Hi Keith,

your message is not bouncing, it shows here: http://dev.list.galaxyproject.org/

Your setup seems correct to me, does Galaxy have permission to read files in the given folders?

Also Galaxy will auto-create folders if set the `user_library_import_dir` to be the same as ftp and use `#user_library_import_dir_auto_creation: false`

M.

On Fri, Jan 25, 2019 at 4:58 PM Keith Suderman suderman@cs.vassar.edu wrote:

I have been creating directories for the users, but putting files in (for example) /home/galaxy/database/ftp/user@example.com does not make them available for the user@example.com user in Galaxy.

Also for the list admins... I never did see my message appear on the list and the message Cicada replied to appears to be from galaxy-dev-bounces@lists.galaxyproject.org. Any ideas why my message(s) appear to be bouncing. I am pretty sure I am sending from the correct address.

Cheers, Keith

On Jan 25, 2019, at 4:36 PM, Dennis, H. E. Cicada Brokaw hbrokaw@iu.edu wrote:

I think you have to create the user's directories under /home/galaxy/database/ftp. I don't think Galaxy will create them if they are not there. Cicada

---

From: galaxy-dev galaxy-dev-bounces@lists.galaxyproject.org on behalf of Keith Suderman suderman@cs.vassar.edu Sent: Friday, January 25, 2019 4:01 PM To: Galaxy Dev List Subject: [External] [galaxy-dev] Copying files to FTP upload directory

Hello,

I am trying to (ab)use the FTP file upload functionality to get data from an external service into Galaxy. From my reading of the docs I simply need to configure the ftp_upload_dir and ftp_upload_site in my galaxy.ini (haven't migrated to yaml yet) and Galaxy will expect to find subdirectories named after the user's account (email) in the ftp_upload_dir.

I have configured the ftp_upload_dir (/home/galaxy/database/ftp in our case) and the "Choose FTP File" button is now available in the Upload dialog, however regardless of where I put files, or what I name them, Galaxy always reports that "Your FTP directory does not contain any files." For example, if I have the user account user@example.org I would expect to be able to place files in /home/galaxy/database/ftp/user@example.org and they will be available in the Upload dialog for the user@example.org user. However, this is not working; am I missing something?

Thanks, Keith

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It turns out I had fat-fingered the key name in the config and had specified ftp_upoload_dir, once I noticed the typo and changed it to ftp_upload_dir everything works as expected. What threw me was that the "Choose FTP file" button appeared in the upload dialog even though the ftp_upload_dir was not specified. Looking at the log files I see 403 errors for GET /api/remote_files and when I try that URL in a browser I get some JSON with the error message, "The configuration of this Galaxy instance does not allow upload from FTP directories."

I am not familiar enough with the Javascript client, but it looks like the logic used to determine whether or not to show the "Choose FTP file" button only checks if ftp_upload_site has been specified and not if ftp_upload_dir has been defined.

- Keith

On Jan 25, 2019, at 7:29 PM, Keith Suderman suderman@cs.vassar.edu wrote:

Hi Martin,

Yes, Galaxy has permission to read the files. I have only tested on my own workstation, so Galaxy runs as me, all the files/directories are owned by me, etc. but I will try on our dev server and see if it makes any difference. Would using an admin account be a problem?

And just to clarify, I am assuming I can do the following to get a file available in Galaxy (where the ftp_upload_dir is /home/galaxy/database/ftp):

$> mkdir -p /home/galaxy/database/ftp/suderman@cs.vassar mailto:home/galaxy/database/ftp/suderman@cs.vassar.edu $> echo "Hello world." > /home/galaxy/database/ftp/suderman@cs.vassar.edu mailto:home/galaxy/database/ftp/suderman@cs.vassar.edu/Hello.txt $> chown -R galaxy:galaxy /home/galaxy/database/ftp

Thanks, Keith

...

On Jan 25, 2019, at 5:07 PM, Martin Čech <emulatorer@gmail.com mailto:emulatorer@gmail.com> wrote:

Hi Keith,

your message is not bouncing, it shows here: http://dev.list.galaxyproject.org/ http://dev.list.galaxyproject.org/ Your setup seems correct to me, does Galaxy have permission to read files in the given folders?

Also Galaxy will auto-create folders if set the `user_library_import_dir` to be the same as ftp and use `#user_library_import_dir_auto_creation: false`

M.

On Fri, Jan 25, 2019 at 4:58 PM Keith Suderman <suderman@cs.vassar.edu mailto:suderman@cs.vassar.edu> wrote: I have been creating directories for the users, but putting files in (for example) /home/galaxy/database/ftp/user@example.com mailto:home/galaxy/database/ftp/user@example.com does not make them available for the user@example.com mailto:user@example.com user in Galaxy.

Also for the list admins... I never did see my message appear on the list and the message Cicada replied to appears to be from galaxy-dev-bounces@lists.galaxyproject.org mailto:galaxy-dev-bounces@lists.galaxyproject.org. Any ideas why my message(s) appear to be bouncing. I am pretty sure I am sending from the correct address.

Cheers, Keith

...

On Jan 25, 2019, at 4:36 PM, Dennis, H. E. Cicada Brokaw <hbrokaw@iu.edu mailto:hbrokaw@iu.edu> wrote:

I think you have to create the user's directories under /home/galaxy/database/ftp. I don't think Galaxy will create them if they are not there. Cicada

---

From: galaxy-dev <galaxy-dev-bounces@lists.galaxyproject.org mailto:galaxy-dev-bounces@lists.galaxyproject.org> on behalf of Keith Suderman <suderman@cs.vassar.edu mailto:suderman@cs.vassar.edu> Sent: Friday, January 25, 2019 4:01 PM To: Galaxy Dev List Subject: [External] [galaxy-dev] Copying files to FTP upload directory

...

Hello,

I am trying to (ab)use the FTP file upload functionality to get data from an external service into Galaxy. From my reading of the docs I simply need to configure the ftp_upload_dir and ftp_upload_site in my galaxy.ini (haven't migrated to yaml yet) and Galaxy will expect to find subdirectories named after the user's account (email) in the ftp_upload_dir.

I have configured the ftp_upload_dir (/home/galaxy/database/ftp in our case) and the "Choose FTP File" button is now available in the Upload dialog, however regardless of where I put files, or what I name them, Galaxy always reports that "Your FTP directory does not contain any files." For example, if I have the user account user@example.org mailto:user@example.org I would expect to be able to place files in /home/galaxy/database/ftp/user@example.org mailto:home/galaxy/database/ftp/user@example.org and they will be available in the Upload dialog for the user@example.org mailto:user@example.org user. However, this is not working; am I missing something?

Thanks, Keith

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---

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/ https://lists.galaxyproject.org/

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