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[RFC72] Spring Boot Upgrade #10425

Merged
merged 116 commits into from
Dec 18, 2023
Merged

[RFC72] Spring Boot Upgrade #10425

merged 116 commits into from
Dec 18, 2023

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inodb
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@inodb inodb commented Oct 9, 2023 •
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Introduces Spring Boot into the project. It includes the implementation of several of the items from this ticket: #10356.

Changes

  • Java 11 -> Java 21
  • Spring Boot Application
  • Security has been simplified
  • No more modules. Core moved to it’s own repository (cbioportal/cbioportal-core)

pvannierop and others added 30 commits August 22, 2023 16:46
@pvannierop @haynescd
Initial Commit Updating CbioPortal Backend to spring-boot
12b909f
@haynescd
Merge branch 'master' into demo-rfc72
422822e
@haynescd
🚧 Updated cbioportal project to get a successfull build
1630b6b
@haynescd
🐛 Use correct annotation to set prefix
cfe49fc
@haynescd
Hotfix remove use of PatientMapper.select from SampleMapper.xml
b40cf21
@haynescd
Remove ReadPermissionService
6e8ef49
@JREastonMarks
Fixes for Deployment
d60076f 
Turns off DocRedirectController
Fixes request mapping for ProxyController
@haynescd
🚨 Update peristence module tests to pass within spring… (#10363)
0e3873e 
* 🚨 Update peristence module tests to pass within springboot framework

* Update Persistence Config to update classpath for mybatis
@haynescd
Remove ReadPermissionService IF and update test (#10364)
dcc31ea
@inodb
fix api path in InvolvedCancerStudyExtractorInterceptor
f6b9b9a 
For some reason the path was /api/api
@haynescd
Fix Unit Tests in Web Module (#10371)
eedd9c6
@inodb @fuzhaoyuan
Fix Github Action Core tests (#10369)
b1c71bc 
* re-introduce test settings xml for github

---------

Co-authored-by: Ryan Fu <fuzhaoyuan@gmail.com>
@inodb
Use simpler web docker image (#10377)
e1f0f84 
* Use simpler web docker image

See: https://spring.io/guides/topicals/spring-boot-docker/. It's slower but got an error with the old setup
@inodb
Spring Boot Upgrade: Fix CircleCI build_backend step (#10379)
a001f2a
@haynescd
Fix Api prefix for ProxyController (#10383)
2660f5e
@haynescd
Update postData to set undefined when map is empty
496aa0e
@haynescd
Add SampleTypeHandler to sessionFactory for mybatis
a83aaf3
@haynescd
Update redirect url for patient and results pages
9891e69
@haynescd
Update redirect urls for login and results
c56859f
@haynescd
Fix /Comparison url redirect
3acc7ec
@haynescd
Fix index.do redirect
0f08422
@haynescd
Fix oncoprinter redirect
446b1e7
@haynescd
Update FrontendPropertiesService to handle boolean values
bf82ed7
@haynescd
Add ability to decompress gzip request body
fcba158
@haynescd
Update gzip stream request wrapper to use legacy code
dec8242
@haynescd
Add mutation_mapper to redirect ruleset
04cbc20
@haynescd
support for /study? as well as /study/ redirect
aa3f71a
@haynescd
Update to support encodedRedirect
f2b9eee
@haynescd
Add enable_cross_study_expression frontend property
c9dc56e
@inodb
in docker action login first
545c4a1
haynescd and others added 22 commits December 12, 2023 14:22
@haynescd
Add support for both api/gene-panels/ api/gene-panels apis
05380af
@haynescd
Add ReadPermissionService
0a145d3
@haynescd
Fix failing tests
df43708
@haynescd
Update redirect logout url for optional_oauth2
e2f33b1
@haynescd
🔧 Add Config for Study View Help Button
647739d
@JREastonMarks
Add EOL and Character return to application.properties
5acd918
@JREastonMarks
Merge branch 'master' into demo-rfc72
0af2d91
@JREastonMarks
Revert frontend version to v5.4.9
cfa84e3
@haynescd
Update Login Page
d763dd5
@haynescd
Fix login url
8077828
@JREastonMarks
SonarCube
0cfe5d3 
Copy appliation.properties file
@JREastonMarks
Update Java Version to 21
21885aa
@haynescd
Create LoginController to handle /login endpoint for authentication
c91d8fe
@JREastonMarks
SonarCube Fixes
97b5677 
SonarCube Fixes
@JREastonMarks
Fix bug in jwt correction and molecular data service
ec2c1ad
@JREastonMarks
Remove Pattern.compile
c80d1e1
@haynescd
Fix Logout Page for SAML2
5d6ab51
@haynescd
Fix SessionServiceController
6fa8c67
@JREastonMarks
New Regex for Session Service
4b5521a
@haynescd
Set logout/login page for authenticate=oauth2 with more than one clie…
7aab69e 
…nt setup
@JREastonMarks
Revert REGEX for session service
51dfc38
@JREastonMarks
Fix compilation error
810b920
@JREastonMarks JREastonMarks self-requested a review December 15, 2023 15:49
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Quality Gate Failed Quality Gate failed

Failed conditions

14 Security Hotspots
35 New Bugs (required ≤ 0)
12 New Vulnerabilities (required ≤ 0)
D Security Rating on New Code (required ≥ A)
4 New Blocker Issues (required ≤ 0)

See analysis details on SonarCloud

idea Catch issues before they fail your Quality Gate with our IDE extension SonarLint SonarLint

@JREastonMarks JREastonMarks merged commit 4c3e035 into master Dec 18, 2023
15 of 16 checks passed
@haynescd haynescd deleted the demo-rfc72 branch February 8, 2024 13:57
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@JREastonMarks JREastonMarks JREastonMarks approved these changes

@dippindots dippindots Awaiting requested review from dippindots

@kalletlak kalletlak Awaiting requested review from kalletlak

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4 participants
@inodb @JREastonMarks @pvannierop @haynescd