[API] Add Project endpoint "Dicoms" #6775

spell00 · 2020-06-27T00:20:21Z

Brief summary of changes

This Pull Request adds an endpoint at /projects/<project>/dicoms. It returns a complete list of DICOM files contained in a project (and other pertinent informations)

Testing instructions

Go to https://<hostname>/api/v0.0.3/projects/rye/dicoms in a browser. The page should return a JSON in a string with information on all DICOM contained in the project

Link(s) to related issue(s)

Resolves [API] New Project /dicoms endpoint #6774

christinerogers · 2020-08-03T14:38:16Z

@spell00 Is this PR up to date?
If so, @xlecours do you have time to review this? if not let me know and I'll find someone perhaps Cecile.

modules/api/php/models/projectimagesrow.class.inc

modules/api/php/provisioners/projectdicomsrowprovisioner.class.inc

modules/api/php/models/projectdicomsrow.class.inc

modules/api/php/provisioners/projectdicomsrowprovisioner.class.inc

modules/api/php/provisioners/visitdicomsrowprovisioner.class.inc

cmadjar

@spell00 Nice work!

See my comment on the query. Let me know if I missed something or misunderstood the goal of the endpoint. Thanks!

modules/api/php/provisioners/projectdicomsrowprovisioner.class.inc

xlecours · 2020-08-06T14:53:01Z

modules/api/php/models/projectdicomsrow.class.inc

+     *
+     * @param array $row An array of image propeties
+     */
+    public function __construct(array $row)


That constructor is never called.
PDO:statement fetchall instanciate the objects and set their values using __set.

modules/api/php/endpoints/project/dicoms.class.inc

spell00 · 2020-08-20T07:10:24Z

now I get {"Dicoms":{}} when trying to access <host>/api/v0.0.3/projects/rye/dicoms

spell00 · 2020-08-21T21:55:45Z

it is now working again, including the changes requested

christinerogers · 2020-08-24T21:20:34Z

@xlecours and @kongtiaowang - would you have a few minutes to (re)review this PR this week?

modules/api/php/endpoints/project/dicoms.class.inc

christinerogers · 2020-08-27T19:52:10Z

@spell00 this seems like a minor change request -- can you address it and move this forward today?

spell00 · 2020-09-01T14:40:31Z

ok @christinerogers , I'll take care of it today

modules/api/php/endpoints/project/dicoms.class.inc

spell00 · 2020-09-01T20:55:06Z

This new endpoint is not in the specs for v0.0.3, so the changes suggested in this PR need to be added to the API v0.0.4 initiated in PR #6944, which is in progress.

spell00 · 2020-11-02T20:32:23Z

blocked by #7101

spell00 · 2020-11-05T07:01:41Z

@xlecours @driusan It is now passing Travis and ready for final review

modules/api/docs/LorisRESTAPI.md

modules/api/php/provisioners/projectdicomsobjectprovisioner.class.inc

xlecours

I wouldn't mind having @cmadjar backing on this. Are the properties of the Dicoms items ok?

modules/api/docs/LorisRESTAPI_v0.0.4-dev.md

cmadjar · 2021-06-08T13:14:25Z

@xlecours can you take this PR over please? Thank you :)

outdated

ridz1208 · 2021-07-06T17:31:50Z

@cmadjar it seems like @xlecours 's next to latest review approved the changes and asked you to take a second look at it. I think this one is also in your court in that case

from @xlecours

I wouldn't mind having @cmadjar backing on this. Are the properties of the Dicoms items ok?

Squashed commit of the following: commit 817b148 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Mon Nov 9 15:17:49 2020 -0500 adding comment about since parameter commit f4892d6 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Fri Nov 6 13:12:55 2020 -0500 change classname in construct to include namespace commit b4f7f60 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Thu Nov 5 14:40:50 2020 -0500 corrections commit 65eefba Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Thu Nov 5 00:12:31 2020 -0500 fixing endpoint name commit 226230e Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Thu Nov 5 00:00:42 2020 -0500 remove old files commit cc79194 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Wed Nov 4 16:35:17 2020 -0500 CHANGELOG was not updated commit ec0f492 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Wed Nov 4 16:34:23 2020 -0500 CHANGELOG was not updated commit e8c4ad2 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Wed Nov 4 16:23:51 2020 -0500 updating doc update commit 6f34893 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Wed Nov 4 16:05:12 2020 -0500 getting out of rebase hell and solving conflicts commit 2350ea0 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Wed Nov 4 15:46:16 2020 -0500 Revert "rollback to v1.x" This reverts commit d9db7d7. commit 48fdddd Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Wed Nov 4 15:46:08 2020 -0500 Revert "update" This reverts commit 211d96d. commit 2fbf050 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Wed Nov 4 15:45:59 2020 -0500 Revert "Revert "update"" This reverts commit 0022745. commit c1c90fc Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Wed Nov 4 15:45:33 2020 -0500 Revert "removing change to travis" This reverts commit e7e4cb6. commit e7e4cb6 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Wed Nov 4 15:39:04 2020 -0500 removing change to travis commit 0022745 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Wed Nov 4 15:36:07 2020 -0500 Revert "update" This reverts commit 0e89111. commit 211d96d Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Tue Nov 3 13:01:13 2020 -0500 update commit d9db7d7 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Tue Nov 3 11:48:04 2020 -0500 rollback to v1.x commit f8aae97 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Mon Nov 2 14:16:09 2020 -0500 Changing classes names ProjectDicoms commit 71203c1 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Mon Nov 2 13:37:51 2020 -0500 v0.0.4-dev not v0.0.4 commit e125284 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Thu Oct 29 16:11:27 2020 -0400 LorisApiAuthenticatedTest.php had unnecessary modifications commit 92b9517 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Thu Oct 29 16:09:58 2020 -0400 LorisApiAuthenticatedTest.php had unnecessary modifications commit 8c9df99 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Thu Oct 29 11:31:21 2020 -0400 Trying to readd newline at end of file because git complains commit 2f9359a Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Thu Oct 29 11:30:03 2020 -0400 Trying to readd newline at end of file because git complains commit ba45736 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Thu Oct 29 10:32:18 2020 -0400 fixing things commit 2333bed Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Fri Sep 18 12:17:30 2020 -0400 correct integration test typo commit 682e337 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Fri Sep 18 11:11:22 2020 -0400 [API] Corrects the tests for the new Projects Dicoms endpoint commit 6dd799a Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Fri Sep 4 15:12:43 2020 -0400 Adds the integration tests for \Project Dicoms endpoint commit d6ca120 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Fri Aug 21 17:47:57 2020 -0400 [API] weird new file removed commit d36d982 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Fri Aug 21 17:43:26 2020 -0400 [API] Fix Travis again commit d3bdd67 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Mon Aug 3 15:29:55 2020 -0400 [API] Changed toJSON to jsonSerialize and resored strict_types declaration commit 4b70446 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Mon Jun 29 13:30:08 2020 -0400 [API] In \project dicoms endpoints: Corrected travis errors commit 6606b4f Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Tue Jun 23 16:11:12 2020 -0400 [API] Creation of endpoint /project/{project}/dicoms commit 63be090 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Tue Jun 23 16:08:40 2020 -0400 [API] Creation of endpoint /project/{project}/dicoms commit 5f8c88d Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Tue Sep 1 17:56:07 2020 -0400 [API] adds v0.0.4 in the supported versions of the /candidate dicom endpoint commit 97ef8f6 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Tue Sep 1 16:27:15 2020 -0400 [API] correct travis errors commit 4a67189 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Tue Sep 1 15:24:01 2020 -0400 [API] changes version in new spec document and removes other errors commit fd87690 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Tue Sep 1 15:12:35 2020 -0400 initial commit of transition to api v0.0.4 commit 002e090 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Tue Sep 1 14:58:08 2020 -0400 initial commit of transition to api v0.0.4 commit a55b304 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Tue Sep 1 13:04:02 2020 -0400 [API] Candidates are now filtered by allowed project ids commit fe3cb93 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Tue Sep 1 10:34:35 2020 -0400 [API] Add getProjectID to candidatesrow model commit b192d15 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Thu Oct 29 10:32:18 2020 -0400 fixing things commit 806e9b5 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Fri Sep 18 12:35:46 2020 -0400 Announce of the new version of the API in CHANGELOG.md commit 9eb937e Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Fri Sep 4 16:22:37 2020 -0400 Addresses comment to clean code commit fdef2d8 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Wed Sep 2 14:15:28 2020 -0400 [API] Fixes Travis checks in projectdicomsobject commit 9c1cf05 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Wed Sep 2 14:06:22 2020 -0400 [API] Adds Projects \Dicoms endpoint to the specs and corrects FileName to be displayed commit 51b1169 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Wed Sep 2 13:55:30 2020 -0400 Makes it available only in v0.0.4 and Path changed to filename commit 83903b7 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Tue Sep 1 11:12:49 2020 -0400 [API] Removes useless condition in _hasAccess function commit 40afcfc Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Tue Aug 25 15:07:15 2020 -0400 [API] Adding checkign user permission commit 3cd3a66 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Sun Aug 23 14:28:41 2020 -0400 Solves Possibly zero references to use statement in travis commit 0266890 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Fri Aug 21 17:53:54 2020 -0400 [API] correct mistakes commit 42a8d5f Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Fri Aug 21 17:47:57 2020 -0400 [API] weird new file removed commit 27c00c1 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Fri Aug 21 17:46:26 2020 -0400 [API] weird new file removed commit 9cd209d Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Fri Aug 21 17:43:26 2020 -0400 [API] Fix Travis again commit a961386 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Fri Aug 21 17:38:09 2020 -0400 [API] Restroring useless declare(strict_types=1) commit 069b167 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Fri Aug 21 17:33:35 2020 -0400 [API] Remove useless stuff commit 601a5e6 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Fri Aug 21 17:16:25 2020 -0400 [API] Project Dicoms endpoint works with ObjectProvisioner commit 32d997f Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Thu Aug 20 02:34:15 2020 -0400 [API] Chenged to ProjectDicomsObjectProvisioner commit efedeef Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Tue Aug 4 16:37:26 2020 -0400 [API] redeclare strict types and simplify projectdicomsrowprovisioner commit 39b4a26 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Tue Aug 4 16:08:55 2020 -0400 [API] redeclare strict types and simplify projectdicomsrowprovisioner commit 756f93e Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Mon Aug 3 15:29:55 2020 -0400 [API] Changed toJSON to jsonSerialize and resored strict_types declaration commit 93f2c1d Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Mon Aug 3 14:10:58 2020 -0400 [API] Corrections to pass Travis checks commit 108121d Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Wed Jul 1 14:41:50 2020 -0400 [API] Added information on tarchive commit 6376f72 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Tue Jun 30 15:19:59 2020 -0400 [API] Fix other typos commit 5ac0b5b Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Tue Jun 30 15:16:42 2020 -0400 [API] Fix other typos commit 3c7c1e6 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Tue Jun 30 12:41:15 2020 -0400 [API] added endpoints/project/dicoms.class.inc that was left behind commit a50d83c Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Mon Jun 29 13:30:08 2020 -0400 [API] In \project dicoms endpoints: Corrected travis errors commit 97beb63 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Mon Jun 29 11:53:03 2020 -0400 [API] In \project dicoms endpoints: Corrected travis errors commit 26ef029 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Fri Jun 26 20:05:06 2020 -0400 [API] New Project /dicoms endpoint commit 9c51213 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Tue Jun 23 16:11:12 2020 -0400 [API] Creation of endpoint /project/{project}/dicoms commit 8bdad92 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Tue Jun 23 16:10:52 2020 -0400 [API] Creation of endpoint /project/{project}/dicoms commit 7465fe3 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Tue Jun 23 16:08:40 2020 -0400 [API] Creation of endpoint /project/{project}/dicoms commit cf758cd Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Tue Sep 1 13:04:02 2020 -0400 [API] Candidates are now filtered by allowed project ids commit c3ac7fa Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Tue Sep 1 10:53:09 2020 -0400 [API] Adding UserProjectMatch to candidates endpoint commit 1954102 Author: Simon Pelletier <simonjpelletier@gmail.com> Date: Tue Sep 1 10:34:35 2020 -0400 [API] Add getProjectID to candidatesrow model

ridz1208 · 2021-07-06T17:43:07Z

@xlecours @cmadjar just rebased the PR

cmadjar

@ridz1208 thank you for pinging me on this, I did not see the previous comment. See attached minor suggestions. Let me know your thoughts.

cmadjar · 2021-07-06T18:34:09Z

modules/api/docs/LorisRESTAPI_v0.0.4-dev.md

+      "DicomArchiveID": "1.2.840.113745.101000.1022000.39911.6153.5242769",
+      "Archive": "2018/DCM_2018-04-20_ImagingUpload-13-42-zcoZR0.tar",
+      "Source": "/tmp/ImagingUpload-13-42-zcoZR0",
+      "FileName": "DCM_2018-04-20_ImagingUpload-13-42-zcoZR0.tar"


is there any reason why the following fields are not returned?

AcquisitionCount DicomFileCount ScannerManufacturer ScannerModel ScannerSoftware ScannerSerialNumber

Those are fields I could see as being informative to the user accessing the DICOM archives.

Also, I notice that in the JSON response, keys have all kinds of different convention. I would tend to make them consistent (either stick to CamelCase, or _ separated values, consistent casing etc...).

Sorry, my brain gets easily distracted with inconsistencies ;).

cmadjar · 2021-07-06T18:34:48Z

modules/api/php/provisioners/projectdicomsobjectprovisioner.class.inc

+               t.TarchiveID as tarchiveid,
+               t.DicomArchiveID as DicomArchiveID,
+               t.ArchiveLocation as Archive,
+	           t.SourceLocation as Source


Suggested change

t.SourceLocation as Source

t.SourceLocation as Source

ridz1208 · 2021-07-07T17:56:18Z

@xlecours this one is back in your court

cmadjar · 2021-08-10T13:35:32Z

@xlecours this one is in your court. Should be straightforward though?

xlecours · 2022-11-29T17:17:48Z

This still needs work.

The property names in the response should be case-consistent
I think we should hide : CenterID, tarchiveid and Source since they are only meaningful from within the database of on the filesystem.
There should be a link to the resource (where it can be downloaded)
Documentation should be add in the api specification of the api module (schema.yml)

On a side note: could this be done using /dicom_archive instead?

ridz1208 · 2024-07-02T13:42:12Z

@cmadjar assigning to you to bring up at Imaging meeting see if this is still needed

cmadjar · 2024-07-04T14:31:44Z

Discussed during the imaging call of Jul 4th. It is stale and needs work that will not be done in the short term.

spell00 added the State: Needs work PR awaiting additional work by the author to proceed label Jun 29, 2020

spell00 force-pushed the 2020-06-23-AddEndpointProjectDicoms branch from d93a9bf to 50d007c Compare June 30, 2020 16:46

spell00 added Area: API PR or issue related to the API Category: Feature PR or issue that aims to introduce a new feature and removed State: Needs work PR awaiting additional work by the author to proceed labels Jun 30, 2020

spell00 requested a review from xlecours June 30, 2020 19:29

spell00 changed the base branch from master to main July 23, 2020 14:23

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[API] Add Project endpoint "Dicoms" #6775

[API] Add Project endpoint "Dicoms" #6775

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[API] Add Project endpoint "Dicoms" #6775

[API] Add Project endpoint "Dicoms" #6775

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Brief summary of changes

Testing instructions

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