[imaging browser] Fix download of JSON, Bval and Bvec files when they are on s3 #8354

cmadjar · 2023-02-02T17:44:10Z

Brief summary of changes

This fixes the error 404 users had when they tried to download a JSON, Bval or Bvec file hosted on S3 from the imaging browser.

Fixing this bug also resolved https://github.com/aces/HBCD/issues/227 as new API endpoints needed to be created for those files.

…e used by the imaging browser

php/libraries/Image.class.inc

modules/api/php/endpoints/candidate/visit/image/format.class.inc

modules/api/php/endpoints/candidate/visit/image/format/downloadfile.class.inc

driusan · 2023-02-08T19:45:20Z

modules/api/php/endpoints/candidate/visit/image/format.class.inc

@@ -90,7 +90,11 @@ class Format extends Endpoint
            $handler = new Format\Brainbrowser($this->_image);
            break;
        case 'thumbnail':
-            $handler = new Format\Thumbnail($this->_image);
+        case 'nifti':


aren't thumbnails intended to be displayed inline?

(It looks like the code already had an attachment Content-Disposition, so I guess it doesn't matter..)

yes, the thumbnail is mainly used to be displayed in the imaging browser but it was already available for download in the API and that is the file I used to base all the other classes so I kept it. @driusan does it answer your question?

xlecours

the $_image instance variable is not needed anymore. All the other places are using $this->_info

modules/api/php/endpoints/candidate/visit/image/format/downloadfile.class.inc

xlecours

Xavier is happy as well

driusan · 2023-02-10T17:19:47Z

I'm so happy to hear that @xlecours!

driusan · 2023-02-10T17:20:36Z

modules/api/php/endpoints/candidate/visit/image/format/downloadfile.class.inc

-        if (!$info->isFile()) {
-            error_log('Thumbnail not found');
+        if (!$this->_info->isFile()) {
+            error_log("$this->_file_type file not found");


This should be using the PSR logger, not error_log

@driusan could you elaborate on how to do that? Sorry I am not very versed in the PSR realm apparently...

NDB_Page includes a $this->logger which implements PSR-3 (https://www.php-fig.org/psr/psr-3/) which honours the config settings from the LORIS config. I think this endpoint bypasses NDB_Page, so you might need to copy the initialization from the NDB_Page constructor and then use ie $this->logger->notice("something") (or the appropriate log level)

That would involve changing src/Http/Endpoint to use Psr\Log\LoggerAwareTrait; and add somehting like this in process.

$loris = $request->getAttribute('loris'); $loglevel = $loris->getConfiguration() ->getLogSettings() ->getRequestLogLevel(); $this->logger = new \LORIS\Log\ErrorLogLogger($loglevel);

driusan · 2023-02-10T17:20:49Z

modules/api/php/endpoints/candidate/visit/image/format/downloadfile.class.inc

-        if (!$info->isReadable()) {
-            error_log('Thumbnail exists but is not readable by webserver');
+        if (!$this->_info->isReadable()) {
+            error_log(


src/Http/Endpoint.php

driusan · 2023-02-13T18:42:35Z

modules/api/php/endpoints/candidate/visit/image/format/downloadfile.class.inc

-        if (!$info->isReadable()) {
-            error_log('Thumbnail exists but is not readable by webserver');
+        if (!$this->_info->isReadable()) {
+            $this->logger->notice(


This should probably be logged at the level of "error" log level.

See the different log level definitions in PSR-3. https://www.php-fig.org/psr/psr-3/

The database referencing a file that the server can't read seems more severe than a notice.

Changed to error

xlecours · 2023-02-13T18:58:01Z

I am even more happy now. :)

… are on s3 (aces#8354) This fixes the error 404 users had when they tried to download a JSON, Bval or Bvec file hosted on S3 from the imaging browser. Fixing this bug also resolved aces/HBCD#227 as new API endpoints needed to be created for those files.

cmadjar added 2 commits February 2, 2023 11:10

add download of BIDS JSON, NIfTI + Bval + Bvec to the API so it can b…

a586f1e

…e used by the imaging browser

use API links to download from view session imaging browser

4716737

cmadjar added Bug PR or issue introducing/requiring bug fixes (not mutually exclusive with the Feature label) API PR or issue introducing/requiring modifications to the API code 24.0.0-bugs Issues or bug fix PRs that were raised during the testing of release 24.0.0 labels Feb 2, 2023

cmadjar requested a review from xlecours February 2, 2023 17:44

cmadjar added 3 commits February 2, 2023 12:51

fix phan

c40102c

fix phan

4f3ea96

create one class to do them all

fdb6512

xlecours requested changes Feb 2, 2023

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php/libraries/Image.class.inc Outdated Show resolved Hide resolved

modules/api/php/endpoints/candidate/visit/image/format.class.inc Outdated Show resolved Hide resolved

modules/api/php/endpoints/candidate/visit/image/format/downloadfile.class.inc Outdated Show resolved Hide resolved

cmadjar added 12 commits February 2, 2023 16:12

move switch to the constructor of the class

8bf64cf

fix phpcbf

46aa398

fix phpcbf

e18586b

fix phpcbf

998b34f

fix phpcbf

d0eb91f

fix phpcbf

03a3d42

Xavier's feedback I missed

8c1a236

revert last commit

3f86d70

Xavier's feedback after a good night sleep

1cdce27

remove all ->_check variables

614b334

remove unecessary extra comma

0de005e

remove unecessary extra comma

c1e92b2

xlecours approved these changes Feb 8, 2023

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driusan reviewed Feb 8, 2023

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xlecours requested changes Feb 10, 2023

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cmadjar added 2 commits February 10, 2023 10:22

Xavier's feedback

a76d31c

Make Phan happy

a24a5da

xlecours approved these changes Feb 10, 2023

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driusan reviewed Feb 10, 2023

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cmadjar added 3 commits February 13, 2023 13:01

PSR

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Phan

4fe033a

Phan

55c8dfd

driusan reviewed Feb 13, 2023

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driusan reviewed Feb 13, 2023

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cmadjar added 2 commits February 13, 2023 13:43

Dave's comment

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Dave's comment

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driusan approved these changes Feb 13, 2023

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driusan merged commit 9276ffa into aces:24.1-release Feb 13, 2023

ridz1208 added this to the 24.1.2 milestone Feb 14, 2023

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[imaging browser] Fix download of JSON, Bval and Bvec files when they are on s3 #8354

[imaging browser] Fix download of JSON, Bval and Bvec files when they are on s3 #8354

cmadjar commented Feb 2, 2023

driusan Feb 8, 2023

cmadjar Feb 8, 2023

xlecours left a comment

xlecours left a comment

driusan commented Feb 10, 2023

driusan Feb 10, 2023

cmadjar Feb 10, 2023

driusan Feb 13, 2023

xlecours Feb 13, 2023

driusan Feb 10, 2023

driusan Feb 13, 2023

cmadjar Feb 13, 2023

xlecours commented Feb 13, 2023

[imaging browser] Fix download of JSON, Bval and Bvec files when they are on s3 #8354

[imaging browser] Fix download of JSON, Bval and Bvec files when they are on s3 #8354

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cmadjar commented Feb 2, 2023

Brief summary of changes

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driusan commented Feb 10, 2023

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xlecours commented Feb 13, 2023