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 | * where the job used an Airavata interface.
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7 | *
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8 | */
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9 |
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10 | $email_address = '';
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11 | $queuestatus = '';
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12 | $jobtype = '';
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13 | $db = '';
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14 | $editXMLFilename = '';
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15 | $status = '';
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16 |
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17 | function aira_cleanup( $us3_db, $reqID, $gfac_link )
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18 | {
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19 | global $org_domain;
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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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34 | global $status;
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35 | global $stderr;
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36 | global $stdout;
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37 | global $tarfile;
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38 | global $requestID;
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39 | global $submit_dir;
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40 | $me = 'cleanup_aira.php';
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41 |
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42 | $requestID = $reqID;
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43 | $db = $us3_db;
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44 | write_log( "$me: debug db=$db; requestID=$requestID" );
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45 |
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46 | $us3_link = mysql_connect( $dbhost, $user, $passwd );
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47 |
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48 | if ( ! $us3_link )
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49 | {
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50 | write_log( "$me: could not connect: $dbhost, $user, $passwd" );
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51 | mail_to_user( "fail", "Internal Error $requestID\nCould not connect to DB" );
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52 | return( -1 );
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53 | }
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54 |
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55 | $result = mysql_select_db( $db, $us3_link );
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56 |
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57 | if ( ! $result )
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58 | {
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59 | write_log( "$me: could not select DB $db" );
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60 | mail_to_user( "fail", "Internal Error $requestID\n$could not select DB $db" );
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61 | return( -1 );
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62 | }
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63 |
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64 | // First get basic info for email messages
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65 | $query = "SELECT email, investigatorGUID, editXMLFilename FROM HPCAnalysisRequest " .
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66 | "WHERE HPCAnalysisRequestID=$requestID";
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67 | $result = mysql_query( $query, $us3_link );
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68 |
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69 | if ( ! $result )
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70 | {
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71 | write_log( "$me: Bad query: $query" );
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72 | mail_to_user( "fail", "Internal Error $requestID\n$query\n" . mysql_error( $us3_link ) );
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73 | return( -1 );
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74 | }
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75 |
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76 | list( $email_address, $investigatorGUID, $editXMLFilename ) = mysql_fetch_array( $result );
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77 |
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78 | $query = "SELECT personID FROM people " .
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79 | "WHERE personGUID='$investigatorGUID'";
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80 | $result = mysql_query( $query, $us3_link );
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81 |
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82 | list( $personID ) = mysql_fetch_array( $result );
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83 |
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84 | $query = "SELECT clusterName, submitTime, queueStatus, method " .
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85 | "FROM HPCAnalysisRequest h, HPCAnalysisResult r " .
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86 | "WHERE h.HPCAnalysisRequestID=$requestID " .
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87 | "AND h.HPCAnalysisRequestID=r.HPCAnalysisRequestID";
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88 |
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89 | $result = mysql_query( $query, $us3_link );
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90 |
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91 | if ( ! $result )
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92 | {
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93 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
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94 | return( -1 );
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95 | }
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96 |
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97 | if ( mysql_num_rows( $result ) == 0 )
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98 | {
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99 | write_log( "$me: US3 Table error - No records for requestID: $requestID" );
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100 | return( -1 );
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101 | }
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102 |
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103 | list( $cluster, $submittime, $queuestatus, $jobtype ) = mysql_fetch_array( $result );
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104 |
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105 | // Get the GFAC ID
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106 | $query = "SELECT HPCAnalysisResultID, gfacID FROM HPCAnalysisResult " .
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107 | "WHERE HPCAnalysisRequestID=$requestID";
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108 |
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109 | $result = mysql_query( $query, $us3_link );
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110 |
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111 | if ( ! $result )
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112 | {
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113 | write_log( "$me: Bad query: $query" );
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114 | mail_to_user( "fail", "Internal Error $requestID\n$query\n" . mysql_error( $us3_link ) );
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115 | return( -1 );
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116 | }
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117 |
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118 | list( $HPCAnalysisResultID, $gfacID ) = mysql_fetch_array( $result );
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119 |
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120 | // Get data from global GFAC DB then insert it into US3 DB
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121 |
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122 | $result = mysql_select_db( $gDB, $gfac_link );
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123 |
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124 | if ( ! $result )
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125 | {
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126 | write_log( "$me: Could not connect to DB $gDB" );
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127 | mail_to_user( "fail", "Internal Error $requestID\nCould not connect to DB $gDB" );
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128 | return( -1 );
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129 | }
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130 |
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131 | $query = "SELECT status, cluster, id FROM analysis " .
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132 | "WHERE gfacID='$gfacID'";
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133 |
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134 | $result = mysql_query( $query, $gfac_link );
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135 | if ( ! $result )
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136 | {
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137 | write_log( "$me: Could not select GFAC status for $gfacID" );
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138 | mail_to_user( "fail", "Could not select GFAC status for $gfacID" );
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139 | return( -1 );
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140 | }
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141 |
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142 | list( $status, $cluster, $id ) = mysql_fetch_array( $result );
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143 |
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144 | $is_us3iab = preg_match( "/us3iab/", $cluster );
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145 | $is_local = preg_match( "/-local/", $cluster );
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146 |
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147 | if ( $is_us3iab || $is_local )
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148 | {
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149 | $clushost = $cluster;
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150 | $clushost = preg_replace( "/\-local/", "", $clushost );
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151 | get_local_files( $gfac_link, $clushost, $requestID, $id, $gfacID );
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152 | }
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153 |
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154 |
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155 | $query = "SELECT id FROM analysis " .
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156 | "WHERE gfacID='$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 ) = mysql_fetch_array( $result );
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168 |
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169 | // Get the request guid (LIMS submit dir name)
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170 | $query = "SELECT HPCAnalysisRequestGUID FROM HPCAnalysisRequest " .
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171 | "WHERE HPCAnalysisRequestID = $requestID ";
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172 | $result = mysql_query( $query, $us3_link );
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173 |
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174 | if ( ! $result )
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175 | {
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176 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
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177 | }
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178 |
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179 | list( $requestGUID ) = mysql_fetch_array( $result );
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180 | $output_dir = "$submit_dir/$requestGUID";
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181 |
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182 | // Get stderr,stdout,tarfile from work directory
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183 | if ( ! is_dir( "$output_dir" ) ) mkdir( "$output_dir", 0770 );
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184 | chdir( "$output_dir" );
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185 | //write_log( "$me: gfacID=$gfacID" );
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186 | //write_log( "$me: submit_dir=$submit_dir" );
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187 | //write_log( "$me: requestGUID=$requestGUID" );
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188 | write_log( "$me: output_dir=$output_dir" );
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189 |
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190 | $stderr = "";
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191 | $stdout = "";
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192 | $tarfile = "";
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193 | $fn_stderr = "Ultrascan.stderr";
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194 | $fn_stdout = "Ultrascan.stdout";
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195 | $fn_tarfile = "analysis-results.tar";
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196 | $num_try = 0;
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197 | write_log( "$me: fn_tarfile=$fn_tarfile" );
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198 | while ( ! file_exists( $fn_tarfile ) && $num_try < 3 )
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199 | {
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200 | sleep( 10 );
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201 | $num_try++;
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202 | write_log( "$me: tar-exists: num_try=$num_try" );
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203 | }
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204 |
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205 | $ofiles = scandir( $output_dir );
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206 | foreach ( $ofiles as $ofile )
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207 | {
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208 | if ( preg_match( "/^" . $gfacID . ".*stderr$/", $ofile ) )
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209 | $fn_stderr = $ofile;
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210 | if ( preg_match( "/^" . $gfacID . ".*stdout$/", $ofile ) )
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211 | $fn_stdout = $ofile;
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212 | //write_log( "$me: ofile=$ofile" );
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213 | }
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214 | write_log( "$me: fn_stderr=$fn_stderr" );
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215 | write_log( "$me: fn_stdout=$fn_stdout" );
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216 | if (file_exists($fn_tarfile)) write_log( "$me: fn_tarfile=$fn_tarfile" );
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217 | else write_log( "$me: NOT FOUND: $fn_tarfile" );
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218 |
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219 | $stderr = '';
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220 | $stdout = '';
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221 | $tarfile = '';
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222 | if ( file_exists( $fn_stderr ) ) $stderr = file_get_contents( $fn_stderr );
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223 | if ( file_exists( $fn_stdout ) ) $stdout = file_get_contents( $fn_stdout );
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224 | if ( file_exists( $fn_tarfile ) ) $tarfile = file_get_contents( $fn_tarfile );
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225 | // If stdout,stderr have no content, retry after delay
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226 | if ( strlen( $stdout ) == 0 || strlen( $stderr ) == 0 )
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227 | {
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228 | sleep( 20 );
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229 | if ( file_exists( $fn_stderr ) )
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230 | $stderr = file_get_contents( $fn_stderr );
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231 | if ( file_exists( $fn_stdout ) )
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232 | $stdout = file_get_contents( $fn_stdout );
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233 | }
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234 |
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235 | write_log( "$me: length contents stderr,stdout,tarfile -- "
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236 | . strlen($stderr) . "," . strlen($stdout) . "," . strlen($tarfile) );
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237 |
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238 | if ( $cluster == 'alamo' || $cluster == 'alamo-local' )
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239 | { // Filter "ipath_userinit" lines out of alamo stdout lines
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240 | $prefln = strlen( $stdout );
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241 | $output = array();
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242 | exec( "grep -v 'ipath_userinit' $fn_stdout 2>&1", $output, $err );
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243 | $stdout = implode( "\n", $output );
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244 | $posfln = strlen( $stdout );
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245 | write_log( "$me: fn_stdout : filtered. Length $prefln -> $posfln ." );
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246 | }
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247 |
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248 | // Save queue messages for post-mortem analysis
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249 | $query = "SELECT message, time FROM queue_messages " .
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250 | "WHERE analysisID = $analysisID " .
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251 | "ORDER BY time ";
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252 | $result = mysql_query( $query, $gfac_link );
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253 |
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254 | if ( ! $result )
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255 | {
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256 | // Just log it and continue
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257 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
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258 | }
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259 |
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260 | $now = date( 'Y-m-d H:i:s' );
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261 | $message_log = "US3 DB: $db\n" .
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262 | "RequestID: $requestID\n" .
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263 | "GFAC ID: $gfacID\n" .
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264 | "Processed: $now\n\n" .
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265 | "Queue Messages\n\n" ;
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266 | if ( mysql_num_rows( $result ) > 0 )
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267 | {
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268 | while ( list( $message, $time ) = mysql_fetch_array( $result ) )
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269 | $message_log .= "$time $message\n";
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270 | }
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271 |
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272 | $query = "DELETE FROM queue_messages " .
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273 | "WHERE analysisID = $analysisID ";
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274 |
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275 | $result = mysql_query( $query, $gfac_link );
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276 |
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277 | if ( ! $result )
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278 | {
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279 | // Just log it and continue
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280 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
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281 | }
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282 |
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283 | $query = "SELECT queue_msg FROM analysis " .
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284 | "WHERE gfacID='$gfacID' ";
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285 |
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286 | $result = mysql_query( $query, $gfac_link );
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287 | list( $queue_msg ) = mysql_fetch_array( $result );
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288 |
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289 | // But let's allow for investigation of other large stdout and/or stderr
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290 | if ( strlen( $stdout ) > 20480000 ||
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291 | strlen( $stderr ) > 20480000 )
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292 | write_log( "$me: stdout + stderr larger than 20M - $gfacID\n" );
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293 |
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294 | $message_log .= "\n\n\nStdout Contents\n\n" .
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295 | $stdout .
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296 | "\n\n\nStderr Contents\n\n" .
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297 | $stderr .
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298 | "\n\n\nGFAC Status: $status\n" .
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299 | "GFAC message field: $queue_msg\n";
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300 |
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301 | // Delete data from GFAC DB
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302 | $query = "DELETE from analysis WHERE gfacID='$gfacID'";
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303 |
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304 | $result = mysql_query( $query, $gfac_link );
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305 |
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306 | if ( ! $result )
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307 | {
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308 | // Just log it and continue
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309 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
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310 | }
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311 |
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312 |
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313 | // Try to create it if necessary, and write the file
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314 | // Let's use FILE_APPEND, in case this is the second time around and the
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315 | // GFAC job status was INSERTed, rather than UPDATEd
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316 | if ( ! is_dir( $output_dir ) )
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317 | mkdir( $output_dir, 0775, true );
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318 | $message_filename = "$output_dir/$db-$requestID-messages.txt";
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319 | file_put_contents( $message_filename, $message_log, FILE_APPEND );
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320 | // mysql_close( $gfac_link );
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321 |
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322 | /////////
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323 | // Insert data into HPCAnalysis
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324 |
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325 | $query = "UPDATE HPCAnalysisResult SET " .
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326 | "stderr='" . mysql_real_escape_string( $stderr, $us3_link ) . "', " .
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327 | "stdout='" . mysql_real_escape_string( $stdout, $us3_link ) . "', " .
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328 | "queueStatus='completed' " .
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329 | "WHERE HPCAnalysisResultID=$HPCAnalysisResultID";
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330 |
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331 | $result = mysql_query( $query, $us3_link );
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332 |
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333 | if ( ! $result )
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334 | {
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335 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
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336 | mail_to_user( "fail", "Bad query:\n$query\n" . mysql_error( $us3_link ) );
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337 | return( -1 );
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338 | }
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339 |
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340 | // Delete data from GFAC DB
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341 | $query = "DELETE from analysis WHERE gfacID='$gfacID'";
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342 |
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343 | $result = mysql_query( $query, $gfac_link );
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344 |
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345 | if ( ! $result )
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346 | {
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347 | // Just log it and continue
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348 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
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349 | }
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350 |
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351 | // Expand the tar file
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352 |
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353 | if ( strlen( $tarfile ) == 0 )
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354 | {
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355 | write_log( "$me: No tarfile" );
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356 | mail_to_user( "fail", "No results" );
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357 | return( -1 );
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358 | }
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359 |
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360 | $tar_out = array();
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361 | exec( "tar -xf analysis-results.tar 2>&1", $tar_out, $err );
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362 |
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363 | // Insert the model files and noise files
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364 | $files = file( "analysis_files.txt", FILE_IGNORE_NEW_LINES );
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365 | $noiseIDs = array();
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366 | $modelGUIDs = array();
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367 | $mrecsIDs = array();
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368 | $fns_used = array();
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369 |
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370 | foreach ( $files as $file )
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371 | {
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372 | $split = explode( ";", $file );
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373 |
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374 | if ( count( $split ) > 1 )
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375 | {
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376 | list( $fn, $meniscus, $mc_iteration, $variance ) = explode( ";", $file );
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377 |
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378 | list( $other, $mc_iteration ) = explode( "=", $mc_iteration );
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379 | list( $other, $variance ) = explode( "=", $variance );
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380 | list( $other, $meniscus ) = explode( "=", $meniscus );
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381 | }
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382 | else
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383 | $fn = $file;
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384 |
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385 | if ( preg_match( "/mdl.tmp$/", $fn ) )
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386 | continue;
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387 |
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388 | if ( in_array( $fn, $fns_used ) )
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389 | continue;
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390 |
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391 | $fns_used[] = $fn;
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392 |
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393 | if ( filesize( $fn ) < 100 )
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394 | {
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395 | write_log( "$me:fn is invalid $fn size filesize($fn)" );
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396 | mail_to_user( "fail", "Internal error\n$fn is invalid" );
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397 | return( -1 );
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398 | }
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399 |
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400 | if ( preg_match( "/^job_statistics\.xml$/", $fn ) ) // Job statistics file
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401 | {
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402 | $xml = file_get_contents( $fn );
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403 | $statistics = parse_xml( $xml, 'statistics' );
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404 | // $ntries = 0;
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405 | //
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406 | // while ( $statistics['cpucount'] < 1 && $ntries < 3 )
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407 | // { // job_statistics file not totally copied, so retry
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408 | // sleep( 10 );
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409 | // $xml = file_get_contents( $fn );
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410 | // $statistics = parse_xml( $xml, 'statistics' );
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411 | // $ntries++;
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412 | //write_log( "$me:jobstats retry $ntries" );
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413 | // }
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414 | //write_log( "$me:cputime=$statistics['cputime']" );
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415 |
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416 | $otherdata = parse_xml( $xml, 'id' );
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417 |
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418 | $query = "UPDATE HPCAnalysisResult SET " .
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419 | "wallTime = {$statistics['walltime']}, " .
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420 | "CPUTime = {$statistics['cputime']}, " .
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421 | "CPUCount = {$statistics['cpucount']}, " .
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422 | "max_rss = {$statistics['maxmemory']}, " .
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423 | "startTime = '{$otherdata['starttime']}', " .
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424 | "endTime = '{$otherdata['endtime']}', " .
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425 | "mgroupcount = {$otherdata['groupcount']} " .
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---|
426 | "WHERE HPCAnalysisResultID=$HPCAnalysisResultID";
|
---|
427 | $result = mysql_query( $query, $us3_link );
|
---|
428 |
|
---|
429 | if ( ! $result )
|
---|
430 | {
|
---|
431 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
|
---|
432 | }
|
---|
433 |
|
---|
434 | file_put_contents( "$output_dir/$fn", $xml ); // Copy to submit dir
|
---|
435 |
|
---|
436 | $file_type = "job_stats";
|
---|
437 | $id = 1;
|
---|
438 | }
|
---|
439 |
|
---|
440 | else if ( preg_match( "/\.noise/", $fn ) > 0 ) // It's a noise file
|
---|
441 | {
|
---|
442 | $xml = file_get_contents( $fn );
|
---|
443 | $noise_data = parse_xml( $xml, "noise" );
|
---|
444 | $type = ( $noise_data[ 'type' ] == "ri" ) ? "ri_noise" : "ti_noise";
|
---|
445 | $desc = $noise_data[ 'description' ];
|
---|
446 | $modelGUID = $noise_data[ 'modelGUID' ];
|
---|
447 | $noiseGUID = $noise_data[ 'noiseGUID' ];
|
---|
448 |
|
---|
449 | $query = "INSERT INTO noise SET " .
|
---|
450 | "noiseGUID='$noiseGUID'," .
|
---|
451 | "modelGUID='$modelGUID'," .
|
---|
452 | "editedDataID=1, " .
|
---|
453 | "modelID=1, " .
|
---|
454 | "noiseType='$type'," .
|
---|
455 | "description='$desc'," .
|
---|
456 | "xml='" . mysql_real_escape_string( $xml, $us3_link ) . "'";
|
---|
457 |
|
---|
458 | // Add later after all files are processed: editDataID, modelID
|
---|
459 |
|
---|
460 | $result = mysql_query( $query, $us3_link );
|
---|
461 |
|
---|
462 | if ( ! $result )
|
---|
463 | {
|
---|
464 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
|
---|
465 | mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) );
|
---|
466 | return( -1 );
|
---|
467 | }
|
---|
468 |
|
---|
469 | $id = mysql_insert_id( $us3_link );
|
---|
470 | $file_type = "noise";
|
---|
471 | $noiseIDs[] = $id;
|
---|
472 |
|
---|
473 | // Keep track of modelGUIDs for later, when we replace them
|
---|
474 | $modelGUIDs[ $id ] = $modelGUID;
|
---|
475 |
|
---|
476 | }
|
---|
477 |
|
---|
478 | else if ( preg_match( "/\.mrecs/", $fn ) > 0 ) // It's an mrecs file
|
---|
479 | {
|
---|
480 | $xml = file_get_contents( $fn );
|
---|
481 | $mrecs_data = parse_xml( $xml, "modelrecords" );
|
---|
482 | $desc = $mrecs_data[ 'description' ];
|
---|
483 | $editGUID = $mrecs_data[ 'editGUID' ];
|
---|
484 | write_log( "$me: mrecs file editGUID=$editGUID" );
|
---|
485 | if ( strlen( $editGUID ) < 36 )
|
---|
486 | $editGUID = "12345678-0123-5678-0123-567890123456";
|
---|
487 | $mrecGUID = $mrecs_data[ 'mrecGUID' ];
|
---|
488 | $modelGUID = $mrecs_data[ 'modelGUID' ];
|
---|
489 |
|
---|
490 | $query = "INSERT INTO pcsa_modelrecs SET " .
|
---|
491 | "editedDataID=" .
|
---|
492 | "(SELECT editedDataID FROM editedData WHERE editGUID='$editGUID')," .
|
---|
493 | "modelID=0, " .
|
---|
494 | "mrecsGUID='$mrecGUID'," .
|
---|
495 | "description='$desc'," .
|
---|
496 | "xml='" . mysql_real_escape_string( $xml, $us3_link ) . "'";
|
---|
497 |
|
---|
498 | // Add later after all files are processed: editDataID, modelID
|
---|
499 |
|
---|
500 | $result = mysql_query( $query, $us3_link );
|
---|
501 |
|
---|
502 | if ( ! $result )
|
---|
503 | {
|
---|
504 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
|
---|
505 | mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) );
|
---|
506 | return( -1 );
|
---|
507 | }
|
---|
508 |
|
---|
509 | $id = mysql_insert_id( $us3_link );
|
---|
510 | $file_type = "mrecs";
|
---|
511 | $mrecsIDs[] = $id;
|
---|
512 |
|
---|
513 | // Keep track of modelGUIDs for later, when we replace them
|
---|
514 | $rmodlGUIDs[ $id ] = $modelGUID;
|
---|
515 | //write_log( "$me: mrecs file inserted into DB : id=$id" );
|
---|
516 | }
|
---|
517 |
|
---|
518 | else if ( preg_match( "/\.model/", $fn ) > 0 ) // It's a model file
|
---|
519 | {
|
---|
520 | $xml = file_get_contents( $fn );
|
---|
521 | $model_data = parse_xml( $xml, "model" );
|
---|
522 | $description = $model_data[ 'description' ];
|
---|
523 | $modelGUID = $model_data[ 'modelGUID' ];
|
---|
524 | $editGUID = $model_data[ 'editGUID' ];
|
---|
525 |
|
---|
526 | if ( $mc_iteration > 1 )
|
---|
527 | {
|
---|
528 | $miter = sprintf( "_mcN%03d", $mc_iteration );
|
---|
529 | $description = preg_replace( "/_mc[0-9]+/", $miter, $description );
|
---|
530 | write_log( "$me: MODELUpd: O:description=$description" );
|
---|
531 | }
|
---|
532 |
|
---|
533 | $query = "INSERT INTO model SET " .
|
---|
534 | "modelGUID='$modelGUID'," .
|
---|
535 | "editedDataID=" .
|
---|
536 | "(SELECT editedDataID FROM editedData WHERE editGUID='$editGUID')," .
|
---|
537 | "description='$description'," .
|
---|
538 | "MCIteration='$mc_iteration'," .
|
---|
539 | "meniscus='$meniscus'," .
|
---|
540 | "variance='$variance'," .
|
---|
541 | "xml='" . mysql_real_escape_string( $xml, $us3_link ) . "'";
|
---|
542 |
|
---|
543 | $result = mysql_query( $query, $us3_link );
|
---|
544 |
|
---|
545 | if ( ! $result )
|
---|
546 | {
|
---|
547 | write_log( "$me: Bad query:\n$query " . mysql_error( $us3_link ) );
|
---|
548 | mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) );
|
---|
549 | return( -1 );
|
---|
550 | }
|
---|
551 |
|
---|
552 | $modelID = mysql_insert_id( $us3_link );
|
---|
553 | $id = $modelID;
|
---|
554 | $file_type = "model";
|
---|
555 |
|
---|
556 | $query = "INSERT INTO modelPerson SET " .
|
---|
557 | "modelID=$modelID, personID=$personID";
|
---|
558 | $result = mysql_query( $query, $us3_link );
|
---|
559 | }
|
---|
560 |
|
---|
561 | else // Undetermined type: skip result data update
|
---|
562 | continue;
|
---|
563 |
|
---|
564 | $query = "INSERT INTO HPCAnalysisResultData SET " .
|
---|
565 | "HPCAnalysisResultID='$HPCAnalysisResultID', " .
|
---|
566 | "HPCAnalysisResultType='$file_type', " .
|
---|
567 | "resultID=$id";
|
---|
568 |
|
---|
569 | $result = mysql_query( $query, $us3_link );
|
---|
570 |
|
---|
571 | if ( ! $result )
|
---|
572 | {
|
---|
573 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
|
---|
574 | mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) );
|
---|
575 | return( -1 );
|
---|
576 | }
|
---|
577 | }
|
---|
578 |
|
---|
579 | // Now fix up noise entries
|
---|
580 | // For noise files, there is, at most two: ti_noise and ri_noise
|
---|
581 | // In this case there will only be one modelID
|
---|
582 |
|
---|
583 | foreach ( $noiseIDs as $noiseID )
|
---|
584 | {
|
---|
585 | $modelGUID = $modelGUIDs[ $noiseID ];
|
---|
586 | $query = "UPDATE noise SET " .
|
---|
587 | "editedDataID=" .
|
---|
588 | "(SELECT editedDataID FROM model WHERE modelGUID='$modelGUID')," .
|
---|
589 | "modelID=" .
|
---|
590 | "(SELECT modelID FROM model WHERE modelGUID='$modelGUID')" .
|
---|
591 | "WHERE noiseID=$noiseID";
|
---|
592 |
|
---|
593 | $result = mysql_query( $query, $us3_link );
|
---|
594 |
|
---|
595 | if ( ! $result )
|
---|
596 | {
|
---|
597 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
|
---|
598 | mail_to_user( "fail", "Bad query\n$query\n" . mysql_error( $us3_link ) );
|
---|
599 | return( -1 );
|
---|
600 | }
|
---|
601 | }
|
---|
602 |
|
---|
603 | // Now possibly fix up mrecs entries
|
---|
604 |
|
---|
605 | foreach ( $mrecsIDs as $mrecsID )
|
---|
606 | {
|
---|
607 | $modelGUID = $rmodlGUIDs[ $mrecsID ];
|
---|
608 | $query = "UPDATE pcsa_modelrecs SET " .
|
---|
609 | "modelID=" .
|
---|
610 | "(SELECT modelID FROM model WHERE modelGUID='$modelGUID')" .
|
---|
611 | "WHERE mrecsID=$mrecsID";
|
---|
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: mrecs entry updated : mrecsID=$mrecsID" );
|
---|
622 | }
|
---|
623 | //write_log( "$me: mrecs entries updated" );
|
---|
624 |
|
---|
625 | // Copy results to LIMS submit directory (files there are deleted after 7 days)
|
---|
626 | global $submit_dir; // LIMS submit files dir
|
---|
627 |
|
---|
628 | // Get the request guid (LIMS submit dir name)
|
---|
629 | $query = "SELECT HPCAnalysisRequestGUID FROM HPCAnalysisRequest " .
|
---|
630 | "WHERE HPCAnalysisRequestID = $requestID ";
|
---|
631 | $result = mysql_query( $query, $us3_link );
|
---|
632 |
|
---|
633 | if ( ! $result )
|
---|
634 | {
|
---|
635 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
|
---|
636 | }
|
---|
637 |
|
---|
638 | // list( $requestGUID ) = mysql_fetch_array( $result );
|
---|
639 | //
|
---|
640 | // chdir( "$submit_dir/$requestGUID" );
|
---|
641 | // $f = fopen( "analysis-results.tar", "w" );
|
---|
642 | // fwrite( $f, $tarfile );
|
---|
643 | // fclose( $f );
|
---|
644 |
|
---|
645 | // Clean up
|
---|
646 | // chdir ( $work );
|
---|
647 | // exec( "rm -rf $gfacID" );
|
---|
648 |
|
---|
649 | mysql_close( $us3_link );
|
---|
650 |
|
---|
651 | /////////
|
---|
652 | // Send email
|
---|
653 |
|
---|
654 | mail_to_user( "success", "" );
|
---|
655 | }
|
---|
656 |
|
---|
657 | function mail_to_user( $type, $msg )
|
---|
658 | {
|
---|
659 | // Note to me. Just changed subject line to include a modified $status instead
|
---|
660 | // of the $type variable passed. More informative than just "fail" or "success."
|
---|
661 | // See how it works for awhile and then consider removing $type parameter from
|
---|
662 | // function.
|
---|
663 | global $email_address;
|
---|
664 | global $submittime;
|
---|
665 | global $queuestatus;
|
---|
666 | global $status;
|
---|
667 | global $cluster;
|
---|
668 | global $jobtype;
|
---|
669 | global $org_name;
|
---|
670 | global $admin_email;
|
---|
671 | global $db;
|
---|
672 | global $dbhost;
|
---|
673 | global $requestID;
|
---|
674 | global $gfacID;
|
---|
675 | global $editXMLFilename;
|
---|
676 | global $stdout;
|
---|
677 | global $org_domain;
|
---|
678 |
|
---|
679 | global $me;
|
---|
680 | write_log( "$me mail_to_user(): sending email to $email_address for $gfacID" );
|
---|
681 |
|
---|
682 | // Get GFAC status and message
|
---|
683 | // function get_gfac_message() also sets global $status
|
---|
684 | $gfac_message = get_gfac_message( $gfacID );
|
---|
685 | if ( $gfac_message === false ) $gfac_message = "Job Finished";
|
---|
686 |
|
---|
687 | // Create a status to put in the subject line
|
---|
688 | switch ( $status )
|
---|
689 | {
|
---|
690 | case "COMPLETE":
|
---|
691 | $subj_status = 'completed';
|
---|
692 | break;
|
---|
693 |
|
---|
694 | case "CANCELLED":
|
---|
695 | case "CANCELED":
|
---|
696 | $subj_status = 'canceled';
|
---|
697 | break;
|
---|
698 |
|
---|
699 | case "FAILED":
|
---|
700 | $subj_status = 'failed';
|
---|
701 | if ( preg_match( "/^US3-A/i", $gfacID ) )
|
---|
702 | { // For A/Thrift FAIL, get error message
|
---|
703 | $gfac_message = getExperimentErrors( $gfacID );
|
---|
704 | //$gfac_message .= "Test ERROR MESSAGE";
|
---|
705 | }
|
---|
706 | break;
|
---|
707 |
|
---|
708 | case "ERROR":
|
---|
709 | $subj_status = 'unknown error';
|
---|
710 | break;
|
---|
711 |
|
---|
712 | default:
|
---|
713 | $subj_status = $status; // For now
|
---|
714 | break;
|
---|
715 |
|
---|
716 | }
|
---|
717 |
|
---|
718 | $queuestatus = $subj_status;
|
---|
719 | $limshost = $dbhost;
|
---|
720 | if ( $limshost == 'localhost' )
|
---|
721 | {
|
---|
722 | $limshost = gethostname();
|
---|
723 | if ( ! preg_match( "/\./", $limshost ) )
|
---|
724 | $limshost = $limshost . $org_domain;
|
---|
725 | }
|
---|
726 |
|
---|
727 | // Parse the editXMLFilename
|
---|
728 | list( $runID, $editID, $dataType, $cell, $channel, $wl, $ext ) =
|
---|
729 | explode( ".", $editXMLFilename );
|
---|
730 |
|
---|
731 | $headers = "From: $org_name Admin<$admin_email>" . "\n";
|
---|
732 | $headers .= "Cc: $org_name Admin<$admin_email>" . "\n";
|
---|
733 |
|
---|
734 | // Set the reply address
|
---|
735 | $headers .= "Reply-To: $org_name<$admin_email>" . "\n";
|
---|
736 | $headers .= "Return-Path: $org_name<$admin_email>" . "\n";
|
---|
737 |
|
---|
738 | // Try to avoid spam filters
|
---|
739 | $now = time();
|
---|
740 | $headers .= "Message-ID: <" . $now . "cleanup@$dbhost>\n";
|
---|
741 | $headers .= "X-Mailer: PHP v" . phpversion() . "\n";
|
---|
742 | $headers .= "MIME-Version: 1.0" . "\n";
|
---|
743 | $headers .= "Content-Transfer-Encoding: 8bit" . "\n";
|
---|
744 |
|
---|
745 | $subject = "UltraScan Job Notification - $subj_status - " . substr( $gfacID, 0, 16 );
|
---|
746 | $message = "
|
---|
747 | Your UltraScan job is complete:
|
---|
748 |
|
---|
749 | Submission Time : $submittime
|
---|
750 | LIMS Host : $limshost
|
---|
751 | Analysis ID : $gfacID
|
---|
752 | Request ID : $requestID ( $db )
|
---|
753 | RunID : $runID
|
---|
754 | EditID : $editID
|
---|
755 | Data Type : $dataType
|
---|
756 | Cell/Channel/Wl : $cell / $channel / $wl
|
---|
757 | Status : $queuestatus
|
---|
758 | Cluster : $cluster
|
---|
759 | Job Type : $jobtype
|
---|
760 | GFAC Status : $status
|
---|
761 | GFAC Message : $gfac_message
|
---|
762 | Stdout : $stdout
|
---|
763 | ";
|
---|
764 |
|
---|
765 | if ( $type != "success" ) $message .= "Grid Ctrl Error : $msg\n";
|
---|
766 |
|
---|
767 | // Handle the error case where an error occurs before fetching the
|
---|
768 | // user's email address
|
---|
769 | if ( $email_address == "" ) $email_address = $admin_email;
|
---|
770 |
|
---|
771 | mail( $email_address, $subject, $message, $headers );
|
---|
772 | }
|
---|
773 |
|
---|
774 | function parse_xml( $xml, $type )
|
---|
775 | {
|
---|
776 | $parser = new XMLReader();
|
---|
777 | $parser->xml( $xml );
|
---|
778 |
|
---|
779 | $results = array();
|
---|
780 |
|
---|
781 | while ( $parser->read() )
|
---|
782 | {
|
---|
783 | if ( $parser->name == $type )
|
---|
784 | {
|
---|
785 | while ( $parser->moveToNextAttribute() )
|
---|
786 | {
|
---|
787 | $results[ $parser->name ] = $parser->value;
|
---|
788 | }
|
---|
789 |
|
---|
790 | break;
|
---|
791 | }
|
---|
792 | }
|
---|
793 |
|
---|
794 | $parser->close();
|
---|
795 | return $results;
|
---|
796 | }
|
---|
797 |
|
---|
798 | // Function to get information about the current job GFAC
|
---|
799 | function get_gfac_message( $gfacID )
|
---|
800 | {
|
---|
801 | global $serviceURL;
|
---|
802 | global $me;
|
---|
803 |
|
---|
804 | $hex = "[0-9a-fA-F]";
|
---|
805 | if ( ! preg_match( "/^US3-Experiment/i", $gfacID ) &&
|
---|
806 | ! preg_match( "/^US3-$hex{8}-$hex{4}-$hex{4}-$hex{4}-$hex{12}$/", $gfacID ) )
|
---|
807 | {
|
---|
808 | // Then it's not a GFAC job
|
---|
809 | return false;
|
---|
810 | }
|
---|
811 |
|
---|
812 | $url = "$serviceURL/jobstatus/$gfacID";
|
---|
813 | try
|
---|
814 | {
|
---|
815 | $post = new HttpRequest( $url, HttpRequest::METH_GET );
|
---|
816 | $http = $post->send();
|
---|
817 | $xml = $post->getResponseBody();
|
---|
818 | }
|
---|
819 | catch ( HttpException $e )
|
---|
820 | {
|
---|
821 | write_log( "$me: Job status not available - $gfacID" );
|
---|
822 | return false;
|
---|
823 | }
|
---|
824 |
|
---|
825 | // Parse the result
|
---|
826 | $gfac_message = parse_message( $xml );
|
---|
827 |
|
---|
828 | return $gfac_message;
|
---|
829 | }
|
---|
830 |
|
---|
831 | function parse_message( $xml )
|
---|
832 | {
|
---|
833 | global $status;
|
---|
834 | $status = "";
|
---|
835 | $gfac_message = "";
|
---|
836 |
|
---|
837 | $parser = new XMLReader();
|
---|
838 | $parser->xml( $xml );
|
---|
839 |
|
---|
840 | $results = array();
|
---|
841 |
|
---|
842 | while( $parser->read() )
|
---|
843 | {
|
---|
844 | $type = $parser->nodeType;
|
---|
845 |
|
---|
846 | if ( $type == XMLReader::ELEMENT )
|
---|
847 | $name = $parser->name;
|
---|
848 |
|
---|
849 | else if ( $type == XMLReader::TEXT )
|
---|
850 | {
|
---|
851 | if ( $name == "status" )
|
---|
852 | $status = $parser->value;
|
---|
853 | else
|
---|
854 | $gfac_message = $parser->value;
|
---|
855 | }
|
---|
856 | }
|
---|
857 |
|
---|
858 | $parser->close();
|
---|
859 | return $gfac_message;
|
---|
860 | }
|
---|
861 |
|
---|
862 | function get_local_files( $gfac_link, $cluster, $requestID, $id, $gfacID )
|
---|
863 | {
|
---|
864 | global $work;
|
---|
865 | global $work_remote;
|
---|
866 | global $me;
|
---|
867 | global $db;
|
---|
868 | global $status;
|
---|
869 | $is_us3iab = preg_match( "/us3iab/", $cluster );
|
---|
870 |
|
---|
871 | // Figure out remote directory
|
---|
872 | $remoteDir = sprintf( "$work_remote/$db-%06d", $requestID );
|
---|
873 | write_log( "$me: is_us3iab=$is_us3iab remoteDir=$remoteDir" );
|
---|
874 |
|
---|
875 | // Get stdout, stderr, output/analysis-results.tar
|
---|
876 | $output = array();
|
---|
877 |
|
---|
878 | if ( $is_us3iab == 0 )
|
---|
879 | {
|
---|
880 | // Figure out local working directory
|
---|
881 | if ( ! is_dir( "$work/$gfacID" ) ) mkdir( "$work/$gfacID", 0770 );
|
---|
882 | $pwd = chdir( "$work/$gfacID" );
|
---|
883 |
|
---|
884 | $cmd = "scp us3@$cluster.uthscsa.edu:$remoteDir/output/analysis-results.tar . 2>&1";
|
---|
885 |
|
---|
886 | exec( $cmd, $output, $stat );
|
---|
887 | if ( $stat != 0 )
|
---|
888 | write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
|
---|
889 |
|
---|
890 | $cmd = "scp us3@$cluster.uthscsa.edu:$remoteDir/stdout . 2>&1";
|
---|
891 |
|
---|
892 | exec( $cmd, $output, $stat );
|
---|
893 | if ( $stat != 0 )
|
---|
894 | {
|
---|
895 | write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
|
---|
896 | sleep( 10 );
|
---|
897 | write_log( "$me: RETRY" );
|
---|
898 | exec( $cmd, $output, $stat );
|
---|
899 | if ( $stat != 0 )
|
---|
900 | write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
|
---|
901 | }
|
---|
902 |
|
---|
903 | $cmd = "scp us3@$cluster.uthscsa.edu:$remoteDir/stderr . 2>&1";
|
---|
904 |
|
---|
905 | exec( $cmd, $output, $stat );
|
---|
906 | if ( $stat != 0 )
|
---|
907 | {
|
---|
908 | write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
|
---|
909 | sleep( 10 );
|
---|
910 | write_log( "$me: RETRY" );
|
---|
911 | exec( $cmd, $output, $stat );
|
---|
912 | if ( $stat != 0 )
|
---|
913 | write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
|
---|
914 | }
|
---|
915 | }
|
---|
916 | else
|
---|
917 | {
|
---|
918 | $pwd = chdir( "$remoteDir" );
|
---|
919 | write_log( "$me: IS US3IAB: pwd=$pwd $remoteDir");
|
---|
920 | }
|
---|
921 |
|
---|
922 |
|
---|
923 | // Write the files to gfacDB
|
---|
924 |
|
---|
925 | if ( file_exists( "stderr" ) )
|
---|
926 | { // Filter stderr to not have libnnls debug lines
|
---|
927 | exec( "mv stderr stderr+nnls", $output, $stat );
|
---|
928 | exec( "grep -vi nnls stderr+nnls >stderr", $output, $stat );
|
---|
929 | $stderr = file_get_contents( "stderr" );
|
---|
930 | }
|
---|
931 | else
|
---|
932 | $stderr = "";
|
---|
933 | if ( file_exists( "stdout" ) ) $stdout = file_get_contents( "stdout" );
|
---|
934 | $fn1_tarfile = "analysis-results.tar";
|
---|
935 | $fn2_tarfile = "output/" . $fn1_tarfile;
|
---|
936 | if ( file_exists( $fn1_tarfile ) )
|
---|
937 | $tarfile = file_get_contents( $fn1_tarfile );
|
---|
938 | else if ( file_exists( $fn2_tarfile ) )
|
---|
939 | $tarfile = file_get_contents( $fn2_tarfile );
|
---|
940 |
|
---|
941 | $lense = strlen( $stderr );
|
---|
942 | if ( $lense > 1000000 )
|
---|
943 | { // Replace exceptionally large stderr with smaller version
|
---|
944 | exec( "mv stderr stderr-orig", $output, $stat );
|
---|
945 | exec( "head -n 5000 stderr-orig >stderr-h", $output, $stat );
|
---|
946 | exec( "tail -n 5000 stderr-orig >stderr-t", $output, $stat );
|
---|
947 | exec( "cat stderr-h stderr-t >stderr", $output, $stat );
|
---|
948 | $stderr = file_get_contents( "stderr" );
|
---|
949 | }
|
---|
950 | $lent = strlen( $tarfile );
|
---|
951 | write_log( "$me: tarfile size: $lent");
|
---|
952 | $lene = strlen( $stderr );
|
---|
953 | write_log( "$me: stderr size: $lene (was $lense)");
|
---|
954 | $leno = strlen( $stdout );
|
---|
955 | write_log( "$me: stdout size: $leno");
|
---|
956 | $estarf=mysql_real_escape_string($tarfile,$gfac_link);
|
---|
957 | $lenf = strlen($estarf);
|
---|
958 | write_log( "$me: es-tarfile size: $lenf");
|
---|
959 | $esstdo=mysql_real_escape_string($stdout,$gfac_link);
|
---|
960 | $leno = strlen($esstdo);
|
---|
961 | write_log( "$me: es-stdout size: $leno");
|
---|
962 | $esstde=mysql_real_escape_string($stderr,$gfac_link);
|
---|
963 | $lene = strlen($esstde);
|
---|
964 | write_log( "$me: es-stderr size: $lene");
|
---|
965 | $query = "UPDATE analysis SET " .
|
---|
966 | "stderr='" . mysql_real_escape_string( $stderr, $gfac_link ) . "'," .
|
---|
967 | "stdout='" . mysql_real_escape_string( $stdout, $gfac_link ) . "'," .
|
---|
968 | "tarfile='" . mysql_real_escape_string( $tarfile, $gfac_link ) . "'";
|
---|
969 |
|
---|
970 | $result = mysql_query( $query, $gfac_link );
|
---|
971 |
|
---|
972 | if ( ! $result )
|
---|
973 | {
|
---|
974 | write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
|
---|
975 | echo "Bad query\n";
|
---|
976 | return( -1 );
|
---|
977 | }
|
---|
978 | }
|
---|
979 | ?>
|
---|