// TODO: move to sitedef.php $df_dir1 = df_available($dir1); // check if /data/ directory is externally mounted (returns array) $devloc = str_replace("/", "\\/", $EXT_MOUNT_DIR); // read from device location stored in /xGDBvm/admin/devloc via sitedef.php $dir1_mount = preg_match("/{$devloc}/", $df_dir1[0]) ? "<span class=\"checked_mount\">Ext vol mounted</span>" : "<span class=\"lightgrayfont\">Ext vol not mounted</span>"; //flag for dir1 mount $dir1_status = "<span class=\"normalfont \" style=\"font-weight:normal\"><a class='help-button' title='Mount status of /xGDBvm/data/' id='config_input_ebs'> {$dir1_mount} </a></span>"; } # data store directory:/input/ ($dir2) $dir2_status = ""; if (file_exists("/xGDBvm/admin/iplant")) { // xGDBvm-iPlant only $dir2 = "{$inputDirRoot}"; // TODO: move to sitedef.php $df_dir2 = df_available($dir2); // check if /input/ directory is fuse-mounted (returns array) $dir2_dropdown = $df_dir2[0] == "fuse" || $df_dir2[0] == "irodsFs" ? "/xGDBvm/input/" : ""; //only show input dir if fuse-mounted $dir2_mount = $df_dir2[0] == "fuse" || $df_dir2[0] == "irodsFs" ? "<span class=\"checked_mount nowrap\">DataStore mounted</span>" : "<span class=\"lightgrayfont\">DataStore not mounted</span>"; //flag for dir2 mount (Data Store) top of form $mount_status_alert = $df_dir2[0] == "fuse" || $df_dir2[0] == "irodsFs" ? "<span class=\"checked nowrap\">DataStore mounted</span>" : "<span class=\"warning\">DataStore not mounted</span>"; //more intrusive flag $dir2_status = "<span class=\"normalfont \" style=\"font-weight:normal\"><a class='help-button' title='Mount status of {$inputDirRoot}' id='config_input_irods'> {$dir2_mount} </a></span>"; } ## Get GTH GSQ app info $gsq_query = "SELECT app_id from {$global_DB1}.apps WHERE program='GeneSeqer-MPI' AND is_default='Y' "; $get_gsq = mysql_query($gsq_query); while ($row = mysql_fetch_array($get_gsq)) { $gsq_default = $row["app_id"]; }
$df_array1 = df_available($path1); $filesys1 = $df_array1[0]; $available1 = $df_array1[1]; $gb1 = round($available1 / 1000000, 1); $path2 = "/xGDBvm/data/"; $df_array2 = df_available($path2); $filesys2 = $df_array2[0]; $available2 = $df_array2[1]; $gb2 = round($available2 / 1000000, 1); $path3 = "/xGDBvm/data/scratch/"; $df_array3 = df_available($path3); $filesys3 = $df_array3[0]; $available3 = $df_array3[1]; $gb3 = round($available3 / 1000000, 1); $path4 = "/xGDBvm/data/mysql/"; $df_array4 = df_available($path4); $filesys4 = $df_array4[0]; $available4 = $df_array4[1]; $gb4 = round($available4 / 1000000, 1); ## License key status # Validate license keys (conf_functions.inc.php validate_dir($dir, $target, $description, $present, $absent) $validate_gm = validate_dir($GENEMARK_KEY_DIR, $GENEMARK_KEY, "GeneMark License Key", "installed", "not installed"); $gm_valid = $validate_gm[0]; $gm_class = $validate_gm[1]; $validate_gth = validate_dir($GENOMETHREADER_KEY_DIR, $GENOMETHREADER_KEY, "GenomeThreader License Key", "installed", "not installed"); $gth_valid = $validate_gth[0]; $gth_class = $validate_gth[1]; $validate_vm = validate_dir($VMATCH_KEY_DIR, $VMATCH_KEY, "Vmatch License Key", "installed", "not installed"); $vm_valid = $validate_vm[0]; $vm_class = $validate_vm[1]; ## Set GDB message (list items) based on status totals
// 1-26-16 if (file_exists("/xGDBvm/admin/iplant")) { // xGDBvm-iPlant only $df_dir1 = df_available($dir1_dropdown); // check if /data/ directory is externally mounted (returns array) $devloc = str_replace("/", "\\/", $ext_mount_dir); // read from device location stored in /xGDBvm/admin/devloc via sitedef.php $dir1_mount = preg_match("/{$devloc}/", $df_dir1[0]) ? "<span class=\"checked_mount\">Ext vol mounted</span>" : "<span class=\"lightgrayfont\">Ext vol not mounted</span>"; //flag for dir1 mount } # data store directory:/input/ ($dir2) $dir2_dropdown = "{$inputDir}"; // 1-26-16 if (file_exists("/xGDBvm/admin/iplant")) { // xGDBvm-iPlant only $df_dir2 = df_available($dir2_dropdown); // check if /input/ directory is fuse-mounted (returns array) # $dir2_dropdown=($df_dir2[0]=="fuse" || $df_dir2[0]=="irodsFs")?"/xGDBvm/input/":""; //only show input dir if fuse-mounted. REMOVED THIS REQUIREMENT 4/16/2014 $dir2_mount = $df_dir2[0] == "fuse" || $df_dir2[0] == "irodsFs" ? "<span class=\"checked_mount\">DataStore mounted</span>" : "<span class=\"lightgrayfont\">DataStore not mounted</span>"; //flag for dir1 mount } $dir3_dropdown = "/xGDBvm/examples/"; // TODO: move to sitedef.php $input_dirlist = dirlist_dropdown($dir1_dropdown, $dir2_dropdown, $dir3_dropdown, "{$Input_Data_Path}"); //build dropdown for input dir(s), to include /xGDBvm/input (preferred) or /xGDBvm/data #$input_dirlist=dirlist_dropdown("", $dir2_dropdown, $dir3_dropdown, "$Input_Data_Path");// To prevent use of /xGDBvm/data for inputs, uncomment this line and comment out previous. # display mount status (iPlant only) $dir1_status = file_exists("/xGDBvm/admin/iplant") ? "<span class=\"normalfont\" style=\"font-weight:normal\"> <a class='help-button' title='Mount status of /xGDBvm/data/' id='config_output_dir_mount'> {$dir1_mount} </a></span>" : ""; $dir2_status = file_exists("/xGDBvm/admin/iplant") ? "<span class=\"normalfont\" style=\"font-weight:normal\"> <a class='help-button' title='Mount status of /xGDBvm/input/' id='config_input_datastore'> {$dir2_mount} </a></span>" : ""; # repeat mask directory and files $dir4_dropdown = "{$inputDir}/repeatmask/";
//$data_directory4=data_directory($path4);// permissions prevents listing $mount4 = $df_array4[2]; #$location4=($filesys4==$filesys1)?"Internal":"External"; $path5 = "/xGDBvm/data/tmp"; $df_array5 = df_available($path5); $filesys5 = $df_array5[0]; $available5 = $df_array5[1]; $gb5 = $available5 / 1000000; $gb5_display = round($gb5, 0); $available5 = preg_replace('/(?<=\\d)(?=(\\d\\d\\d)+$)/', ',', $available5); $data_directory5 = data_directory($path5); // list entire directory contents as a string $mount5 = $df_array5[2]; #$location5=($filesys4==$filesys1)?"Internal":"External"; $path6 = $inputDirRoot; $df_array6 = df_available($path6); $filesys6 = $df_array6[0]; $available6 = $df_array6[1]; $gb6 = $available6 / 1000000; $gb6_display = round($gb6, 0); $available6 = preg_replace('/(?<=\\d)(?=(\\d\\d\\d)+$)/', ',', $available6); $data_directory6 = data_directory($path6); // list entire directory contents as a string $mount6 = $df_array6[2]; #$location6=($filesys6==$filesys1)?"Internal":"External"; ## Validate volumes $validate_mysql = validate_dir("/xGDBvm/data/", "mysql", "mysql directory", "present", "missing"); $mysql_valid = $validate_mysql[0]; $mysql_class = $validate_mysql[1]; $validate_scratch = validate_dir("/xGDBvm/data/", "scratch", "scratch directory", "present", "missing"); $scratch_valid = $validate_scratch[0];