<?php
#Copyright 2008 Aaron Day-Williams <hide@address.com>
#
#This file is part of Generic Genetic Studies Database (GGSD).
#
#GGSD is free software: you can redistribute it and/or modify
#it under the terms of the GNU General Public License as published by
#the Free Software Foundation, either version 3 of the License, or
#(at your option) any later version.
#
#GGSD is distributed in the hope that it will be useful,
#but WITHOUT ANY WARRANTY; without even the implied warranty of
#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#GNU General Public License for more details.
#
#You should have received a copy of the GNU General Public License
#along with GGSD. If not, see <http://www.gnu.org/licenses/>.
header('Content-type: text/html');
session_cache_limiter('private');
session_start();
require 'html_lib.inc';
require 'sql_lib.inc';
require 'file_system_lib.inc';
#NAME link_pedigrees_to_pedigree_groups.php
#TYPE PHP
#USES html_lib.inc(??)
# sql_lib.inc(authenticate existsValue insertPedigreePedigreeGroupLink)
#PURPOSE To get pedigree data to insert into a pedigree group in the database
#USAGE link_pedigrees_to_pedigree_groups.php
#PARAMETERS
# authorized user auth_user int optional
# insert_from_file insert_from_file int optional
# pedigree group id ped_group_id int optional
# pedigree table id ped_id list optional
#RETURNS
# nothing
#DATASTRUCTURES No special datastructures
#FUNCTIONAL DESCRIPTION The script will authenticate the user. Then determine
# whether they want to insert from a file or from the web
# site. If from a file, parse the file and insert pedigree pedigre group links.
# If from website, give them a form to fill out and insert the
# values they supply.
#ASSUMPTIONS
#LIMITATIONS
#COMMENTS
#PRELIMINARY DESIGN
# 1 Get Args
# 2 Authenticate User
# 3 Determine Whether they want to upload file
# 4 If from Website give form
# 5 Insert Pedigree Pedigree Group Link from webform
# 6 Get File
# 7 Parse File and Insert
echo "<html>\n";
echo " <head>\n";
if (isset($_POST['end_session'])){echo " <META HTTP-EQUIV=Refresh CONTENT=\"$logout_refresh_time;URL=../right.html\">\n";}
else {echo " <META HTTP-EQUIV=Refresh CONTENT=\"$normal_refresh_time; URL=$_SERVER[SCRIPT_NAME]\">\n";}
echo " <title>Populate Pedigree Groups</title>\n";
echo " </head>\n";
echo "<body bgcolor = \"white\">\n";
echo "<center><h3>Populate Pedigree Groups</h3></center>\n";
echo "<hr>\n";
printHomeNavBar();
echo "<br>\n";
#1 Get Args
$access_type_required = 'administrative';
$DEBUG = '0';
$start_time = date('Y-m-d H:i:s');
$insert_from_file = $_POST['insert_from_file'];
$upload_file = $_POST['upload_file'];
$file_on_server = $_POST['file_name'];
$ped_group_id = $_POST['pedigree_group_id'];
$ped_table_id = $_POST['pedigree_id']; #Value from printPedigreeSelectList
$ped_ids = $_POST['ped_id']; #Value from printPedigreeCheckList
$ped_multiple_pages = $_POST['ped_multiple_pages'];#Binary let knowing if more pedigrees to look at
$function_to_call = $_POST['function_to_call'];
$table_name = $_POST['table_name'];
$field_list = $_POST['field_list'];
$term = $_POST['term'];
$mode = $_POST['mode'];
$order_by = $_POST['order_by'];
$last_record_retrieved = $_POST['last_record_retrieved'];
$ret_val = connect();
if ($ret_val != '1')
{
$date = date('Y-m-d H:i:s');
echo "Error #1: $date<br>\n";
echo "Error in call to connect from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$ret_val<br><br>\n";
echo "Please email the above error using the Comments/Help/Support link \n";
echo "in the left navigation bar.<br>\n";
echo "</body></html>\n";
exit;
}
#2 Authenticate User
if (isset($_POST['end_session']))#if want to end session
{
#if (key_exists('files_on_server',$_SESSION))
# {
# $files_to_delete_array = $_SESSION['files_on_server'];
# $ret_val = deleteFiles($files_to_delete_array);
# if ($ret_val != '1')
# {
# $date = date('Y-m-d H:i:s');
# echo "Error #2: $date<br>\n";
# echo "Error in call to deleteFiles from link_pedigrees_to_pedigree_groups.php<br>\n";
# echo "$ret_val<br><br>\n";
# echo "Please email the above error using Comments/Help/Support link \n";
# echo "in the left navigation bar.<br>\n";
# echo "</body></html>\n";
# session_unset();
# session_destroy();
# $ret_val = disconnect();
# exit;
# }#end error in call to deleteFiles
# }#end if files that need to be deleted
if (is_dir("../data/download_data/$_SESSION[user_name]"))
{
$ret_val = deleteExpiredFiles($_SESSION['user_name']);
if ($ret_val != '1')
{
$date = date('Y-m-d H:i:s');
echo "Error #3: $date<br>\n";
echo "Error in call to deleteExpiredFiles from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$ret_val<br><br>\n";
echo "Please email the above error using Comments/Help/Support link \n";
echo "in the left navigation bar.<br>\n";
echo "</body></html>\n";
session_unset();
session_destroy();
$ret_val = disconnect();
exit;
}#end error in call to deleteExpiredFiles
}#end if user has own directory in download_data directory
session_unset();
session_destroy();
echo "You have successfully logged out of the system.<br>\n";
#echo "To log back in click on any of the links on the left navigation bar.<br>\n";
$ret_val = disconnect();
exit;
}#end if want to end session
else#don't want to end session
{
if ((!session_is_registered('user_name')) and (!session_is_registered('user_passwd')))
{
if ((!preg_match('/\w+/',$_POST['user_name'])) and (!preg_match('/\w+/',$_POST['user_passwd'])))
{
$ret_val = printLoginPage('link_pedigrees_to_pedigree_groups.php');
if ($ret_val != '1')
{
$date = date('Y-m-d H:i:s');
echo "Error #4: $date<br>\n";
echo "Error in call to printLoginPage from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$ret_val<br><br>\n";
echo "Please email the above error using Comments/Help/Support link \n";
echo "in the left navigation bar.<br>\n";
echo "</body></html>\n";
session_unset();
session_destroy();
$ret_val = disconnect();
exit;
}#end if error in call to printLoginPage
}#end if haven't started a session yet
else #have started a session
{
$auth_user = authenticate($_POST['user_name'],$_POST['user_passwd'],$_POST['rand'],$access_type_required,$_POST['database_id']);
if (($auth_user != '1') and ($auth_user != '0'))
{
$date = date('Y-m-d H:i:s');
echo "Error #5: $date<br>\n";
echo "Error in call to authenticate from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$auth_user<br>\n";
echo "Please email the above error using Comments/Help/Support link \n";
echo "in the left navigation bar.<br>\n";
echo "</body></html>\n";
session_unset();
session_destroy();
$ret_val = disconnect();
exit;
}
if ($auth_user == '0')
{
echo "You are not an authorized user of this website!!<br><br>\n";
echo "You must be an authorized user to access the data contained in this site.\n";
echo "If you feel like you should be an authorized user, or want to see if you can\n";
echo "become an authorized user please contact $contact_person at \n";
echo "<a href=\"mailto:$contact_email\">$contact_email</a>\n";
echo "</body></html>\n";
session_unset();
session_destroy();
$ret_val = disconnect();
exit;
}
if ($auth_user == '1')
{
$_SESSION['user_name'] = $_POST['user_name'];
$_SESSION['user_passwd'] = $_POST['user_passwd'];
$_SESSION['database_id'] = $_POST['database_id'];
$_SESSION['rand'] = $_POST['rand'];
$_SESSION['entry_time'] = time();
session_write_close();
}
}#end else have user name an passwd
}#end if session variables not registered
else #session variable are registered
{
if ((time() - $_SESSION['entry_time']) > $session_expiration_time)#if session has expired
{
#if (key_exists('files_on_server',$_SESSION))
# {
# $files_to_delete_array = $_SESSION['files_on_server'];
# $ret_val = deleteFiles($files_to_delete_array);
# if ($ret_val != 1)
# {
# $date = date('Y-m-d H:i:s');
# echo "Error #6: $date<br>\n";
# echo "Error in call to deleteFiles from link_pedigrees_to_pedigree_groups.php<br>\n";
# echo "$ret_val<br><br>\n";
# echo "Please email the above error using Comments/Help/Support link \n";
# echo "in the left navigation bar.<br>\n";
# session_unset();
# session_destroy();
# $ret_val = disconnect();
# exit;
# }#end if error in call to deleteFiles
# }#end if files that need to be deleted
if (is_dir("../data/download_data/$_SESSION[user_name]"))
{
$ret_val = deleteExpiredFiles($_SESSION['user_name']);
if ($ret_val != 1)
{
$date = date('Y-m-d H:i:s');
echo "Error #7: $date<br>\n";
echo "Error in call to deleteExpiredFiles from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$ret_val<br><br>\n";
echo "Please email the above error using Comments/Help/Support link \n";
echo "in the left navigation bar.<br>\n";
session_unset();
session_destroy();
$ret_val = disconnect();
exit;
}#end if error in call to deleteExpiredFiles
}#end if user has a data directory
session_unset();
session_destroy();
echo "<b>Your Session has expired. You must log back into the system.</b><br><br><br>\n";
$ret_val = printLoginPage('link_pedigrees_to_pedigree_groups.php');
if ($ret_val != '1')
{
$date = date('Y-m-d H:i:s');
echo "Error #8: $date<br>\n";
echo "Error in call to printLoginPage from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$ret_val<br><br>\n";
echo "Please email the above error using Comments/Help/Support link \n";
echo "in the left navigation bar.<br>\n";
echo "</body></html>\n";
session_unset();
session_destroy();
$ret_val = disconnect();
exit;
}#end if error in call to printLoginPage
}#end if session has expired
else #session hasn't expired
{
if ((!session_is_registered('database_id')) and (!isset($_POST['database_id'])))
{
$ret_val = printDatabaseSelectPage('link_pedigrees_to_pedigree_groups.php');
if ($ret_val != '1')
{
$date = date('Y-m-d H:i:s');
echo "Error #9: $date<br>\n";
echo "Error in call to printDatabaseSelectPage from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$ret_val<br><br>\n";
echo "Please email the above error using Comments/Help/Support link \n";
echo "in the left navigation bar.<br>\n";
echo "</body></html>\n";
session_unset();
session_destroy();
$ret_val = disconnect();
exit;
}#end if error in call to printDatabaseSelectPage
}#end if the database id session variable isn't set and haven't selected
else #all the session variables are set
{
$user_name = $_SESSION['user_name'];
$user_passwd = $_SESSION['user_passwd'];
if (session_is_registered('database_id')){$database_id = $_SESSION['database_id'];}
else #set database id session variable
{
$database_id = $_POST['database_id'];
$_SESSION['database_id'] = $_POST['database_id'];
}#end else set database id session variable
$rand = $_SESSION['rand'];
$_SESSION['entry_time'] = time();
$auth_user = authenticate($user_name,$user_passwd,$rand,$access_type_required,$database_id);
if (($auth_user != '1') and ($auth_user != '0'))
{
$date = date('Y-m-d H:i:s');
echo "Error #10: $date<br>\n";
echo "Error in call to authenticate from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$auth_user<br>\n";
echo "Please email the above error using Comments/Help/Support link \n";
echo "in the left navigation bar.<br>\n";
echo "</body></html>\n";
session_unset();
session_destroy();
$ret_val = disconnect();
exit;
}
if ($auth_user == '0')
{
echo "You are not an authorized user of this website!!<br><br>\n";
echo "You must be an authorized user to access the data contained in this site.\n";
echo "If you feel like you should be an authorized user, or want to see if you can\n";
echo "become an authorized user please contact $contact_person \n";
echo "at <a href=\"mailto:$contact_email\">$contact_email</a>\n";
echo "</body></html>\n";
session_unset();
session_destroy();
$ret_val = disconnect();
exit;
}
}#end else all the session variables are set
}#end else session hasn't expired
}#end else registered values
}#end else not ending session
if ($auth_user == '1')
{
$database_id = $_SESSION['database_id'];
#3 Determine Whether Insert from File or Web
if (!preg_match('/\d+/',$insert_from_file))
{
echo "<form action=\"link_pedigrees_to_pedigree_groups.php\" name=\"form\" method=\"POST\" target=\"main\">\n";
echo "This form allows you to populate Pedigree Groups with Pedigrees that are in the database. There are two options \n";
echo "for the way to do this. If you have multiple pedigrees to link, you can store their \n";
echo "information in a comma-separated file and upload that file to the site. Or if you only have \n";
echo "one or two pedigrees to link, you can use a web form to insert their data. Please choose the method \n";
echo "you would like to choose below.<br><br>\n";
echo "<table>\n";
echo "<tr><td><input type=\"radio\" name=\"insert_from_file\" value=\"0\"></td><td>Populate Pedigree Group with a Single Pedigree</td></tr>\n";
echo "<tr><td><input type=\"radio\" name=\"insert_from_file\" value=\"1\"></td><td>Populate Pedigree Group with Several Pedigrees</td></tr>\n";
echo "<tr><td><input type=\"radio\" name=\"insert_from_file\" value=\"2\" checked</td><td>Populate Pedigree Group from a File</td></tr>\n";
echo "</table>\n";
echo "<br>\n";
echo "<center>\n";
echo "<input type=\"submit\" name=\"submit\" value=\"Populate Pedigree Group\">\n";
echo "<input type=\"reset\" name=\"reset\" value=\"Reset Selection\">\n";
echo "</center>\n";
echo "</form>\n";
echo "<br><br>\n";
$ret_val = printLogOutButton('link_pedigrees_to_pedigree_groups.php');
}#end if (!preg_match('/\d+/',insert_from_file))
#4 If Insert from Web form
if (($insert_from_file == '0') and
(!preg_match('/^\d+$/',$ped_group_id)) and
(!preg_match('/^\d+$/',$ped_table_id))
)
{
echo "<form action=\"link_pedigrees_to_pedigree_groups.php\" name=\"form\" method=\"POST\" target=\"main\" onSubmit=\"return(Validate(this))\">\n";
echo "Please select the Pedigree Group to populate and the Pedigree to populate it with, then press the submit button. The \n";
echo "information will then be entered into the database.<br><br>\n";
echo "<table>\n";
echo "<tr><td>Pedigree Group:</td><td>\n";
$jscript_1 = printPedigreeGroupSelectList($database_id);
if ($jscript_1 == '0')
{
$date = date('Y-m-d H:i:s');
echo "Error #11: $date<br>\n";
echo "Error in call to printPedigreeGroupSelectList from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "See the error message from printPedigreeGroupSelectList above for an explanation.<br><br>\n";
echo "Please email the above error message using the Comments/Help/Support link on \n";
echo "the left navigation bar\n";
echo "</form>\n";
echo "</body></html>\n";
$ret_val = disconnect();
exit;
}#end error in call to printPedigreeGroupSelectList
if ($jscript_1 == 'no_defined_pedigree_groups')
{
$date = date('Y-m-d H:i:s');
echo "This message was generated at $date.\n";
$ret_val = disconnect();
exit;
}
echo "</td></tr>\n";
echo "<tr><td> </td></tr>\n";
echo "<tr><td>Pedigree ID:</td><td>\n";
$jscript_2 = printPedigreeSelectList($database_id);
if ($jscript_2 == '0')
{
$date = date('Y-m-d H:i:s');
echo "Error #12: $date<br>\n";
echo "Error in call to printPedigreeSelectList from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "See the error message from printPedigreeSelectList above for an explanation.<br><br>\n";
echo "Please email the above error message using the Comments/Help/Support link on \n";
echo "the left navigation bar\n";
echo "</form>\n";
echo "</body></html>\n";
$ret_val = disconnect();
exit;
}#end error in call to printPedigreeSelectList
if ($jscript_2 == 'no_defined_pedigrees')
{
$date = date('Y-m-d H:i:s');
echo "This message was generated at $date.\n";
$ret_val = disconnect();
exit;
}
echo "</td></tr>\n";
echo "</table>\n";
echo "<br><br>\n";
echo "<input type=\"hidden\" name=\"insert_from_file\" value=\"0\">\n";
echo "<center>\n";
echo "<input type=\"submit\" name=\"submit\" value=\"Insert Pedigree into Pedigree Group\">\n";
echo "<input type=\"reset\" name=\"reset\" value=\"Reset Values\">\n";
echo "</form>\n";
echo "</center>\n";
echo "<br><br>\n";
$ret_val = printLogOutButton('link_pedigrees_to_pedigree_groups.php');
echo "\n\n";
$jscript_1 = preg_replace('/ else \{return true;\}\n\}/','',$jscript_1);
$jscript_2 = preg_replace('/^\{\n/','',$jscript_2);
$jscript_2 = preg_replace('/ else \{return true;\}\n\}/','',$jscript_2);
$jscript = "$jscript_1\n$jscript_2\n return true;\n}";
echo "<script>\n";
echo "function Validate(form)\n";
echo "$jscript\n";
echo "</script>\n";
}#end if from web but no values
#If Select Multiple Pedigrees, but no pedigree group or pedigrees
if (($insert_from_file == '1') and
(!preg_match('/^\d+$/',$ped_group_id)) and
(!preg_match('/^\d$/',$ped_multiple_pages)) and
(sizeof($indv_ids) == '0')
)
{
$field_list = array('pedigree_table_id');
$num_peds = countTableQuery('pedigree_table',$database_id,$field_list,'_','wildcard');
if (!preg_match('/^\d+$/',$num_peds))
{
$date = date('Y-m-d H:i:s');
echo "Error #13: $date<br>\n";
echo "Error in call to countTableQuery from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$num_peds<br><br>\n";
echo "Please email the above error using the Comments/Help/Support link \n";
echo "on the left navigation bar.\n";
echo "</body></html>\n";
$ret_val = disconnect();
exit;
}#end if error in call to countTableQuery
if ($num_peds == '0')
{
$date = date('Y-m-d H:i:s');
echo "Currently there are no Pedigrees in the database, so you cannot populate an Pedigree Group.<br>\n";
echo "This message was generated at $date.<br><br>\n";
printLogOutButton('link_pedigrees_to_pedigree_groups.php');
$ret_val = disconnect();
exit;
}
if ($num_peds > $max_records_to_print_per_page)
{
$indiv_multiple_pages = 1;
$from = 0;
$to = $max_records_to_print_per_page - 1;
$range = "$from"."-"."$to";
if ($db_type == 'mysql'){$order_by = 'pedigree_id+0';}
if ($db_type == 'pgsql'){$order_by = 'pedigree_id::text::integer';}
$ped_rec_list = tableQuery('pedigree_table',$database_id,$field_list,'_','wildcard',$range,$order_by);
if (!is_array($ped_rec_list))
{
$date = date('Y-m-d H:i:s');
echo "Error #14: $date<br>\n";
echo "Error in call to tableQuery from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$ped_rec_list<br><br>\n";
echo "Please email the above error using the Comments/Help/Support link \n";
echo "on the left navigation bar.\n";
echo "</body></html>\n";
$ret_val = disconnect();
exit;
}#end if error in call to tableQuery
$final_function_call = 'tableQuery';
$final_table_name = 'pedigree_table';
$final_field_list = $field_list;
$final_term = '_';
$final_mode = 'wildcard';
$final_order_by = $order_by;
$last_record_retrieved = $max_records_to_print_per_page;
}#end if multiple pages
else #only a single page of pedigrees
{
$ped_multiple_pages = 0;
$range = "all";
if ($db_type == 'mysql'){$order_by = 'pedigree_id+0';}
if ($db_type == 'pgsql'){$order_by = 'pedigree_id::text::integer';}
$ped_rec_list = tableQuery('pedigree_table',$database_id,$field_list,'_','wildcard',$range,$order_by);
if (!is_array($ped_rec_list))
{
$date = date('Y-m-d H:i:s');
echo "Error #15: $date<br>\n";
echo "Error in call to tableQuery from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$ped_rec_list<br><br>\n";
echo "Please email the above error using the Comments/Help/Support link \n";
echo "on the left navigation bar.\n";
echo "</body></html>\n";
$ret_val = disconnect();
exit;
}#end if error in call to tableQuery
}#end else only a single page of pedigrees
echo "Select the Pedigree Group you want to insert Pedigrees into, and the Pedigrees to insert.<br><br>\n";
$ret_val = printLogOutButton('link_pedigrees_to_pedigree_groups.php');
echo "<br><br>\n";
if ($ped_multiple_pages == '1')
{
echo "<table align=\"center\">\n";
echo "<form action=\"link_pedigrees_to_pedigree_groups.php\" name=\"skip_form1\" method=\"POST\" target=\"main\" onSubmit=\"return(Validate(form))\">\n";
echo "<input type=\"hidden\" name=\"insert_from_file\" value=\"$insert_from_file\">\n";
echo "<input type=\"hidden\" name=\"pedigree_group_id\" value=\"\">\n";
echo "<input type=\"hidden\" name=\"ped_id\" value=\"\">\n";
echo "<input type=\"hidden\" name=\"ped_mulitple_pages\" value=\"0\">\n";
echo "<tr>\n";
echo "<td><input type=\"submit\" name=\"submit\" value=\"Insert Selected Pedigree(s)\" onClick=\"copyData('skip_form1')\"></td>\n";
echo "</form>\n";
echo "<form action=\"link_pedigrees_to_pedigree_groups.php\" name=\"form\" method=\"POST\" target=\"main\">\n";
$records_left = $num_peds - $max_records_to_print_per_page;
if ($records_left > $max_records_to_print_per_page)
{echo "<td><input type=\"submit\" name=\"submit\" value=\"Get Next $max_records_to_print_per_page Pedigrees\"></td>\n";}
else
{echo "<td><input type=\"submit\" name=\"submit\" value=\"Get Next $records_left Pedigrees\"></td>\n";}
echo "</tr>\n";
echo "</table>\n";
echo "<br>\n";
echo "<table align=\"center\">\n";
echo "<tr>\n";
echo "<td> </td>\n";
echo "<td><input type=\"reset\" name=\"reset\" value=\"Reset Selected Pedigree(s)\"></td>\n";
echo "</tr>\n";
echo "</table>\n";
}#end if multiple pages of pedigrees
else #only a single page of pedigrees
{
echo "<form action=\"link_pedigrees_to_pedigree_groups.php\" name=\"form\" method=\"POST\" target=\"main\" onSubmit=\"return(Validate(form))\">\n";
echo "<table align=\"center\">\n";
echo "<tr>\n";
echo "<td><input type=\"submit\" name=\"submit\" value=\"Insert Selected Pedigree(s)\"></td>\n";
echo "<td><input type=\"reset\" name=\"reset\" value=\"Reset Selected Pedigree(s)\"></td>\n";
echo "</tr>\n";
echo "</table>\n";
}#end else only a single page of pedigrees
echo "<br><br>\n";
echo "<table align=\"center\">\n";
echo "<tr><td><b>Pedigree Group:</td><td>\n";
$jscript_1 = printPedigreeGroupSelectList($database_id);
if ($jscript_1 == '0')
{
$date = date('Y-m-d H:i:s');
echo "Error #16: $date<br>\n";
echo "Error in call to printPedigreeGroupSelectList from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "See the error message from printPedigreeGroupSelectList above for an explanation.<br><br>\n";
echo "Please email the above error message using the Comments/Help/Support link on \n";
echo "the left navigation bar\n";
echo "</form>\n";
echo "</body></html>\n";
$ret_val = disconnect();
exit;
}#end error in call to printPedigreeGroupSelectList
if ($jscript_1 == 'no_defined_pedigree_groups')
{
$date = date('Y-m-d H:i:s');
echo "This message was generated at $date.\n";
$ret_val = disconnect();
exit;
}
echo "</td></tr>\n";
echo "</table>\n";
echo "<br>\n";
$jscript_2 = printPedigreeCheckList($ped_rec_list,$database_id);
if ($jscript_2 == '0')
{
$date = date('Y-m-d H:i:s');
echo "Error #17: $date $date<br>\n";
echo "Error in call to printPedigreeCheckList from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "See above error message from printPedigreeCheckList for an explanation<br><br>\n";
echo "Please email the above error using the Comments/Help/Support link on the \n";
echo "left navigation bar.\n";
echo "</form>\n";
echo "</body></html>\n";
$ret_val = disconnect();
exit;
}#end if error in call to printPedigreeCheckList
echo "<br><br>\n";
echo "<input type=\"hidden\" name=\"insert_from_file\" value=\"$insert_from_file\">\n";
echo "<input type=\"hidden\" name=\"ped_multiple_pages\" value=\"$ped_multiple_pages\">\n";
if ($ped_multiple_pages)
{
echo "<input type=\"hidden\" name=\"function_to_call\" value=\"$final_function_call\">\n";
echo "<input type=\"hidden\" name=\"table_name\" value=\"$final_table_name\">\n";
foreach ($final_field_list as $field){echo "<input type=\"hidden\" name=\"field_list[]\" value=\"$field\">\n";}
if (is_array($final_term)){foreach ($final_term as $term){echo "<input type=\"hidden\" name=\"term[]\" value=\"$term\">\n";}}
else {echo "<input type=\"hidden\" name=\"term\" value=\"$final_term\">\n";}
if (is_array($final_mode)){foreach ($final_mode as $mode){echo "<input type=\"hidden\" name=\"mode[]\" value=\"$mode\">\n";}}
else {echo "<input type=\"hidden\" name=\"mode\" value=\"$final_mode\">\n";}
echo "<input type=\"hidden\" name=\"order_by\" value=\"$final_order_by\">\n";
echo "<input type=\"hidden\" name=\"last_record_retrieved\" value=\"$last_record_retrieved\">\n";
echo "<table align=\"center\">\n";
echo "<tr>\n";
echo "<td> </td>\n";
echo "<td><input type=\"reset\" name=\"reset\" value=\"Reset Selected Pedigree(s)\"></td>\n";
echo "</tr>\n";
echo "</table>\n";
echo "<table align=\"center\">\n";
echo "<tr>\n";
if ($records_left > $max_records_to_print_per_page)
{echo "<td><input type=\"submit\" name=\"submit\" value=\"Get Next $max_records_to_print_per_page Pedigrees\"></td>\n";}
else
{echo "<td><input type=\"submit\" name=\"submit\" value=\"Get Next $records_left Pedigrees\"></td>\n";}
echo "</form>\n";
echo "<form action=\"unlink_pedigrees_to_pedigree_groups.php\" name=\"skip_form2\" method=\"POST\" target=\"main\" onSubmit=\"return(Validate(form))\">\n";
echo "<input type=\"hidden\" name=\"want_list\" value=\"$want_list\">\n";
echo "<input type=\"hidden\" name=\"pedigree_group_id\" value=\"\">\n";
echo "<input type=\"hidden\" name=\"ped_id\" value=\"\">\n";
echo "<input type=\"hidden\" name=\"ped_mulitple_pages\" value=\"0\">\n";
echo "<td><input type=\"submit\" name=\"submit\" value=\"Insert Selected Pedigree(s)\" onClick=\"copyData('skip_form2')\"></td>\n";
echo "</form>\n";
echo "</tr>\n";
echo "</table>\n";
}#end if multiple_pages
else #only a single page
{
echo "<table align=\"center\">\n";
echo "<tr>\n";
echo "<td><input type=\"submit\" name=\"submit\" value=\"Insert Pedigree(s) from Pedigree Group\"></td>\n";
echo "<td><input type=\"reset\" name=\"reset\" value=\"Reset Selected Pedigree(s)\"></td>\n";
echo "</tr>\n";
echo "</form>\n";
echo "</table>\n";
}#end else only a single page
echo "<br><br>\n";
$ret_val = printLogOutButton('unlink_pedigrees_to_pedigree_groups.php');
echo "\n\n";
$jscript_1 = preg_replace('/ else \{return true;\}\n\}/','',$jscript_1);
$jscript_2 = preg_replace('/^\{\n/','',$jscript_2);
$jscript = "$jscript_1\n$jscript_2";
echo "<script>\n";
echo "function Validate(form)\n";
echo "$jscript\n";
if ($ped_multiple_pages)
{
echo "\n";
echo "function copyData(form_to_copy_to)\n";
echo "{\n";
echo " var ped_string = new Array();\n";
echo " var length = 0;\n";
echo " for (var i=0; i<document.form.elements['ped_id[]'].length; i++){\n";
echo " if (document.form.elements['ped_id[]'][i].checked){\n";
echo " length = ped_string.length;\n";
echo " ped_string[length] = document.form.elements['ped_id[]'][i].value;}}\n";
echo " if (form_to_copy_to == \"skip_form1\"){\n";
echo " document.skip_form1.pedigree_group_id.value = document.form.pedigree_group_id.value;\n";
echo " document.skip_form1.ped_id.value = ped_string;}\n";
echo " if (form_to_copy_to == \"skip_form2\"){\n";
echo " document.skip_form2.pedigree_group_id.value = document.form.pedigree_group_id.value;\n";
echo " document.skip_form2.ped_id.value = ped_string;}\n";
echo "}\n";
}#end if multiple pages
echo "</script>\n";
}#end if Select Multiple Pedigrees, but not pedigree group or pedigrees
#If Select Multiple Pedigrees, have pedigree group but more pedigrees to see
if (($insert_from_file == '1') and
(preg_match('/^\d+$/',$ped_group_id)) and
($ped_multiple_pages == '1')
)
{
$ped_group_field_list = array('pedigree_group_id');
$ped_group_name_array = distinctTableQuery('pedigree_group_name','pedigree_group_table',$database_id,$ped_group_field_list,$ped_group_id,'equal','all');
if (!is_array($ped_group_name_array))
{
$date = date('Y-m-d H:i:s');
echo "Error #18: $date<br>\n";
echo "Error in call to distinctTableQuery from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$ped_group_name_array<br><br>\n";
echo "Please email the above error using The Comments/Help/Support link on the \n";
echo "left navigation bar.\n";
echo "</form>\n";
echo "</body></html>\n";
$ret_val = disconnect();
exit;
}#end error in call to distinctTableQuery
if (sizeof($ped_group_name_array) == '0')
{
$date = date('Y-m-d H:i:s');
echo "The Pedigree Group you selected to delete Pedigrees from appears to have been deleted from the database. \n";
echo "Therefore, there are no longer any pedigrees associated with it.<br>\n";
echo "This message was generated at $date.<br><br>\n";
printLogOutButton('link_pedigrees_to_pedigree_groups.php');
$ret_val = disconnect();
exit;
}#end if pedigree group has been deleted
elseif (sizeof($ped_group_name_array) == '1'){$ped_group_name = $ped_group_name_array[0];unset($ped_group_name_array);}
else #error in data integrity
{
$date = date('Y-m-d H:i:s');
echo "Error #19: $date<br>\n";
echo "!!!Error in Database Data Integrity!!!!<br>\n";
echo "Stop using the data in the database until Database Administrator tells you all data is okay.<br>\n";
echo "Error in execution of link_pedigrees_to_pedigree_groups.php<br>\n";
echo "The user wants to delete an pedigree from pedigree group with pedigree_group_id $ped_group_id in database_id $database_id, \n";
echo "but when query the pedigree group table with that data multiple records are returned.<br><br>\n";
echo "Please email the above error using the Comments/Help/Support link \n";
echo "on the left navigation bar.\n";
echo "</body></html>\n";
$ret_val = disconnect();
exit;
}#end error in data integrity
if ($function_to_call == 'tableQuery')
{
$num_of_peds = countTableQuery($table_name,$database_id,$field_list,$term,$mode);
if (!preg_match('/^\d+$/',$num_of_peds))
{
$date = date('Y-m-d H:i:s');
echo "Error #20: $date<br>\n";
echo "Error in call to countTableQuery from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$num_of_peds<br><br>\n";
echo "Please email the above error using The Comments/Help/Support link on the \n";
echo "left navigation bar.\n";
echo "</form>\n";
echo "</body></html>\n";
$ret_val = disconnect();
exit;
}#end error in call to countTableQuery
$records_yet_to_be_retrieved = $num_of_peds - $last_record_retrieved;
if ($records_yet_to_be_retrieved > $max_records_to_print_per_page)
{
$ped_multiple_pages = 1;
$from = $last_record_retrieved;
$to = ($last_record_retrieved-1) + $max_records_to_print_per_page;
$range = "$from"."-"."$to";
$ped_rec_list = tableQuery($table_name,$database_id,$field_list,$term,$mode,$range,$order_by);
if (!is_array($ped_rec_list))
{
$date = date('Y-m-d H:i:s');
echo "Error #21: $date<br>\n";
echo "Error in call to tableQuery from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$ped_rec_list<br><br>\n";
echo "Please email the above error using The Comments/Help/Support link on the \n";
echo "left navigation bar.\n";
echo "</form>\n";
echo "</body></html>\n";
$ret_val = disconnect();
exit;
}#end if (!is_array(ped_rec_list))
if (sizeof($ped_rec_list) == 0)
{
$date = date('Y-m-d H:i:s');
echo "Error #22: $date<br>\n";
echo "Error in call to link_pedigrees_to_pedigree_groups.php<br>\n";
echo "There should be records returned for tableQuery search with parameters:<br>\n";
echo "table_name = $table_name<br>\n";
echo "field_list = ".join(',',$field_list)."<br>\n";
echo "term = $term<br>\n";
echo "mode = $mode<br>\n";
echo "range = $range<br>\n";
echo "order_by = $order_by<br>\n";
echo "But no records were returned<br><br>\n";
echo "Please email the above error using The Comments/Help/Support link on the \n";
echo "left navigation bar.\n";
echo "</form>\n";
echo "</body></html>\n";
$ret_val = disconnect();
exit;
}#end if no records returned
$last_record_retrieved = $to + 1;
}#end if more than a single page
else #only a single page
{
$ped_multiple_pages = 0;
$from = $last_record_retrieved;
$to = $num_of_peds - 1;
$range = "$from"."-"."$to";
$ped_rec_list = tableQuery($table_name,$database_id,$field_list,$term,$mode,$range,$order_by);
if (!is_array($ped_rec_list))
{
$date = date('Y-m-d H:i:s');
echo "Error #23: $date<br>\n";
echo "Error in call to tableQuery from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$ped_rec_list<br><br>\n";
echo "Please email the above error using The Comments/Help/Support link on the \n";
echo "left navigation bar.\n";
echo "</form>\n";
echo "</body></html>\n";
$ret_val = disconnect();
exit;
}#end if (!is_array(ped_rec_list))
if (sizeof($ped_rec_list) == 0)
{
$date = date('Y-m-d H:i:s');
echo "Error #24: $date<br>\n";
echo "Error in call to link_pedigrees_to_pedigree_groups.php<br>\n";
echo "There should be records returned for tableQuery search with parameters:<br>\n";
echo "table_name = $table_name<br>\n";
echo "field_list = ".join(',',$field_list)."<br>\n";
echo "term = $term<br>\n";
echo "mode = $mode<br>\n";
echo "range = $range<br>\n";
echo "order_by = $order_by<br>\n";
echo "But no records were returned<br><br>\n";
echo "Please email the above error using The Comments/Help/Support link on the \n";
echo "left navigation bar.\n";
echo "</form>\n";
echo "</body></html>\n";
$ret_val = disconnect();
exit;
}#end if no records returned
}#end else only a single page
}#end if tableQuery
echo "Please select which Pedigree(s) you want to insert into the Pedigree Group $ped_group_name.<br><br>\n";
$ret_val = printLogOutButton('link_pedigrees_to_pedigree_groups.php');
echo "<br><br>\n";
if ($ped_multiple_pages)
{
echo "<table align=\"center\">\n";
echo "<form action=\"link_pedigrees_to_pedigree_groups.php\" name=\"skip_form1\" method=\"POST\" target=\"main\" onSubmit=\"return(Validate(form))\">\n";
echo "<input type=\"hidden\" name=\"insert_from_file\" value=\"$insert_from_file\">\n";
echo "<input type=\"hidden\" name=\"pedigree_group_id\" value=\"$ped_group_id\">\n";
echo "<input type=\"hidden\" name=\"ped_id\" value=\"\">\n";
echo "<input type=\"hidden\" name=\"ped_mulitple_pages\" value=\"0\">\n";
echo "<tr>\n";
echo "<td><input type=\"submit\" name=\"submit\" value=\"Insert Selected Pedigree(s)\" onClick=\"copyData('skip_form1')\"></td>\n";
echo "</form>\n";
echo "<form action=\"link_pedigrees_to_pedigree_groups.php\" name=\"form\" method=\"POST\" target=\"main\">\n";
$records_left = $num_peds - $last_record_retrieved;
if ($records_left > $max_records_to_print_per_page)
{echo "<td><input type=\"submit\" name=\"submit\" value=\"Get Next $max_records_to_print_per_page Pedigrees\"></td>\n";}
else
{echo "<td><input type=\"submit\" name=\"submit\" value=\"Get Next $records_left Pedigrees\"></td>\n";}
echo "</tr>\n";
echo "</table>\n";
echo "<br>\n";
echo "<table align=\"center\">\n";
echo "<tr>\n";
echo "<td> </td>\n";
echo "<td><input type=\"reset\" name=\"reset\" value=\"Reset Selected Pedigree(s)\"></td>\n";
echo "</tr>\n";
echo "</table>\n";
}#end if multiple_pages
else #only a single page
{
echo "<form action=\"link_pedigrees_to_pedigree_groups.php\" name=\"form\" method=\"POST\" target=\"main\" onSubmit=\"return(Validate(form))\">\n";
echo "<table align=\"center\">\n";
echo "<tr>\n";
echo "<td><input type=\"submit\" name=\"submit\" value=\"Insert Selected Pedigree(s)\"></td>\n";
echo "<td><input type=\"reset\" name=\"reset\" value=\"Reset Selected Pedigree(s)\"></td>\n";
echo "</tr>\n";
echo "</table>\n";
}#end else only a single page
echo "<br><br>\n\n";
$jscript = printPedigreeCheckList($ped_rec_list,$database_id);
if ($jscript == '0')
{
$date = date('Y-m-d H:i:s');
echo "Error #25: $date<br>\n";
echo "Error in call to printPedigreeCheckList from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "See above error message from printPedigreeCheckList for an explanation<br><br>\n";
echo "Please email the above error using the Comments/Help/Support link on the \n";
echo "left navigation bar.\n";
echo "</form>\n";
echo "</body></html>\n";
$ret_val = disconnect();
exit;
}#end if (jscript == '0')
echo "<br><br>\n";
echo "<input type=\"hidden\" name=\"insert_from_file\" value=\"$insert_from_file\">\n";
echo "<input type=\"hidden\" name=\"pedigree_group_id\" value=\"$ped_group_id\">\n";
echo "<input type=\"hidden\" name=\"ped_multiple_pages\" value=\"$ped_multiple_pages\">\n";
if (sizeof($ped_id) > '0')
{
if (!is_array($ped_id)){echo "<input type=\"hidden\" name=\"ped_id[]\" value=\"$ped_id\">\n";}
else
{
$term = join($ped_id,',');
echo "<input type=\"hidden\" name=\"ped_id[]\" value=\"$term\">\n";
unset($term);
}
}#end if have ids from previous page(s)
if ($ped_multiple_pages)
{
echo "<input type=\"hidden\" name=\"function_to_call\" value=\"$function_to_call\">\n";
echo "<input type=\"hidden\" name=\"table_name\" value=\"$table_name\">\n";
foreach ($field_list as $field){echo "<input type=\"hidden\" name=\"field_list[]\" value=\"$field\">\n";}
if (is_array($term)){foreach ($term as $sub_term){echo "<input type=\"hidden\" name=\"term[]\" value=\"$sub_term\">\n";}}
else {echo "<input type=\"hidden\" name=\"term\" value=\"$term\">\n";}
if (is_array($mode)){foreach ($mode as $sub_mode){echo "<input type=\"hidden\" name=\"mode[]\" value=\"$sub_mode\">\n";}}
else {echo "<input type=\"hidden\" name=\"mode\" value=\"$final_mode\">\n";}
echo "<input type=\"hidden\" name=\"order_by\" value=\"$order_by\">\n";
echo "<input type=\"hidden\" name=\"last_record_retrieved\" value=\"$last_record_retrieved\">\n";
echo "<table align=\"center\">\n";
echo "<tr>\n";
echo "<td> </td>\n";
echo "<td><input type=\"reset\" name=\"reset\" value=\"Reset Selected Pedigree(s)\"></td>\n";
echo "</tr>\n";
echo "</table>\n";
echo "<table align=\"center\">\n";
echo "<tr>\n";
if ($records_left > $max_records_to_print_per_page)
{echo "<td><input type=\"submit\" name=\"submit\" value=\"Get Next $max_records_to_print_per_page Pedigrees\"></td>\n";}
else
{echo "<td><input type=\"submit\" name=\"submit\" value=\"Get Next $records_left Pedigrees\"></td>\n";}
echo "</form>\n";
echo "<form action=\"unlink_pedigrees_to_pedigree_groups.php\" name=\"skip_form2\" method=\"POST\" target=\"main\" onSubmit=\"return(Validate(form))\">\n";
echo "<input type=\"hidden\" name=\"insert_from_file\" value=\"$insert_from_file\">\n";
echo "<input type=\"hidden\" name=\"pedigree_group_id\" value=\"$ped_group_id\">\n";
echo "<input type=\"hidden\" name=\"ped_id\" value=\"\">\n";
echo "<input type=\"hidden\" name=\"ped_mulitple_pages\" value=\"0\">\n";
echo "<td><input type=\"submit\" name=\"submit\" value=\"Insert Selected Pedigree(s)\" onClick=\"copyData('skip_form2')\"></td>\n";
echo "</form>\n";
echo "</tr>\n";
echo "</table>\n";
}#end if multiple_pages
else #only a single page
{
echo "<table align=\"center\">\n";
echo "<tr>\n";
echo "<td><input type=\"submit\" name=\"submit\" value=\"Insert Pedigree(s) from Pedigree Group\"></td>\n";
echo "<td><input type=\"reset\" name=\"reset\" value=\"Reset Selected Pedigree(s)\"></td>\n";
echo "</tr>\n";
echo "</form>\n";
echo "</table>\n";
}#end else only a single page
echo "<br><br>\n";
$ret_val = printLogOutButton('link_pedigrees_to_pedigree_groups.php');
echo "\n\n";
echo "<script>\n";
echo "function Validate(form)\n";
echo "$jscript\n";
if ($ped_multiple_pages)
{
echo "\n";
echo "function copyData(form_to_copy_to)\n";
echo "{\n";
echo " var ped_string = new Array();\n";
echo " var length = 0;\n";
echo " for (var i=0; i<document.form.elements['ped_id[]'].length; i++){\n";
echo " if (document.form.elements['ped_id[]'][i].type == \"hidden\"){\n";
echo " length = ped_string.length;\n";
echo " ped_string[length] = document.form.elements['ped_id[]'][i].value;}\n";
echo " else{\n";
echo " if (document.form.elements['ped_id[]'][i].checked){\n";
echo " length = ped_string.length;\n";
echo " ped_string[length] = document.form.elements['ped_id[]'][i].value;}}}\n";
echo " if (form_to_copy_to == \"skip_form1\"){\n";
echo " document.skip_form1.ped_id.value = ped_string;}\n";
echo " if (form_to_copy_to == \"skip_form2\"){\n";
echo " document.skip_form2.ped_id.value = ped_string;}\n";
echo "}\n";
}#end if multiple pages
echo "</script>\n";
}#end if select multiple pedigrees, have pedigree group but more pedigrees to see
#5 Insert values from Web form
if ((($insert_from_file == '0') and
(preg_match('/^\d+$/',$ped_group_id)) and
(preg_match('/^\d+$/',$ped_table_id))
)or
(($insert_from_file == '1') and
(preg_match('/^\d+$/',$ped_group_id)) and
($ped_multiple_pages == '0') and
(sizeof($ped_ids) > '0')
)
)
{
$rand = rand();
$tmp_log_file = "log_file_"."$rand".".txt";
$log_file_handle = fopen("../data/$tmp_log_file","w");
if (!$log_file_handle)
{
$date = date('Y-m-d H:i:s');
echo "Error #26: $date<br>\n";
echo "Error in call to fopen from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "Unable to open log file to keep track of when, what, and by whom data is altered in the database<br><br>\n";
echo "Please email the above error using the Comments/Help/Support link \n";
echo "on the left navigation bar.\n";
echo "</body></html>\n";
$ret_val = disconnect();
exit;
}#end error in call to fopen
$log_file_statement = "";
$pedigree_field_array = array('pedigree_group_id');
$pedigree_value_array = array($ped_group_id);
$exists_pedigree_group = existsValue('pedigree_group_table',$pedigree_field_array,$pedigree_value_array,$database_id);
if (!preg_match('/\d+/',$exists_pedigree_group))
{
$date = date('Y-m-d H:i:s');
echo "Error #27: $date<br>\n";
echo "Error in call to existsValue from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$exists_pedigree_group<br><br>\n";
echo "Please email the above error message using the Comments/Help/Support link on \n";
echo "the left navigation bar\n";
echo "</form>\n";
echo "</body></html>\n";
fclose($log_file_handle);
chmod("../data/$tmp_log_file",0777);
$command = "rm ../data/$tmp_log_file";
exec($command,$output_array,$return_code);
$ret_val = disconnect();
exit;
}#end if error in call to existsValue
if ($exists_pedigree_group == '0')
{
$date = date('Y-m-d H:i:s');
echo "Pedigree Group ID $ped_group_id is not a pedigree group in the database. It appears that it was deleted \n";
echo "from the database before you submitted your request to add pedigrees to it.<br>\n";
echo "This message was generated at $date.\n";
fclose($log_file_handle);
chmod("../data/$tmp_log_file",0777);
$command = "rm ../data/$tmp_log_file";
exec($command,$output_array,$return_code);
$ret_val = disconnect();
exit;
}#end if pedigree group not already in the database
$field_list = array('pedigree_group_id');
$ped_group_rec_list = tableQuery('pedigree_group_table',$database_id,$field_list,$ped_group_id,'equal','all');
if (!is_array($ped_group_rec_list))
{
$date = date('Y-m-d H:i:s');
echo "Error #28: $date<br>\n";
echo "Error in call to tableQuery from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$ped_group_rec_list<br><br>\n";
echo "Please email the above error message using the Comments/Help/Support link on \n";
echo "the left navigation bar\n";
echo "</form>\n";
echo "</body></html>\n";
fclose($log_file_handle);
chmod("../data/$tmp_log_file",0777);
$command = "rm ../data/$tmp_log_file";
exec($command,$output_array,$return_code);
$ret_val = disconnect();
exit;
}#end if error in call to tableQuery
$ped_group_rec = $ped_group_rec_list[0];
if ($insert_from_file == '0')
{
$pedigree_field_array = array('pedigree_table_id');
$pedigree_value_array = array($ped_table_id);
$exists_pedigree = existsValue('pedigree_table',$pedigree_field_array,$pedigree_value_array,$database_id);
if (!preg_match('/\d+/',$exists_pedigree))
{
$date = date('Y-m-d H:i:s');
echo "Error #29: $date<br>\n";
echo "Error in call to existsValue from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$exists_pedigree<br><br>\n";
echo "Please email the above error message using the Comments/Help/Support link on \n";
echo "the left navigation bar\n";
echo "</form>\n";
echo "</body></html>\n";
fclose($log_file_handle);
chmod("../data/$tmp_log_file",0777);
$command = "rm ../data/$tmp_log_file";
exec($command,$output_array,$return_code);
$ret_val = disconnect();
exit;
}#end if error in call to existsValue
if ($exists_pedigree == '0')
{
$date = date('Y-m-d H:i:s');
echo "Pedigree Table ID $ped_table_id is not a pedigree in the database. It appears that it was deleted \n";
echo "from the database before you submitted your request to add it to the pedigree group $ped_group_rec[pedigree_group_name].<br>\n";
echo "This message was generated at $date.\n";
fclose($log_file_handle);
chmod("../data/$tmp_log_file",0777);
$command = "rm ../data/$tmp_log_file";
exec($command,$output_array,$return_code);
$ret_val = disconnect();
exit;
}#end if pedigree not already in the database
$field_list = array('pedigree_table_id');
$ped_rec_list = tableQuery('pedigree_table',$database_id,$field_list,$ped_table_id,'equal','all');
if (!is_array($ped_rec_list))
{
$date = date('Y-m-d H:i:s');
echo "Error #30: $date<br>\n";
echo "Error in call to tableQuery from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$ped_rec_list<br><br>\n";
echo "Please email the above error message using the Comments/Help/Support link on \n";
echo "the left navigation bar\n";
echo "</form>\n";
echo "</body></html>\n";
fclose($log_file_handle);
chmod("../data/$tmp_log_file",0777);
$command = "rm ../data/$tmp_log_file";
exec($command,$output_array,$return_code);
$ret_val = disconnect();
exit;
}#end if error in call to tableQuery
$ped_rec = $ped_rec_list[0];
#Test to see if pedigree already in the pedigree group
$field_list_array = array('pedigree_group_id','pedigree_table_id');
$term_array = array($ped_group_id,$ped_table_id);
$mode_array = array('equal','equal');
$linked = countCompoundTableQuery('pedigree_pedigree_group_link_table',$database_id,$field_list_array,$term_array,$mode_array,'and');
if (!preg_match('/^\d+$/',$linked))
{
$date = date('Y-m-d H:i:s');
echo "Error #31: $date<br>\n";
echo "Error in call to countCompoundTableQuery from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$linked<br><br>\n";
echo "Please email the above error message using the Comments/Help/Support link on \n";
echo "the left navigation bar\n";
echo "</form>\n";
echo "</body></html>\n";
fclose($log_file_handle);
chmod("../data/$tmp_log_file",0777);
$command = "rm ../data/$tmp_log_file";
exec($command,$output_array,$return_code);
$ret_val = disconnect();
exit;
}#end if error in call to countCompoundTableQuery
if ($linked > '0')
{
$date = date('Y-m-d H:i:s');
echo "The Pedigree $ped_rec[pedigree_id] is already in the Pedigree Group $ped_group_rec[pedigree_group_name].<br>\n";
echo "This message was generated at $date.<br><br>\n";
echo "</form>\n";
printLogOutButton('link_pedigrees_to_pedigree_groups.php');
echo "</body></html>\n";
fclose($log_file_handle);
chmod("../data/$tmp_log_file",0777);
$command = "rm ../data/$tmp_log_file";
exec($command,$output_array,$return_code);
$ret_val = disconnect();
exit;
}#end if pedigree already linked to pedigree group
$ret_val = insertPedigreePedigreeGroupLink($database_id,$ped_table_id,$ped_group_id);
if ($ret_val != '1')
{
$date = date('Y-m-d H:i:s');
echo "Error #32: $date<br>\n";
echo "Error in call to insertPedigreePedigreeGroupLink from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$ret_val<br><br>\n";
echo "Please email the above error message using the Comments/Help/Support link on \n";
echo "the left navigation bar\n";
echo "</form>\n";
echo "</body></html>\n";
fclose($log_file_handle);
chmod("../data/$tmp_log_file",0777);
$command = "rm ../data/$tmp_log_file";
exec($command,$output_array,$return_code);
$ret_val = disconnect();
exit;
}#end if error in call to insertPedigreePedigreeGroupLink
$field_list = array('pedigree_table_id','pedigree_group_id');
$term_array = array($ped_table_id,$ped_group_id);
$mode_array = array('equal','equal');
$ped_ped_group_link_id_array = distinctCompoundTableQuery('pedigree_pedigree_group_link_id','pedigree_pedigree_group_link_table',$database_id,$field_list,$term_array,$mode_array,'and','all');
if (!is_array($ped_ped_group_link_id_array))
{
$date = date('Y-m-d H:i:s');
echo "Error #33: $date<br>\n";
echo "Error in call to distinctCompoundTableQuery from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$ped_ped_group_link_id_array<br><br>\n";
echo "Please email the above error message using the Comments/Help/Support link on \n";
echo "the left navigation bar\n";
echo "</form>\n";
echo "</body></html>\n";
fclose($log_file_handle);
chmod("../data/$tmp_log_file",0777);
$command = "rm ../data/$tmp_log_file";
exec($command,$output_array,$return_code);
$ret_val = disconnect();
exit;
}#end if error in call to distinctCompoundTableQuery
if ((sizeof($ped_ped_group_link_id_array) == 0) or (sizeof($ped_ped_group_link_id_array) > 1))
{
$date = date('Y-m-d H:i:s');
echo "Error #34: $date<br>\n";
echo "Error in execution of link_pedigrees_to_pedigree_groups.php<br>\n";
echo "The call to insertPedigreePedigreeGroupLink returned success for Pedigree Table ID $ped_table_id and ";
echo "Pedigree Group ID $ped_group_id.<br>\n";
echo "But when query database ".sizeof($ped_ped_group_link_id_array)." records are returned.<br>\n";
echo "Please email the above error using the Comments/Help/Support link on the \n";
echo "left navigation bar.<br><br>\n";
echo "</form>\n";
echo "</body></html>\n";
fclose($log_file_handle);
chmod("../data/$tmp_log_file",0777);
$command = "rm ../data/$tmp_log_file";
exec($command,$output_array,$return_code);
$ret_val = disconnect();
exit;
}#end if error in data integrity
$date = date('Y-m-d H:i:s');
$log_file_statement.= "$date:\t$_SESSION[user_name] Inserted a new Pedigree-Pedigree Group Link into Database ID $database_id for ";
$log_file_statement.= "Pedigree Table ID $ped_table_id and Pedigree Group ID $ped_group_id, assigned Pedigree-Pedigree Group Link ID ";
$log_file_statement.= "$ped_ped_group_link_id_array[0].\n";
fwrite($log_file_handle,$log_file_statement);
fclose($log_file_handle);
chmod("../data/$tmp_log_file",0777);
$command = "cat ../data/$tmp_log_file >> ../data/log_file.txt";
exec($command,$output_array,$return_code);
$command = "rm ../data/$tmp_log_file";
exec($command,$output_array,$return_code);
echo "Successfully added Pedigree $ped_rec[pedigree_id] to Pedigree Group $ped_group_rec[pedigree_group_name]<br><br>\n";
}#end if inserting only a single pedigree
if ($insert_from_file == '1')
{
$log_file_statement = "";
$inserted_peds = array();
$skipped_peds = array();
if (!is_array($ped_ids))
{
if (preg_match('/,/',$ped_ids))#if a comma-separated list
{
$insert_array = explode(',',$ped_ids);
foreach ($insert_array as $ped_table_id)
{
$pedigree_field_array = array('pedigree_table_id');
$pedigree_value_array = array($ped_table_id);
$exists_pedigree = existsValue('pedigree_table',$pedigree_field_array,$pedigree_value_array,$database_id);
if (!preg_match('/\d+/',$exists_pedigree))
{
$date = date('Y-m-d H:i:s');
echo "Error #35: $date<br>\n";
echo "Error in call to existsValue from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$exists_pedigree<br><br>\n";
echo "Please email the above error message using the Comments/Help/Support link on \n";
echo "the left navigation bar\n";
echo "</form>\n";
echo "</body></html>\n";
fclose($log_file_handle);
chmod("../data/$tmp_log_file",0777);
$command = "cat ../data/$tmp_log_file >> ../data/log_file.txt";
exec($command,$output_array,$return_code);
$command = "rm ../data/$tmp_log_file";
exec($command,$output_array,$return_code);
$ret_val = disconnect();
exit;
}#end if error in call to existsValue
if ($exists_pedigree == '0')
{
$skipped_peds[] = $ped_table_id;
continue;
}#end if pedigree not already in the database
$field_list = array('pedigree_table_id');
$ped_rec_list = tableQuery('pedigree_table',$database_id,$field_list,$ped_table_id,'equal','all');
if (!is_array($ped_rec_list))
{
$date = date('Y-m-d H:i:s');
echo "Error #36: $date<br>\n";
echo "Error in call to tableQuery from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$ped_rec_list<br><br>\n";
echo "Please email the above error message using the Comments/Help/Support link on \n";
echo "the left navigation bar\n";
echo "</form>\n";
echo "</body></html>\n";
fclose($log_file_handle);
chmod("../data/$tmp_log_file",0777);
$command = "rm ../data/$tmp_log_file";
exec($command,$output_array,$return_code);
$ret_val = disconnect();
exit;
}#end if error in call to tableQuery
$ped_rec = $ped_rec_list[0];
#Test to see if pedigree already in the pedigree group
$field_list_array = array('pedigree_group_id','pedigree_table_id');
$term_array = array($ped_group_id,$ped_table_id);
$mode_array = array('equal','equal');
$linked = countCompoundTableQuery('pedigree_pedigree_group_link_table',$database_id,$field_list_array,$term_array,$mode_array,'and');
if (!preg_match('/^\d+$/',$linked))
{
$date = date('Y-m-d H:i:s');
echo "Error #37: $date<br>\n";
echo "Error in call to countCompoundTableQuery from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$linked<br><br>\n";
echo "Please email the above error message using the Comments/Help/Support link on \n";
echo "the left navigation bar\n";
echo "</form>\n";
echo "</body></html>\n";
fclose($log_file_handle);
chmod("../data/$tmp_log_file",0777);
$command = "rm ../data/$tmp_log_file";
exec($command,$output_array,$return_code);
$ret_val = disconnect();
exit;
}#end if error in call to countCompoundTableQuery
if ($linked > '0')
{
$skipped_peds[] = $ped_rec['pedigree_id'];
continue;
}#end if pedigree already linked to pedigree group
$ret_val = insertPedigreePedigreeGroupLink($database_id,$ped_table_id,$ped_group_id);
if ($ret_val != '1')
{
$date = date('Y-m-d H:i:s');
echo "Error #38: $date<br>\n";
echo "Error in call to insertPedigreePedigreeGroupLink from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$ret_val<br><br>\n";
echo "Please email the above error message using the Comments/Help/Support link on \n";
echo "the left navigation bar\n";
echo "</form>\n";
echo "</body></html>\n";
fclose($log_file_handle);
chmod("../data/$tmp_log_file",0777);
$command = "cat ../data/$tmp_log_file >> ../data/log_file.txt";
exec($command,$output_array,$return_code);
$command = "rm ../data/$tmp_log_file";
exec($command,$output_array,$return_code);
$ret_val = disconnect();
exit;
}#end if error in call to insertPedigreePedigreeGroupLink
$date = date('Y-m-d H:i:s');
$field_list = array('pedigree_table_id','pedigree_group_id');
$term_array = array($ped_table_id,$ped_group_id);
$mode_array = array('equal','equal');
$ped_ped_group_link_id_array = distinctCompoundTableQuery('pedigree_pedigree_group_link_id','pedigree_pedigree_group_link_table',$database_id,$field_list,$term_array,$mode_array,'and','all');
if (!is_array($ped_ped_group_link_id_array))
{
$date = date('Y-m-d H:i:s');
echo "Error #39: $date<br>\n";
echo "Error in call to distinctCompoundTableQuery from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$ped_ped_group_link_id_array<br><br>\n";
echo "Please email the above error message using the Comments/Help/Support link on \n";
echo "the left navigation bar\n";
echo "</form>\n";
echo "</body></html>\n";
fclose($log_file_handle);
chmod("../data/$tmp_log_file",0777);
$command = "cat ../data/$tmp_log_file >> ../data/log_file.txt";
exec($command,$output_array,$return_code);
$command = "rm ../data/$tmp_log_file";
exec($command,$output_array,$return_code);
$ret_val = disconnect();
exit;
}#end if error in call to distinctCompoundTableQuery
if ((sizeof($ped_ped_group_link_id_array) == 0) or (sizeof($ped_ped_group_link_id_array) > 1))
{
$date = date('Y-m-d H:i:s');
echo "Error #40: $date<br>\n";
echo "Error in execution of link_pedigrees_to_pedigree_groups.php<br>\n";
echo "The call to insertPedigreePedigreeGroupLink returned success for Pedigree Table ID $ped_table_id and ";
echo "Pedigree Group ID $ped_group_id.<br>\n";
echo "But when query database ".sizeof($ped_ped_group_link_id_array)." records are returned.<br>\n";
echo "Please email the above error using the Comments/Help/Support link on the \n";
echo "left navigation bar.<br><br>\n";
echo "</form>\n";
echo "</body></html>\n";
fclose($log_file_handle);
chmod("../data/$tmp_log_file",0777);
$command = "cat ../data/$tmp_log_file >> ../data/log_file.txt";
exec($command,$output_array,$return_code);
$command = "rm ../data/$tmp_log_file";
exec($command,$output_array,$return_code);
$ret_val = disconnect();
exit;
}#end if error in data integrity
$log_file_statement = "$date:\t$_SESSION[user_name] Inserted a new Pedigree-Pedigree Group Link ID ";
$log_file_statement.= "$ped_ped_group_link_id_array[0] into Database ID $database_id ";
$log_file_statement.= "for Pedigree Group ID $ped_group_id and Pedigree Table ID $ped_table_id.\n";
fwrite($log_file_handle,$log_file_statement);
$inserted_peds[] = $ped_rec['pedigree_id'];
}#end foreach pedigree to insert
}#end if ped_ids is a comma-separated list
else #only a single ped_id
{
$pedigree_field_array = array('pedigree_table_id');
$pedigree_value_array = array($ped_ids);
$exists_pedigree = existsValue('pedigree_table',$pedigree_field_array,$pedigree_value_array,$database_id);
if (!preg_match('/\d+/',$exists_pedigree))
{
$date = date('Y-m-d H:i:s');
echo "Error #41: $date<br>\n";
echo "Error in call to existsValue from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$exists_pedigree<br><br>\n";
echo "Please email the above error message using the Comments/Help/Support link on \n";
echo "the left navigation bar\n";
echo "</form>\n";
echo "</body></html>\n";
fclose($log_file_handle);
chmod("../data/$tmp_log_file",0777);
$command = "rm ../data/$tmp_log_file";
exec($command,$output_array,$return_code);
$ret_val = disconnect();
exit;
}#end if error in call to existsValue
if ($exists_pedigree == '0')
{
$date = date('Y-m-d H:i:s');
echo "Pedigree Table ID $ped_ids is not an pedigree in the database. It appears that it was deleted \n";
echo "from the database before you submitted your request to add it to the pedigree group $ped_group_rec[pedigree_group_name].<br>\n";
echo "This message was generated at $date.\n";
fclose($log_file_handle);
chmod("../data/$tmp_log_file",0777);
$command = "rm ../data/$tmp_log_file";
exec($command,$output_array,$return_code);
$ret_val = disconnect();
exit;
}#end if pedigree not already in the database
$field_list = array('pedigree_table_id');
$ped_rec_list = tableQuery('pedigree_table',$database_id,$field_list,$ped_table_id,'equal','all');
if (!is_array($ped_rec_list))
{
$date = date('Y-m-d H:i:s');
echo "Error #42: $date<br>\n";
echo "Error in call to tableQuery from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$ped_rec_list<br><br>\n";
echo "Please email the above error message using the Comments/Help/Support link on \n";
echo "the left navigation bar\n";
echo "</form>\n";
echo "</body></html>\n";
fclose($log_file_handle);
chmod("../data/$tmp_log_file",0777);
$command = "rm ../data/$tmp_log_file";
exec($command,$output_array,$return_code);
$ret_val = disconnect();
exit;
}#end if error in call to tableQuery
$ped_rec = $ped_rec_list[0];
#Test to see if pedigree already in the pedigree group
$field_list_array = array('pedigree_group_id','pedigree_table_id');
$term_array = array($ped_group_id,$ped_table_id);
$mode_array = array('equal','equal');
$linked = countCompoundTableQuery('pedigree_pedigree_group_link_table',$database_id,$field_list_array,$term_array,$mode_array,'and');
if (!preg_match('/^\d+$/',$linked))
{
$date = date('Y-m-d H:i:s');
echo "Error #43: $date<br>\n";
echo "Error in call to countCompoundTableQuery from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$linked<br><br>\n";
echo "Please email the above error message using the Comments/Help/Support link on \n";
echo "the left navigation bar\n";
echo "</form>\n";
echo "</body></html>\n";
fclose($log_file_handle);
chmod("../data/$tmp_log_file",0777);
$command = "rm ../data/$tmp_log_file";
exec($command,$output_array,$return_code);
$ret_val = disconnect();
exit;
}#end if error in call to countCompoundTableQuery
if ($linked > '0')
{
$date = date('Y-m-d H:i:s');
echo "The Pedigree $ped_rec[pedigree_id] is already in the Pedigree Group $ped_group_rec[pedigree_group_name].<br>\n";
echo "This message was generated at $date.<br><br>\n";
echo "</form>\n";
printLogOutButton('link_pedigrees_to_pedigree_groups.php');
echo "</body></html>\n";
fclose($log_file_handle);
chmod("../data/$tmp_log_file",0777);
$command = "rm ../data/$tmp_log_file";
exec($command,$output_array,$return_code);
$ret_val = disconnect();
exit;
}#end if pedigree already linked to pedigree group
$ret_val = insertPedigreePedigreeGroupLink($database_id,$ped_ids,$ped_group_id);
if ($ret_val != '1')
{
$date = date('Y-m-d H:i:s');
echo "Error #44: $date<br>\n";
echo "Error in call to insertPedigreePedigreeGroupLink from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$ret_val<br><br>\n";
echo "Please email the above error message using the Comments/Help/Support link on \n";
echo "the left navigation bar\n";
echo "</form>\n";
echo "</body></html>\n";
fclose($log_file_handle);
chmod("../data/$tmp_log_file",0777);
$command = "rm ../data/$tmp_log_file";
exec($command,$output_array,$return_code);
$ret_val = disconnect();
exit;
}#end if error in call to insertPedigreePedigreeGroupLink
$date = date('Y-m-d H:i:s');
$field_list = array('pedigree_table_id','pedigree_group_id');
$term_array = array($ped_ids,$ped_group_id);
$mode_array = array('equal','equal');
$ped_ped_group_link_id_array = distinctCompoundTableQuery('pedigree_pedigree_group_link_id','pedigree_pedigree_group_link_table',$database_id,$field_list,$term_array,$mode_array,'and','all');
if (!is_array($ped_ped_group_link_id_array))
{
$date = date('Y-m-d H:i:s');
echo "Error #45: $date<br>\n";
echo "Error in call to distinctCompoundTableQuery from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$ped_ped_group_link_id_array<br><br>\n";
echo "Please email the above error message using the Comments/Help/Support link on \n";
echo "the left navigation bar\n";
echo "</form>\n";
echo "</body></html>\n";
fclose($log_file_handle);
chmod("../data/$tmp_log_file",0777);
$command = "rm ../data/$tmp_log_file";
exec($command,$output_array,$return_code);
$ret_val = disconnect();
exit;
}#end if error in call to distinctCompoundTableQuery
if ((sizeof($ped_ped_group_link_id_array) == 0) or (sizeof($ped_ped_group_link_id_array) > 1))
{
$date = date('Y-m-d H:i:s');
echo "Error #46: $date<br>\n";
echo "Error in execution of link_pedigrees_to_pedigree_groups.php<br>\n";
echo "The call to insertPedigreePedigreeGroupLink returned success for Pedigree Table ID $ped_ids and ";
echo "Pedigree Group ID $ped_group_id.<br>\n";
echo "But when query database ".sizeof($ped_ped_group_link_id_array)." records are returned.<br>\n";
echo "Please email the above error using the Comments/Help/Support link on the \n";
echo "left navigation bar.<br><br>\n";
echo "</form>\n";
echo "</body></html>\n";
fclose($log_file_handle);
chmod("../data/$tmp_log_file",0777);
$command = "rm ../data/$tmp_log_file";
exec($command,$output_array,$return_code);
$ret_val = disconnect();
exit;
}#end if error in data integrity
$log_file_statement = "$date:\t$_SESSION[user_name] Inserted Pedigree-Pedigree Group Link ID ";
$log_file_statement.= "$ped_ped_group_link_id_array[0] into Database ID $database_id ";
$log_file_statement.= "for Pedigree Group ID $ped_group_id and Pedigree Table ID $ped_ids.\n";
fwrite($log_file_handle,$log_file_statement);
$inserted_peds[] = $ped_rec['pedigree_id'];
}#end only single ped_id
}#end if ped_ids is not an array
else #ped_ids is an array
{
$insert_term = join($ped_ids,',');
$insert_array = explode(',',$insert_term);
foreach ($insert_array as $ped_table_id)
{
$pedigree_field_array = array('pedigree_table_id');
$pedigree_value_array = array($ped_table_id);
$exists_pedigree = existsValue('pedigree_table',$pedigree_field_array,$pedigree_value_array,$database_id);
if (!preg_match('/\d+/',$exists_pedigree))
{
$date = date('Y-m-d H:i:s');
echo "Error #47: $date<br>\n";
echo "Error in call to existsValue from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$exists_pedigree<br><br>\n";
echo "Please email the above error message using the Comments/Help/Support link on \n";
echo "the left navigation bar\n";
echo "</form>\n";
echo "</body></html>\n";
fclose($log_file_handle);
chmod("../data/$tmp_log_file",0777);
$command = "cat ../data/$tmp_log_file >> ../data/log_file.txt";
exec($command,$output_array,$return_code);
$command = "rm ../data/$tmp_log_file";
exec($command,$output_array,$return_code);
$ret_val = disconnect();
exit;
}#end if error in call to existsValue
if ($exists_pedigree == '0')
{
$skipped_peds[] = $ped_table_id;
continue;
}#end if pedigree not already in the database
$field_list = array('pedigree_table_id');
$ped_rec_list = tableQuery('pedigree_table',$database_id,$field_list,$ped_table_id,'equal','all');
if (!is_array($ped_rec_list))
{
$date = date('Y-m-d H:i:s');
echo "Error #48: $date<br>\n";
echo "Error in call to tableQuery from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$ped_rec_list<br><br>\n";
echo "Please email the above error message using the Comments/Help/Support link on \n";
echo "the left navigation bar\n";
echo "</form>\n";
echo "</body></html>\n";
fclose($log_file_handle);
chmod("../data/$tmp_log_file",0777);
$command = "rm ../data/$tmp_log_file";
exec($command,$output_array,$return_code);
$ret_val = disconnect();
exit;
}#end if error in call to tableQuery
$ped_rec = $ped_rec_list[0];
#Test to see if pedigree already in the pedigree group
$field_list_array = array('pedigree_group_id','pedigree_table_id');
$term_array = array($ped_group_id,$ped_table_id);
$mode_array = array('equal','equal');
$linked = countCompoundTableQuery('pedigree_pedigree_group_link_table',$database_id,$field_list_array,$term_array,$mode_array,'and');
if (!preg_match('/^\d+$/',$linked))
{
$date = date('Y-m-d H:i:s');
echo "Error #49: $date<br>\n";
echo "Error in call to countCompoundTableQuery from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$linked<br><br>\n";
echo "Please email the above error message using the Comments/Help/Support link on \n";
echo "the left navigation bar\n";
echo "</form>\n";
echo "</body></html>\n";
fclose($log_file_handle);
chmod("../data/$tmp_log_file",0777);
$command = "rm ../data/$tmp_log_file";
exec($command,$output_array,$return_code);
$ret_val = disconnect();
exit;
}#end if error in call to countCompoundTableQuery
if ($linked > '0')
{
$skipped_peds[] = $ped_rec['pedigree_id'];
continue;
}#end if pedigree already linked to pedigree group
$ret_val = insertPedigreePedigreeGroupLink($database_id,$ped_table_id,$ped_group_id);
if ($ret_val != '1')
{
$date = date('Y-m-d H:i:s');
echo "Error #50: $date<br>\n";
echo "Error in call to insertPedigreePedigreeGroupLink from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$ret_val<br><br>\n";
echo "Please email the above error message using the Comments/Help/Support link on \n";
echo "the left navigation bar\n";
echo "</form>\n";
echo "</body></html>\n";
fclose($log_file_handle);
chmod("../data/$tmp_log_file",0777);
$command = "cat ../data/$tmp_log_file >> ../data/log_file.txt";
exec($command,$output_array,$return_code);
$command = "rm ../data/$tmp_log_file";
exec($command,$output_array,$return_code);
$ret_val = disconnect();
exit;
}#end if error in call to insertPedigreePedigreeGroupLink
$field_list = array('pedigree_table_id','pedigree_group_id');
$term_array = array($ped_table_id,$ped_group_id);
$mode_array = array('equal','equal');
$ped_ped_group_link_id_array = distinctCompoundTableQuery('pedigree_pedigree_group_link_id','pedigree_pedigree_group_link_table',$database_id,$field_list,$term_array,$mode_array,'and','all');
if (!is_array($ped_ped_group_link_id_array))
{
$date = date('Y-m-d H:i:s');
echo "Error #51: $date<br>\n";
echo "Error in call to distinctCompoundTableQuery from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$ped_ped_group_link_id_array<br><br>\n";
echo "Please email the above error message using the Comments/Help/Support link on \n";
echo "the left navigation bar\n";
echo "</form>\n";
echo "</body></html>\n";
fclose($log_file_handle);
chmod("../data/$tmp_log_file",0777);
$command = "cat ../data/$tmp_log_file >> ../data/log_file.txt";
exec($command,$output_array,$return_code);
$command = "rm ../data/$tmp_log_file";
exec($command,$output_array,$return_code);
$ret_val = disconnect();
exit;
}#end if error in call to distinctCompoundTableQuery
if ((sizeof($ped_ped_group_link_id_array) == 0) or (sizeof($ped_ped_group_link_id_array) > 1))
{
$date = date('Y-m-d H:i:s');
echo "Error #52: $date<br>\n";
echo "Error in execution of link_pedigrees_to_pedigree_groups.php<br>\n";
echo "The call to insertPedigreePedigreeGroupLink returned success for Pedigree Table ID $ped_table_id and ";
echo "Pedigree Group ID $ped_group_id.<br>\n";
echo "But when query database ".sizeof($ped_ped_group_link_id_array)." records are returned.<br>\n";
echo "Please email the above error using the Comments/Help/Support link on the \n";
echo "left navigation bar.<br><br>\n";
echo "</form>\n";
echo "</body></html>\n";
fclose($log_file_handle);
chmod("../data/$tmp_log_file",0777);
$command = "cat ../data/$tmp_log_file >> ../data/log_file.txt";
exec($command,$output_array,$return_code);
$command = "rm ../data/$tmp_log_file";
exec($command,$output_array,$return_code);
$ret_val = disconnect();
exit;
}#end if error in data integrity
$date = date('Y-m-d H:i:s');
$log_file_statement = "$date:\t$_SESSION[user_name] Inserted Pedigree-Pedigree Group Link ID ";
$log_file_statement.= "$ped_ped_ped_group_link_array[0] into Database ID $database_id for ";
$log_file_statement.= "Pedigree Group ID $ped_group_id and Pedigree Table ID $ped_table_id.\n";
fwrite($log_file_handle,$log_file_statement);
$inserted_peds[] = $ped_rec['pedigree_id'];
}#end foreach pedigree to insert
}#end else ped_ids is an array
fclose($log_file_handle);
chmod("../data/$tmp_log_file",0777);
$command = "cat ../data/$tmp_log_file >> ../data/log_file.txt";
exec($command,$output_array,$return_code);
$command = "rm ../data/$tmp_log_file";
exec($command,$output_array,$return_code);
echo "Successfully added the following ".sizeof($inserted_peds)." Pedigrees to Pedigree Group $ped_group_rec[pedigree_group_name]:<br>\n";
echo "<table border=\"1\">\n";
echo "<tr><th>Pedigree ID</th></tr>\n";
foreach ($inserted_peds as $inserted_ped){echo "<tr><td align=\"center\">$inserted_ped</td></tr>\n";}
echo "</table>\n";
echo "<br><br>\n";
if (sizeof($skipped_peds) > '0')
{
echo "The remaining ".sizeof($skipped_peds)." Pedigrees <b>were not</b> inserted into the pedigree group becasue they \n";
echo "were no longer in the database OR because they were already in the pedigree group.<br>\n";
}#end if pedigrees skipped<br><br>\n";
}#end if inserting from checklist
echo "Now emailing all the users of the database to inform them of the new information in the database.<br>\n";
$database_rec_list = getDatabase($database_id);
if (!is_array($database_rec_list))
{
$date = date('Y-m-d H:i:s');
echo "Error #53: $date<br>\n";
echo "Error in call to getDatabase from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$database_rec_list<br><br>\n";
echo "Please email the above error using the Comments/Help/Support link on the \n";
echo "left navigation bar.\n";
echo "</body></html>\n";
$ret_val = disconnect();
exit;
}#end error in call to getDatabase
$database_rec = $database_rec_list[0];
$user_rec_list = getAllUsers();
if (!is_array($user_rec_list))
{
$date = date('Y-m-d H:i:s');
echo "Error #54: $date<br>\n";
echo "Error in call to getAllUsers from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$user_rec_list<br><br>\n";
echo "Please email the above error using the Comments/Help/Support link on the \n";
echo "left navigation bar.\n";
echo "</body></html>\n";
$ret_val = disconnect();
exit;
}#end error in call to getAllUsers
foreach ($user_rec_list as $user_rec)
{
if ($user_rec['user_name'] == 'root') {$root_email = $user_rec['user_email'];}
}#end foreach user
if ($insert_from_file == '0')
{
$subject = "Added new Pedigree to a Pedigree Group in your Genetic Studies Database";
$message = "The Pedigree $ped_rec[pedigree_id] was added to Pedigree Group $ped_group_rec[pedigree_group_name] ";
$message.= "in database $database_rec[database_name].\n";
}#end if only inserted a single pedigree
if ($insert_from_file == '1')
{
$subject = "New Pedigrees added to a Pedigree Group in your Genetic Studies Database";
$message = "There were ".sizeof($inserted_peds)." Pedigrees inserted into Pedigree Group $ped_group_rec[pedigree_group_name] ";
$message.= "in database $database_rec[database_name]";
}#end if inserted from checklist
$header = "From: $root_email";
$field_list = array('user_database_link_id');
$user_database_link_rec_list = tableQuery('user_database_link_table',$database_id,$field_list,'_','wildcard','all');
if (!is_array($user_database_link_rec_list))
{
$date = date('Y-m-d H:i:s');
echo"Error #55: $date<br>\n";
echo "Error in call to tableQuery from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$user_database_link_rec_list<br><br>\n";
echo "Please email the above error using the Comments/Help/Support link on the \n";
echo "left navigation bar.\n";
echo "</body></html>\n";
$ret_val = disconnect();
exit;
}#end error in call to tableQuery
if (sizeof($user_database_link_rec_list) > '0')
{
foreach ($user_database_link_rec_list as $user_database_link_rec)
{
$user_id = $user_database_link_rec['user_id'];
$field_list = array('user_id');
$user_rec_list = getUser($user_id);
if (!is_array($user_rec_list))
{
$date = date('Y-m-d H:i:s');
echo "Error #56: $date<br>\n";
echo "Error in call to getUser from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$user_rec_list<br><br>\n";
echo "Please email the above error using the Comments/Help/Support link on the \n";
echo "left navigation bar.\n";
echo "</body></html>\n";
$ret_val = disconnect();
exit;
}#end error in call to getUser
if (sizeof($user_rec_list) == '0') {continue;}
elseif (sizeof($user_rec_list) == '1') {$user_rec = $user_rec_list[0];}
else
{
$date = date('Y-m-d H:i:s');
echo "Error #57: $date<br>\n";
echo "Tried to send an update email to user id $user_id, but when queried the user table \n";
echo "with that id multiple records were returned.<br><br>\n";
echo "Please email the above error using the Comments/Help/Support link on the \n";
echo "left navigation bar.\n";
echo "</body></html>\n";
$ret_val = disconnect();
exit;
}#end error in data integrity
$user_email_address = $user_rec['user_email'];
$ret_val = mail($user_email_address,$subject,$message,$header);
#if (!$ret_val) {echo "Unable to send an update email to user $user_rec[user_name]<br>\n";}
#else {echo "Sent an update email to user $user_name<br>\n";}
}#end foreach user associated with database
}#end if have users associated with database
echo "Finished sending update emails to all the users<br><br>\n";
if ($insert_from_file == '0')
{
echo " <form action=\"link_pedigrees_to_pedigree_groups.php\" name=\"form\" method=\"POST\" target=\"main\">\n";
echo " If you would like to insert more pedigrees please click the button below.<br><br>\n";
echo "<center>\n";
echo "<input type=\"submit\" name=\"submit\" value=\"Insert More Pedigrees\">\n";
echo "</center>\n";
echo "</form>\n";
echo "<br><br>\n";
}#end if only inserted a single pedigree
$ret_val = printLogOutButton('link_pedigrees_to_pedigree_groups.php');
}#end if insert from web and have values
#6 Want to insert from file, but haven't said if file on server or users computer
if (($insert_from_file == '2') and
(!preg_match('/^\d$/',$upload_file)) and
((!is_uploaded_file($_FILES['ped_group_file']['tmp_name'])) and (!preg_match('/\w+/',$file_on_server)))
)
{
echo "Please select whether you would like to upload a file from your computer, or \n";
echo "select a file that is already in your 'Uploaded Data' directory on the server.<br><br>\n";
echo "<form action=\"link_pedigrees_to_pedigree_groups.php\" name=\"form\" method=\"POST\" target=\"main\">\n";
echo "<input type=\"hidden\" name=\"insert_from_file\" value=\"$insert_from_file\">\n";
echo "<table align=\"center\">\n";
echo "<tr><td><input type=\"radio\" name=\"upload_file\" value=\"0\" checked></td><td>Select File in 'Uploaded Data' directory</td></tr>\n";
echo "<tr><td><input type=\"radio\" name=\"upload_file\" value=\"1\"></td><td>Upload File from Your Computer</td></tr>\n";
echo "</table>\n";
echo "<br>\n";
echo "<table align=\"center\">\n";
echo "<tr>\n";
echo "<td><input type=\"submit\" name=\"submit\" value=\"Select File to Insert From\"></td>\n";
echo "<td><input type=\"reset\" name=\"reset\" value=\"Reset Method to Select File\"></td>\n";
echo "</tr>\n";
echo "</table>\n";
echo "<br><br>\n";
printLogOutButton('link_pedigrees_to_pedigree_groups.php');
}#end if want to upload file but haven't select way to select
#7 Get File
if (($insert_from_file == '2') and
(preg_match('/^\d$/',$upload_file)) and
((!is_uploaded_file($_FILES['ped_group_file']['tmp_name'])) and (!preg_match('/\w+/',$file_on_server)))
)
{
if ($upload_file == 1)
{echo "<form action=\"link_pedigrees_to_pedigree_groups.php\" enctype=\"multipart/form-data\" name=\"form\" method=\"POST\" target=\"main\" onSubmit=\"return(Validate(this))\">\n";}
else #file on server
{echo "<form action=\"link_pedigrees_to_pedigree_groups.php\" name=\"form\" method=\"POST\" target=\"main\" onSubmit=\"return(Validate(this))\">\n";}
echo "This form will allow you to upload a file that contains the pedigrees you would like to populate the selected pedigree group with.<br> \n";
echo "The file must be in a specific format for the insertion to be done properly. The file must contain 1 \n";
echo "column of pedigree ids. Each pedigree must be on its own line, and all the pedigrees must \n";
echo "already be in the database. (Click <a href=\"../data/test_data/pedigree_pedigree_group_link_test_data.txt\" target=\"_blank\">here</a> for an example data file.)<br> ";
echo "<center><b>Upload your file below:</b></center> <br><br>\n";
echo "<input type=\"hidden\" name=\"insert_from_file\" value=\"$insert_from_file\">\n";
echo "<input type=\"hidden\" name=\"upload_file\" value=\"$upload_file\">\n";
if ($upload_file == 1){echo "<input type=\"hidden\" name=\"MAX_FILE_SIZE\" value=\"1000000000\">\n";}
echo "<table align=\"center\">\n";
echo "<tr><td>Pedigree Group:</td><td>\n";
$jscript_1 = printPedigreeGroupSelectList($database_id);
if ($jscript_1 == '0')
{
$date = date('Y-m-d H:i:s');
echo "Error #58: $date<br>\n";
echo "Error in call to printPedigreeGroupSelectList from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "See error from printPedigreeGroupSelectList above for an explanation.<br><br>\n";
echo "Please email the above error message using the Comments/Help/Support link on \n";
echo "the left navigation bar\n";
echo "</form>\n";
echo "</body></html>\n";
$ret_val = disconnect();
exit;
}#end error in call to printPedigreeGroupSelectList
if ($jscript_1 == 'no_defined_pedigree_groups')
{
$date = date('Y-m-d H:i:s');
echo "This message was generated at $date.<br>\n";
$ret_val = disconnect();
exit;
}
echo "</td></tr>\n";
echo "<tr><td> </td></tr>\n";
echo "<tr><td> </td></tr>\n";
echo "<tr><td>File Name:</td><td>\n";
if ($upload_file == 1){echo "<input type=\"file\" name=\"ped_group_file\" size=\"20\"></td></tr>\n";}
else #file on server
{
$jscript_2 = printFileSelectList($_SESSION['user_name'],$database_id,'upload');
if ($jscript_2 == '0')
{
echo "</td></tr>\n";
echo "</table>\n";
echo "</form>\n";
echo "<br><br>\n";
$date = date('Y-m-d H:i:s');
echo "Error #59: $date<br>\n";
echo "Error in call to printFileSelectList from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "See above error message from printFileSelectList for an explanation.<br><br>\n";
echo "Please email the above error message using the Comments/Help/Support link on \n";
echo "the left navigation bar.\n";
echo "</body></html>\n";
$ret_val = disconnect();
exit;
}#end if error in call to printFileSelectList
if ($jscript_2 == '1')
{
echo "</td></tr>\n";
echo "</table>\n";
echo "</form>\n";
echo "<br><br>\n";
echo "<center>\n";
echo "<b>There are no files stored for user $_SESSION[user_name] in their uploaded_data directory.</b><br>\n";
echo "This means either you have not transfered the file to the server, or the file has expired and has been \n";
echo "deleted from the server.<br> So you need to either transfer the file you are looking for to the server and put it \n";
echo "in your uploaded_data directory, or upload the file directly from your computer in order to insert the data.<br><br>\n";
echo "</center>\n\n";
$ret_val = printLogOutButton('link_pedigrees_to_pedigree_groups.php');
echo "</body></html>\n";
$ret_val = disconnect();
exit;
}#end if no files in users directory to upload
echo "</td></tr>\n";
}#end else file on server
echo "</table>\n";
echo "<br>\n";
echo "<table align=\"center\">\n";
echo "<tr>\n";
echo "<td><input type=\"submit\" name=\"submit\" value=\"Upload File\"></td>\n";
echo "<td><input type=\"reset\" name=\"reset\" value=\"Reset Selected File\"></td>\n";
echo "</tr>\n";
echo "</form>\n";
echo "</table>\n";
echo "<br><br>\n";
$ret_val = printLogOutButton('link_pedigrees_to_pedigree_groups.php');
echo "\n\n";
$jscript_1 = preg_replace('/ else \{return true;\}\n\}/','',$jscript_1);
echo "<script>\n";
echo "function Validate(form)\n";
echo "$jscript\n";
if ($upload_file == 1)
{
echo " if (form.ped_group_file.value == \"\"){\n";
echo " alert(\"You must select a file to upload.\");\n";
echo " return false;}\n";
echo " return true;\n";
echo "}\n";
}#end if file upload
else #file on server
{
$jscript_2 = preg_replace('/^\{/','',$jscript_2);
echo "$jscript_2\n";
}#end else file on server
echo "</script>\n";
}#end get file
#8 Parse File and Insert
if ((
($insert_from_file == '2') and
(preg_match('/^\d$/',$upload_file)) and
(preg_match('/^\d+$/',$ped_group_id)) and
(is_uploaded_file($_FILES['ped_group_file']['tmp_name']))
) or
(
($insert_from_file == '2') and
(preg_match('/^\d$/',$upload_file)) and
(preg_match('/^\d+$/',$ped_group_id)) and
(preg_match('/\w+/',$file_on_server))
)
)
{
if ($upload_file == 1)
{
$rand_num = rand();
$file_name = "ped_group_data_upload_".$rand_num.".txt";
$ret_val = move_uploaded_file($_FILES['ped_group_file']['tmp_name'],"../data/uploaded_data/$_SESSION[user_name]/$file_name");
if (!$ret_val)
{
$date = date('Y-m-d H:i:s');
echo "Error #60: $date<br>\n";
echo "Error in call to link_pedigrees_to_pedigree_groups.php<br>\n";
echo "Unable to move uploaded file inorder to read it.<br>\n";
echo "Please email the above error message using the Comments/Help/Support link on \n";
echo "the left navigation bar\n";
echo "</body></html>\n";
$ret_val = disconnect();
exit;
}#end if (!ret_val)
$uploaded_file_name = "../../data/uploaded_data/$_SESSION[user_name]/$file_name";
$uploaded_file_size = @filesize("../data/uploaded_data/$_SESSION[user_name]/$file_name");
if (!$uploaded_file_size)
{
$command = "stat -c %s ../data/uploaded_data/$_SESSION[user_name]/$file_name";
exec($command,$output_array);
$uploaded_file_size = $output_array[0];
}#end if file too big for php
}#end if file uploaded
else #file on server
{
$uploaded_file_name = "../"."$file_on_server";
$uploaded_file_size = @filesize("$file_on_server");
if (!$uploaded_file_size)
{
$command = "stat -c %s $file_on_server";
exec($command,$output_array);
$uploaded_file_size = $output_array[0];
}#end if file too big for php
}#end else file on server
$pedigree_group_field_array = array('pedigree_group_id');
$pedigree_group_value_array = array($ped_group_id);
$exists_pedigree_group = existsValue('pedigree_group_table',$pedigree_group_field_array,$pedigree_group_value_array,$database_id);
if (!preg_match('/\d+/',$exists_pedigree_group))
{
$date = date('Y-m-d H:i:s');
echo "Error #61: $date<br>\n";
echo "Error in call to existsValue from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$exists_pedigree_group<br><br>\n";
echo "Please email the above error message using the Comments/Help/Support link on \n";
echo "the left navigation bar\n";
echo "</form>\n";
echo "</body></html>\n";
#$ret_val = unlink("../data/uploaded_data/$_SESSION[user_name]/$file_name");
fclose($log_file_handle);
chmod("../data/$tmp_log_file",0777);
fclose($uploaded_file_handle);
$ret_val = disconnect();
exit;
}#end if error in call to existsValue
if ($exists_pedigree_group == '0')
{
$date = date('Y-m-d H:i:s');
echo "Pedigree Group ID $ped_group_id is not already a pedigree in the database. It appears that this pedigree group was deleted from \n";
echo "the database before you submited your request to populate it with pedigrees.<br>\n";
echo "This message was generated at $date.\n";
#$ret_val = unlink("../data/uploaded_data/$_SESSION[user_name]/$file_name");
fclose($log_file_handle);
chmod("../data/$tmp_log_file",0777);
fclose($uploaded_file_handle);
$ret_val = disconnect();
exit;
}#end if pedigree group not already in the database
else #pedigree group already in the database
{
$field_list = array('pedigree_group_id');
$ped_group_rec_list = tableQuery('pedigree_group_table',$database_id,$field_list,$ped_group_id,'equal','all');
if (!is_array($ped_group_rec_list))
{
$date = date('Y-m-d H:i:s');
echo "Error #62: $date<br><br>\n";
echo "Error in call to tableQuery from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$ped_group_rec_list<br><br>\n";
echo "Please email the above error message using the Comments/Help/Support link on \n";
echo "the left navigation bar\n";
echo "</form>\n";
echo "</body></html>\n";
#$ret_val = unlink("../data/uploaded_data/$_SESSION[user_name]/$file_name");
fclose($log_file_handle);
chmod("../data/$tmp_log_file",0777);
fclose($uploaded_file_handle);
$ret_val = disconnect();
exit;
}#end error in call to tableQuery
if (sizeof($ped_group_rec_list) == '0')
{
$date = date('Y-m-d H:i:s');
echo "Error #63: $date<br>\n";
echo "Error in data integrity. existsValue says that pedigree group id $ped_group_id is a pedigree group in database id $database_id, \n";
echo "but when query the pedigree group table with that id no records are returned.<br><br>\n";
echo "Please email the above error message using the Comments/Help/Support link on \n";
echo "the left navigation bar\n";
echo "</form>\n";
echo "</body></html>\n";
#$ret_val = unlink("../data/uploaded_data/$_SESSION[user_name]/$file_name");
fclose($log_file_handle);
chmod("../data/$tmp_log_file",0777);
fclose($uploaded_file_handle);
$ret_val = disconnect();
exit;
}#end error in data integrity
elseif (sizeof($ped_group_rec_list) == '1') {$ped_group_rec = $ped_group_rec_list[0];}
else
{
$date = date('Y-m-d H:i:s');
echo "Error #64: $date<br>\n";
echo "Error in data integrity. Error in data integrity. existsValue says that pedigree group id $ped_group_id is a pedigree group \n";
echo "in database id $database_id, but when query the pedigree table with that id multiple records are returned.<br><br>\n";
echo "Please email the above error message using the Comments/Help/Support link on \n";
echo "the left navigation bar\n";
echo "</form>\n";
echo "</body></html>\n";
#$ret_val = unlink("../data/uploaded_data/$_SESSION[user_name]/$file_name");
fclose($log_file_handle);
chmod("../data/$tmp_log_file",0777);
fclose($uploaded_file_handle);
$ret_val = disconnect();
exit;
}#end error in data integrity
}#end else pedigree group already in the database
$ped_group_name = $ped_group_rec['pedigree_group_name'];
echo "Preparing to insert Pedigrees from the file into the Pedigree Group. This may take a few minutes depending on how many \n";
echo "pedigrees are in the uploaded file.<br><br><br>\n";
$ret_val = chdir("../bin/database_query_scripts/");
if (!$ret_val)
{
$date = date('Y-m-d H:i:s');
echo "Error #65: $date<br>\n";
echo "Error in call to chdir from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "Unable to change directory to database query scripts directory<br><br>\n";
echo "Please email the above error using Comments/Help/Support link \n";
echo "in the left navigation bar.<br>\n";
echo "</body></html>\n";
$ret_val = disconnect();
exit;
}#end error in call to chdir
if ($uploaded_file_size > $max_file_size_to_wait_to_run)
{
$background_flag = 1;
if ($uploaded_file_size >= $max_file_size_not_to_split)
{
$found = preg_match('/^(.+\/)([^\/]+)$/',$uploaded_file_name,$captured);
$path = $captured[1];
$file_name = $captured[2];
$sub_file_name = "sub_"."$file_name";
$prefix = "$path"."$sub_file_name";
$prefix = preg_replace('/\.\w+$/','_',$prefix);
$command = "split -a5 --lines=$num_lines_to_split_files $uploaded_file_name $prefix";
if (sizeof($output_array) > '0'){$output_array = array();}
exec($command,$output_array,$return_code);
if ($return_code)
{
$err_msg = implode("\n",$output_array);
$date = date('Y-m-d H:i:s');
echo "Error #66: $date<br>\n";
echo "Error in call to exec to split file from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "$err_msg<br><br>\n";
echo "Please email the above error using the Comments/Help/Support link on the \n";
echo "left navigation bar.\n";
echo "</form>\n";
echo "</body></html>\n";
$ret_val = disconnect();
exit;
}#end if error in exec call to split file
$file_array = glob("$prefix*");
$num_files_split = sizeof($file_array);
sort($file_array);
foreach ($file_array as $key=>$file)
{
$command = "./insert_data_into_database.php '$file' '$database_id' 'Populate Pedigree Groups' '$_SESSION[user_name]'";
$command.= " '$background_flag' '$ped_group_id' '$ped_group_name' >> dummy_insert_data_background_output.txt &";
$last_line = system($command,$sys_ret_val);
if ($sys_ret_val != '0')
{
$date = date('Y-m-d H:i:s');
echo "Error #67: $date<br>\n";
echo "Error in system call to insert_data_into_database.php from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "The return value of the sytem call was $sys_ret_val<br><br>\n";
echo "Please email the above error using the Comments/Help/Support link on the \n";
echo "left navigation bar.\n";
echo "</form>\n";
echo "</body></html>\n";
$ret_val = disconnect();
exit;
}#end if error in system call
}#end foreach sub file
}#end if file too big for php
else #don't need to split file
{
$command = "./insert_data_into_database.php '$uploaded_file_name' '$database_id' 'Populate Pedigree Groups' '$_SESSION[user_name]'";
$command.= " '$background_flag' '$ped_group_id' '$ped_group_name' >> dummy_insert_data_background_output.txt &";
$last_line = system($command,$sys_ret_val);
if ($sys_ret_val != '0')
{
$date = date('Y-m-d H:i:s');
echo "Error #68: $date<br>\n";
echo "Error in system call to insert_data_into_database.php from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "The return value of the sytem call was $sys_ret_val<br><br>\n";
echo "Please email the above error using the Comments/Help/Support link on the \n";
echo "left navigation bar.\n";
echo "</form>\n";
echo "</body></html>\n";
$ret_val = disconnect();
exit;
}#end if error in system call
}#end else don't need to split file
}#end if run in background
else #run in foreground
{
$background_flag = 0;
$command = "./insert_data_into_database.php '$uploaded_file_name' '$database_id' 'Populate Pedigree Groups' '$_SESSION[user_name]'";
$command.= " '$background_flag' '$ped_group_id' '$ped_group_name'";
passthru($command,$sys_ret_val);
if ($sys_ret_val != '0')
{
echo "<br><br>\n";
$date = date('Y-m-d H:i:s');
echo "Error #69: $date<br>\n";
echo "Error in system call to insert_data_into_database.php from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "See the error message above for an explanation of the error<br><br>\n";
echo "Please email the above error using the Comments/Help/Support link on the \n";
echo "left navigation bar.\n";
echo "</form>\n";
echo "</body></html>\n";
$ret_val = disconnect();
exit;
}#end if error in system call
}#end else run in foreground
$ret_val = chdir("../../cgi-bin/");
if (!$ret_val)
{
$date = date('Y-m-d H:i:s');
echo "Error #70: $date<br>\n";
echo "Error in call to chdir from link_pedigrees_to_pedigree_groups.php<br>\n";
echo "Unable to change directory to cgi-bin directory<br><br>\n";
echo "Please email the above error using Comments/Help/Support link \n";
echo "in the left navigation bar.<br>\n";
echo "</body></html>\n";
$ret_val = disconnect();
exit;
}#end error in call to chdir
if ($background_flag)
{
echo "<center>\n";
echo "<b>The data you uploaded is being inserted into the database.<br>\n";
if ($uploaded_file_size >= $max_file_size_not_to_split)
{
echo "The file was too large to handle, so it was split into $num_files_split sub files, and each \n";
echo "sub file is being processed separately. So you will recieve an email when the data in each sub file\n";
echo "has been inserted into the database \n";
}#end if split file
else {echo "You will receive an email when all the data has been inserted into the database \n";}
echo "detailing the results of the file upload and any errors.</b><br><br>\n";
echo "</center>\n";
echo "</body></html>\n";
$ret_val = disconnect();
exit;
}#end if running in background
if (!$background_flag){echo "Finished sending update emails to all the users<br>\n";}
}#end parse file and insert
}#end if (auth_user == '1')
$ret_val = disconnect();
echo "</body></html>\n";
?>