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java upgrade #940

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wants to merge 59 commits into from
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java upgrade #940

wants to merge 59 commits into from

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@jcschaff jcschaff commented Jul 14, 2023 •
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see #848

  • separation from SciJava parent POM
  • migrate from SciJava services to Guice dependency injection
  • upgrade to latest Oracle drivers from maven central, remove vcell-oracle module
  • upgrade from Java 8 to Java 17
    • modular JVMs with better container support (uses ALL-MODULE-PATH for now in jlink)
    • new language features
    • support for modern java frameworks,
    • eventual support for GraalVM native deployments (beyond scope of this PR).
  • upgrade Install4J and new client-side JVMs.
  • split VCellClientTest into VCellClientMain (for client-server) and VCellClientDevMain (for local dev)

additional refactoring/clean-up

  • removed vcell-imagej and vcell-imagej-helper modules
  • removed unused /PythonScripts/ python projects (VCell_API, VCell_ImageJ and VCell_Opt)
  • removed unused Thrift specs: ImageDataset.thrift, VCellImage.thrift, pyVCell.thrift
  • moved /PythonScripts/VCell_VTK to its own Poetry project /pythonVtk.
  • remove dependencies from vcell-cli on vcell-server, vcell-admin and vcell-client.

@jcschaff jcschaff self-assigned this Jul 14, 2023
@jcschaff jcschaff linked an issue Jul 14, 2023 that may be closed by this pull request
Need to Upgrade VCell to later versions of Java #848
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github-advanced-security[bot]
github-advanced-security bot found potential problems Jul 28, 2023
View reviewed changes
vcell-api/src/main/java/org/vcell/rest/VCellApiMain.java
// keystorePassword may be encrypted with dbPassword, if it is decypt it.
//
String dbPassword = PropertyLoader.getSecretValue(PropertyLoader.dbPasswordValue, PropertyLoader.dbPasswordFile);
SecretKeyFactory kf = SecretKeyFactory.getInstance("PBEWithMD5AndDES");

Check failure

Code scanning / CodeQL

Use of a broken or risky cryptographic algorithm

Cryptographic algorithm [PBEWithMD5AndDES](1) is weak and should not be used.
vcell-api/src/main/java/org/vcell/rest/VCellApiMain.java
String dbPassword = PropertyLoader.getSecretValue(PropertyLoader.dbPasswordValue, PropertyLoader.dbPasswordFile);
SecretKeyFactory kf = SecretKeyFactory.getInstance("PBEWithMD5AndDES");
SecretKey key = kf.generateSecret(new PBEKeySpec(dbPassword.toCharArray()));
Cipher pbeCipher = Cipher.getInstance("PBEWithMD5AndDES");

Check failure

Code scanning / CodeQL

Use of a broken or risky cryptographic algorithm

Cryptographic algorithm [PBEWithMD5AndDES](1) is weak and should not be used.
@jcschaff
remove scijava parent POM and use Java 11 source/target
883dd32
@jcschaff
specify Java 17 - passes tests
9dd4207
@jcschaff
WIP: updating Docker
2eb6cf2
@jcschaff
WIP: rebased and pushed so it doesn't get lost
f6231d2
@jcschaff
WIP: install4j
4b52e38
@jcschaff
specify java 17 for github actions
98e259d
@jcschaff
fix .yml indent
f6ad0fb
@jcschaff
rm no-op test in vcell-apiclient, test groups not defined (vcell-utils)
7abcc34
@jcschaff
use Java 17 and Python 3.9 in multistage build for biosimulators_vcell
8484bf9
@jcschaff
vcell-batch to ghcr.io/virtualcell/vcell-solvers:v0.0.42 (Java 17/py3.9)
8108d3b
@jcschaff
rest of Docker images to Java 17 and Python 3.9 (as needed)
c4fb003
@jcschaff
Java 17 is container aware (no UseCGroupMemoryLimitForHeap)
b37de01
@jcschaff
replace SciJava Dependency Injection (for ExternalDataIdentifierService)
acd7bef
@jcschaff
replace SciJava Dependency Injection (for LocalVCellConnectionService)
6782094
@jcschaff
replace SciJava Dependency Injection (for RegistrationService)
5502dec
@jcschaff
replace SciJava Dependency Injection (for VCMessagingService)
17a3a8b
@jcschaff
explicit java9 modules for JVM and update java cli switches
511b46d
@jcschaff
updated documentation for vcell-batch
ba6825a
@jcschaff
remove remaining of SciJava dependency injection
e36898c
@jcschaff
remove python-copasi and python-libsbml refs
c0b0b3b
@jcschaff
default constructor for AccessTokenRepresentation
e81ac64
@jcschaff
remove vcell-oracle module, use simple Oracle/Postgres factory
358ca8a
@jcschaff
completed removal of vcell-oracle, use newer oracle driver name
93823a7
@jcschaff
move static client access from VCellClientTest to VCellClient
347148d
@jcschaff
remove vcell-imagej and vcell-imagej-helper, mv to separare repo(s)
a7b8f63
@jcschaff
update poetry lock for copasi/opt with python 3.10
784aa9f
@jcschaff
fix initialization for vcell-submit after dependency injection refactor
87bc2b6
@jcschaff
make VCellClientMain --api-host optional (vcell.serverHost is default)
5dd1055
@jcschaff
upgrade Install4j from 8.0.5 to 10.0.5
688b02d
@jcschaff
let Install4J manage bundling of JREs
ab56a82
@jcschaff
use Java 17 for all github actions.
aacf349
@jcschaff
add pythonVtk to CI - verify all python package installs with pytest
ddc0e37
@jcschaff
remove vcell-cli-utils dependencies on python 3.10 syntax (for now)
eb6deea
@jcschaff
add ignored zip file to project used in test fixture.
7430fee
@jcschaff
keep one zip file for test fixture - exclude from zip rule.
91a6382
@jcschaff
fix path in test fixture
e831eea
@jcschaff
inject dummy test in pythonVtk so that CI passes
4aa65cf
@jcschaff
add ignored fixture files with .log and .zip suffixes.
699847d
@jcschaff
configure cliWorkingDir for SEDMLExporter round trip validation tests
d77bbc4
@jcschaff
remove reference to provided client JREs
2a550f0
@jcschaff
clean up top level maven pom file
38bf50c
@jcschaff
add fonts to openjdk to run install4jc in docker
6b5d391
@jcschaff
remove remaining references to supplied client JREs
c6e120e
@jcschaff
use new named Install4J license key for version 10
6b2c5c1
@jcschaff
versioned deploy_dir_2023_07_30.tar (was deploy_dir.tar) for back compat
31f7789
@jcschaff
fixed conflicting maven dependencies, enforce versions with properties
d61b2fa
@jcschaff
allow maven 3.8 or higher.
0ae373e
@jcschaff
bring missing java modules into vcell-batch
0809e15
@jcschaff
use ucp11 when using ojdbc11
4b31a84
@jcschaff
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replaced by #994 (fresh branch for merging with master).

@jcschaff jcschaff closed this Oct 20, 2023
@jcschaff jcschaff deleted the 848-java-upgrade branch October 20, 2023 03:34
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VCell-7.6.0
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Need to Upgrade VCell to later versions of Java
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