This is an automated email from the ASF dual-hosted git repository.
yasith pushed a change to branch cybershuttle-dev
in repository https://gitbox.apache.org/repos/asf/airavata.git
discard eec2402b5b fix api server assembly after the dependency update.
discard a650ea74df fix dozer deprecations, add httpclient dep
discard 3f7df10a72 fix rabbitmq deprecation
discard 80b4bd40e4 no functional changes - just removing unused imports and
reordering them.
discard a02e87b430 deprecation fixing round 2. cleanup unused imports of most
files.
discard 46197be2ea partially update deprecated code
discard 1f2e18be3b consolidate POM deps to non-deprecated versions
discard 23c31506cc move portal to research-framework
discard c9012d4007 initial research framework
discard bf8d62291d Initial research-framework portal
discard ad2d1c367f cleanup code. add placeholders for job monitor email/pw in
airavata-server.properties
discard d0dd7633c7 fix issues with helix participant and job engine starter
discard 8a750ed8aa get hibernate orm to validate against test db. manually
specify catalog for conflicting entities.
discard abc7bfd0ef migrate openjpa to hibernate, update pool and dbcp deps to
pool2 and dbcp2.
discard 51feea9d4a parametrize pom versions. add maven-enforcer rule for
dependency convergence and fix version issues.
discard acf6937ec1 regenerated thrift stubs with version 0.21.0 and fix issues
discard feaee51f77 migrate javax.mail to jakarta.mail to fix email-monitor
bug. exclude conflicting angus-mail dependency. add missing @Deprecated tags.
discard 7dbeb40772 simplify devcontainer. unify maven-compiler plugin version.
discard 05e63d7a3f migrate openjpa to 4.0.1. update javax.persistence to
jakarta.persistence.
discard 25ca66b871 fix pom issues when running in devcontainer
discard 722beff41e fix generated protos unused issue
discard b4f5e8d14a update rabbitmq and proto versions, fix proto path in
agent-service
discard 550df6a64b change protobuf plugin to a maintained one
discard 6d6865530a bump all jdk deps to 17. get devcontainer to working state.
add launch.json for vscode integration. add openjpa runtimeoptimization tag to
persistence.xml. bump mysql connector to 8.0.31. add dns tags to keystore
generation script (browser https compatibility), move keystores to top-level
and add build-time copy to project resources. fix Serializable warning in
UserPK.java
discard bed9c6ac83 move docker-compose file to .devcontainer
discard 1fa520acbb rename devcontainer to Airavata
discard 5882ed9e50 add AF2Complex notebook
discard 4c8d9db1b4 updated devcontainer and compose for easy use in vscode
discard 33402f2a6c create devcontainer.json and integrate with docker-compose
file. fix bugs.
discard dda0b48d49 move self-signed certs to a single location
discard 2d17099ce5 partial solution for keycloak update in ide-integration
add 93b84c9d82 ui for adding repos
add 7093a25c62 Add X-Claims header to swagger ui requests
add c2b8f28974 Allow for repository creation, project creation, and
resource search
add d6bd1eb6fc frontend integration for adding projects
add 4ac99eb259 frontend for project repo search
add 80a9911508 support for adding project datasets
add 9383a5e4af mvp working
add 058d9b9021 Merge pull request #497 from ganning127/post-projects
add a734f7ec61 update DevDbInitializer project list
add 30036b8322 Support multiple datasets
add 54686b01e0 Merge pull request #498 from ganning127/more-fixes
add 95b508db6d CyberFaCES docker file
add 397f1cdaf6 add file ops to jupyter magics, cleanup code, update
agent.sh
add 741815f673 temp commit to get cyberfaces meeting poc
add 896f11c016 update data tar and analysis script
add 684711d180 add airavata magics to dev-tools/, make airavata-agent/
build generic
add 9394c945fd reorganize agent-framework related code. make
airavata-magics a python package.
add 17012d556b revise jupyterhub spawned notebooks, add makefiles
add 3560c00c2d initial experiment sdk implementation
add 8b9cacf758 improve auth flow, add python code invocation, add plan
crud apis and file ul/dl apis, reduce settings.ini deps, fix bugs
add a9594b965b venv support for agent, update notebooks, show tables as
pandas df, update dir refs, fix bugs.
add 1046150be6 make settings.ini lean, add runtime picker {by cluster,
category}. change agent base dir.
add 47d882e396 add pre-submission validator, update storage dir, take
CONNECTION_SVC_URL and FILEMGR_SVC_URL from settings.ini, cleanup runtime.py,
add fallback apis to airavata.py, rearrange files, setup file ul/dl apis,
improve ux, update notebooks, add agent scripts, refine code, fix bugs
add 599fba45fd fix bug in code execution, remove jupyter kernel start from
agent add support to cold-start analysis agents reset changes to
sftp_file_handling_client update notebooks remove verbose log from remote code
execution separate python env creation and code execution steps. always return
stdout+err for command/script executions lock agent to python 3.12 and update
pyproject.toml update file listing and python execution cmds
add fa6a4207a0 bump version to 0.0.16 add AlphaFold2 and Gaussian
applications update realm from 10000000 -> default add GROMACS and AMBER to MD
SDK
add 83052b074d choose group/project from API, silent plan launch,
add_replica() -> create_task(), display task state, planid and taskid, improve
messaging
add 8061e070b5 add back kernel launcher to agent
add ca369fc700 refine Makefiles, move app-scripts to agent-framework/, fix
bugs in agent.go and sample Dockerfile
add d7d5275990 regenerate thrift specs
add 251edd3890 cleanup airavata_sdk wrappers, error-handling in
airavata_experiments
add c3273418ba add type-hinting imports to __init__ files
add 86425b63dd cleanup imports, fix bugs found by type checker
add 118b1dcc18 enabled micromamba base when starting the kernel
add de6c7f04af fix bugs in airavata-jupyter-magic package
add 9776da5d14 fix dependency issue in cyberfaces agent
add 8b9cfeae02 organize code, add other deployment files, partially redo
airavata_jupyter_magic for runtime switching
add 56bee085dc refine code flow in airavata_jupyter_magic. bump version to
1.0.5, update notebook, fix bugs
add 94319b5951 updated notebooks
add 7716162705 rename platform x86_64 -> amd64. fix issues in cyberfaces
dockerfile. update notebooks. move environment files.
add c96c793730 updated the agent dependencies
add d3c191c8f3 gkeyll agent image and notebook sample
add 5f42822a16 updated the gkeyll notebook script
add 238b9d1ab5 Changed the uploading file size in enveomics gateway
add 3420f70e16 ide-integration docker-compose changes
add 7a7a4715bc Added keycloak.conf, Updated docker-compose.yml, Updated
airavata.jks
add cea66cb840 Replaced airavata.jks with an updated version
add 148a93ea73 modified keycloak.conf
add f884cb1914 removed duplicate keycloak volume
add 619578bf19 Merge pull request #468 from riccog/master
add 96381137fa Bump golang.org/x/crypto in
/modules/agent-framework/airavata-agent
add 0de85939af Merge pull request #492 from
apache/dependabot/go_modules/modules/agent-framework/airavata-agent/golang.org/x/crypto-0.35.0
add fe8d4e54f4 gateway switching for local agent (#469)
add b3046107b2 Delete unused SSHCredentialGenerator (#240)
add 361544c204 Merge branch 'master' into cybershuttle-staging
add 497b86d76e update agent.sh to initialize scratch
new f0a8350d1b bump JDK to v17. create devcontainer setup. bump rabbitmq
and proto versions. consolidate maven-compiler plugin versions. migrate openjpa
to 4.0.1. update javax to jakarta. regenerate certs. fix bugs.
new ebdbeabaec regenerated thrift stubs with version 0.21.0 and fix issues
new 8429960eca parametrize pom versions. add maven-enforcer rule for
dependency convergence and fix version issues.
new 668fc39273 migrate openjpa to hibernate, update pool and dbcp deps to
pool2 and dbcp2.
new cf17a29c07 get hibernate orm to validate against test db. manually
specify catalog for conflicting entities.
new 843edb3c13 fix issues with helix participant and job engine starter
new fba22eaa1c fix deprecations, cleanup code. add placeholders for job
monitor email/pw in airavata-server.properties
This update added new revisions after undoing existing revisions.
That is to say, some revisions that were in the old version of the
branch are not in the new version. This situation occurs
when a user --force pushes a change and generates a repository
containing something like this:
* -- * -- B -- O -- O -- O (eec2402b5b)
\
N -- N -- N refs/heads/cybershuttle-dev (fba22eaa1c)
You should already have received notification emails for all of the O
revisions, and so the following emails describe only the N revisions
from the common base, B.
Any revisions marked "omit" are not gone; other references still
refer to them. Any revisions marked "discard" are gone forever.
The 7 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "add" were already present in the repository and have only
been added to this reference.
Summary of changes:
.gitignore | 2 +-
airavata-local-agent/main/background.js | 71 +-
airavata-local-agent/package.json | 2 +-
.../renderer/components/HeaderBox.jsx | 4 +-
airavata-local-agent/renderer/lib/Contexts.js | 107 +-
airavata-local-agent/renderer/pages/_app.jsx | 6 +-
.../renderer/pages/docker-home.jsx | 4 +-
airavata-local-agent/renderer/pages/login.jsx | 55 +-
modules/agent-framework/airavata-agent/agent.sh | 4 +-
modules/agent-framework/airavata-agent/go.mod | 7 +-
.../airavata-jupyter-magic/.gitignore | 3 +
.../airavata-jupyter-magic/README.md | 28 +
.../airavata-jupyter-magic}/__init__.py | 0
.../airavata_jupyter_magic.py | 557 +-
.../airavata-jupyter-magic/device_auth.py | 59 +
.../airavata-jupyter-magic/pyproject.toml | 30 +
.../data/af2complex/AF2Complex_notebook.ipynb | 1021 ---
modules/commons/pom.xml | 3 -
.../src/main/containers/keycloak/keycloak.conf | 7 -
modules/research-framework/pom.xml | 4 +-
modules/research-framework/portal/eslint.config.js | 2 +-
modules/research-framework/portal/index.html | 2 +-
.../research-framework/portal/package-lock.json | 6545 +++++++-------------
modules/research-framework/portal/package.json | 3 +
modules/research-framework/portal/public/vite.svg | 1 -
modules/research-framework/portal/src/App.tsx | 6 +
.../portal/src/components/NavBar.tsx | 58 -
.../portal/src/components/add/AddGitUrl.tsx | 92 +
.../portal/src/components/add/AddProjectMaster.tsx | 139 +
.../portal/src/components/add/AddRepoMaster.tsx | 67 +
.../src/components/add/ConfirmRepoDetails.tsx | 150 +
.../portal/src/components/add/DatasetSearch.tsx | 165 +
.../portal/src/components/add/RepoSearch.tsx | 157 +
.../portal/src/components/add/index.tsx | 35 +
.../portal/src/components/datasets/DatasetCard.tsx | 70 -
.../src/components/datasets/DatasetDetails.tsx | 54 -
.../portal/src/components/home/ProjectsSection.tsx | 15 +-
.../portal/src/components/home/ResourceCard.tsx | 154 +-
.../home/StartSessionFromProjectButton.tsx | 4 +-
.../portal/src/components/home/index.tsx | 9 +
.../portal/src/components/models/ModelCard.tsx | 34 -
.../portal/src/components/models/ModelDetails.tsx | 96 -
.../src/components/notebooks/NotebookCard.tsx | 64 -
.../src/components/notebooks/ProjectDetails.tsx | 98 -
.../src/components/repositories/GitHubFileTree.tsx | 32 +-
.../src/components/repositories/RepositoryCard.tsx | 39 -
.../repositories/RepositorySpecificDetails.tsx | 3 -
.../src/components/resources/ResourceDetails.tsx | 25 +-
.../components/resources/ResourceSyncButton.tsx | 216 +
.../portal/src/interfaces/ProjectType.tsx | 7 +
.../interfaces/Requests/CreateProjectRequest.tsx | 6 +
.../interfaces/Requests/CreateResourceRequest.tsx | 10 +
.../portal/src/layouts/NavBar.tsx | 5 +
.../research-framework/portal/src/lib/constants.ts | 2 +-
.../research-framework/portal/tsconfig.app.json | 2 +-
modules/research-framework/portal/tsconfig.json | 2 +-
.../research-framework/portal/tsconfig.node.json | 2 +-
modules/research-framework/portal/vite.config.ts | 2 +-
.../proto/research-service.proto | 11 -
.../research-framework/research-service/pom.xml | 6 +-
.../research/ResearchServiceApplication.java | 13 -
.../research/service/config/AuthzTokenFilter.java | 5 +
.../service/config/DevDataInitializer.java | 18 +
.../research/service/config/OpenApiConfig.java | 22 +-
.../service/controller/ProjectController.java | 18 +-
.../service/controller/ResearchHubController.java | 2 +-
.../service/controller/ResourceController.java | 55 +-
.../research/service/dto/CreateProjectRequest.java | 42 +
.../service/dto/CreateResourceRequest.java | 62 +
.../service/dto/ModifyResourceRequest.java | 13 +
.../{ResponseTypes => dto}/RedirectResponse.java | 2 +-
.../{ResponseTypes => dto}/ResourceResponse.java | 2 +-
.../research/service/handlers/ProjectHandler.java | 48 +
.../service/handlers/ResearchHubHandler.java | 25 +-
.../research/service/handlers/ResourceHandler.java | 84 +-
.../service/model/repo/ProjectRepository.java | 4 +
.../service/model/repo/ResourceRepository.java | 11 +
.../src/main/resources/application.yml | 2 +-
pom.xml | 12 +-
79 files changed, 4368 insertions(+), 6436 deletions(-)
create mode 100644 modules/agent-framework/airavata-jupyter-magic/.gitignore
create mode 100644 modules/agent-framework/airavata-jupyter-magic/README.md
copy {airavata-api/airavata-client-sdks/airavata-python-sdk =>
modules/agent-framework/airavata-jupyter-magic}/__init__.py (100%)
copy
airavata-api/airavata-client-sdks/airavata-python-sdk/airavata_jupyter_magic/__init__.py
=> modules/agent-framework/airavata-jupyter-magic/airavata_jupyter_magic.py
(55%)
create mode 100644
modules/agent-framework/airavata-jupyter-magic/device_auth.py
create mode 100644
modules/agent-framework/airavata-jupyter-magic/pyproject.toml
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/af2complex/AF2Complex_notebook.ipynb
delete mode 100644 modules/research-framework/portal/public/vite.svg
delete mode 100644 modules/research-framework/portal/src/components/NavBar.tsx
create mode 100644
modules/research-framework/portal/src/components/add/AddGitUrl.tsx
create mode 100644
modules/research-framework/portal/src/components/add/AddProjectMaster.tsx
create mode 100644
modules/research-framework/portal/src/components/add/AddRepoMaster.tsx
create mode 100644
modules/research-framework/portal/src/components/add/ConfirmRepoDetails.tsx
create mode 100644
modules/research-framework/portal/src/components/add/DatasetSearch.tsx
create mode 100644
modules/research-framework/portal/src/components/add/RepoSearch.tsx
create mode 100644
modules/research-framework/portal/src/components/add/index.tsx
delete mode 100644
modules/research-framework/portal/src/components/datasets/DatasetCard.tsx
delete mode 100644
modules/research-framework/portal/src/components/datasets/DatasetDetails.tsx
delete mode 100644
modules/research-framework/portal/src/components/models/ModelCard.tsx
delete mode 100644
modules/research-framework/portal/src/components/models/ModelDetails.tsx
delete mode 100644
modules/research-framework/portal/src/components/notebooks/NotebookCard.tsx
delete mode 100644
modules/research-framework/portal/src/components/notebooks/ProjectDetails.tsx
delete mode 100644
modules/research-framework/portal/src/components/repositories/RepositoryCard.tsx
create mode 100644
modules/research-framework/portal/src/components/resources/ResourceSyncButton.tsx
create mode 100644
modules/research-framework/portal/src/interfaces/Requests/CreateProjectRequest.tsx
create mode 100644
modules/research-framework/portal/src/interfaces/Requests/CreateResourceRequest.tsx
delete mode 100644 modules/research-framework/proto/research-service.proto
delete mode 100644
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/ResearchServiceApplication.java
create mode 100644
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/dto/CreateProjectRequest.java
create mode 100644
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/dto/CreateResourceRequest.java
create mode 100644
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/dto/ModifyResourceRequest.java
rename
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/{ResponseTypes
=> dto}/RedirectResponse.java (84%)
rename
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/{ResponseTypes
=> dto}/ResourceResponse.java (90%)
