NITRC NIDB - Neuroinformatics Database Forum: help

RE: install glitch

Greg Book — Thu, 01 Nov 2012 20:22:10 GMT

You'll need to edit the /nidb/programs/config.pl file to reflect your server's hostname, and the usernames/passwords. Then try running it again.

You may need to delete the lock files in /nidb/programs/lock

RE: install glitch

Jenifer Juranek — Thu, 01 Nov 2012 19:08:15 GMT

Looks like a connect problem with mysql?
as root, I tried restarting mysqld services
# service mysqld restart
but still have same outcome.

[nidb@localhost programs]$ perl parsedicom.pl
Found 0 lock files
Creating /nidb/programs/lock/parsedicom.0.
Mysql connect('database=nidb;host=yourhostname','root',...) failed: Unknown MySQL server host 'yourhostname' (1) at parsedicom.pl line 117

RE: install glitch

Greg Book — Thu, 01 Nov 2012 13:19:06 GMT

Great!
You can turn off the Notice messages by editing the /etc/php.ini file (as root) and finding the line that starts with "error_reporting = " and change it to this:
[code]error_reporting = E_ALL & ~E_DEPRECATED & ~E_NOTICE[/code]
To import data, you can place the dicom files in the /nidb/dicomincoming directory. The files themselves need to be in that directory, they can't be in a sub directory. So, you may need to rename files if you have the same filename in different sub directories for your data.

You'll need to make sure the cron job called "parsedicom.pl" is running. This is a program that runs every minute to check the /nidb/dicomincoming directory for new files to import. If the installer got to that point, it should have created a set of cron jobs under the nidb user.

If you login to Webmin, which is http://localhost:10000 , then to System -> Scheduled cron jobs, you should see a list of cron jobs for the nidb user account. Do you see these? If not, we'll need to set them up manually. If they are there, but are disabled, check off the nidb jobs and click Enable Selected Jobs.

If none of this works, you can run it manually by doing the following (as the nidb user)
[code]cd /nidb/programs
perl parsedicom.pl[/code]
Let me know how that goes.

RE: install glitch

Jenifer Juranek — Wed, 31 Oct 2012 18:34:52 GMT

I just tried your suggestion to restart httpd services...and it worked!
I now see a new splash screen (with an error message about an undefined variable)...what's recommended for testing its handling of dicom data?
CHEERS!
Jenifer

Notice: Undefined variable: totalseries in /var/www/html/index.php on line 61

Notice: Undefined variable: totalsize in /var/www/html/index.php on line 62

[table][tr]
[td]
[size= 20pt]Welcome to [img]http://localhost/images/A.png[/img]ll [/size][size= 20pt][img]http://localhost/images/D.png[/img]ata [img]http://localhost/images/O.png[/img]nline [img]http://localhost/images/2.png[/img]


[b]Available Data:[/b]

0 subjects

0 studies

[table]
[tr]
[th][b]Series[/b][/th]
[th][b]Count[/b][/th]
[th][b]Size[/b][/th]
[/tr]
[tr]
[td]BINARY[/td]
[td]0[/td]
[td]0.0 B[/td]
[/tr]
[tr]
[td]CR[/td]
[td]0[/td]
[td]0.0 B[/td]
[/tr]
[tr]
[td]CT[/td]
[td]0[/td]
[td]0.0 B[/td]
[/tr]
[tr]
[td]EEG[/td]
[td]0[/td]
[td]0.0 B[/td]
[/tr]
[tr]
[td]ET[/td]
[td]0[/td]
[td]0.0 B[/td]
[/tr]
[tr]
[td]MR[/td]
[td]0[/td]
[td]0.0 B[/td]
[/tr]
[tr]
[td]OT[/td]
[td]0[/td]
[td]0.0 B[/td]
[/tr]
[tr]
[td]PPI[/td]
[td]0[/td]
[td]0.0 B[/td]
[/tr]
[tr]
[td]SR[/td]
[td]0[/td]
[td]0.0 B[/td]
[/tr]
[tr]
[td]US[/td]
[td]0[/td]
[td]0.0 B[/td]
[/tr]
[tr]
[td]VIDEO[/td]
[td]0[/td]
[td]0.0 B[/td]
[/tr]
[tr]
[td]XA[/td]
[td]0[/td]
[td]0.0 B[/td]
[/tr]
[tr]
[td]Total[/td]
[td]0[/td]
[td]0.0 B[/td]
[/tr]
[/table]
[/size]

[/td]
[td]
[table]
[tr]
[td]
[b]Most recent studies[/b]

Collected in past 72 hours
[/td]
[/tr]
[tr]
[th]Subject ID[/th]
[th]Study ID[/th]
[th]Study Date[/th]
[th]Modality[/th]
[th]Project[/th]
[/tr]
[/table]
[/td]
[/tr]
[tr]
[td]

[url=http://localhost/stats.php]NIDB statistics[/url][/td][/tr][/table]

RE: install glitch

Greg Book — Wed, 31 Oct 2012 15:32:04 GMT

Hmm, I'm not seeing the reply I posted, so I'll try it again.

I'm stumped about the problem, but if you are willing to try IM, skype, maybe we can solve it faster. Otherwise, I think the best path would be to download the VM or install CentOS 6.3 on your server and follow the installation instructions.

RE: install glitch

Greg Book — Tue, 30 Oct 2012 19:54:46 GMT

I'm still stumped on this one. Maybe we can try one last thing?

> service httpd restart

After that, I'd suggest downloading the VM and running it on either a Windows PC or a Linux box so you can test it out. Or, if you are able to, format the server you are testing on and install CentOS 6.3 with the suggested installation, and then install using the NIDB installer. If you really want to install on Redhat, maybe can try remote access, instant message, or skype and solve this faster?

RE: install glitch

Jenifer Juranek — Mon, 22 Oct 2012 19:55:33 GMT

It looks like 1 row is populated in the users table under nidb.
Do the cell contents look okay?[table][tr][th] [/th][/tr][tr][th] [/th][/tr]

[tr][td]<input id="id_rows_to_delete0_left" class="multi_checkbox" name="rows_to_delete[%60users%60.%60user_id%60+%3D+1]" type="checkbox" value="DELETE FROM `nidb`.`users` WHERE `users`.`user_id` = 1" /><input class="condition_array" type="hidden" value="{" /> [/td][td]
[url=http://localhost/phpMyAdmin/tbl_change.php?db=nidb&table=users&where_clause=%60users%60.%60user_id%60+%3D+1&clause_is_unique=1&sql_query=SELECT+%2A+FROM+%60users%60&goto=sql.php&default_action=update&token=411a64653831f80c7eaba8c2311b91d3][img]http://localhost/phpMyAdmin/themes/dot.gif[/img] Edit[/url]
<input class="where_clause" type="hidden" value="%60users%60.%60user_id%60+%3D+1" />[/td][td]
[url=http://localhost/phpMyAdmin/tbl_change.php?db=nidb&table=users&where_clause=%60users%60.%60user_id%60+%3D+1&clause_is_unique=1&sql_query=SELECT+%2A+FROM+%60users%60&goto=sql.php&default_action=insert&token=411a64653831f80c7eaba8c2311b91d3][img]http://localhost/phpMyAdmin/themes/dot.gif[/img] Copy[/url]
<input class="where_clause" type="hidden" value="%60users%60.%60user_id%60+%3D+1" />[/td][td]
[url=http://localhost/phpMyAdmin/sql.php?db=nidb&table=users&sql_query=DELETE+FROM+%60nidb%60.%60users%60+WHERE+%60users%60.%60user_id%60+%3D+1&message_to_show=The+row+has+been+deleted&goto=sql.php%3Fdb%3Dnidb%26table%3Dusers%26sql_query%3DSELECT%2B%252A%2BFROM%2B%2560users%2560%26message_to_show%3DThe%2Brow%2Bhas%2Bbeen%2Bdeleted%26goto%3Dtbl_structure.php%26token%3D411a64653831f80c7eaba8c2311b91d3&token=411a64653831f80c7eaba8c2311b91d3][img]http://localhost/phpMyAdmin/themes/dot.gif[/img] Delete[/url]
[/td][td]1[/td]
[td]admin[/td]
[td]901924565[/td]
[td]Standard[/td]
[td]Administrator[/td]
[td]admin@nidb.org[/td]
[td]2012-10-10 16:46:02[/td]
[td]0[/td]
[td]1[/td]
[td]1[/td]
[td]0[/td]
[td]2012-10-10 16:46:02[/td][/tr][/table]

RE: install glitch

Greg Book — Mon, 22 Oct 2012 17:31:35 GMT

Interesting...
Ok, so lets try this:

Go to http://localhost/phpMyAdmin. Login with root/password

Go to the database list on the left and click 'nidb'. It will show a list of tables. Find the 'users' table. It should list out the rows in the users table, if not, click 'Browse' at the top of the page. Do any records show up, especially one with a username of 'admin'?

I'm thinking you may have downloaded an old version of the installer that didn't automatically setup the admin user account.

RE: install glitch

Jenifer Juranek — Fri, 19 Oct 2012 18:11:44 GMT

Those are the values I am entering at the Olin login portal when I get the error message.

RE: install glitch

Greg Book — Fri, 19 Oct 2012 18:09:52 GMT

The username for NIDB login should be "admin" and password "password"