View uploaded files

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View uploaded files

pieter coussement-2

Hi,

I just updated galaxy, and now I seem to be unable to view the contents of the files.

So i'm able to upload, and can work with them and see the attributes.

If however I want to open them ('the eye' on the left), I get an error (as do my collegues)

I checked on the full path and the file is there.

permission on the file:

-rw-r--r--  1 galaxy galaxy        16 mrt  1 12:10 dataset_140.dat


nginx vhost      

        ##
        # Galaxy
        ##

        upstream galaxy_app {
                server 127.0.0.1:8080;
        }

        proxy_next_upstream off;

        server {
                client_max_body_size 10G;
                # ... other server stuff ...
                location / {
                        proxy_pass   http://galaxy_app;
                        proxy_set_header   X-Forwarded-Host $host;
                        proxy_set_header   X-Forwarded-For  $proxy_add_x_forwarded_for;
                }

                location /static {
                        alias /home/galaxy/Software/galaxy/static;
                        expires 24h;

                }

                location /static/style {
                        alias /home/galaxy/Software/galaxy/static/style/blue;
                        expires 24h;
                }

                location /static/scripts {
                        alias /home/galaxy/Software/galaxy/static/scripts;
                }

                location /favicon.ico {
                        alias /home/galaxy/Software/galaxy/static/favicon.ico;
                }

                location /robots.txt {
                        alias /home/galaxy/Software/galaxy/static/robots.txt;
                }

                # serve static content for visualization and interactive environment plugins
                location ~ ^/plugins/(?<plug_type>.+?)/(?<vis_name>.+?)/static/(?<static_file>.*?)$ {
                        alias /home/galaxy/Software/galaxy/config/plugins/$plug_type/$vis_name/static/$static_file;
                }

                location /_x_accel_redirect/ {
                        internal;
                        alias /;
                }

                location ~ \.php$ {
                        fastcgi_pass 127.0.0.1:9000;
                        include /etc/nginx/conf.d/*.conf;
                        include /etc/nginx/sites-enabled/*;

                        fastcgi_intercept_errors        on;
                        error_page 404 /error/404.php;
                }
        }


I would guess a permission error of some kind but I seem unable to find it.

Nginx spits out:

2017/03/01 17:23:39 [error] 28783#0: *1457 open() "/usr/share/nginx/htmltrue/home/galaxy/Software/galaxy/database/files/000/dataset_14
0.dat" failed (2: No such file or directory), client: 172.19.40.126, server: , request: "GET /datasets/32d48e3506ae8cf7/display/?previ
ew=True HTTP/1.1", upstream: "http://127.0.0.1:8080/datasets/32d48e3506ae8cf7/display/?preview=True", host: "172.19.32.42", referrer:
"http://172.19.32.42/"

the file is in home/galaxy/Software/galaxy/database/files/000/dataset_140.dat

but the folder /usr/share/nginx/htmltrue does not exists...


Any help on this one?

Best regards,

Pieter

--

ir. Pieter Coussement, PhD
[hidden email]
+32 (0) 485 42 79 72




www.inbiose.com
Registered address: Inbiose N.V., Technologiepark Zwijnaarde 3 – bus 41, B-9052 Gent, Belgium - rpr gent: 0534 887 593

Confidentiality notice: The information contained in this e-mail, including any attachments, is confidential and may be the subject of legal professional privilege. It is intended for the authorized use of the individual or entity addressed. If the receiver or reader of this message is not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is prohibited. If this email is received in error, please accept our apologies, delete all copies from your system, and notify the sender by return e-mail and delete this e-mail, including any attachments. Disclaimer: The author of this e-mail has taken every effort to ensure that the information and advice provided are accurate and up-to-date, based upon the information available at the time of writing. The information and advice can only be binding for Inbiose when this is clearly intended in the message and is contained in the information made available.


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Re: View uploaded files

John Chilton-4
Do you have ``nginx_x_accel_redirect_base = /_x_accel_redirect`` set in your Galaxy ini file?

Do you know what user nginx runs as?

If yes, do you know if it has access to /home/galaxy/Software/galaxy/database/files/000/dataset_140.dat?

I'd su to become that nginx user and just make sure it can cd into that directory and read that file.

If it can't read the directory - my common recommendation is to create a Galaxy group, make sure the nginx user belongs to it, and ensure all of Galaxy's data files are group readable.

If the permissions are not the problem - I'm at a bit of a loss.

-John


On Wed, Mar 1, 2017 at 11:35 AM, pieter coussement <[hidden email]> wrote:

Hi,

I just updated galaxy, and now I seem to be unable to view the contents of the files.

So i'm able to upload, and can work with them and see the attributes.

If however I want to open them ('the eye' on the left), I get an error (as do my collegues)

I checked on the full path and the file is there.

permission on the file:

-rw-r--r--  1 galaxy galaxy        16 mrt  1 12:10 dataset_140.dat


nginx vhost      

        ##
        # Galaxy
        ##

        upstream galaxy_app {
                server 127.0.0.1:8080;
        }

        proxy_next_upstream off;

        server {
                client_max_body_size 10G;
                # ... other server stuff ...
                location / {
                        proxy_pass   http://galaxy_app;
                        proxy_set_header   X-Forwarded-Host $host;
                        proxy_set_header   X-Forwarded-For  $proxy_add_x_forwarded_for;
                }

                location /static {
                        alias /home/galaxy/Software/galaxy/static;
                        expires 24h;

                }

                location /static/style {
                        alias /home/galaxy/Software/galaxy/static/style/blue;
                        expires 24h;
                }

                location /static/scripts {
                        alias /home/galaxy/Software/galaxy/static/scripts;
                }

                location /favicon.ico {
                        alias /home/galaxy/Software/galaxy/static/favicon.ico;
                }

                location /robots.txt {
                        alias /home/galaxy/Software/galaxy/static/robots.txt;
                }

                # serve static content for visualization and interactive environment plugins
                location ~ ^/plugins/(?<plug_type>.+?)/(?<vis_name>.+?)/static/(?<static_file>.*?)$ {
                        alias /home/galaxy/Software/galaxy/config/plugins/$plug_type/$vis_name/static/$static_file;
                }

                location /_x_accel_redirect/ {
                        internal;
                        alias /;
                }

                location ~ \.php$ {
                        fastcgi_pass 127.0.0.1:9000;
                        include /etc/nginx/conf.d/*.conf;
                        include /etc/nginx/sites-enabled/*;

                        fastcgi_intercept_errors        on;
                        error_page 404 /error/404.php;
                }
        }


I would guess a permission error of some kind but I seem unable to find it.

Nginx spits out:

2017/03/01 17:23:39 [error] 28783#0: *1457 open() "/usr/share/nginx/htmltrue/home/galaxy/Software/galaxy/database/files/000/dataset_14
0.dat" failed (2: No such file or directory), client: 172.19.40.126, server: , request: "GET /datasets/32d48e3506ae8cf7/display/?previ
ew=True HTTP/1.1", upstream: "http://127.0.0.1:8080/datasets/32d48e3506ae8cf7/display/?preview=True", host: "172.19.32.42", referrer:
"http://172.19.32.42/"

the file is in home/galaxy/Software/galaxy/database/files/000/dataset_140.dat

but the folder /usr/share/nginx/htmltrue does not exists...


Any help on this one?

Best regards,

Pieter

--

ir. Pieter Coussement, PhD
[hidden email]
<a href="tel:+32%20485%2042%2079%2072" value="+32485427972" target="_blank">+32 (0) 485 42 79 72




www.inbiose.com
Registered address: Inbiose N.V., Technologiepark Zwijnaarde 3 – bus 41, B-9052 Gent, Belgium - rpr gent: 0534 887 593

Confidentiality notice: The information contained in this e-mail, including any attachments, is confidential and may be the subject of legal professional privilege. It is intended for the authorized use of the individual or entity addressed. If the receiver or reader of this message is not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is prohibited. If this email is received in error, please accept our apologies, delete all copies from your system, and notify the sender by return e-mail and delete this e-mail, including any attachments. Disclaimer: The author of this e-mail has taken every effort to ensure that the information and advice provided are accurate and up-to-date, based upon the information available at the time of writing. The information and advice can only be binding for Inbiose when this is clearly intended in the message and is contained in the information made available.


___________________________________________________________
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/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:
  https://lists.galaxyproject.org/

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

pieter coussement-2

Hi,

Thanks a lot.

``nginx_x_accel_redirect_base = /_x_accel_redirect`` seems to have fixed it. this was somehow set to ''true'' (could be my mistake, I don't seem to remember anymore).

Anyway, it works now.


Thanks!


On 14-03-17 13:39, John Chilton wrote:
Do you have ``nginx_x_accel_redirect_base = /_x_accel_redirect`` set in your Galaxy ini file?

Do you know what user nginx runs as?

If yes, do you know if it has access to /home/galaxy/Software/galaxy/database/files/000/dataset_140.dat?

I'd su to become that nginx user and just make sure it can cd into that directory and read that file.

If it can't read the directory - my common recommendation is to create a Galaxy group, make sure the nginx user belongs to it, and ensure all of Galaxy's data files are group readable.

If the permissions are not the problem - I'm at a bit of a loss.

-John


On Wed, Mar 1, 2017 at 11:35 AM, pieter coussement <[hidden email]> wrote:

Hi,

I just updated galaxy, and now I seem to be unable to view the contents of the files.

So i'm able to upload, and can work with them and see the attributes.

If however I want to open them ('the eye' on the left), I get an error (as do my collegues)

I checked on the full path and the file is there.

permission on the file:

-rw-r--r--  1 galaxy galaxy        16 mrt  1 12:10 dataset_140.dat


nginx vhost      

        ##
        # Galaxy
        ##

        upstream galaxy_app {
                server 127.0.0.1:8080;
        }

        proxy_next_upstream off;

        server {
                client_max_body_size 10G;
                # ... other server stuff ...
                location / {
                        proxy_pass   http://galaxy_app;
                        proxy_set_header   X-Forwarded-Host $host;
                        proxy_set_header   X-Forwarded-For  $proxy_add_x_forwarded_for;
                }

                location /static {
                        alias /home/galaxy/Software/galaxy/static;
                        expires 24h;

                }

                location /static/style {
                        alias /home/galaxy/Software/galaxy/static/style/blue;
                        expires 24h;
                }

                location /static/scripts {
                        alias /home/galaxy/Software/galaxy/static/scripts;
                }

                location /favicon.ico {
                        alias /home/galaxy/Software/galaxy/static/favicon.ico;
                }

                location /robots.txt {
                        alias /home/galaxy/Software/galaxy/static/robots.txt;
                }

                # serve static content for visualization and interactive environment plugins
                location ~ ^/plugins/(?<plug_type>.+?)/(?<vis_name>.+?)/static/(?<static_file>.*?)$ {
                        alias /home/galaxy/Software/galaxy/config/plugins/$plug_type/$vis_name/static/$static_file;
                }

                location /_x_accel_redirect/ {
                        internal;
                        alias /;
                }

                location ~ \.php$ {
                        fastcgi_pass 127.0.0.1:9000;
                        include /etc/nginx/conf.d/*.conf;
                        include /etc/nginx/sites-enabled/*;

                        fastcgi_intercept_errors        on;
                        error_page 404 /error/404.php;
                }
        }


I would guess a permission error of some kind but I seem unable to find it.

Nginx spits out:

2017/03/01 17:23:39 [error] 28783#0: *1457 open() "/usr/share/nginx/htmltrue/home/galaxy/Software/galaxy/database/files/000/dataset_14
0.dat" failed (2: No such file or directory), client: 172.19.40.126, server: , request: "GET /datasets/32d48e3506ae8cf7/display/?previ
ew=True HTTP/1.1", upstream: "http://127.0.0.1:8080/datasets/32d48e3506ae8cf7/display/?preview=True", host: "172.19.32.42", referrer:
"http://172.19.32.42/"

the file is in home/galaxy/Software/galaxy/database/files/000/dataset_140.dat

but the folder /usr/share/nginx/htmltrue does not exists...


Any help on this one?

Best regards,

Pieter

--

ir. Pieter Coussement, PhD
[hidden email]
<a moz-do-not-send="true" href="tel:+32%20485%2042%2079%2072" value="+32485427972" target="_blank">+32 (0) 485 42 79 72




www.inbiose.com
Registered address: Inbiose N.V., Technologiepark Zwijnaarde 3 – bus 41, B-9052 Gent, Belgium - rpr gent: 0534 887 593

Confidentiality notice: The information contained in this e-mail, including any attachments, is confidential and may be the subject of legal professional privilege. It is intended for the authorized use of the individual or entity addressed. If the receiver or reader of this message is not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is prohibited. If this email is received in error, please accept our apologies, delete all copies from your system, and notify the sender by return e-mail and delete this e-mail, including any attachments. Disclaimer: The author of this e-mail has taken every effort to ensure that the information and advice provided are accurate and up-to-date, based upon the information available at the time of writing. The information and advice can only be binding for Inbiose when this is clearly intended in the message and is contained in the information made available.


___________________________________________________________
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/mailinglists/


--

ir. Pieter Coussement, PhD
[hidden email]
+32 (0) 485 42 79 72




www.inbiose.com
Registered address: Inbiose N.V., Technologiepark Zwijnaarde 3 – bus 41, B-9052 Gent, Belgium - rpr gent: 0534 887 593

Confidentiality notice: The information contained in this e-mail, including any attachments, is confidential and may be the subject of legal professional privilege. It is intended for the authorized use of the individual or entity addressed. If the receiver or reader of this message is not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is prohibited. If this email is received in error, please accept our apologies, delete all copies from your system, and notify the sender by return e-mail and delete this e-mail, including any attachments. Disclaimer: The author of this e-mail has taken every effort to ensure that the information and advice provided are accurate and up-to-date, based upon the information available at the time of writing. The information and advice can only be binding for Inbiose when this is clearly intended in the message and is contained in the information made available.


___________________________________________________________
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/mailinglists/
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