Shanoir issue#1602 nifti management #1849

jcomedouteau · 2023-09-04T13:07:13Z

No description provided.

- Move conversion to microservice

# Conflicts: # shanoir-ng-datasets/src/main/java/org/shanoir/ng/importer/dto/ImportJob.java # shanoir-ng-datasets/src/main/java/org/shanoir/ng/studycard/service/CardsProcessingService.java # shanoir-ng-import/src/main/java/org/shanoir/ng/importer/ImporterApi.java # shanoir-ng-import/src/main/java/org/shanoir/ng/importer/ImporterApiController.java # shanoir-ng-import/src/main/java/org/shanoir/ng/importer/dcm2nii/NIfTIConverter.java # shanoir-ng-import/src/main/java/org/shanoir/ng/importer/dcm2nii/NIfTIConverterApi.java # shanoir-ng-import/src/main/java/org/shanoir/ng/importer/dcm2nii/NIfTIConverterApiController.java # shanoir-ng-nifti-conversion/src/main/java/org/shanoir/ng/service/DatasetsCreatorAndNIfTIConverterService.java

- Merge develop - Management of DB (not resolved yet)

- nifti-conversion compilation - Import correctly

- unify download logic

# Conflicts: # shanoir-ng-datasets/src/main/java/org/shanoir/ng/dataset/controler/CarminDataApi.java # shanoir-ng-datasets/src/main/java/org/shanoir/ng/dataset/controler/CarminDataApiController.java # shanoir-ng-datasets/src/main/java/org/shanoir/ng/dataset/controler/DatasetApi.java # shanoir-ng-datasets/src/main/java/org/shanoir/ng/dataset/service/DatasetDownloaderServiceImpl.java # shanoir-ng-front/src/app/datasets/dataset/dataset.component.ts # shanoir-ng-front/src/app/import/shared/import.service.ts # shanoir-ng-import/src/main/java/org/shanoir/ng/importer/ImporterApi.java # shanoir-ng-import/src/main/java/org/shanoir/ng/importer/ImporterApiController.java # shanoir-ng-import/src/main/java/org/shanoir/ng/importer/dcm2nii/NIfTIConverter.java # shanoir-ng-import/src/main/java/org/shanoir/ng/importer/dcm2nii/NIfTIConverterType.java # shanoir-ng-import/src/main/resources/scripts/import.sql # shanoir-ng-nifti-conversion/src/main/java/org/shanoir/ng/service/DatasetsCreatorAndNIfTIConverterService.java

# Conflicts: # shanoir-ng-front/src/app/shared/mass-download/download-setup/download-setup.component.html # shanoir-ng-front/src/app/shared/mass-download/download-setup/download-setup.component.ts

- Clean old files from import - Reorganise nifti conversion logic

- Clean old converters and old windows files - Reorganise nifti conversion logic in the front - Correct mriconverter - Move dicomifier (and remove bruker2dicom microservice)

- Remove from application yml

- Correct tests

- Clean code from nifti dataset expression generation - SQL script

jcomedouteau · 2023-11-16T14:57:41Z

What I've done in the PR:

Factorize code in the front to download, now we have almost only one entry to download datasets.
Factorize code in the back to download, now both (multiple download and single) use the same logic.
Move all nifti converters to new microservice
Including dicomifier that is now included in the nifti-conversion micro-service (the bruker2dicom disapeared)
Clean up useless old converters
Remove nifti conversion from import (and all code associated)
Allow mass reconversion in nifti incorporated with new mass download logic.
Download correctly EEG and BIDS datasets too

What to test:

Every f*ing types of download:

EEG only
BIDS only
Nifti, single, multiple
Dicom, single, multiple
Processed dataset
Mixed datasets

All import

Bruker import (important)
Dicom
Bids
EEG
Processed dataset
Processed dataset with ANIMA image (yes yes)

- Clean code from nimport MS - Refactor front code

- Clean code for alt methods - Deployment logic

- Firefox logic

- Add conversion logic to BIDS where necessary

shanoir-ng-front/src/app/shared/mass-download/mass-download.service.ts

julien-louis · 2023-11-21T12:39:46Z

shanoir-ng-preclinical/src/main/java/org/shanoir/ng/preclinical/bruker/BrukerApiController.java


-		if (!HttpStatus.OK.equals(response.getStatusCode()) && !HttpStatus.NO_CONTENT.equals(response.getStatusCode())) {
-			LOG.error(ERROR_BRUKER2DICOM_REQUEST);
+		boolean result = (boolean) rabbitTemplate.convertSendAndReceive(RabbitMQConfiguration.BRUKER_CONVERSION_QUEUE, request);


I have

Caused by: java.lang.NullPointerException: Cannot invoke "java.lang.Boolean.booleanValue()" because the return value of "org.springframework.amqp.rabbit.core.RabbitTemplate.convertSendAndReceive(String, Object)" is null qualif-preclinical-1 | at org.shanoir.ng.preclinical.bruker.BrukerApiController.startBruker2Dicom(BrukerApiController.java:145) qualif-preclinical-1 | at org.shanoir.ng.preclinical.bruker.BrukerApiController.uploadBrukerFile(BrukerApiController.java:108) qualif-preclinical-1 | ... 95 common frames omitted

when I try to upload a bruker file at the beginning of a bruker import.
The file works in prod.

I'll check !

julien-louis · 2023-11-21T14:57:57Z

reminder : add an error msg when the nifti convertion fails

- Don't write errors

# Conflicts: # shanoir-ng-datasets/src/main/java/org/shanoir/ng/bids/service/BIDSServiceImpl.java # shanoir-ng-datasets/src/main/java/org/shanoir/ng/dataset/controler/DatasetApi.java # shanoir-ng-datasets/src/main/java/org/shanoir/ng/dataset/controler/DatasetApiController.java # shanoir-ng-datasets/src/main/java/org/shanoir/ng/dataset/service/DatasetDownloaderServiceImpl.java # shanoir-ng-datasets/src/main/java/org/shanoir/ng/download/WADODownloaderService.java # shanoir-ng-datasets/src/main/java/org/shanoir/ng/shared/service/SubjectStudyServiceImpl.java # shanoir-ng-datasets/src/main/java/org/shanoir/ng/studycard/service/CardsProcessingService.java # shanoir-ng-datasets/src/main/java/org/shanoir/ng/vip/controller/ExecutionDataApiController.java # shanoir-ng-front/src/app/datasets/dataset/dataset.component.html # shanoir-ng-front/src/app/shared/mass-download/mass-download.service.ts # shanoir-ng-front/src/app/solr/solr.search.component.ts # shanoir-ng-front/src/app/subjects/tree/subject-node.component.ts # shanoir-ng-import/src/main/java/org/shanoir/ng/importer/SerieToDatasetsSeparator.java # shanoir-ng-import/src/main/java/org/shanoir/ng/importer/dcm2nii/DatasetsCreatorAndNIfTIConverterService.java # shanoir-ng-import/src/main/java/org/shanoir/ng/importer/dcm2nii/SerieToDatasetsSeparator.java # shanoir-ng-ms-common/src/main/java/org/shanoir/ng/shared/dicom/SerieToDatasetsSeparator.java

# Conflicts: # shanoir-ng-datasets/src/main/java/org/shanoir/ng/dataset/service/DatasetDownloaderServiceImpl.java

# Conflicts: # shanoir-ng-import/src/main/java/org/shanoir/ng/importer/dcm2nii/DatasetsCreatorAndNIfTIConverterService.java

# Conflicts: # shanoir-ng-import/src/main/java/org/shanoir/ng/importer/dcm2nii/NIfTIConverter.java # shanoir-ng-import/src/main/java/org/shanoir/ng/importer/dcm2nii/NIfTIConverterApi.java # shanoir-ng-ms-common/src/main/java/org/shanoir/ng/shared/configuration/RabbitMQConfiguration.java # shanoir-ng-nifti-conversion/src/main/java/org/shanoir/ng/utils/ShanoirExec.java # shanoir-uploader/src/test/java/org/shanoir/uploader/test/importer/ZipFileImportTest.java

# Conflicts: # shanoir-ng-datasets/src/main/java/org/shanoir/ng/download/WADODownloaderService.java # shanoir-ng-front/src/app/import/pre-clinical-context/pre-clinical-context.component.ts

…b.com/jcomedouteau/shanoir-ng into shanoir-issue#1602-nifti-management

# Conflicts: # shanoir-ng-front/src/app/examinations/examination/examination.component.ts

julien-louis · 2024-03-08T10:53:01Z

@jcomedouteau the download fixes & evolutions pr has been merged, maybe I could do the merge in your pr ? Maybe I will try a pr on your branch ? (I had bad experiences with prs on prs but we will be careful !)

julien-louis · 2024-03-08T14:49:49Z

@jcomedouteau I'm currently working on the merge

jcomedouteau · 2024-03-08T14:57:50Z

Thanks !

jcomedouteau · 2024-03-14T09:05:15Z

replaced by #2143

jcomedouteau added 21 commits July 5, 2023 13:47

fli-iam#1602-nifti-management

bb4cd96

- Move conversion to microservice

fli-iam#1602 - add dicomifier

29ae50f

Nifti conversion

d3e6438

fli-iam#1602 nifti management - Remove import / study card conversion

9550d2f

fli-iam#1602 Nift-management

e90bb67

- Merge develop - Management of DB (not resolved yet)

fli-iam#1602-nifti-management

88bd386

- nifti-conversion compilation - Import correctly

fli-iam#1602 nifti conversion

869f017

- unify download logic

fli-iam#1602 - develop merge

be17625

fli-iam#1602 - develop merge

b135622

Merge branch 'develop' into shanoir-issue#1602-nifti-management

01975b9

# Conflicts: # shanoir-ng-front/src/app/shared/mass-download/download-setup/download-setup.component.html # shanoir-ng-front/src/app/shared/mass-download/download-setup/download-setup.component.ts

Merge branch 'develop' into shanoir-issue#1602-nifti-management

9f9d1cb

Merge branch 'develop' into shanoir-issue#1602-nifti-management

1bd642e

# Conflicts: # shanoir-ng-front/src/app/shared/mass-download/download-setup/download-setup.component.html # shanoir-ng-front/src/app/shared/mass-download/download-setup/download-setup.component.ts

fli-iam#1602 Nifti reconversion

c1d221a

- Clean old files from import - Reorganise nifti conversion logic

fli-iam#1602 Nifti reconversion

6a5c479

- Clean old converters and old windows files - Reorganise nifti conversion logic in the front - Correct mriconverter - Move dicomifier (and remove bruker2dicom microservice)

fli-iam#1602 Nifti reconversion

3a95fae

- Remove from application yml

Merge branch 'develop' into shanoir-issue#1602-nifti-management

fbe46db

fli-iam#1602 Nifti reconversion

fa69f1c

- Correct tests

fli-iam#1602 Nifti reconversion

dd43e6b

- Clean code from nifti dataset expression generation - SQL script

jcomedouteau marked this pull request as ready for review November 16, 2023 14:41

jcomedouteau added the REVIEWABLE Has to be reviewed label Nov 16, 2023

jcomedouteau added 4 commits November 17, 2023 10:31

fli-iam#1602 Nifti reconversion

6494568

- Clean code from nimport MS - Refactor front code

fli-iam#1602 Nifti reconversion

6247443

- Clean code for alt methods - Deployment logic

fli-iam#1602 Nifti reconversion

81c8e52

- Firefox logic

fli-iam#1602-nifti-mangement

fe48e45

- Add conversion logic to BIDS where necessary

julien-louis requested changes Nov 21, 2023

View reviewed changes

jcomedouteau added 17 commits November 24, 2023 09:00

1602 - merge develop

e2925e4

fli-iam#1602 -nifti-management

405d83e

- Don't write errors

fli-iam#1602 - manage executions

11d4091

Merge branch 'develop' into shanoir-issue#1602-nifti-management

11c0f82

# Conflicts: # shanoir-ng-datasets/src/main/java/org/shanoir/ng/dataset/service/DatasetDownloaderServiceImpl.java

fli-iam#1602 - invert condition for nifti conversion

dad6e08

Merge branch 'develop' into shanoir-issue#1602-nifti-management

297ecb2

# Conflicts: # shanoir-ng-import/src/main/java/org/shanoir/ng/importer/dcm2nii/DatasetsCreatorAndNIfTIConverterService.java

fli-iam#1602 update execution front to get nifti converter

a193d10

Merge branch 'develop' into shanoir-issue#1602-nifti-management

8b099b8

fli-iam#1602 add converter to execution

910d41b

fli-iam#1602 add converter to execution

7847174

fli-iam#1602 Correct error management when mass downloading

7cd6278

fli-iam#1602 Correct error management when mass downloading

125bf30

fli-iam#1602 Correct error management when mass downloading

46a0e7f

fli-iam#1602 Correct error management when mass downloading

4948132

fli-iam#1602 Correct error management when mass downloading

a0a4eea

jcomedouteau requested a review from julien-louis February 19, 2024 09:03

jcomedouteau and others added 6 commits February 28, 2024 16:34

Merge branch 'develop' into shanoir-issue#1602-nifti-management

ec72a27

# Conflicts: # shanoir-ng-datasets/src/main/java/org/shanoir/ng/download/WADODownloaderService.java # shanoir-ng-front/src/app/import/pre-clinical-context/pre-clinical-context.component.ts

Merge branch 'develop' into shanoir-issue#1602-nifti-management

892d200

fli-iam#1602 - nifti management - compilation

c25dc0d

Merge branch 'shanoir-issue#1602-nifti-management' of git+ssh://githu…

9f41495

…b.com/jcomedouteau/shanoir-ng into shanoir-issue#1602-nifti-management

Merge branch 'develop' into shanoir-issue#1602-nifti-management

38e34bd

# Conflicts: # shanoir-ng-front/src/app/examinations/examination/examination.component.ts

fli-iam#1602 - dicomifier

8c64d27

julien-louis mentioned this pull request Mar 13, 2024

Nifti pr merge #2143

Closed

jcomedouteau closed this Mar 14, 2024

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Shanoir issue#1602 nifti management #1849

Shanoir issue#1602 nifti management #1849

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Shanoir issue#1602 nifti management #1849

Shanoir issue#1602 nifti management #1849

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