1 | <?php
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2 | /*
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3 | * cleanup_gfac.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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9 | $us3bin = exec( "ls -d ~us3/lims/bin" );
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10 | include_once "$us3bin/listen-config.php";
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11 | $me = 'cleanup_gfac.php';
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12 | $email_address = '';
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13 | $queuestatus = '';
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14 | $jobtype = '';
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15 | $db = '';
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16 | $editXMLFilename = '';
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17 | $status = '';
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18 |
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19 | function gfac_cleanup( $us3_db, $reqID, $gfac_link )
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20 | {
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21 | global $dbhost;
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22 | global $user;
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23 | global $passwd;
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24 | global $db;
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25 | global $guser;
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26 | global $gpasswd;
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27 | global $gDB;
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28 | global $me;
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29 | global $work;
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30 | global $email_address;
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31 | global $queuestatus;
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32 | global $jobtype;
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33 | global $editXMLFilename;
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34 | global $submittime;
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35 | global $status;
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36 | global $stdout;
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37 | global $requestID;
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38 |
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39 | $requestID = $reqID;
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40 | $db = $us3_db;
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41 | write_log( "$me: debug db=$db; requestID=$requestID" );
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42 |
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43 | $us3_link = mysql_connect( $dbhost, $user, $passwd );
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44 |
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45 | if ( ! $us3_link )
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46 | {
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47 | write_log( "$me: could not connect: $dbhost, $user, $passwd" );
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48 | mail_to_user( "fail", "Internal Error $requestID\nCould not connect to DB" );
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49 | return( -1 );
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50 | }
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51 |
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52 | $result = mysql_select_db( $db, $us3_link );
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53 |
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54 | if ( ! $result )
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55 | {
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56 | write_log( "$me: could not select DB $db" );
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57 | mail_to_user( "fail", "Internal Error $requestID\n$could not select DB $db" );
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58 | return( -1 );
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59 | }
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60 |
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61 | // First get basic info for email messages
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62 | $query = "SELECT email, investigatorGUID, editXMLFilename FROM HPCAnalysisRequest " .
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63 | "WHERE HPCAnalysisRequestID=$requestID";
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64 | $result = mysql_query( $query, $us3_link );
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65 |
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66 | if ( ! $result )
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67 | {
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68 | write_log( "$me: Bad query: $query" );
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69 | mail_to_user( "fail", "Internal Error $requestID\n$query\n" . mysql_error( $us3_link ) );
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70 | return( -1 );
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71 | }
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72 |
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73 | list( $email_address, $investigatorGUID, $editXMLFilename ) = mysql_fetch_array( $result );
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74 |
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75 | $query = "SELECT personID FROM people " .
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76 | "WHERE personGUID='$investigatorGUID'";
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77 | $result = mysql_query( $query, $us3_link );
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78 |
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79 | list( $personID ) = mysql_fetch_array( $result );
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80 |
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81 | /*
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82 | $query = "SELECT clusterName, submitTime, queueStatus, method " .
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83 | "FROM HPCAnalysisRequest h LEFT JOIN HPCAnalysisResult " .
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84 | "ON h.HPCAnalysisRequestID=HPCAnalysisResult.HPCAnalysisRequestID " .
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85 | "WHERE h.HPCAnalysisRequestID=$requestID";
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86 | */
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87 | $query = "SELECT clusterName, submitTime, queueStatus, method " .
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88 | "FROM HPCAnalysisRequest h, HPCAnalysisResult r " .
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89 | "WHERE h.HPCAnalysisRequestID=$requestID " .
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90 | "AND h.HPCAnalysisRequestID=r.HPCAnalysisRequestID";
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91 |
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92 | $result = mysql_query( $query, $us3_link );
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93 |
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94 | if ( ! $result )
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95 | {
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96 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
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97 | return( -1 );
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98 | }
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99 |
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100 | if ( mysql_num_rows( $result ) == 0 )
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101 | {
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102 | write_log( "$me: US3 Table error - No records for requestID: $requestID" );
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103 | return( -1 );
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104 | }
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105 |
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106 | list( $cluster, $submittime, $queuestatus, $jobtype ) = mysql_fetch_array( $result );
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107 |
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108 | // Get the GFAC ID
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109 | $query = "SELECT HPCAnalysisResultID, gfacID FROM HPCAnalysisResult " .
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110 | "WHERE HPCAnalysisRequestID=$requestID";
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111 |
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112 | $result = mysql_query( $query, $us3_link );
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113 |
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114 | if ( ! $result )
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115 | {
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116 | write_log( "$me: Bad query: $query" );
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117 | mail_to_user( "fail", "Internal Error $requestID\n$query\n" . mysql_error( $us3_link ) );
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118 | return( -1 );
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119 | }
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120 |
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121 | list( $HPCAnalysisResultID, $gfacID ) = mysql_fetch_array( $result );
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122 |
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123 | ////////
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124 | // Get data from global GFAC DB and insert it into US3 DB
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125 | // $gfac_link = mysql_connect( $dbhost, $guser, $gpasswd );
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126 |
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127 | $result = mysql_select_db( $gDB, $gfac_link );
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128 |
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129 | if ( ! $result )
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130 | {
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131 | write_log( "$me: Could not connect to DB $gDB" );
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132 | mail_to_user( "fail", "Internal Error $requestID\nCould not connect to DB $gDB" );
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133 | return( -1 );
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134 | }
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135 |
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136 | $query = "SELECT status, cluster, id FROM analysis " .
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137 | "WHERE gfacID='$gfacID'";
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138 |
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139 | $result = mysql_query( $query, $gfac_link );
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140 | if ( ! $result )
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141 | {
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142 | write_log( "$me: Could not select GFAC status for $gfacID" );
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143 | mail_to_user( "fail", "Could not select GFAC status for $gfacID" );
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144 | return( -1 );
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145 | }
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146 |
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147 | $num_rows = mysql_num_rows( $result );
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148 | if ( $num_rows == 0 )
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149 | {
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150 | write_log( "$me: Cleanup analysis query found 0 entries for $gfacID" );
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151 | return( 0 );
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152 | }
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153 | //else
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154 | //{
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155 | //write_log( "$me: db=$db; num_rows=$num_rows; queuestatus=$queuestatus" );
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156 | //}
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157 |
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158 | list( $status, $cluster, $id ) = mysql_fetch_array( $result );
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159 | //write_log( "$me: db=$db; requestID=$requestID; status=$status; cluster=$cluster" );
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160 |
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161 | // if ( $cluster == 'bcf-local' || $cluster == 'alamo-local' )
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162 | if ( preg_match( "/\-local/", $cluster ) ||
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163 | preg_match( "/us3iab/", $cluster ) )
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164 | {
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165 | // $clushost = $cluster;
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166 | // $clushost = preg_replace( "/\-local/", "", $clushost );
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167 | $parts = explode( "-", $cluster );
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168 | $clushost = $parts[ 0 ];
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169 | get_local_files( $gfac_link, $clushost, $requestID, $id, $gfacID );
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170 | write_log( "$me: clushost=$clushost reqID=$requestID get_local_files() gfacID=$gfacID" );
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171 | }
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172 | else
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173 | write_log( "$me: NO get_local_files()" );
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174 |
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175 | $query = "SELECT id, stderr, stdout, tarfile FROM analysis " .
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176 | "WHERE gfacID='$gfacID'";
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177 |
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178 | $result = mysql_query( $query, $gfac_link );
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179 |
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180 | if ( ! $result )
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181 | {
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182 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
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183 | mail_to_user( "fail", "Internal error " . mysql_error( $gfac_link ) );
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184 | return( -1 );
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185 | }
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186 |
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187 | $num_rows = mysql_num_rows( $result );
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188 | if ( $num_rows == 0 )
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189 | {
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190 | write_log( "$me: Cleanup analysis query found 0 entries for $gfacID" );
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191 | return( 0 );
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192 | }
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193 |
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194 | list( $analysisID, $stderr, $stdout, $tarfile ) = mysql_fetch_array( $result );
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195 |
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196 | if ( strlen( $tarfile ) > 0 )
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197 | { // Log success at fetch attempt
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198 | write_log( "$me: Successful data fetch: $requestID $gfacID" );
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199 | }
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200 | else
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201 | { // Log failure at fetch attempt
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202 | write_log( "$me: Failed data fetch: $requestID $gfacID" );
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203 | if ( $analysisID == '' )
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204 | $analysisID = '0';
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205 | }
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206 |
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207 | // Save queue messages for post-mortem analysis
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208 | $query = "SELECT message, time FROM queue_messages " .
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209 | "WHERE analysisID = $analysisID " .
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210 | "ORDER BY time ";
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211 | $result = mysql_query( $query, $gfac_link );
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212 |
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213 | if ( ! $result )
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214 | {
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215 | // Just log it and continue
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216 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
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217 | }
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218 |
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219 | $now = date( 'Y-m-d H:i:s' );
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220 | $message_log = "US3 DB: $db\n" .
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221 | "RequestID: $requestID\n" .
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222 | "GFAC ID: $gfacID\n" .
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223 | "Processed: $now\n\n" .
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224 | "Queue Messages\n\n" ;
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225 |
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226 | $need_finish = ( $status == 'COMPLETE' );
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227 |
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228 | if ( mysql_num_rows( $result ) > 0 )
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229 | {
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230 | $time_msg = time();
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231 | while ( list( $message, $time ) = mysql_fetch_array( $result ) )
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232 | {
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233 | //write_log( "$me: message=$message" );
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234 | $message_log .= "$time $message\n";
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235 | if ( preg_match( "/^Finished/i", $message ) )
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236 | $need_finish = false;
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237 | $time_msg = strtotime( $time );
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238 | }
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239 |
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240 | if ( $need_finish )
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241 | { // No 'Finished' yet: forget if too much time has passed
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242 | $time_now = time();
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243 | $tdelta = $time_now - $time_msg;
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244 | write_log( "$me: no-Finish time: tnow=$time_now, tmsg=$time_msg, tdelt=$tdelta" );
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245 | if ( $tdelta > 600 )
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246 | $need_finish = false;
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247 | }
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248 | //write_log( "$me: no-Finish time: tnow=$time_now, tmsg=$time_msg, tdelt=$tdelta" );
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249 | }
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250 | else
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251 | {
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252 | write_log( "$me: No messages for analysisID=$analysisID ." );
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253 | $need_finish = false;
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254 | }
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255 |
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256 | if ( $need_finish )
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257 | {
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258 | write_log( "$me: Cleanup has not yet found 'Finished' for $gfacID" );
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259 | return( 0 );
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260 | }
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261 |
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262 | $query = "DELETE FROM queue_messages " .
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263 | "WHERE analysisID = $analysisID ";
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264 |
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265 | $result = mysql_query( $query, $gfac_link );
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266 |
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267 | if ( ! $result )
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268 | {
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269 | // Just log it and continue
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270 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
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271 | }
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272 |
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273 | // Save stdout, stderr, etc. for message log
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274 | $query = "SELECT stdout, stderr, status, queue_msg FROM analysis " .
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275 | "WHERE gfacID='$gfacID' ";
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276 | $result = mysql_query( $query, $gfac_link );
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277 | try
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278 | {
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279 | // What if this is too large?
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280 | list( $stdout, $stderr, $status, $queue_msg ) = mysql_fetch_array( $result );
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281 | }
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282 | catch ( Exception $e )
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283 | {
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284 | write_log( "$me: stdout + stderr larger than 128M - $gfacID\n" . mysql_error( $gfac_link ) );
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285 | // Just go ahead and clean up
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286 | }
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287 |
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288 | // But let's allow for investigation of other large stdout and/or stderr
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289 | if ( strlen( $stdout ) > 20480000 ||
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290 | strlen( $stderr ) > 20480000 )
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291 | write_log( "$me: stdout + stderr larger than 20M - $gfacID\n" );
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292 |
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293 | $message_log .= "\n\n\nStdout Contents\n\n" .
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294 | $stdout .
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295 | "\n\n\nStderr Contents\n\n" .
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296 | $stderr .
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297 | "\n\n\nGFAC Status: $status\n" .
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298 | "GFAC message field: $queue_msg\n";
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299 |
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300 | // Delete data from GFAC DB
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301 | $query = "DELETE from analysis WHERE gfacID='$gfacID'";
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302 |
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303 | $result = mysql_query( $query, $gfac_link );
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304 |
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305 | if ( ! $result )
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306 | {
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307 | // Just log it and continue
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308 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
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309 | }
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310 | write_log( "$me: GFAC DB entry deleted" );
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311 |
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312 | // Copy queue messages to LIMS submit directory (files there are deleted after 7 days)
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313 | global $submit_dir;
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314 |
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315 | // Get the request guid (LIMS submit dir name)
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316 | $query = "SELECT HPCAnalysisRequestGUID FROM HPCAnalysisRequest " .
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317 | "WHERE HPCAnalysisRequestID = $requestID ";
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318 | $result = mysql_query( $query, $us3_link );
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319 |
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320 | if ( ! $result )
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321 | {
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322 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
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323 | }
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324 |
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325 | list( $requestGUID ) = mysql_fetch_array( $result );
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326 | $output_dir = "$submit_dir/$requestGUID";
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327 | write_log( "$me: Output dir determined: $output_dir" );
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328 |
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329 | // Try to create it if necessary, and write the file
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330 | // Let's use FILE_APPEND, in case this is the second time around and the
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331 | // GFAC job status was INSERTed, rather than UPDATEd
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332 | if ( ! is_dir( $output_dir ) )
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333 | mkdir( $output_dir, 0775, true );
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334 | $message_filename = "$output_dir/$db-$requestID-messages.txt";
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335 | file_put_contents( $message_filename, $message_log, FILE_APPEND );
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336 | // mysql_close( $gfac_link );
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337 | write_log( "$me: *messages.txt written" );
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338 |
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339 | /////////
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340 | // Insert data into HPCAnalysis
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341 |
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342 | $query = "UPDATE HPCAnalysisResult SET " .
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343 | "stderr='" . mysql_real_escape_string( $stderr, $us3_link ) . "', " .
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344 | "stdout='" . mysql_real_escape_string( $stdout, $us3_link ) . "' " .
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345 | "WHERE HPCAnalysisResultID=$HPCAnalysisResultID";
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346 |
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347 | $result = mysql_query( $query, $us3_link );
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348 |
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349 | if ( ! $result )
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350 | {
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351 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
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352 | mail_to_user( "fail", "Bad query:\n$query\n" . mysql_error( $us3_link ) );
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353 | return( -1 );
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354 | }
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355 |
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356 | // Save the tarfile and expand it
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357 |
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358 | if ( strlen( $tarfile ) == 0 )
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359 | {
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360 | write_log( "$me: No tarfile" );
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361 | mail_to_user( "fail", "No results" );
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362 | return( -1 );
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363 | }
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364 |
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365 | // Shouldn't happen
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366 | if ( ! is_dir( "$work" ) )
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367 | {
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368 | write_log( "$me: $work directory does not exist" );
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369 | mail_to_user( "fail", "$work directory does not exist" );
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370 | return( -1 );
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371 | }
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372 |
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373 | if ( ! is_dir( "$work/$gfacID" ) ) mkdir( "$work/$gfacID", 0770 );
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374 | chdir( "$work/$gfacID" );
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375 |
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376 | $f = fopen( "analysis-results.tar", "w" );
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377 | fwrite( $f, $tarfile );
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378 | fclose( $f );
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379 | //write_log( "$me: analysis-results.tar file written to work dir" );
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380 |
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381 | $tar_out = array();
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382 | exec( "tar -xf analysis-results.tar 2>&1", $tar_out, $err );
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383 |
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384 | if ( $err != 0 )
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385 | {
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386 | chdir( $work );
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387 | exec( "rm -r $gfacID" );
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388 | $output = implode( "\n", $tar_out );
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389 |
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390 | write_log( "$me: Bad output tarfile: $output" );
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391 | mail_to_user( "fail", "Bad output file" );
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392 | return( -1 );
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393 | }
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394 | //write_log( "$me: tar files extracted" );
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395 |
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396 | // Insert the model files and noise files
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397 | $files = file( "analysis_files.txt", FILE_IGNORE_NEW_LINES );
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398 | $noiseIDs = array();
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399 | $modelGUIDs = array();
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400 | $mrecsIDs = array();
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401 | $rmodlGUIDs = array();
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402 |
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403 | foreach ( $files as $file )
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404 | {
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405 | $split = explode( ";", $file );
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406 |
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407 | if ( count( $split ) > 1 )
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408 | {
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409 | list( $fn, $meniscus, $mc_iteration, $variance ) = explode( ";", $file );
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410 |
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411 | list( $other, $mc_iteration ) = explode( "=", $mc_iteration );
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412 | list( $other, $variance ) = explode( "=", $variance );
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413 | list( $other, $meniscus ) = explode( "=", $meniscus );
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414 | }
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415 | else
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416 | $fn = $file;
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417 |
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418 | if ( preg_match( "/mdl.tmp$/", $fn ) )
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419 | continue;
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420 |
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421 | if ( filesize( $fn ) < 100 )
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422 | {
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423 | write_log( "$me:fn is invalid $fn" );
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424 | mail_to_user( "fail", "Internal error\n$fn is invalid" );
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425 | return( -1 );
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426 | }
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427 | //write_log( "$me: handling file: $fn" );
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428 |
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429 | if ( preg_match( "/^job_statistics\.xml$/", $fn ) ) // Job statistics file
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430 | {
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431 | $xml = file_get_contents( $fn );
|
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432 | $statistics = parse_xml( $xml, 'statistics' );
|
---|
433 | $otherdata = parse_xml( $xml, 'id' );
|
---|
434 |
|
---|
435 | $query = "UPDATE HPCAnalysisResult SET " .
|
---|
436 | "wallTime = {$statistics['walltime']}, " .
|
---|
437 | "CPUTime = {$statistics['cputime']}, " .
|
---|
438 | "CPUCount = {$statistics['cpucount']}, " .
|
---|
439 | "max_rss = {$statistics['maxmemory']}, " .
|
---|
440 | "startTime = '{$otherdata['starttime']}', " .
|
---|
441 | "endTime = '{$otherdata['endtime']}', " .
|
---|
442 | "mgroupcount = {$otherdata['groupcount']} " .
|
---|
443 | "WHERE HPCAnalysisResultID=$HPCAnalysisResultID";
|
---|
444 | $result = mysql_query( $query, $us3_link );
|
---|
445 |
|
---|
446 | if ( ! $result )
|
---|
447 | {
|
---|
448 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
|
---|
449 | }
|
---|
450 |
|
---|
451 | file_put_contents( "$output_dir/$fn", $xml ); // Copy to submit dir
|
---|
452 | $file_type = "job_stats";
|
---|
453 | //write_log( "$me: job_statistics file updated in Result and written" );
|
---|
454 |
|
---|
455 | }
|
---|
456 |
|
---|
457 | else if ( preg_match( "/\.noise/", $fn ) > 0 ) // It's a noise file
|
---|
458 | {
|
---|
459 | $xml = file_get_contents( $fn );
|
---|
460 | $noise_data = parse_xml( $xml, "noise" );
|
---|
461 | $type = ( $noise_data[ 'type' ] == "ri" ) ? "ri_noise" : "ti_noise";
|
---|
462 | $desc = $noise_data[ 'description' ];
|
---|
463 | $modelGUID = $noise_data[ 'modelGUID' ];
|
---|
464 | $noiseGUID = $noise_data[ 'noiseGUID' ];
|
---|
465 |
|
---|
466 | $query = "INSERT INTO noise SET " .
|
---|
467 | "noiseGUID='$noiseGUID'," .
|
---|
468 | "modelGUID='$modelGUID'," .
|
---|
469 | "editedDataID=2, " .
|
---|
470 | "modelID=1, " .
|
---|
471 | "noiseType='$type'," .
|
---|
472 | "description='$desc'," .
|
---|
473 | "xml='" . mysql_real_escape_string( $xml, $us3_link ) . "'";
|
---|
474 |
|
---|
475 | // Add later after all files are processed: editDataID, modelID
|
---|
476 |
|
---|
477 | $result = mysql_query( $query, $us3_link );
|
---|
478 |
|
---|
479 | if ( ! $result )
|
---|
480 | {
|
---|
481 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
|
---|
482 | mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) );
|
---|
483 | return( -1 );
|
---|
484 | }
|
---|
485 |
|
---|
486 | $id = mysql_insert_id( $us3_link );
|
---|
487 | $file_type = "noise";
|
---|
488 | $noiseIDs[] = $id;
|
---|
489 |
|
---|
490 | // Keep track of modelGUIDs for later, when we replace them
|
---|
491 | $modelGUIDs[ $id ] = $modelGUID;
|
---|
492 | //write_log( "$me: noise file inserted into DB : id=$id" );
|
---|
493 |
|
---|
494 | }
|
---|
495 |
|
---|
496 | else if ( preg_match( "/\.mrecs/", $fn ) > 0 ) // It's an mrecs file
|
---|
497 | {
|
---|
498 | $xml = file_get_contents( $fn );
|
---|
499 | $mrecs_data = parse_xml( $xml, "modelrecords" );
|
---|
500 | $desc = $mrecs_data[ 'description' ];
|
---|
501 | $editGUID = $mrecs_data[ 'editGUID' ];
|
---|
502 | write_log( "$me: mrecs file editGUID=$editGUID" );
|
---|
503 | if ( strlen( $editGUID ) < 36 )
|
---|
504 | $editGUID = "12345678-0123-5678-0123-567890123456";
|
---|
505 | $mrecGUID = $mrecs_data[ 'mrecGUID' ];
|
---|
506 | $modelGUID = $mrecs_data[ 'modelGUID' ];
|
---|
507 |
|
---|
508 | $query = "INSERT INTO pcsa_modelrecs SET " .
|
---|
509 | "editedDataID=" .
|
---|
510 | "(SELECT editedDataID FROM editedData WHERE editGUID='$editGUID')," .
|
---|
511 | "modelID=0, " .
|
---|
512 | "mrecsGUID='$mrecGUID'," .
|
---|
513 | "description='$desc'," .
|
---|
514 | "xml='" . mysql_real_escape_string( $xml, $us3_link ) . "'";
|
---|
515 |
|
---|
516 | // Add later after all files are processed: editDataID, modelID
|
---|
517 |
|
---|
518 | $result = mysql_query( $query, $us3_link );
|
---|
519 |
|
---|
520 | if ( ! $result )
|
---|
521 | {
|
---|
522 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
|
---|
523 | mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) );
|
---|
524 | return( -1 );
|
---|
525 | }
|
---|
526 |
|
---|
527 | $id = mysql_insert_id( $us3_link );
|
---|
528 | $file_type = "mrecs";
|
---|
529 | $mrecsIDs[] = $id;
|
---|
530 |
|
---|
531 | // Keep track of modelGUIDs for later, when we replace them
|
---|
532 | $rmodlGUIDs[ $id ] = $modelGUID;
|
---|
533 | //write_log( "$me: mrecs file inserted into DB : id=$id" );
|
---|
534 | }
|
---|
535 |
|
---|
536 | else if ( preg_match( "/\.model/", $fn ) > 0 ) // It's a model file
|
---|
537 | {
|
---|
538 | $xml = file_get_contents( $fn );
|
---|
539 | $model_data = parse_xml( $xml, "model" );
|
---|
540 | $description = $model_data[ 'description' ];
|
---|
541 | $modelGUID = $model_data[ 'modelGUID' ];
|
---|
542 | $editGUID = $model_data[ 'editGUID' ];
|
---|
543 |
|
---|
544 | if ( $mc_iteration > 1 )
|
---|
545 | {
|
---|
546 | //write_log( "$me: MODELUpd: mc_iteration=$mc_iteration" );
|
---|
547 | $miter = sprintf( "_mcN%03d", $mc_iteration );
|
---|
548 | //write_log( "$me: MODELUpd: miter=$miter" );
|
---|
549 | //write_log( "$me: MODELUpd: I:description=$description" );
|
---|
550 | $description = preg_replace( "/_mc[0-9]+/", $miter, $description );
|
---|
551 | write_log( "$me: MODELUpd: O:description=$description" );
|
---|
552 | }
|
---|
553 |
|
---|
554 | $query = "INSERT INTO model SET " .
|
---|
555 | "modelGUID='$modelGUID'," .
|
---|
556 | "editedDataID=" .
|
---|
557 | "(SELECT editedDataID FROM editedData WHERE editGUID='$editGUID')," .
|
---|
558 | "description='$description'," .
|
---|
559 | "MCIteration='$mc_iteration'," .
|
---|
560 | "meniscus='$meniscus'," .
|
---|
561 | "variance='$variance'," .
|
---|
562 | "xml='" . mysql_real_escape_string( $xml, $us3_link ) . "'";
|
---|
563 |
|
---|
564 | $result = mysql_query( $query, $us3_link );
|
---|
565 |
|
---|
566 | if ( ! $result )
|
---|
567 | {
|
---|
568 | write_log( "$me: Bad query:\n$query " . mysql_error( $us3_link ) );
|
---|
569 | mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) );
|
---|
570 | return( -1 );
|
---|
571 | }
|
---|
572 |
|
---|
573 | $modelID = mysql_insert_id( $us3_link );
|
---|
574 | $id = $modelID;
|
---|
575 | $file_type = "model";
|
---|
576 |
|
---|
577 | $query = "INSERT INTO modelPerson SET " .
|
---|
578 | "modelID=$modelID, personID=$personID";
|
---|
579 | $result = mysql_query( $query, $us3_link );
|
---|
580 | //write_log( "$me: model file inserted into DB : id=$id" );
|
---|
581 | }
|
---|
582 |
|
---|
583 | $query = "INSERT INTO HPCAnalysisResultData SET " .
|
---|
584 | "HPCAnalysisResultID='$HPCAnalysisResultID', " .
|
---|
585 | "HPCAnalysisResultType='$file_type', " .
|
---|
586 | "resultID=$id";
|
---|
587 |
|
---|
588 | $result = mysql_query( $query, $us3_link );
|
---|
589 |
|
---|
590 | if ( ! $result )
|
---|
591 | {
|
---|
592 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
|
---|
593 | mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) );
|
---|
594 | return( -1 );
|
---|
595 | }
|
---|
596 | //write_log( "$me: ResultData updated : file_type=$file_type" );
|
---|
597 | }
|
---|
598 |
|
---|
599 | // Now fix up noise entries
|
---|
600 | // For noise files, there is, at most two: ti_noise and ri_noise
|
---|
601 | // In this case there will only be one modelID
|
---|
602 |
|
---|
603 | foreach ( $noiseIDs as $noiseID )
|
---|
604 | {
|
---|
605 | $modelGUID = $modelGUIDs[ $noiseID ];
|
---|
606 | $query = "UPDATE noise SET " .
|
---|
607 | "editedDataID=" .
|
---|
608 | "(SELECT editedDataID FROM model WHERE modelGUID='$modelGUID')," .
|
---|
609 | "modelID=" .
|
---|
610 | "(SELECT modelID FROM model WHERE modelGUID='$modelGUID')" .
|
---|
611 | "WHERE noiseID=$noiseID";
|
---|
612 |
|
---|
613 | $result = mysql_query( $query, $us3_link );
|
---|
614 |
|
---|
615 | if ( ! $result )
|
---|
616 | {
|
---|
617 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
|
---|
618 | mail_to_user( "fail", "Bad query\n$query\n" . mysql_error( $us3_link ) );
|
---|
619 | return( -1 );
|
---|
620 | }
|
---|
621 | //write_log( "$me: noise entry updated : noiseID=$noiseID" );
|
---|
622 | }
|
---|
623 | //write_log( "$me: noise entries updated" );
|
---|
624 |
|
---|
625 | // Now possibly fix up mrecs entries
|
---|
626 |
|
---|
627 | foreach ( $mrecsIDs as $mrecsID )
|
---|
628 | {
|
---|
629 | $modelGUID = $rmodlGUIDs[ $mrecsID ];
|
---|
630 | $query = "UPDATE pcsa_modelrecs SET " .
|
---|
631 | "modelID=" .
|
---|
632 | "(SELECT modelID FROM model WHERE modelGUID='$modelGUID')" .
|
---|
633 | "WHERE mrecsID=$mrecsID";
|
---|
634 |
|
---|
635 | $result = mysql_query( $query, $us3_link );
|
---|
636 |
|
---|
637 | if ( ! $result )
|
---|
638 | {
|
---|
639 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
|
---|
640 | mail_to_user( "fail", "Bad query\n$query\n" . mysql_error( $us3_link ) );
|
---|
641 | return( -1 );
|
---|
642 | }
|
---|
643 | //write_log( "$me: mrecs entry updated : mrecsID=$mrecsID" );
|
---|
644 | }
|
---|
645 | //write_log( "$me: mrecs entries updated" );
|
---|
646 |
|
---|
647 | // Copy results to LIMS submit directory (files there are deleted after 7 days)
|
---|
648 | global $submit_dir; // LIMS submit files dir
|
---|
649 |
|
---|
650 | // Get the request guid (LIMS submit dir name)
|
---|
651 | $query = "SELECT HPCAnalysisRequestGUID FROM HPCAnalysisRequest " .
|
---|
652 | "WHERE HPCAnalysisRequestID = $requestID ";
|
---|
653 | $result = mysql_query( $query, $us3_link );
|
---|
654 |
|
---|
655 | if ( ! $result )
|
---|
656 | {
|
---|
657 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
|
---|
658 | }
|
---|
659 |
|
---|
660 | list( $requestGUID ) = mysql_fetch_array( $result );
|
---|
661 |
|
---|
662 | chdir( "$submit_dir/$requestGUID" );
|
---|
663 | $f = fopen( "analysis.tar", "w" );
|
---|
664 | fwrite( $f, $tarfile );
|
---|
665 | fclose( $f );
|
---|
666 |
|
---|
667 | // Clean up
|
---|
668 | chdir ( $work );
|
---|
669 | // exec( "rm -rf $gfacID" );
|
---|
670 |
|
---|
671 | mysql_close( $us3_link );
|
---|
672 |
|
---|
673 | /////////
|
---|
674 | // Send email
|
---|
675 |
|
---|
676 | mail_to_user( "success", "" );
|
---|
677 | }
|
---|
678 | ?>
|
---|