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Imaging Browser: Add DICOM download: Redmine 12580 #3501

Merged
merged 11 commits into from
May 16, 2018
Merged

Imaging Browser: Add DICOM download: Redmine 12580 #3501

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9ce94ae
Imaging Browser: Add DICOM download: Redmine 12580
MounaSafiHarab Feb 19, 2018
8f24d2e
update README
MounaSafiHarab Feb 20, 2018
1a9275e
test plan: specify the download dicom option
MounaSafiHarab Feb 20, 2018
94269b3
remove unused key as per Melanies feedback
MounaSafiHarab Feb 22, 2018
b7e0974
rebase aces minor
MounaSafiHarab Feb 26, 2018
1ca82fd
Cecile feedback on View Session
MounaSafiHarab Mar 5, 2018
ed1b8b4
update comment based on Daves feedback
MounaSafiHarab Mar 23, 2018
389d76a
Daves feedback
MounaSafiHarab Mar 23, 2018
821b78a
manual PHPCS to address Daves concern and Nicks feedback for basename
MounaSafiHarab Apr 17, 2018
1cfb14b
nicks comment on missing $
MounaSafiHarab Apr 25, 2018
11d1cdc
Merge remote-tracking branch 'aces/minor' into ImagBrowserCCNAOverrid…
MounaSafiHarab May 10, 2018
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30 changes: 26 additions & 4 deletions htdocs/mri/jiv/get_file.php
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Original file line number Diff line number Diff line change
Expand Up @@ -38,20 +38,26 @@
}

// Checks that config settings are set
$config =& NDB_Config::singleton();
$paths = $config->getSetting('paths');
$config =& NDB_Config::singleton();
$paths = $config->getSetting('paths');
$pipeline = $config->getSetting('imaging_pipeline');

// Basic config validation
$imagePath = $paths['imagePath'];
$DownloadPath = $paths['DownloadPath'];
$mincPath = $paths['mincPath'];
if (empty($imagePath) || empty($DownloadPath) || empty($mincPath)) {
$tarchivePath = $pipeline['tarchiveLibraryDir'];
if (empty($imagePath) || empty($DownloadPath)
|| empty($mincPath) || empty($tarchivePath)
) {
error_log("ERROR: Config settings are missing");
header("HTTP/1.1 500 Internal Server Error");
exit(1);
}

if ($imagePath === '/' || $DownloadPath === '/' || $mincPath === '/') {
if ($imagePath === '/' || $DownloadPath === '/'
|| $mincPath === '/' || tarchivePath === '/'
) {
error_log("ERROR: Path can not be root for security reasons.");
header("HTTP/1.1 500 Internal Server Error");
exit(2);
Expand All @@ -72,6 +78,7 @@
// Find the extension
$path_parts = pathinfo($File);
$FileExt = $path_parts['extension'];
$FileBase = $path_parts['basename'];

//make sure that we have a .nii.gz image if FileExt equal gz
if (strcmp($FileExt, "gz") == 0) {
Expand All @@ -92,6 +99,15 @@
exit(4);
}

// If basename of $File starts with "DCM_", prefix automatically
// inserted by the LORIS-MRI pipeline, identify it as $FileExt:
// "DICOMTAR"
// Caveat: this is not a real file extension, but a LORIS-MRI
// convention to identify archived DICOMs
if (strpos($FileBase, "DCM_") === 0) {
$FileExt = "DICOMTAR";
}

switch($FileExt) {
case 'mnc':
$FullPath = $mincPath . '/' . $File;
Expand Down Expand Up @@ -133,6 +149,12 @@
$MimeType = 'image/vnd.nrrd';
$DownloadFilename = basename($File);
break;
case 'DICOMTAR':
// ADD case for DICOMTAR
$FullPath = $tarchivePath . '/' . $File;
$MimeType = 'application/x-tar';
$DownloadFilename = basename($File);
break;
default:
$FullPath = $DownloadPath . '/' . $File;
$MimeType = 'application/octet-stream';
Expand Down
13 changes: 8 additions & 5 deletions modules/imaging_browser/README.md
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Expand Up @@ -59,7 +59,7 @@ tblScanTypes - This setting determines which scan types are considered "NEW" for
main imaging browser menu page.

ImagingBrowserLinkedInstruments - This setting defines which instruments to
include a link to on the viewsession page.
include a link to on the "View Session" page.

useProjects - This setting determines whether "project" filtering dropdowns exist
on the menu page.
Expand All @@ -68,7 +68,7 @@ useEDC - This setting determines whether "EDC" filtering dropdowns exist
on the menu page.

mantis_url - This setting defines a URL for LORIS to include a link to for bug reporting
on the viewsession page.
on the "View Session" page.

## Interactions with LORIS

Expand All @@ -78,7 +78,10 @@ mantis_url - This setting defines a URL for LORIS to include a link to for bug r
`$LORIS/tools/CouchDB_Import_MRI.php` alongside all other CouchDB
import scripts, but should logically be considered part of this module.)
- The imaging browser module includes links to BrainBrowser to visualize data.
- The control panel on the viewsession page includes links to the instruments
- The control panel on the "View Session" page includes links to instruments
named "mri_parameter_form" and "radiologyreview" if they exist for the
currently viewed session.
- The control panel on the "View Session" page includes links to the instruments
as configured by the study.
- The control panel on the viewsession page includes links to the DICOM Archive
for any DICOM tars associated with the given session.
- The control panel on the "View Session" page includes links to the DICOM Archive
and download capabilities for any DICOM tars associated with the given session.
13 changes: 10 additions & 3 deletions modules/imaging_browser/php/imaging_session_controlpanel.class.inc
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Expand Up @@ -105,13 +105,20 @@ class Imaging_Session_ControlPanel
$params['PCandID'] = $timePoint->getCandID();
$params['PVL'] = $timePoint->getVisitLabel();
}
$tarchiveIDs = $DB->pselect(
"SELECT TarchiveID
// To enable DICOM download: Add pair: tarchiveID, ArchiveLocation
$qresult = $DB->pselect(
"SELECT TarchiveID, ArchiveLocation
FROM tarchive
WHERE PatientName LIKE $ID",
$params
);
$subjectData['tarchiveids'] = $tarchiveIDs;

$tarIDToTarLoc =array();
foreach ($qresult as $v) {
$tarchiveID = $v['TarchiveID'];
$tarIDToTarLoc[$tarchiveID] = $v['ArchiveLocation'];
}
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suggest using array_values() instead of foreach. Prevent unused variable $k.

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removed unused $k. thanks!

$subjectData['tarchiveIDLoc'] = $tarIDToTarLoc;

$config =& \NDB_Config::singleton();

Expand Down
9 changes: 7 additions & 2 deletions modules/imaging_browser/templates/imaging_session_controlpanel.tpl
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Expand Up @@ -35,8 +35,13 @@
{foreach from=$subject.links item=link}
<li><a href="{$baseurl}/{$subject.candid}/{$subject.sessionID}/{$link.BEName}/?commentID={$link.CommentID}">{$link.FEName}</a></li>
{/foreach}
{foreach from=$subject.tarchiveids item=tarchive}
<li><a href="{$baseurl}/dicom_archive/viewDetails/?tarchiveID={$tarchive.TarchiveID}&backURL={$backURL|escape:"url"}">DICOM Archive {$tarchive.TarchiveID}</a></li>{/foreach}
{foreach from=$subject.tarchiveIDLoc key=tarchive item=tarchiveLoc}
<li><a href="{$baseurl}/dicom_archive/viewDetails/?tarchiveID={$tarchive}&backURL={$backURL|escape:"url"}">DICOM Archive {$tarchive}</a></li>
<li><a href="/mri/jiv/get_file.php?file={$tarchiveLoc}" class="btn btn-primary btn-small">
<span class="glyphicon glyphicon-cloud-download"></span><span class="hidden-xs"> Download DICOM {$tarchive}</span>
</a>
</li>
{/foreach}
{if $mantis}
<li><a target="mantis" href="{$mantis}">Report a Bug (Mantis)</a></li>
{/if}
Expand Down
2 changes: 1 addition & 1 deletion modules/imaging_browser/test/imaging_browser_test_plan.md
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Expand Up @@ -11,7 +11,7 @@

### B. ViewSession / Volume List

8. Sidebar: all links work. Ensure that projects can customize (add/remove) their list of instruments that can be linked to from the Configuration/Imaging Modules/Imaging Browser Links to Insruments
8. Sidebar: all links work, including the Download DICOM option. Ensure that projects can customize (add/remove) their list of instruments that can be linked to from the Configuration/Imaging Modules/Imaging Browser Links to Insruments
9. 3d panel overlay etc - they work. Add panel checkbox works. 3D only or 3D+Overlay loads files if at least one image exists and is selected
10. "Visit Level Feedback" - pops up QC window (see section E below)
11. Visit level QC controls (Pass/Fail, Pending, Visit Level Caveat) viewable to all, editable IFF permission imaging_browser_qc
Expand Down