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