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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,150 @@ | ||
| <?php | ||
|
|
||
| namespace SynchWeb\Downstream; | ||
|
|
||
| use SynchWeb\Downstream\DownstreamPlugin; | ||
| use SynchWeb\Downstream\DownstreamResult; | ||
|
|
||
| class BigEPPhasing extends DownstreamPlugin { | ||
| var $has_images = true; | ||
| var $has_mapmodel = array(1, 1); | ||
|
|
||
| function results() { | ||
| $dat = array(); | ||
|
|
||
| if (array_key_exists('program_id', $this->process['PARAMETERS'])) { | ||
| $integrator = $this->_lookup_autoproc( | ||
| $this->process['PARAMETERS']['program_id'] | ||
| ); | ||
| if ($integrator) { | ||
| $dat['PARENTAUTOPROCPROGRAM'] = | ||
| $integrator['PROCESSINGPROGRAMS']; | ||
| $dat['PARENTAUTOPROCPROGRAMID'] = | ||
| $integrator['AUTOPROCPROGRAMID']; | ||
| } | ||
| } | ||
|
|
||
| $image = $this->_get_image(); | ||
| $dat['IMAGE'] = file_exists($image); | ||
|
|
||
| $model = $this->_get_attachments('big_ep_model_ispyb.json'); | ||
| $dat['HASMODEL'] = $model && file_exists($model['FILE']); | ||
| if ($model) { | ||
| if (file_exists($model['FILE'])) { | ||
| $json_str = file_get_contents($model['FILE']); | ||
| $json_data = json_decode($json_str, true); | ||
| foreach ( | ||
| array( | ||
| 'RESID' => array('total', 0), | ||
| 'FRAGM' => array('fragments', 0), | ||
| 'MAXLEN' => array('max', 0), | ||
| 'MAPCC' => array('mapcc', 2), | ||
| 'MAPRESOL' => array('mapcc_dmin', 2), | ||
| ) | ||
| as $k => $v | ||
| ) { | ||
| if (array_key_exists($v[0], $json_data)) { | ||
| $dat[$k] = number_format($json_data[$v[0]], $v[1]); | ||
| } else { | ||
| $dat[$k] = null; | ||
| } | ||
| } | ||
| } | ||
| } | ||
|
|
||
| # Read SHELXC logs | ||
| $shx_log = $this->_get_attachments(null, null, "shelxc.log"); | ||
| if (sizeof($shx_log)) { | ||
| $shx_log = $shx_log[0]['FILE']; | ||
| $graph_patterns = array( | ||
| 'CHISQ' => array('Chi-sq', 2), | ||
| 'ISIGI' => array('<I/sig>', 2), | ||
| 'DSIG' => array('<d"/sig>', 2), | ||
| 'CC12' => array('CC(1/2)', 2), | ||
| 'RESO' => array('Resl.', 3), | ||
| ); | ||
|
|
||
|
|
||
| if (file_exists($shx_log)) { | ||
| $lst = explode("\n", file_get_contents($shx_log)); | ||
| $graphs = array(); | ||
| foreach ($lst as $l) { | ||
| foreach ($graph_patterns as $k => $gr) { | ||
| if (strpos($l, $gr[0]) == 1) { | ||
| $graphs[$k] = array_map( | ||
| 'floatval', | ||
| array_slice(preg_split('/\s+/', $l), $gr[1]) | ||
| ); | ||
| } | ||
| } | ||
| } | ||
|
|
||
| $dat['SHELXC'] = array(); | ||
| foreach (array_keys($graph_patterns) as $k) { | ||
| if ($k != 'RESO' and array_key_exists($k, $graphs)) { | ||
| $dat['SHELXC'][$k] = array(); | ||
| } | ||
| } | ||
| if (array_key_exists('RESO', $graphs)) { | ||
| foreach ($graphs['RESO'] as $i => $r) { | ||
| foreach (array_keys($dat['SHELXC']) as $k) { | ||
| if (array_key_exists($i, $graphs[$k])) { | ||
| array_push($dat['SHELXC'][$k], array( | ||
| 1.0 / pow($r, 2), | ||
| $graphs[$k][$i], | ||
| )); | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
|
|
||
| $results = new DownstreamResult($this); | ||
| $results->data = $dat; | ||
|
|
||
| return $results; | ||
| } | ||
|
|
||
| function _get_image() { | ||
| $images = $this->_get_attachments(null, null, '.png'); | ||
| if (sizeof($images)) { | ||
| return $images[0]['FILEPATH'] . '/' . $images[0]['FILENAME']; | ||
| } | ||
| } | ||
|
|
||
| function images($n = 0) { | ||
| return $this->_get_image(); | ||
| } | ||
|
|
||
| function mapmodel($n = 0, $map = false) { | ||
| if ($map) { | ||
| $maps = $this->_get_attachments(null, null, '.map'); | ||
| if (!sizeof($maps)) { | ||
| return; | ||
| } | ||
| $map = $maps[0]; | ||
|
|
||
| $out = | ||
| '/tmp/' . | ||
| $this->autoprocprogramid . | ||
| '_' . | ||
| $this->type . | ||
| '_map.gz'; | ||
| if (!file_exists($out) && file_exists($map['FILE'])) { | ||
| file_put_contents( | ||
| $out, | ||
| gzencode(file_get_contents($map['FILE'])) | ||
| ); | ||
| } | ||
|
|
||
| return $out; | ||
| } else { | ||
| $pdbs = $this->_get_attachments(null, null, '.pdb'); | ||
| if (!sizeof($pdbs)) { | ||
| return; | ||
| } | ||
| return $pdbs[0]['FILE']; | ||
| } | ||
| } | ||
| } |
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