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Merge pre-release/2024-R4.2 into master (#830)
* LIMS-1432: Add shelxt downstream view (#818) * LIMS-1436: Use auth provider provided logout URL when SSO is enabled (#822) * LIMS-1108: Improve message re international shipping (#721) * LIMS-1396: Use shipping service callback URL to only send emails once shipment is booked (#814) * LIMS-1435: Put CCP4 location into config variable (#821) * LIMS-656: Show auto subsamples if they have data (#817) --------- Co-authored-by: Dean Keeble <[email protected]> Co-authored-by: Guilherme Francisco <[email protected]> Co-authored-by: Mark Williams <[email protected]>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -122,5 +122,10 @@ function validate($service, $ticket) | |
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| return rtrim($resp); | ||
| } | ||
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| function logout() | ||
| { | ||
| return false; | ||
| } | ||
| } | ||
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||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -26,4 +26,9 @@ function authenticate($login, $password) | |
| { | ||
| return true; | ||
| } | ||
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| function logout() | ||
| { | ||
| return false; | ||
| } | ||
| } | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -66,4 +66,9 @@ function authenticate($login, $password) | |
| } | ||
| } | ||
| } | ||
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| function logout() | ||
| { | ||
| return false; | ||
| } | ||
| } | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,91 @@ | ||
| <?php | ||
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| namespace SynchWeb\Downstream\Type; | ||
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| use SynchWeb\Downstream\DownstreamPlugin; | ||
| use SynchWeb\Downstream\DownstreamResult; | ||
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| class Shelxt extends DownstreamPlugin { | ||
| var $has_images = true; | ||
| var $friendlyname = 'Shelxt'; | ||
| var $has_mapmodel = array(1, 0); | ||
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| function _get_shelxt_results_json() { | ||
| $appid = array($this->autoprocprogramid); | ||
| $filepath = $this->db->pq( | ||
| "SELECT app.filePath from autoprocprogramattachment app where autoprocprogramid = :1 and filename = 'shelxt_results.json' ", | ||
| $appid | ||
| ); | ||
| return $filepath; | ||
| } | ||
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| function _get_shelxt_results_png() { | ||
| $appid = array($this->autoprocprogramid); | ||
| $filepath = $this->db->pq( | ||
| "SELECT app.filepath, app.filename from autoprocprogramattachment app where autoprocprogramid = :1 and filename like '%.png%' ", | ||
| $appid | ||
| ); | ||
| return $filepath; | ||
| } | ||
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| function _get_pdb() { | ||
| $appid = array($this->autoprocprogramid); | ||
| $filepath = $this->db->pq( | ||
| "SELECT app.filepath, app.filename from autoprocprogramattachment app where autoprocprogramid = :1 and filename like '%.pdb%' ", | ||
| $appid | ||
| ); | ||
| if (sizeof($filepath)) { | ||
| return $filepath[0]["FILEPATH"] . "/" . $filepath[0]["FILENAME"]; | ||
| } else { | ||
| return; | ||
| } | ||
| } | ||
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| function results() { | ||
| $json_filepath = $this->_get_shelxt_results_json(); | ||
| if (sizeof($json_filepath)) { | ||
| $json_path = $json_filepath[0]["FILEPATH"] . "/shelxt_results.json" ; | ||
| $json_data = file_get_contents($json_path); | ||
| } else { | ||
| $json_data = "[]"; | ||
| } | ||
| $dat = array(); | ||
| $dat['BLOBS'] = 1; | ||
| $dat['SOLUTIONS'] = json_decode($json_data); | ||
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| // scaling_id should always be present, but just in case... | ||
| if (array_key_exists('scaling_id', $this->process['PARAMETERS'])) { | ||
| $integrator = $this->_lookup_autoproc( | ||
| null, | ||
| $this->process['PARAMETERS']['scaling_id'] | ||
| ); | ||
| if ($integrator) { | ||
| $dat['PARENTAUTOPROCPROGRAM'] = $integrator['PROCESSINGPROGRAMS']; | ||
| $dat['PARENTAUTOPROCPROGRAMID'] = $integrator['AUTOPROCPROGRAMID']; | ||
| } | ||
| } | ||
| $results = new DownstreamResult($this); | ||
| $results->data = $dat; | ||
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| return $results; | ||
| } | ||
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| function images($n = 0) { | ||
| $png = $this->_get_shelxt_results_png(); | ||
| if (sizeof($png)) { | ||
| return $png[0]["FILEPATH"] . "/" . $png[0]["FILENAME"]; | ||
| } else { | ||
| return; | ||
| } | ||
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| } | ||
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| function mapmodel($n = 0, $map = false) { | ||
| $pdb = $this->_get_pdb(); | ||
| if (!$pdb) { | ||
| return; | ||
| } else { | ||
| return $pdb; | ||
| } | ||
| } | ||
| } |
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