Ok, it is not the same problem we have encountered a few years ago.

I doubt, that it is a system permission issue. All data files belong to galaxy (or the user the galaxy server is running as), and the access is regulated by the PostgreSQL (or MySQL or SQlite) database. I can only imagine the following case: you have restarted the Galaxy server as a different user than before?

To me, it rather looks like something has changed in the apache set-up and I am not an expert on this. I hope some-else can pick up this e-mail thread

Hans-Rudolf

On 09/21/2015 02:05 PM, Zuzanna K. Filutowska wrote:

Dnia 2015-09-21, pon o godzinie 13:55 +0200, Hans-Rudolf Hotz pisze:

...

Hi Zuzanna

This sort of rings a bell...can you give some more details:

• Have you always used external authentication? or do you get this

problem after switching to external authentication?

Yes, I always used external auth.

...

• what do you mean by "new LDAP users"?

Users that newly log on Galaxy today.

...

• Are you sure, you get the "correct information" back from the LDAP

server? Maybe the LDAP server gave you e-mail addresses in all lower cases, and now somebody has changed something , and the LDAP server returns e-mail addresses in camel case?

Yes, old users can log in, and new users also can log in but they can't upload files or histories - they are getting internal server error while uploading and 403 errors while trying to upload history and the error shows "This API requires authentication"

...

• Have a look at Admin -> Manage users Do you have duplications of

users?

No.

...

• Have you looked into the PostgreSQL database and checked the

ownership of the histories in question.

How can I do that?

...

I hope this gives you a few points to look into

I have a hunch that this maybe something in system permissions but I looked throught the galaxy tree and I see galaxy is the owner of all files. I am used mod_xsendfile.

Dnia 2015-09-21, pon o godzinie 15:14 +0200, Hans-Rudolf Hotz pisze:

I have created a new test user, and here is the output, when trying to import and show imported histories (/history/view_multiple) { "agent": "Mozilla/5.0 (X11; Fedora; Linux x86_64; rv:40.0) Gecko/20100101 Firefox/40.0", "url": "http://galaxy.man.poznan.pl/history/view_multipl/api/histories/85b413e771c18...", "data": "", "options": { "data": {}, "silent": true, "parse": true, "emulateHTTP": false, "emulateJSON": false }, "xhr": { "readyState": 4, "responseText": "{"err_msg": "API authentication required for this request", "err_code": 403001}", "responseJSON": { "err_msg": "API authentication required for this request", "err_code": 403001 }, "status": 403, "statusText": "Forbidden", "responseHeaders": { "Date": "Mon, 21 Sep 2015 14:37:59 GMT\r", "Server": "PasteWSGIServer/0.5 Python/2.7.10\r", "X-Frame-Options": "SAMEORIGIN\r", "Content-Type": "text/html; charset=UTF-8\r", "Vary": "Accept-Encoding\r", "Content-Encoding": "gzip\r", "Connection": "close\r", "Transfer-Encoding": "chunked\r" } }, "source": [], "user": { "username": "plgjdoe", "quota_percent": null, "total_disk_usage": 20139875, "nice_total_disk_usage": "19.2 MB", "email": "plgjdoe@galaxy.man.poznan.pl", "is_admin": false, "tags_used": [], "model_class": "User", "id": "3cc0effd29705aa3" } }

Dnia 2015-09-21, pon o godzinie 13:29 -0400, Carl Eberhard pisze:

I'm stumped: * I'm not sure how that url ("http://galaxy.man.poznan.pl/history/view_multipl/api/histories/85b413e771c18...") could have been formed * Calling that link from a local galaxy results in 'No route for' when the error is an api authentication 403 Maybe it's possible that an authentication error is confounding/combining with a client error?

Client is only a user of a browser (I have checked several browsers).

Zuzanna, can you: * tell us what version of Galaxy you're using?

It is newest from git - 15.07.

  * open a javascript console on the history/view_multiple page
    and see what it says 'galaxy_conf.root' equals?

I can't find anything like that (I am using openjdk with firefox built in js console). This is what it shows me: URL żądania: http://galaxy.man.poznan.pl/api/histories/85b413e771c184a9/contents Metoda żądania: GET Kod stanu: HTTP/1.1 403 Forbidden Nagłówki żądania 20:54:21.000 X-Requested-With: XMLHttpRequest User-Agent: Mozilla/5.0 (X11; Fedora; Linux x86_64; rv:40.0) Gecko/20100101 Firefox/40.0 Referer: http://galaxy.man.poznan.pl/history/view_multiple Host: galaxy.man.poznan.pl Connection: keep-alive Authorization: Basic cGxnamRvZTpONG4zazQuMjMyMw== Accept-Language: pl,en-US;q=0.7,en;q=0.3 Accept-Encoding: gzip, deflate Accept: application/json, text/javascript, */*; q=0.01 Nagłówki odpowiedzi Δ27ms X-Frame-Options: SAMEORIGIN Vary: Accept-Encoding Transfer-Encoding: chunked Server: PasteWSGIServer/0.5 Python/2.7.10 Date: Mon, 21 Sep 2015 18:54:21 GMT Content-Type: text/html; charset=UTF-8 Content-Encoding: gzip Connection: close However my galaxy root is /home/galaxy/galaxy-dist (I am using mod_rewrite).

I think this problem has been introduced with galaxy multiprocess setup, but it affects new users therefore we didn't find it before workshop. Old users works fine. I checked my ldap server and those users are in there.

Glad you figured it out! So a page served via https is generating links for http references that should have been https?

On Mon, Sep 21, 2015 at 5:15 PM, Zuzanna K. Filutowska < platyna@man.poznan.pl> wrote:

Dnia 2015-09-21, pon o godzinie 13:29 -0400, Carl Eberhard pisze:

...

I'm stumped: * I'm not sure how that url ("

http://galaxy.man.poznan.pl/history/view_multipl/api/histories/85b413e771c18...") could have been formed

...

  * Calling that link from a local galaxy results in 'No route
    for' when the error is an api authentication 403

Maybe it's possible that an authentication error is confounding/combining with a client error?

Zuzanna, can you: * tell us what version of Galaxy you're using? * open a javascript console on the history/view_multiple page and see what it says 'galaxy_conf.root' equals?

It took me 13 hours to figure it out but it seems that the problem was caused by this: RequestHeader set X-URL-SCHEME https

inside my <Location />.

I have set it according to the docs: https://wiki.galaxyproject.org/Admin/Config/ApacheProxy as I use apache proxy with SSL, but without it the proxy works fine, as well as uploads and history import. Maybe this case is worth mentioning in the docs.

--

Pozdrawiam,

-- Zuzanna K. Filutowska, HPC Systems Administrator Poznan Supercomputing and Networking Center Institute of Bioorganic Chemistry Polish Academy of Sciences Seize the day boys! Make your lifes extraordinary! --John Keating

---

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/

Dnia 2015-09-21, pon o godzinie 13:55 +0200, Hans-Rudolf Hotz pisze:

After turning off mod_xsendfile nothing changed, so I assume it is not at fault.