[base] Help please - upgrade to 1.2.17 and now no user edits or uploads

Wed, 19 Apr 2006 05:37:10 -0700


Hi,
I have just updated BASE to v1.2.17. All seemed to go well and followed instructions as expected, ran the db migrate and quota php scripts fine,  but have found that I now cannot get to edit user accounts, or view uploaded files (from any account including the superuser account).  
If choosing to edit a user's info, all I get is a page with "Edit User" as the title and nothing elsebelow except  the return link.
Similarly if i access uploads - then for both my own and others uploaded files I get a title only for the page/frame)
Also - If I try to add a new raw data file from one already available (ie from adding  "new" raw data sets) I get a blank page on  clicking continue.
it is not a DB access  problem generally  as other things work, such as logging on, news, viewing users and groups lists, samples, etc etc

in terms of logs, A few things have shown up:
in the base logs folder I got a file called debug.unknownSearchField.000 which is geiven at the end
which contained the following (I've removed the addresses and substituted XXX etc)

Other errors in the httpd error log included: (one copy of each presented here)

[error] PHP Fatal error:  Call to undefined function:  setfilename() in /Library/WebServer/Documents/base/hyb_result.phtml on line 124
 [error] PHP Fatal error:  Call to undefined function:  getfilequota() in /Library/WebServer/Documents/base/upload_list.phtml on line 63

[error] MySQL query failed: "INSERT INTO Upload (`name`,`descr`,`addedDate`,`owner`,`removed`,`fileSize`,`mimeType`,`gid`,`groupAccess`,`worldAccess`) VALUES ('_084382R1_S01_A01.gpr', '', '2006-04-13 16:32:22', '19', '3', '3829012', 'text/plain', '0', '0', '0')" : Duplicate entry '19-_084382R1_S01_A01.gpr' for key 2 

[error] PHP Warning:  Missing argument 4 for transformationshow() in /usr/local/base/include/web/experiment_common.inc.php on line 656
[error] PHP Warning:  Missing argument 5 for transformationshow() in /usr/local/base/include/web/experiment_common.inc.php on line 656
[error] PHP Notice:  Undefined variable:  editable in /usr/local/base/include/web/experiment_common.inc.php on line 720
[error] PHP Notice:  Undefined variable:  channels in /usr/local/base/include/web/experiment_common.inc.php on line 780
[error] PHP Notice:  Undefined variable:  channels in /usr/local/base/include/web/experiment_common.inc.php on line 784
[error] PHP Fatal error:  Call to undefined function:  setfilename() in /Library/WebServer/Documents/base/hyb_result.phtml on line 124
[error] PHP Fatal error:  Call to undefined function:  getfilequota() in /Library/WebServer/Documents/base/upload_list.phtml on line 63
[error] Undefined search field type 'minint1_2' in search 1980. logged to /Volumes/RAID3/base-data/logs/debug.unknownSearchField.000

the missing arguments for lines 656 and 720 are $editable and $channels - I guess these should be something else? $edit and ?
Likewise is setFilename() supposed to be something else?

Error logged at 2006-04-19 11:32:17

_SERVER: array (
  'CONTENT_LENGTH' => '71',
  'CONTENT_TYPE' => 'application/x-www-form-urlencoded',
  'DOCUMENT_ROOT' => '/Library/WebServer/Documents',
  'HTTP_ACCEPT' => 'text/xml,application/xml,application/xhtml+xml,text/html;q=0.9,text/plain;q=0.8,image/png,*/*;q=0.5',
  'HTTP_ACCEPT_CHARSET' => 'ISO-8859-1,utf-8;q=0.7,*;q=0.7',
  'HTTP_ACCEPT_ENCODING' => 'gzip,deflate',
  'HTTP_ACCEPT_LANGUAGE' => 'en-gb,en;q=0.5',
  'HTTP_CACHE_CONTROL' => 'max-age=259200',
  'HTTP_CONNECTION' => 'keep-alive',
  'HTTP_COOKIE' => 'session=20afcd867317dd3e6639f766397e5561',
  'HTTP_HOST' => 'xxxxx.xxxxx.xxx.xx',
  'HTTP_KEEP_ALIVE' => '300',
  'HTTP_USER_AGENT' => 'Mozilla/5.0 (Windows; U; Windows NT 5.1; en-GB; rv:1.7.12) Gecko/20050919 Firefox/1.0.7',
  'HTTP_VIA' => '1.0 xxxxx.xxxxx.xxx.xx:3128 (squid/2.5.STABLE3)',
  'HTTP_X_FORWARDED_FOR' => 'xxxxx.xxxxx.xxx.xx',
  'PATH' => '/bin:/sbin:/usr/bin:/usr/sbin:/usr/libexec:/System/Library/CoreServices',
  'REMOTE_ADDR' => 'xxxxx.xxxxx.xxx.xx',
  'REMOTE_PORT' => '39525',
  'SCRIPT_FILENAME' => '/Library/WebServer/Documents/base/experiment_edit.phtml',
  'SCRIPT_URI' => 'xxxxx.xxxxx.xxx.xx/base/experiment_edit.phtml',
  'SCRIPT_URL' => '/base/experiment_edit.phtml',
  'SERVER_ADDR' => '128.243.149.39',
  'SERVER_ADMIN' => '[EMAIL PROTECTED]',
  'SERVER_NAME' => 'xxxxx.xxxxx.xxx.xx',
  'SERVER_PORT' => '80',
  'SERVER_SIGNATURE' => '<ADDRESS>Apache/1.3.33 Server at xxxxx.xxxxx.xxx.xx Port 80</ADDRESS>
',
  'SERVER_SOFTWARE' => 'Apache/1.3.33 (Darwin) PHP/4.3.10 mod_perl/1.26',
  'GATEWAY_INTERFACE' => 'CGI/1.1',
  'SERVER_PROTOCOL' => 'HTTP/1.0',
  'REQUEST_METHOD' => 'POST',
  'QUERY_STRING' => 'i_e=16',
  'REQUEST_URI' => '/base/experiment_edit.phtml?i_e=16',
  'SCRIPT_NAME' => '/base/experiment_edit.phtml',
  'PATH_TRANSLATED' => '/Library/WebServer/Documents/base/experiment_edit.phtml',
  'PHP_SELF' => '/base/experiment_edit.phtml',
  'argv' =>
  array (
    0 => 'i_e=16',
  ),
  'argc' => 1,
)

_REQUEST: array (
  'i_e' => '16',
  'location' => 'experiment_list.phtml',
  'i_tran' => '487',
  'i_setedit' => '0',
  'i_page1' => '',
  'i_sort1' => '',
  'session' => '20afcd867317dd3e6639f766397e5561',
)

INFO: class searchcriterion {
  var $search = 1980;
  var $position = 1;
  var $field = 'minint1_2';
  var $op = 0;
  var $searchString = '50';
  var $translated = '';
  var $viewable = NULL;
  var $fieldType = false;
}



"An expert is a person who has made all the mistakes that can be made in a very narrow field". Niels Bohr Danish physicist (1885 - 1962)

__
Dr Paddy Tighe
Associate Professor in Molecular Biology
Division of Immunology 
and 
Institute of Infection, immunity and Inflammation
University Hospital
Nottingham NG7 2UH
Tel: (44) 115 82 30734
Fax (44) 115 82 30759

Group website: http://immune2.nottingham.ac.uk/immunology/research/immunomo.htm
Genomics Facility website: http://genomics.nottingham.ac.uk


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