[1] | 1 | <?php
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| 2 | /*
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| 3 | * cleanup.php
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| 4 | *
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| 5 | * functions relating to copying results and cleaning up the gfac DB
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[10] | 6 | * where the job used an Airavata interface.
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[1] | 7 | *
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| 8 | */
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| 9 |
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| 10 | $email_address = '';
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| 11 | $queuestatus = '';
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| 12 | $jobtype = '';
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| 13 | $db = '';
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| 14 | $editXMLFilename = '';
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[4] | 15 | $status = '';
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[1] | 16 |
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[10] | 17 | function aira_cleanup( $us3_db, $reqID, $gfac_link )
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[1] | 18 | {
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| 19 | global $dbhost;
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| 20 | global $user;
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| 21 | global $passwd;
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| 22 | global $db;
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| 23 | global $guser;
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| 24 | global $gpasswd;
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| 25 | global $gDB;
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| 26 | global $me;
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| 27 | global $work;
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| 28 | global $email_address;
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| 29 | global $queuestatus;
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| 30 | global $jobtype;
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| 31 | global $editXMLFilename;
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| 32 | global $submittime;
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[4] | 33 | global $status;
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[10] | 34 | global $stderr;
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[5] | 35 | global $stdout;
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[10] | 36 | global $tarfile;
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[6] | 37 | global $requestID;
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[10] | 38 | global $submit_dir;
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| 39 | $me = 'cleanup_aira.php';
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[1] | 40 |
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[6] | 41 | $requestID = $reqID;
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[1] | 42 | $db = $us3_db;
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| 43 | write_log( "$me: debug db=$db; requestID=$requestID" );
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| 44 |
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| 45 | $us3_link = mysql_connect( $dbhost, $user, $passwd );
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| 46 |
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| 47 | if ( ! $us3_link )
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| 48 | {
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| 49 | write_log( "$me: could not connect: $dbhost, $user, $passwd" );
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| 50 | mail_to_user( "fail", "Internal Error $requestID\nCould not connect to DB" );
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| 51 | return( -1 );
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| 52 | }
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| 53 |
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| 54 | $result = mysql_select_db( $db, $us3_link );
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| 55 |
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| 56 | if ( ! $result )
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| 57 | {
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| 58 | write_log( "$me: could not select DB $db" );
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| 59 | mail_to_user( "fail", "Internal Error $requestID\n$could not select DB $db" );
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| 60 | return( -1 );
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| 61 | }
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| 62 |
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| 63 | // First get basic info for email messages
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| 64 | $query = "SELECT email, investigatorGUID, editXMLFilename FROM HPCAnalysisRequest " .
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| 65 | "WHERE HPCAnalysisRequestID=$requestID";
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| 66 | $result = mysql_query( $query, $us3_link );
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| 67 |
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| 68 | if ( ! $result )
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| 69 | {
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| 70 | write_log( "$me: Bad query: $query" );
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| 71 | mail_to_user( "fail", "Internal Error $requestID\n$query\n" . mysql_error( $us3_link ) );
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| 72 | return( -1 );
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| 73 | }
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| 74 |
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| 75 | list( $email_address, $investigatorGUID, $editXMLFilename ) = mysql_fetch_array( $result );
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| 76 |
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| 77 | $query = "SELECT personID FROM people " .
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| 78 | "WHERE personGUID='$investigatorGUID'";
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| 79 | $result = mysql_query( $query, $us3_link );
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| 80 |
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| 81 | list( $personID ) = mysql_fetch_array( $result );
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| 82 |
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| 83 | $query = "SELECT clusterName, submitTime, queueStatus, method " .
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| 84 | "FROM HPCAnalysisRequest h, HPCAnalysisResult r " .
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| 85 | "WHERE h.HPCAnalysisRequestID=$requestID " .
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| 86 | "AND h.HPCAnalysisRequestID=r.HPCAnalysisRequestID";
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| 87 |
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| 88 | $result = mysql_query( $query, $us3_link );
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| 89 |
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| 90 | if ( ! $result )
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| 91 | {
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| 92 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
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| 93 | return( -1 );
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| 94 | }
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| 95 |
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| 96 | if ( mysql_num_rows( $result ) == 0 )
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| 97 | {
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| 98 | write_log( "$me: US3 Table error - No records for requestID: $requestID" );
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| 99 | return( -1 );
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| 100 | }
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| 101 |
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| 102 | list( $cluster, $submittime, $queuestatus, $jobtype ) = mysql_fetch_array( $result );
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| 103 |
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| 104 | // Get the GFAC ID
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| 105 | $query = "SELECT HPCAnalysisResultID, gfacID FROM HPCAnalysisResult " .
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| 106 | "WHERE HPCAnalysisRequestID=$requestID";
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| 107 |
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| 108 | $result = mysql_query( $query, $us3_link );
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| 109 |
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| 110 | if ( ! $result )
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| 111 | {
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| 112 | write_log( "$me: Bad query: $query" );
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| 113 | mail_to_user( "fail", "Internal Error $requestID\n$query\n" . mysql_error( $us3_link ) );
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| 114 | return( -1 );
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| 115 | }
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| 116 |
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| 117 | list( $HPCAnalysisResultID, $gfacID ) = mysql_fetch_array( $result );
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| 118 |
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[10] | 119 | // Get data from global GFAC DB then insert it into US3 DB
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[1] | 120 |
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| 121 | $result = mysql_select_db( $gDB, $gfac_link );
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| 122 |
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| 123 | if ( ! $result )
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| 124 | {
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| 125 | write_log( "$me: Could not connect to DB $gDB" );
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| 126 | mail_to_user( "fail", "Internal Error $requestID\nCould not connect to DB $gDB" );
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| 127 | return( -1 );
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| 128 | }
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| 129 |
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| 130 | $query = "SELECT status, cluster, id FROM analysis " .
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| 131 | "WHERE gfacID='$gfacID'";
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| 132 |
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| 133 | $result = mysql_query( $query, $gfac_link );
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| 134 | if ( ! $result )
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| 135 | {
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| 136 | write_log( "$me: Could not select GFAC status for $gfacID" );
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| 137 | mail_to_user( "fail", "Could not select GFAC status for $gfacID" );
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| 138 | return( -1 );
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| 139 | }
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| 140 |
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| 141 | list( $status, $cluster, $id ) = mysql_fetch_array( $result );
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| 142 |
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| 143 | if ( $cluster == 'bcf-local' || $cluster == 'alamo-local' )
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| 144 | {
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| 145 | $clushost = $cluster;
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| 146 | $clushost = preg_replace( "/\-local/", "", $clushost );
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| 147 | get_local_files( $gfac_link, $clushost, $requestID, $id, $gfacID );
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| 148 | }
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| 149 |
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[10] | 150 |
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| 151 | $query = "SELECT id FROM analysis " .
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[1] | 152 | "WHERE gfacID='$gfacID'";
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| 153 |
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| 154 | $result = mysql_query( $query, $gfac_link );
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| 155 |
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| 156 | if ( ! $result )
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| 157 | {
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| 158 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
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| 159 | mail_to_user( "fail", "Internal error " . mysql_error( $gfac_link ) );
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| 160 | return( -1 );
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| 161 | }
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| 162 |
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[10] | 163 | list( $analysisID ) = mysql_fetch_array( $result );
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[1] | 164 |
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[10] | 165 | // Get the request guid (LIMS submit dir name)
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| 166 | $query = "SELECT HPCAnalysisRequestGUID FROM HPCAnalysisRequest " .
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| 167 | "WHERE HPCAnalysisRequestID = $requestID ";
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| 168 | $result = mysql_query( $query, $us3_link );
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| 169 |
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| 170 | if ( ! $result )
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| 171 | {
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| 172 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
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| 173 | }
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| 174 |
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| 175 | list( $requestGUID ) = mysql_fetch_array( $result );
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| 176 | $output_dir = "$submit_dir/$requestGUID";
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| 177 |
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| 178 | // Get stderr,stdout,tarfile from work directory
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| 179 | if ( ! is_dir( "$output_dir" ) ) mkdir( "$output_dir", 0770 );
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| 180 | chdir( "$output_dir" );
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| 181 | //write_log( "$me: gfacID=$gfacID" );
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| 182 | //write_log( "$me: submit_dir=$submit_dir" );
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| 183 | //write_log( "$me: requestGUID=$requestGUID" );
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| 184 | write_log( "$me: output_dir=$output_dir" );
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| 185 |
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| 186 | $stderr = "";
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| 187 | $stdout = "";
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| 188 | $tarfile = "";
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| 189 | $fn_stderr = "Ultrascan.stderr";
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| 190 | $fn_stdout = "Ultrascan.stdout";
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| 191 | $fn_tarfile = "analysis-results.tar";
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| 192 | $num_try = 0;
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| 193 | while ( ! file_exists( $fn_tarfile ) && $num_try < 3 )
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| 194 | {
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| 195 | sleep( 10 );
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| 196 | $num_try++;
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| 197 | }
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| 198 |
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| 199 | $ofiles = scandir( $output_dir );
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| 200 | foreach ( $ofiles as $ofile )
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| 201 | {
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[16] | 202 | if ( preg_match( "/.*stderr$/", $ofile ) )
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[10] | 203 | $fn_stderr = $ofile;
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[16] | 204 | if ( preg_match( "/.*stdout$/", $ofile ) )
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[10] | 205 | $fn_stdout = $ofile;
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| 206 | //write_log( "$me: ofile=$ofile" );
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| 207 | }
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| 208 | write_log( "$me: fn_stderr=$fn_stderr" );
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| 209 | write_log( "$me: fn_stdout=$fn_stdout" );
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| 210 | if (file_exists($fn_tarfile)) write_log( "$me: fn_tarfile=$fn_tarfile" );
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| 211 | else write_log( "$me: NOT FOUND: $fn_tarfile" );
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| 212 |
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| 213 | if ( file_exists( $fn_stderr ) ) $stderr = file_get_contents( $fn_stderr );
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| 214 | if ( file_exists( $fn_stdout ) ) $stdout = file_get_contents( $fn_stdout );
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| 215 | if ( file_exists( $fn_tarfile ) ) $tarfile = file_get_contents( $fn_tarfile );
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| 216 |
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| 217 | if ( $cluster == 'alamo' || $cluster == 'alamo-local' )
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| 218 | { // Filter "ipath_userinit" lines out of alamo stdout lines
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| 219 | $prefln = strlen( $stdout );
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| 220 | $output = array();
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| 221 | exec( "grep -v 'ipath_userinit' $fn_stdout 2>&1", $output, $err );
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| 222 | $stdout = implode( "\n", $output );
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| 223 | $posfln = strlen( $stdout );
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| 224 | write_log( "$me: fn_stdout : filtered. Length $prefln -> $posfln ." );
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| 225 | }
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| 226 |
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[1] | 227 | // Save queue messages for post-mortem analysis
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| 228 | $query = "SELECT message, time FROM queue_messages " .
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| 229 | "WHERE analysisID = $analysisID " .
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| 230 | "ORDER BY time ";
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| 231 | $result = mysql_query( $query, $gfac_link );
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| 232 |
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| 233 | if ( ! $result )
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| 234 | {
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| 235 | // Just log it and continue
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| 236 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
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| 237 | }
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| 238 |
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| 239 | $now = date( 'Y-m-d H:i:s' );
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| 240 | $message_log = "US3 DB: $db\n" .
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| 241 | "RequestID: $requestID\n" .
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| 242 | "GFAC ID: $gfacID\n" .
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| 243 | "Processed: $now\n\n" .
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| 244 | "Queue Messages\n\n" ;
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| 245 | if ( mysql_num_rows( $result ) > 0 )
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| 246 | {
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| 247 | while ( list( $message, $time ) = mysql_fetch_array( $result ) )
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| 248 | $message_log .= "$time $message\n";
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| 249 | }
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| 250 |
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| 251 | $query = "DELETE FROM queue_messages " .
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| 252 | "WHERE analysisID = $analysisID ";
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| 253 |
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| 254 | $result = mysql_query( $query, $gfac_link );
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| 255 |
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| 256 | if ( ! $result )
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| 257 | {
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| 258 | // Just log it and continue
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| 259 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
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| 260 | }
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| 261 |
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[10] | 262 | $query = "SELECT queue_msg FROM analysis " .
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| 263 | "WHERE gfacID='$gfacID' ";
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| 264 |
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[1] | 265 | $result = mysql_query( $query, $gfac_link );
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[10] | 266 | list( $queue_msg ) = mysql_fetch_array( $result );
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[1] | 267 |
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| 268 | // But let's allow for investigation of other large stdout and/or stderr
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| 269 | if ( strlen( $stdout ) > 20480000 ||
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| 270 | strlen( $stderr ) > 20480000 )
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| 271 | write_log( "$me: stdout + stderr larger than 20M - $gfacID\n" );
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| 272 |
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| 273 | $message_log .= "\n\n\nStdout Contents\n\n" .
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| 274 | $stdout .
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| 275 | "\n\n\nStderr Contents\n\n" .
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| 276 | $stderr .
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| 277 | "\n\n\nGFAC Status: $status\n" .
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| 278 | "GFAC message field: $queue_msg\n";
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| 279 |
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| 280 | // Delete data from GFAC DB
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| 281 | $query = "DELETE from analysis WHERE gfacID='$gfacID'";
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| 282 |
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| 283 | $result = mysql_query( $query, $gfac_link );
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| 284 |
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| 285 | if ( ! $result )
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| 286 | {
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| 287 | // Just log it and continue
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| 288 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
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| 289 | }
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| 290 |
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| 291 |
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| 292 | // Try to create it if necessary, and write the file
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| 293 | // Let's use FILE_APPEND, in case this is the second time around and the
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| 294 | // GFAC job status was INSERTed, rather than UPDATEd
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| 295 | if ( ! is_dir( $output_dir ) )
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| 296 | mkdir( $output_dir, 0775, true );
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| 297 | $message_filename = "$output_dir/$db-$requestID-messages.txt";
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| 298 | file_put_contents( $message_filename, $message_log, FILE_APPEND );
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| 299 | // mysql_close( $gfac_link );
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| 300 |
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| 301 | /////////
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| 302 | // Insert data into HPCAnalysis
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| 303 |
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| 304 | $query = "UPDATE HPCAnalysisResult SET " .
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| 305 | "stderr='" . mysql_real_escape_string( $stderr, $us3_link ) . "', " .
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[10] | 306 | "stdout='" . mysql_real_escape_string( $stdout, $us3_link ) . "', " .
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| 307 | "queueStatus='completed' " .
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[1] | 308 | "WHERE HPCAnalysisResultID=$HPCAnalysisResultID";
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| 309 |
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| 310 | $result = mysql_query( $query, $us3_link );
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| 311 |
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| 312 | if ( ! $result )
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| 313 | {
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| 314 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
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| 315 | mail_to_user( "fail", "Bad query:\n$query\n" . mysql_error( $us3_link ) );
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| 316 | return( -1 );
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| 317 | }
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| 318 |
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[10] | 319 | // Delete data from GFAC DB
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| 320 | $query = "DELETE from analysis WHERE gfacID='$gfacID'";
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[1] | 321 |
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[10] | 322 | $result = mysql_query( $query, $gfac_link );
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| 323 |
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| 324 | if ( ! $result )
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| 325 | {
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| 326 | // Just log it and continue
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| 327 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
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| 328 | }
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| 329 |
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| 330 | // Expand the tar file
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| 331 |
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[1] | 332 | if ( strlen( $tarfile ) == 0 )
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| 333 | {
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| 334 | write_log( "$me: No tarfile" );
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| 335 | mail_to_user( "fail", "No results" );
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| 336 | return( -1 );
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| 337 | }
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| 338 |
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| 339 | $tar_out = array();
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[10] | 340 | exec( "tar -xf analysis-results.tar 2>&1", $tar_out, $err );
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[1] | 341 |
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| 342 | // Insert the model files and noise files
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| 343 | $files = file( "analysis_files.txt", FILE_IGNORE_NEW_LINES );
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| 344 | $noiseIDs = array();
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| 345 | $modelGUIDs = array();
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[17] | 346 | $mrecsIDs = array();
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| 347 | $fns_used = array();
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[1] | 348 |
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| 349 | foreach ( $files as $file )
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| 350 | {
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| 351 | $split = explode( ";", $file );
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| 352 |
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| 353 | if ( count( $split ) > 1 )
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| 354 | {
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| 355 | list( $fn, $meniscus, $mc_iteration, $variance ) = explode( ";", $file );
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| 356 |
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| 357 | list( $other, $mc_iteration ) = explode( "=", $mc_iteration );
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| 358 | list( $other, $variance ) = explode( "=", $variance );
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| 359 | list( $other, $meniscus ) = explode( "=", $meniscus );
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| 360 | }
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| 361 | else
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| 362 | $fn = $file;
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| 363 |
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[10] | 364 | if ( preg_match( "/mdl.tmp$/", $fn ) )
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| 365 | continue;
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| 366 |
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[17] | 367 | if ( in_array( $fn, $fns_used ) )
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| 368 | continue;
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| 369 |
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| 370 | $fns_used[] = $fn;
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| 371 |
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[1] | 372 | if ( filesize( $fn ) < 100 )
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| 373 | {
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[10] | 374 | write_log( "$me:fn is invalid $fn size filesize($fn)" );
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[1] | 375 | mail_to_user( "fail", "Internal error\n$fn is invalid" );
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| 376 | return( -1 );
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| 377 | }
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| 378 |
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| 379 | if ( preg_match( "/^job_statistics\.xml$/", $fn ) ) // Job statistics file
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| 380 | {
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| 381 | $xml = file_get_contents( $fn );
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| 382 | $statistics = parse_xml( $xml, 'statistics' );
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[10] | 383 | // $ntries = 0;
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| 384 | //
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| 385 | // while ( $statistics['cpucount'] < 1 && $ntries < 3 )
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| 386 | // { // job_statistics file not totally copied, so retry
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| 387 | // sleep( 10 );
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| 388 | // $xml = file_get_contents( $fn );
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| 389 | // $statistics = parse_xml( $xml, 'statistics' );
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| 390 | // $ntries++;
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| 391 | //write_log( "$me:jobstats retry $ntries" );
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| 392 | // }
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| 393 | //write_log( "$me:cputime=$statistics['cputime']" );
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| 394 |
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[1] | 395 | $otherdata = parse_xml( $xml, 'id' );
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| 396 |
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| 397 | $query = "UPDATE HPCAnalysisResult SET " .
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| 398 | "wallTime = {$statistics['walltime']}, " .
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| 399 | "CPUTime = {$statistics['cputime']}, " .
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| 400 | "CPUCount = {$statistics['cpucount']}, " .
|
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| 401 | "max_rss = {$statistics['maxmemory']}, " .
|
---|
| 402 | "startTime = '{$otherdata['starttime']}', " .
|
---|
| 403 | "endTime = '{$otherdata['endtime']}', " .
|
---|
| 404 | "mgroupcount = {$otherdata['groupcount']} " .
|
---|
| 405 | "WHERE HPCAnalysisResultID=$HPCAnalysisResultID";
|
---|
| 406 | $result = mysql_query( $query, $us3_link );
|
---|
| 407 |
|
---|
| 408 | if ( ! $result )
|
---|
| 409 | {
|
---|
| 410 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
|
---|
| 411 | }
|
---|
| 412 |
|
---|
| 413 | file_put_contents( "$output_dir/$fn", $xml ); // Copy to submit dir
|
---|
| 414 |
|
---|
[18] | 415 | $file_type = "jobstats";
|
---|
[1] | 416 | }
|
---|
| 417 |
|
---|
| 418 | else if ( preg_match( "/\.noise/", $fn ) > 0 ) // It's a noise file
|
---|
| 419 | {
|
---|
| 420 | $xml = file_get_contents( $fn );
|
---|
| 421 | $noise_data = parse_xml( $xml, "noise" );
|
---|
| 422 | $type = ( $noise_data[ 'type' ] == "ri" ) ? "ri_noise" : "ti_noise";
|
---|
| 423 | $desc = $noise_data[ 'description' ];
|
---|
| 424 | $modelGUID = $noise_data[ 'modelGUID' ];
|
---|
| 425 | $noiseGUID = $noise_data[ 'noiseGUID' ];
|
---|
| 426 |
|
---|
| 427 | $query = "INSERT INTO noise SET " .
|
---|
| 428 | "noiseGUID='$noiseGUID'," .
|
---|
| 429 | "modelGUID='$modelGUID'," .
|
---|
| 430 | "editedDataID=1, " .
|
---|
| 431 | "modelID=1, " .
|
---|
| 432 | "noiseType='$type'," .
|
---|
| 433 | "description='$desc'," .
|
---|
| 434 | "xml='" . mysql_real_escape_string( $xml, $us3_link ) . "'";
|
---|
| 435 |
|
---|
| 436 | // Add later after all files are processed: editDataID, modelID
|
---|
| 437 |
|
---|
| 438 | $result = mysql_query( $query, $us3_link );
|
---|
| 439 |
|
---|
| 440 | if ( ! $result )
|
---|
| 441 | {
|
---|
| 442 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
|
---|
| 443 | mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) );
|
---|
| 444 | return( -1 );
|
---|
| 445 | }
|
---|
| 446 |
|
---|
| 447 | $id = mysql_insert_id( $us3_link );
|
---|
| 448 | $file_type = "noise";
|
---|
| 449 | $noiseIDs[] = $id;
|
---|
| 450 |
|
---|
| 451 | // Keep track of modelGUIDs for later, when we replace them
|
---|
| 452 | $modelGUIDs[ $id ] = $modelGUID;
|
---|
| 453 |
|
---|
| 454 | }
|
---|
[10] | 455 |
|
---|
| 456 | else if ( preg_match( "/\.mrecs/", $fn ) > 0 ) // It's an mrecs file
|
---|
[1] | 457 | {
|
---|
| 458 | $xml = file_get_contents( $fn );
|
---|
[10] | 459 | $mrecs_data = parse_xml( $xml, "modelrecords" );
|
---|
| 460 | $desc = $mrecs_data[ 'description' ];
|
---|
| 461 | $editGUID = $mrecs_data[ 'editGUID' ];
|
---|
| 462 | write_log( "$me: mrecs file editGUID=$editGUID" );
|
---|
| 463 | if ( strlen( $editGUID ) < 36 )
|
---|
| 464 | $editGUID = "12345678-0123-5678-0123-567890123456";
|
---|
| 465 | $mrecGUID = $mrecs_data[ 'mrecGUID' ];
|
---|
| 466 | $modelGUID = $mrecs_data[ 'modelGUID' ];
|
---|
| 467 |
|
---|
| 468 | $query = "INSERT INTO pcsa_modelrecs SET " .
|
---|
| 469 | "editedDataID=" .
|
---|
| 470 | "(SELECT editedDataID FROM editedData WHERE editGUID='$editGUID')," .
|
---|
| 471 | "modelID=0, " .
|
---|
| 472 | "mrecsGUID='$mrecGUID'," .
|
---|
| 473 | "description='$desc'," .
|
---|
| 474 | "xml='" . mysql_real_escape_string( $xml, $us3_link ) . "'";
|
---|
| 475 |
|
---|
| 476 | // Add later after all files are processed: editDataID, modelID
|
---|
| 477 |
|
---|
| 478 | $result = mysql_query( $query, $us3_link );
|
---|
| 479 |
|
---|
| 480 | if ( ! $result )
|
---|
| 481 | {
|
---|
| 482 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
|
---|
| 483 | mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) );
|
---|
| 484 | return( -1 );
|
---|
| 485 | }
|
---|
| 486 |
|
---|
| 487 | $id = mysql_insert_id( $us3_link );
|
---|
| 488 | $file_type = "mrecs";
|
---|
| 489 | $mrecsIDs[] = $id;
|
---|
| 490 |
|
---|
| 491 | // Keep track of modelGUIDs for later, when we replace them
|
---|
| 492 | $rmodlGUIDs[ $id ] = $modelGUID;
|
---|
| 493 | //write_log( "$me: mrecs file inserted into DB : id=$id" );
|
---|
| 494 | }
|
---|
| 495 |
|
---|
| 496 | else // It's a model file
|
---|
| 497 | {
|
---|
| 498 | $xml = file_get_contents( $fn );
|
---|
[1] | 499 | $model_data = parse_xml( $xml, "model" );
|
---|
| 500 | $description = $model_data[ 'description' ];
|
---|
| 501 | $modelGUID = $model_data[ 'modelGUID' ];
|
---|
| 502 | $editGUID = $model_data[ 'editGUID' ];
|
---|
| 503 |
|
---|
[10] | 504 | if ( $mc_iteration > 1 )
|
---|
| 505 | {
|
---|
| 506 | $miter = sprintf( "_mcN%03d", $mc_iteration );
|
---|
| 507 | $description = preg_replace( "/_mc[0-9]+/", $miter, $description );
|
---|
| 508 | write_log( "$me: MODELUpd: O:description=$description" );
|
---|
| 509 | }
|
---|
| 510 |
|
---|
[1] | 511 | $query = "INSERT INTO model SET " .
|
---|
| 512 | "modelGUID='$modelGUID'," .
|
---|
| 513 | "editedDataID=" .
|
---|
| 514 | "(SELECT editedDataID FROM editedData WHERE editGUID='$editGUID')," .
|
---|
| 515 | "description='$description'," .
|
---|
| 516 | "MCIteration='$mc_iteration'," .
|
---|
| 517 | "meniscus='$meniscus'," .
|
---|
| 518 | "variance='$variance'," .
|
---|
| 519 | "xml='" . mysql_real_escape_string( $xml, $us3_link ) . "'";
|
---|
| 520 |
|
---|
| 521 | $result = mysql_query( $query, $us3_link );
|
---|
| 522 |
|
---|
| 523 | if ( ! $result )
|
---|
| 524 | {
|
---|
| 525 | write_log( "$me: Bad query:\n$query " . mysql_error( $us3_link ) );
|
---|
| 526 | mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) );
|
---|
| 527 | return( -1 );
|
---|
| 528 | }
|
---|
| 529 |
|
---|
| 530 | $modelID = mysql_insert_id( $us3_link );
|
---|
| 531 | $id = $modelID;
|
---|
| 532 | $file_type = "model";
|
---|
| 533 |
|
---|
| 534 | $query = "INSERT INTO modelPerson SET " .
|
---|
| 535 | "modelID=$modelID, personID=$personID";
|
---|
| 536 | $result = mysql_query( $query, $us3_link );
|
---|
| 537 | }
|
---|
| 538 |
|
---|
| 539 | $query = "INSERT INTO HPCAnalysisResultData SET " .
|
---|
| 540 | "HPCAnalysisResultID='$HPCAnalysisResultID', " .
|
---|
| 541 | "HPCAnalysisResultType='$file_type', " .
|
---|
| 542 | "resultID=$id";
|
---|
| 543 |
|
---|
| 544 | $result = mysql_query( $query, $us3_link );
|
---|
| 545 |
|
---|
| 546 | if ( ! $result )
|
---|
| 547 | {
|
---|
| 548 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
|
---|
| 549 | mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) );
|
---|
| 550 | return( -1 );
|
---|
| 551 | }
|
---|
| 552 | }
|
---|
| 553 |
|
---|
| 554 | // Now fix up noise entries
|
---|
| 555 | // For noise files, there is, at most two: ti_noise and ri_noise
|
---|
| 556 | // In this case there will only be one modelID
|
---|
| 557 |
|
---|
| 558 | foreach ( $noiseIDs as $noiseID )
|
---|
| 559 | {
|
---|
| 560 | $modelGUID = $modelGUIDs[ $noiseID ];
|
---|
| 561 | $query = "UPDATE noise SET " .
|
---|
| 562 | "editedDataID=" .
|
---|
[6] | 563 | "(SELECT editedDataID FROM model WHERE modelGUID='$modelGUID')," .
|
---|
[1] | 564 | "modelID=" .
|
---|
| 565 | "(SELECT modelID FROM model WHERE modelGUID='$modelGUID')" .
|
---|
| 566 | "WHERE noiseID=$noiseID";
|
---|
| 567 |
|
---|
| 568 | $result = mysql_query( $query, $us3_link );
|
---|
| 569 |
|
---|
| 570 | if ( ! $result )
|
---|
| 571 | {
|
---|
| 572 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
|
---|
| 573 | mail_to_user( "fail", "Bad query\n$query\n" . mysql_error( $us3_link ) );
|
---|
| 574 | return( -1 );
|
---|
| 575 | }
|
---|
| 576 | }
|
---|
| 577 |
|
---|
[13] | 578 | // Now possibly fix up mrecs entries
|
---|
| 579 |
|
---|
| 580 | foreach ( $mrecsIDs as $mrecsID )
|
---|
| 581 | {
|
---|
| 582 | $modelGUID = $rmodlGUIDs[ $mrecsID ];
|
---|
| 583 | $query = "UPDATE pcsa_modelrecs SET " .
|
---|
| 584 | "modelID=" .
|
---|
| 585 | "(SELECT modelID FROM model WHERE modelGUID='$modelGUID')" .
|
---|
| 586 | "WHERE mrecsID=$mrecsID";
|
---|
| 587 |
|
---|
| 588 | $result = mysql_query( $query, $us3_link );
|
---|
| 589 |
|
---|
| 590 | if ( ! $result )
|
---|
| 591 | {
|
---|
| 592 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
|
---|
| 593 | mail_to_user( "fail", "Bad query\n$query\n" . mysql_error( $us3_link ) );
|
---|
| 594 | return( -1 );
|
---|
| 595 | }
|
---|
| 596 | write_log( "$me: mrecs entry updated : mrecsID=$mrecsID" );
|
---|
| 597 | }
|
---|
| 598 | //write_log( "$me: mrecs entries updated" );
|
---|
| 599 |
|
---|
[1] | 600 | // Copy results to LIMS submit directory (files there are deleted after 7 days)
|
---|
| 601 | global $submit_dir; // LIMS submit files dir
|
---|
| 602 |
|
---|
| 603 | // Get the request guid (LIMS submit dir name)
|
---|
| 604 | $query = "SELECT HPCAnalysisRequestGUID FROM HPCAnalysisRequest " .
|
---|
| 605 | "WHERE HPCAnalysisRequestID = $requestID ";
|
---|
| 606 | $result = mysql_query( $query, $us3_link );
|
---|
| 607 |
|
---|
| 608 | if ( ! $result )
|
---|
| 609 | {
|
---|
| 610 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
|
---|
| 611 | }
|
---|
| 612 |
|
---|
[10] | 613 | // list( $requestGUID ) = mysql_fetch_array( $result );
|
---|
| 614 | //
|
---|
| 615 | // chdir( "$submit_dir/$requestGUID" );
|
---|
| 616 | // $f = fopen( "analysis-results.tar", "w" );
|
---|
| 617 | // fwrite( $f, $tarfile );
|
---|
| 618 | // fclose( $f );
|
---|
[1] | 619 |
|
---|
| 620 | // Clean up
|
---|
[10] | 621 | // chdir ( $work );
|
---|
[1] | 622 | // exec( "rm -rf $gfacID" );
|
---|
| 623 |
|
---|
| 624 | mysql_close( $us3_link );
|
---|
| 625 |
|
---|
| 626 | /////////
|
---|
| 627 | // Send email
|
---|
| 628 |
|
---|
| 629 | mail_to_user( "success", "" );
|
---|
| 630 | }
|
---|
| 631 |
|
---|
| 632 | function mail_to_user( $type, $msg )
|
---|
| 633 | {
|
---|
| 634 | // Note to me. Just changed subject line to include a modified $status instead
|
---|
| 635 | // of the $type variable passed. More informative than just "fail" or "success."
|
---|
| 636 | // See how it works for awhile and then consider removing $type parameter from
|
---|
| 637 | // function.
|
---|
| 638 | global $email_address;
|
---|
| 639 | global $submittime;
|
---|
| 640 | global $queuestatus;
|
---|
| 641 | global $status;
|
---|
| 642 | global $cluster;
|
---|
| 643 | global $jobtype;
|
---|
| 644 | global $org_name;
|
---|
| 645 | global $admin_email;
|
---|
[6] | 646 | global $db;
|
---|
[1] | 647 | global $dbhost;
|
---|
| 648 | global $requestID;
|
---|
| 649 | global $gfacID;
|
---|
| 650 | global $editXMLFilename;
|
---|
[5] | 651 | global $stdout;
|
---|
[1] | 652 |
|
---|
| 653 | global $me;
|
---|
| 654 | write_log( "$me mail_to_user(): sending email to $email_address for $gfacID" );
|
---|
| 655 |
|
---|
| 656 | // Get GFAC status and message
|
---|
[4] | 657 | // function get_gfac_message() also sets global $status
|
---|
| 658 | $gfac_message = get_gfac_message( $gfacID );
|
---|
[10] | 659 | if ( $gfac_message === false ) $gfac_message = "Job Finished";
|
---|
[1] | 660 |
|
---|
| 661 | // Create a status to put in the subject line
|
---|
| 662 | switch ( $status )
|
---|
| 663 | {
|
---|
| 664 | case "COMPLETE":
|
---|
| 665 | $subj_status = 'completed';
|
---|
| 666 | break;
|
---|
| 667 |
|
---|
| 668 | case "CANCELLED":
|
---|
| 669 | case "CANCELED":
|
---|
| 670 | $subj_status = 'canceled';
|
---|
| 671 | break;
|
---|
| 672 |
|
---|
| 673 | case "FAILED":
|
---|
| 674 | $subj_status = 'failed';
|
---|
[10] | 675 | if ( preg_match( "/^US3-A/i", $gfacID ) )
|
---|
| 676 | { // For A/Thrift FAIL, get error message
|
---|
| 677 | $gfac_message = getExperimentErrors( $gfacID );
|
---|
| 678 | //$gfac_message .= "Test ERROR MESSAGE";
|
---|
| 679 | }
|
---|
[1] | 680 | break;
|
---|
| 681 |
|
---|
| 682 | case "ERROR":
|
---|
| 683 | $subj_status = 'unknown error';
|
---|
| 684 | break;
|
---|
| 685 |
|
---|
| 686 | default:
|
---|
| 687 | $subj_status = $status; // For now
|
---|
| 688 | break;
|
---|
| 689 |
|
---|
| 690 | }
|
---|
| 691 |
|
---|
[10] | 692 | $queuestatus = $subj_status;
|
---|
| 693 | $limshost = $dbhost;
|
---|
| 694 | if ( $limshost == 'localhost' )
|
---|
| 695 | $limshost = gethostname();
|
---|
| 696 |
|
---|
[1] | 697 | // Parse the editXMLFilename
|
---|
| 698 | list( $runID, $editID, $dataType, $cell, $channel, $wl, $ext ) =
|
---|
| 699 | explode( ".", $editXMLFilename );
|
---|
| 700 |
|
---|
| 701 | $headers = "From: $org_name Admin<$admin_email>" . "\n";
|
---|
| 702 | $headers .= "Cc: $org_name Admin<$admin_email>" . "\n";
|
---|
| 703 |
|
---|
| 704 | // Set the reply address
|
---|
| 705 | $headers .= "Reply-To: $org_name<$admin_email>" . "\n";
|
---|
| 706 | $headers .= "Return-Path: $org_name<$admin_email>" . "\n";
|
---|
| 707 |
|
---|
| 708 | // Try to avoid spam filters
|
---|
| 709 | $now = time();
|
---|
| 710 | $headers .= "Message-ID: <" . $now . "cleanup@$dbhost>\n";
|
---|
| 711 | $headers .= "X-Mailer: PHP v" . phpversion() . "\n";
|
---|
| 712 | $headers .= "MIME-Version: 1.0" . "\n";
|
---|
| 713 | $headers .= "Content-Transfer-Encoding: 8bit" . "\n";
|
---|
| 714 |
|
---|
| 715 | $subject = "UltraScan Job Notification - $subj_status - " . substr( $gfacID, 0, 16 );
|
---|
| 716 | $message = "
|
---|
| 717 | Your UltraScan job is complete:
|
---|
| 718 |
|
---|
| 719 | Submission Time : $submittime
|
---|
[10] | 720 | LIMS Host : $limshost
|
---|
[1] | 721 | Analysis ID : $gfacID
|
---|
[6] | 722 | Request ID : $requestID ( $db )
|
---|
[1] | 723 | RunID : $runID
|
---|
| 724 | EditID : $editID
|
---|
| 725 | Data Type : $dataType
|
---|
| 726 | Cell/Channel/Wl : $cell / $channel / $wl
|
---|
| 727 | Status : $queuestatus
|
---|
| 728 | Cluster : $cluster
|
---|
| 729 | Job Type : $jobtype
|
---|
| 730 | GFAC Status : $status
|
---|
[4] | 731 | GFAC Message : $gfac_message
|
---|
[5] | 732 | Stdout : $stdout
|
---|
[1] | 733 | ";
|
---|
| 734 |
|
---|
[4] | 735 | if ( $type != "success" ) $message .= "Grid Ctrl Error : $msg\n";
|
---|
[1] | 736 |
|
---|
| 737 | // Handle the error case where an error occurs before fetching the
|
---|
| 738 | // user's email address
|
---|
| 739 | if ( $email_address == "" ) $email_address = $admin_email;
|
---|
| 740 |
|
---|
| 741 | mail( $email_address, $subject, $message, $headers );
|
---|
| 742 | }
|
---|
| 743 |
|
---|
| 744 | function parse_xml( $xml, $type )
|
---|
| 745 | {
|
---|
| 746 | $parser = new XMLReader();
|
---|
| 747 | $parser->xml( $xml );
|
---|
| 748 |
|
---|
| 749 | $results = array();
|
---|
| 750 |
|
---|
| 751 | while ( $parser->read() )
|
---|
| 752 | {
|
---|
| 753 | if ( $parser->name == $type )
|
---|
| 754 | {
|
---|
| 755 | while ( $parser->moveToNextAttribute() )
|
---|
| 756 | {
|
---|
| 757 | $results[ $parser->name ] = $parser->value;
|
---|
| 758 | }
|
---|
| 759 |
|
---|
| 760 | break;
|
---|
| 761 | }
|
---|
| 762 | }
|
---|
| 763 |
|
---|
| 764 | $parser->close();
|
---|
| 765 | return $results;
|
---|
| 766 | }
|
---|
| 767 |
|
---|
| 768 | // Function to get information about the current job GFAC
|
---|
| 769 | function get_gfac_message( $gfacID )
|
---|
| 770 | {
|
---|
| 771 | global $serviceURL;
|
---|
| 772 | global $me;
|
---|
| 773 |
|
---|
| 774 | $hex = "[0-9a-fA-F]";
|
---|
| 775 | if ( ! preg_match( "/^US3-Experiment/i", $gfacID ) &&
|
---|
| 776 | ! preg_match( "/^US3-$hex{8}-$hex{4}-$hex{4}-$hex{4}-$hex{12}$/", $gfacID ) )
|
---|
| 777 | {
|
---|
| 778 | // Then it's not a GFAC job
|
---|
| 779 | return false;
|
---|
| 780 | }
|
---|
| 781 |
|
---|
| 782 | $url = "$serviceURL/jobstatus/$gfacID";
|
---|
| 783 | try
|
---|
| 784 | {
|
---|
| 785 | $post = new HttpRequest( $url, HttpRequest::METH_GET );
|
---|
| 786 | $http = $post->send();
|
---|
| 787 | $xml = $post->getResponseBody();
|
---|
| 788 | }
|
---|
| 789 | catch ( HttpException $e )
|
---|
| 790 | {
|
---|
| 791 | write_log( "$me: Job status not available - $gfacID" );
|
---|
| 792 | return false;
|
---|
| 793 | }
|
---|
| 794 |
|
---|
| 795 | // Parse the result
|
---|
| 796 | $gfac_message = parse_message( $xml );
|
---|
| 797 |
|
---|
| 798 | return $gfac_message;
|
---|
| 799 | }
|
---|
| 800 |
|
---|
| 801 | function parse_message( $xml )
|
---|
| 802 | {
|
---|
[4] | 803 | global $status;
|
---|
[1] | 804 | $status = "";
|
---|
| 805 | $gfac_message = "";
|
---|
| 806 |
|
---|
| 807 | $parser = new XMLReader();
|
---|
| 808 | $parser->xml( $xml );
|
---|
| 809 |
|
---|
| 810 | $results = array();
|
---|
| 811 |
|
---|
| 812 | while( $parser->read() )
|
---|
| 813 | {
|
---|
| 814 | $type = $parser->nodeType;
|
---|
| 815 |
|
---|
| 816 | if ( $type == XMLReader::ELEMENT )
|
---|
| 817 | $name = $parser->name;
|
---|
| 818 |
|
---|
| 819 | else if ( $type == XMLReader::TEXT )
|
---|
| 820 | {
|
---|
| 821 | if ( $name == "status" )
|
---|
| 822 | $status = $parser->value;
|
---|
| 823 | else
|
---|
| 824 | $gfac_message = $parser->value;
|
---|
| 825 | }
|
---|
| 826 | }
|
---|
| 827 |
|
---|
| 828 | $parser->close();
|
---|
| 829 | return $gfac_message;
|
---|
| 830 | }
|
---|
| 831 |
|
---|
| 832 | function get_local_files( $gfac_link, $cluster, $requestID, $id, $gfacID )
|
---|
| 833 | {
|
---|
| 834 | global $work;
|
---|
| 835 | global $work_remote;
|
---|
| 836 | global $me;
|
---|
| 837 | global $db;
|
---|
| 838 | global $status;
|
---|
| 839 |
|
---|
| 840 | // Figure out local working directory
|
---|
| 841 | if ( ! is_dir( "$work/$gfacID" ) ) mkdir( "$work/$gfacID", 0770 );
|
---|
| 842 | $pwd = chdir( "$work/$gfacID" );
|
---|
| 843 |
|
---|
| 844 | // Figure out remote directory
|
---|
| 845 | $remoteDir = sprintf( "$work_remote/$db-%06d", $requestID );
|
---|
| 846 |
|
---|
| 847 | // Get stdout, stderr, output/analysis-results.tar
|
---|
| 848 | $output = array();
|
---|
| 849 | // $cmd = "scp us3@$cluster.uthscsa.edu:$remoteDir/stdout . 2>&1";
|
---|
| 850 | //
|
---|
| 851 | // exec( $cmd, $output, $stat );
|
---|
| 852 | // if ( $stat != 0 )
|
---|
| 853 | // write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
|
---|
| 854 | //
|
---|
| 855 | // $cmd = "scp us3@$cluster.uthscsa.edu:$remoteDir/stderr . 2>&1";
|
---|
| 856 | // exec( $cmd, $output, $stat );
|
---|
| 857 | // if ( $stat != 0 )
|
---|
| 858 | // write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
|
---|
| 859 |
|
---|
| 860 | $cmd = "scp us3@$cluster.uthscsa.edu:$remoteDir/output/analysis-results.tar . 2>&1";
|
---|
| 861 | exec( $cmd, $output, $stat );
|
---|
| 862 | if ( $stat != 0 )
|
---|
| 863 | write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
|
---|
| 864 |
|
---|
| 865 | $cmd = "scp us3@$cluster.uthscsa.edu:$remoteDir/stdout . 2>&1";
|
---|
| 866 | exec( $cmd, $output, $stat );
|
---|
| 867 | if ( $stat != 0 )
|
---|
| 868 | {
|
---|
| 869 | write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
|
---|
| 870 | sleep( 10 );
|
---|
| 871 | write_log( "$me: RETRY" );
|
---|
| 872 | exec( $cmd, $output, $stat );
|
---|
| 873 | if ( $stat != 0 )
|
---|
| 874 | write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
|
---|
| 875 | }
|
---|
| 876 |
|
---|
| 877 | $cmd = "scp us3@$cluster.uthscsa.edu:$remoteDir/stderr . 2>&1";
|
---|
| 878 | exec( $cmd, $output, $stat );
|
---|
| 879 | if ( $stat != 0 )
|
---|
| 880 | {
|
---|
| 881 | write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
|
---|
| 882 | sleep( 10 );
|
---|
| 883 | write_log( "$me: RETRY" );
|
---|
| 884 | exec( $cmd, $output, $stat );
|
---|
| 885 | if ( $stat != 0 )
|
---|
| 886 | write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
|
---|
| 887 | }
|
---|
| 888 |
|
---|
| 889 | // Write the files to gfacDB
|
---|
| 890 |
|
---|
| 891 | if ( file_exists( "stderr" ) ) $stderr = file_get_contents( "stderr" );
|
---|
| 892 | if ( file_exists( "stdout" ) ) $stdout = file_get_contents( "stdout" );
|
---|
| 893 | if ( file_exists( "analysis-results.tar" ) )
|
---|
| 894 | $tarfile = file_get_contents( "analysis-results.tar" );
|
---|
| 895 |
|
---|
| 896 | $query = "UPDATE analysis SET " .
|
---|
| 897 | "stderr='" . mysql_real_escape_string( $stderr, $gfac_link ) . "'," .
|
---|
| 898 | "stdout='" . mysql_real_escape_string( $stdout, $gfac_link ) . "'," .
|
---|
| 899 | "tarfile='" . mysql_real_escape_string( $tarfile, $gfac_link ) . "'";
|
---|
| 900 |
|
---|
| 901 | $result = mysql_query( $query, $gfac_link );
|
---|
| 902 |
|
---|
| 903 | if ( ! $result )
|
---|
| 904 | {
|
---|
| 905 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
|
---|
| 906 | echo "Bad query\n";
|
---|
| 907 | return( -1 );
|
---|
| 908 | }
|
---|
| 909 | }
|
---|
| 910 | ?>
|
---|