TPP 7.0 login screen appears for http://localhost:10401/tpp/cgi-bin/tpp_gui.pl but goes then goes "This site can’t be reached" to

[Robert Willows]

I just finished building and installing TPP 7.0 under Ubuntu. All appears well until I go to http://localhost:10401/tpp/cgi-bin/tpp_gui.pl

The login appears:  

ISB/SPC Trans Proteomic Pipeline ::

.....

 TPP v7.0.0 Arafel, Build 202404151216-exported (Linux-x86_64)

But after entering guest as username and password the pages goes to:

http://tpp/cgi-bin/tpp_gui.pl

and 

This site can’t be reached

Check if there is a typo in tpp.

DNS_PROBE_FINISHED_NXDOMAIN

Apache error logs are empty and access log is:
127.0.1.1:80 ::1 - - [15/Apr/2024:17:47:01 +1000] "GET /tpp/cgi-bin/tpp_gui.pl HTTP/1.1" 200 1076 "-" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/123.0.0.0 Safari/537.36"
127.0.1.1:80 ::1 - - [15/Apr/2024:17:47:53 +1000] "-" 408 0 "-" "-"

Any help or incites as I feel I've exhausted possibilities.

 TPP v7.0.0 Arafel, Build 202404151216-exported (Linux-x86_64)

[David Shteynberg]

Hi Robert,

Thanks for trying to install and use TPP on Ubuntu.  It seems the webserver is somewhat misconfigured for tpp on your system.  Can you share the site.mk file that you are using for this build as this file allows to control the PATHs and URLS used by TPP?

Thanks!

-David

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[David Shteynberg]

To further troubleshoot you can try running the environment checker on the tpp server using the following url on your machine:

http://localhost:10401/tpp/cgi-bin/check_env.pl

This should give you an idea how the tpp environment is configured from the web server’s perspective and perhaps help identify any missing environment variables, specifically HTTP_HOST should be set to "localhost" based on the installation you described.  

To print the tpp_hostname (HTTP_HOST) that is configured in your tpp installation you can run the command "tpp_hostname" on the commandline.

Good luck!

-David

[Robert Willows]

Hi David,

The site.mk file is:

INSTALL_DIR = /usr/local/tpp
TPP_DATADIR = /data
TPP_BASEURL = /tpp
TPP_DATAURL = /tpp/data
TPP_PORT = 10401

The output from http://localhost:10401/tpp/cgi-bin/check_env.pl is

HTTP_ACCEPT = text/html,application/xhtml+xml,application/xml;q=0.9,image/avif,image/webp,image/apng,*/*;q=0.8,application/signed-exchange;v=b3;q=0.7
HTTP_SEC_CH_UA_PLATFORM = "Linux"
REQUEST_URI = /tpp/cgi-bin/check_env.pl
HTTP_SEC_FETCH_MODE = navigate
PATH = /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin
SCRIPT_FILENAME = /usr/local/tpp/cgi-bin/check_env.pl
SERVER_SOFTWARE = Apache/2.4.52 (Ubuntu)
WEBSERVER_ROOT = /usr/local/tpp
SERVER_NAME = localhost
CONTEXT_PREFIX = //tpp/cgi-bin
REMOTE_ADDR = ::1
SCRIPT_URI = http://localhost:10401/tpp/cgi-bin/check_env.pl
TPP_DATADIR = /data
HTTP_CONNECTION = keep-alive
HTTP_SEC_CH_UA = "Google Chrome";v="123", "Not:A-Brand";v="8", "Chromium";v="123"
HTTP_SEC_FETCH_USER = ?1
REQUEST_METHOD = GET
SCRIPT_NAME = /tpp/cgi-bin/check_env.pl
SEQ2MS_SOURCE_URL = _SEQ2MS_SOURCE_URL_
SCRIPT_URL = /tpp/cgi-bin/check_env.pl
HTTP_ACCEPT_ENCODING = gzip, deflate, br, zstd
SERVER_SIGNATURE =Apache/2.4.52 (Ubuntu) Server at localhost Port 10401
HTTP_USER_AGENT = Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/123.0.0.0 Safari/537.36
REMOTE_PORT = 49404
TPP_BASEURL = //tpp
TPP_DATAURL = //tpp/data
USERPROFILE = /usr/local/tpp
GATEWAY_INTERFACE = CGI/1.1
HTTP_HOST = localhost:10401
CONTEXT_DOCUMENT_ROOT = /usr/local/tpp/cgi-bin
HTTP_ACCEPT_LANGUAGE = en-GB,en-US;q=0.9,en;q=0.8
PERL5LIB = /usr/local/tpp/lib/perl
DOCUMENT_ROOT = /var/www/html
REQUEST_SCHEME = http
SEQ2MS_DEFAULT_MODEL = _SEQ2MS_DEFAULT_MODEL_
QUERY_STRING =
SERVER_ADMIN = [no address given]
HTTP_SEC_FETCH_SITE = none
WEBSERVER_TMP = /tmp
SERVER_PROTOCOL = HTTP/1.1
HTTP_UPGRADE_INSECURE_REQUESTS = 1
HTTP_SEC_FETCH_DEST = document
SERVER_PORT = 10401
SERVER_ADDR = ::1
SSRCALC = /usr/local/tpp/conf
HTTP_SEC_CH_UA_MOBILE = ?0
TPP_HOME = /usr/local/tpp

[David Shteynberg]

Hi Robert,

I think I see the problem.  TPP_BASEURL and TPP_DATAURL should be relative, no start with '/',  try changing your site.mk to :

INSTALL_DIR = /usr/local/tpp
TPP_DATADIR = /data

TPP_BASEURL = tpp
TPP_DATAURL = tpp/data
TPP_PORT = 10401

Then you will need to make all and make install from scratch.  The easiest way is to rename the previous build directory.

Cheers!

-David

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[Robert Willows]

Hi David,

I've changed the site.mk and recompiled. 

Deleted the old install in the /usr/local/tpp directory and reinstalled withy make install. 

Restarted everything but still have the same issue.

Still goes to http://tpp/cgi-bin/tpp_gui.pl after entering guest username and password.

I've tried some of the other cgi-bin programs in place of tpp_gui.pl http://localhost:10401/tpp/cgi-bin/XXXXX and they all run and give somewhat of the expected output given no files,  except for http://localhost:10401/tpp/cgi-bin/tpp_gui_config.pl

Internal Server Error

The server encountered an internal error or misconfiguration and was unable to complete your request.

Please contact the server administrator at [no address given] to inform them of the time this error occurred, and the actions you performed just before this error.

More information about this error may be available in the server error log.

[Tue Apr 16 13:08:10.934308 2024] [cgid:error] [pid 841488:tid 140546230744960] (8)Exec format error: AH01241: exec of '/usr/local/tpp/cgi-bin/tpp_gui_config.pl' failed

[Tue Apr 16 13:08:10.934745 2024] [cgid:error] [pid 841395:tid 140546200757824] [client ::1:38680] End of script output before headers: tpp_gui_config.pl

[Robert Willows]

one more piece of puzzle.
The httpd-tpp.conf has:

    ## Set the TPP's environment variables
    SetEnv TPP_HOME    /usr/local/tpp
    SetEnv TPP_DATADIR /data
    SetEnv SEQ2MS_SOURCE_URL _SEQ2MS_SOURCE_URL_
    SetEnv SEQ2MS_DEFAULT_MODEL _SEQ2MS_DEFAULT_MODEL_
    SetEnv TPP_BASEURL /tpp
    SetEnv TPP_DATAURL /tpp/data

When I change the TPP_BASEURL and TPP_DATAURL  to the same as in the site.mk file

    SetEnv TPP_BASEURL tpp
    SetEnv TPP_DATAURL tpp/data

The login screen then goes to:

http://localhost:10401/tpp/cgi-bin/tpp/cgi-bin/tpp_gui.pl

Site not found. 

So it is adding an additional tpp/cgi-bin/ to the path after login as guest.

Is this a webserver config issue or a tpp issue?

[David Shteynberg]

Can you seen if you can access the server at:

 127.0.0.1:10401/tpp 

or

 127.0.0.1:10401/tpp/cgi-bin/tpp_gui.pl

Thanks!

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[David Shteynberg]

This seems to be a configuration issue but I am not sure where, likely in the server.  It appears you are running apache 2.4.x (same as I, on my phone ubuntu emulator ;) which is in configured by http-2.4-tpp.conf. This file should be first configured by site.mk at make install.  You should not have to modify this file, perhaps only for testing.  Is the css stylesheet loading for you on the login screen?  Can you provide a screenshot?  Are you serving any other sites from this server?

Thanks!

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[Robert Willows]

Hi David,

The style sheet isn’t loading. Just a very basic login screen missing the usual TPP style. 

The same when running the other cgi’s from the browser/s.

No not serving any other sites from this server.

Regards

Robert

On 17 Apr 2024, at 12:53 AM, 'David Shteynberg' via spctools-discuss <spctools...@googlegroups.com> wrote:



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[David Shteynberg]

Hi Robert,

The fact that the css is not loading is an strong indication that the apache configuration is not correct.

I just built a 7.0.0 TPP instance on a fresh ubuntu 22.04.4 "jammy" node in the Azure "cloud", using instructions here: 

http://tools.proteomecenter.org/wiki/index.php?title=TPP_7.0.0:_Installing_on_Ubuntu_22.04_LTS#Configuring_the_Apache_web_server

It seems to load as expected.  Sorry, but I am not sure why your specific instance is becoming misconfigured.  Perhaps you can launch another node in the cloud, try setting it up there and if you run into trouble I can log in and help troubleshoot?

Cheers,

-David

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[Robert Willows]

Hi David,

I have solved the issue. A typo in the https-tpp.config file. 

Require ip had the wrong number. I’d typed the ip address number incorrectly. Everything loading and running now with proper style sheet.

Thanks for the help in tracking this down.

Regards

Robert

On 17 Apr 2024, at 7:59 AM, 'David Shteynberg' via spctools-discuss <spctools...@googlegroups.com> wrote:



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[David Shteynberg]

Sounds great!  Let us know should you require further help answering TPP related questions.

To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/AE4DAED6-A080-45EF-8ACD-A71BB6523F37%40gmail.com.