and repacks scripts automatically
>> 3. Finally, make your changes to the code files in
>> client/galaxy/scripts/mvc/upload and reload your browser
>>
>> Let me know if that works for you or if you have any other questions.
>>
>> Thanks,
>> Sam
>>
>> On Wed, Nov 12, 2014 at 4:47 AM, Christophe Antoniewski <
>> christophe.antoniew...@snv.jussieu.fr> wrote:
>>
>>> Hi,
>>>
>>> As we have arranged an sftp upload system through ftp port for our
>>> Galaxy instance, we would need to customize the Upload File tool form, so
>>> that a few more line explain how-to-do in the FTP section of the form, in
>>> addition to the "This Galaxy server allows you to upload files via FTP. To
>>> upload some files, log in to the FTP server at 127.0.0.1 using your Galaxy
>>> credentials (email address and password)."
>>>
>>> I dug into
>>> /home/galaxy/galaxy-dist/static/scripts/mvc/upload/upload-ftp.js
>>> and
>>> /home/galaxy/galaxy-dist/static/scripts/packed/mvc/upload/upload-ftp.js
>>>
>>> but the changes I tried into these files do not show up in the tool form.
>>>
>>> If someone can indicate the right way to intercept this content and
>>> enrich it as mentioned above,  I would be grateful !
>>>
>>> Cheers
>>>
>>> Chris
>>>
>>> Christophe Antoniewski
>>>
>>> Drosophila Genetics and Epigenetics
>>> Institut de Biologie Paris Seine
>>> 
>>> 9, Quai St Bernard, Boîte courrier 24
>>> 75252 Paris Cedex 05
>>>
>>> Tel +33 1 44 27 34 39
>>> Fax +33 1 44 27 34 45
>>> Mobile +33 6 68 60 51 50
>>> christophe.antoniew...@upmc.fr
>>>
>>> http://drosophile.org
>>>
>>>
>>>
>>> ___
>>> 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/
>>>
>>
>>
>> ___
>> 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/
>>
>
>
___
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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To search Galaxy mailing lists use the unified search at:
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Re: [galaxy-dev] customize the Upload File tool form (version 1.1.4)

[Martin Čech]

I updated our wiki with this new build information.
https://wiki.galaxyproject.org/Develop/JSA

M.

On Wed, Nov 12, 2014 at 10:11 AM, Aysam Guerler 
wrote:

> Hi Christophe,
>
> In order to apply the changes scripts have to be packed properly. Please
> follow these steps:
>
> 1. Go to the client/ directory and type 'npm install'
> 2. Now type 'grunt watch'. This will start a listener which captures code
> changes and repacks scripts automatically
> 3. Finally, make your changes to the code files in
> client/galaxy/scripts/mvc/upload and reload your browser
>
> Let me know if that works for you or if you have any other questions.
>
> Thanks,
> Sam
>
> On Wed, Nov 12, 2014 at 4:47 AM, Christophe Antoniewski <
> christophe.antoniew...@snv.jussieu.fr> wrote:
>
>> Hi,
>>
>> As we have arranged an sftp upload system through ftp port for our Galaxy
>> instance, we would need to customize the Upload File tool form, so that a
>> few more line explain how-to-do in the FTP section of the form, in addition
>> to the "This Galaxy server allows you to upload files via FTP. To upload
>> some files, log in to the FTP server at 127.0.0.1 using your Galaxy
>> credentials (email address and password)."
>>
>> I dug into
>> /home/galaxy/galaxy-dist/static/scripts/mvc/upload/upload-ftp.js
>> and
>> /home/galaxy/galaxy-dist/static/scripts/packed/mvc/upload/upload-ftp.js
>>
>> but the changes I tried into these files do not show up in the tool form.
>>
>> If someone can indicate the right way to intercept this content and
>> enrich it as mentioned above,  I would be grateful !
>>
>> Cheers
>>
>> Chris
>>
>> Christophe Antoniewski
>>
>> Drosophila Genetics and Epigenetics
>> Institut de Biologie Paris Seine
>> 
>> 9, Quai St Bernard, Boîte courrier 24
>> 75252 Paris Cedex 05
>>
>> Tel +33 1 44 27 34 39
>> Fax +33 1 44 27 34 45
>> Mobile +33 6 68 60 51 50
>> christophe.antoniew...@upmc.fr
>>
>> http://drosophile.org
>>
>>
>>
>> ___
>> 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/
>>
>
>
> ___
> 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/
>
___
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: [galaxy-dev] customize the Upload File tool form (version 1.1.4)

[Aysam Guerler]

Hi Christophe,

In order to apply the changes scripts have to be packed properly. Please
follow these steps:

1. Go to the client/ directory and type 'npm install'
2. Now type 'grunt watch'. This will start a listener which captures code
changes and repacks scripts automatically
3. Finally, make your changes to the code files in
client/galaxy/scripts/mvc/upload and reload your browser

Let me know if that works for you or if you have any other questions.

Thanks,
Sam

On Wed, Nov 12, 2014 at 4:47 AM, Christophe Antoniewski <
christophe.antoniew...@snv.jussieu.fr> wrote:

> Hi,
>
> As we have arranged an sftp upload system through ftp port for our Galaxy
> instance, we would need to customize the Upload File tool form, so that a
> few more line explain how-to-do in the FTP section of the form, in addition
> to the "This Galaxy server allows you to upload files via FTP. To upload
> some files, log in to the FTP server at 127.0.0.1 using your Galaxy
> credentials (email address and password)."
>
> I dug into
> /home/galaxy/galaxy-dist/static/scripts/mvc/upload/upload-ftp.js
> and
> /home/galaxy/galaxy-dist/static/scripts/packed/mvc/upload/upload-ftp.js
>
> but the changes I tried into these files do not show up in the tool form.
>
> If someone can indicate the right way to intercept this content and enrich
> it as mentioned above,  I would be grateful !
>
> Cheers
>
> Chris
>
> Christophe Antoniewski
>
> Drosophila Genetics and Epigenetics
> Institut de Biologie Paris Seine
> 
> 9, Quai St Bernard, Boîte courrier 24
> 75252 Paris Cedex 05
>
> Tel +33 1 44 27 34 39
> Fax +33 1 44 27 34 45
> Mobile +33 6 68 60 51 50
> christophe.antoniew...@upmc.fr
>
> http://drosophile.org
>
>
>
> ___
> 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/
>
___
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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To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

[galaxy-dev] customize the Upload File tool form (version 1.1.4)

[Christophe Antoniewski]

Hi,

As we have arranged an sftp upload system through ftp port for our Galaxy
instance, we would need to customize the Upload File tool form, so that a
few more line explain how-to-do in the FTP section of the form, in addition
to the "This Galaxy server allows you to upload files via FTP. To upload
some files, log in to the FTP server at 127.0.0.1 using your Galaxy
credentials (email address and password)."

I dug into
/home/galaxy/galaxy-dist/static/scripts/mvc/upload/upload-ftp.js
and
/home/galaxy/galaxy-dist/static/scripts/packed/mvc/upload/upload-ftp.js

but the changes I tried into these files do not show up in the tool form.

If someone can indicate the right way to intercept this content and enrich
it as mentioned above,  I would be grateful !

Cheers

Chris

Christophe Antoniewski

Drosophila Genetics and Epigenetics
Institut de Biologie Paris Seine

9, Quai St Bernard, Boîte courrier 24
75252 Paris Cedex 05

Tel +33 1 44 27 34 39
Fax +33 1 44 27 34 45
Mobile +33 6 68 60 51 50
christophe.antoniew...@upmc.fr

http://drosophile.org
___
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:
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