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 8817f8277a centralize all dependency versions into root pom
discard d7bce90a6d update airavata distribution module to match deployment
structure
discard 6e036df49f fix deprecations, cleanup code. add placeholders for job
monitor email/pw in airavata-server.properties
discard 713918e389 fix issues with helix participant and job engine starter
discard 1d96b1db54 get hibernate orm to validate against test db. manually
specify catalog for conflicting entities.
discard de25688a32 migrate openjpa to hibernate, update pool and dbcp deps to
pool2 and dbcp2.
discard 94915ed231 parametrize pom versions. add maven-enforcer rule for
dependency convergence and fix version issues.
discard bfc028ae60 regenerated thrift stubs with version 0.21.0 and fix issues
discard 55124e8432 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.
add d6241d2c8b may 7 workshop agenda + resource filtering (#501)
add 667a9a5d9d May 7 workshop fixes (#502)
add 06709604cd uncontainerize agent.sh. fix agent.go bug. update makefile
add dddc2431a2 fix bugs
add de6fb8e6ea handle empty args for agent.sh
add bb37f68a4e update messages in python sdk. polish messaging and flow.
add c8f861e18c ability to upload directories to remote
add 0b94fc1dba show stdout and stderr when jobs fail. add live log tail
mode.
add f66ff0ef04 improve looks of live log viewer
add 72273a2883 updated the readme with instructions to run the agent and
execute commands
add a3a4516978 correctly differentiate between files and folders
add 86a1acda5e Adding tunnel creation support to agent
add d35c0271ed fix bugs, add recursive file fetching from remote
add b0e2452f4f Support to terminate tunnel
add 4e118d73d6 fix file upload bug
add 3bb86077ea fix file uploader naming issue. make agents auto-sync
datasets at runtime.
add 44ba9d59c2 fix bug in live printing
add 23feb0c088 Support to run async shell commands
add b46d12fad6 Minor logging improvements
add f1ab4b4bfd Fixing the async command response issues
add a55cf5c1ec add utils for async shells and tunnels
add 583602b111 add terminate async shell function
add 1d2d0be2f1 fix ClassNotFoundExceptions by aligning activation API with
RESTEasy dependencies
add 56f18693b9 Update May7Workshop.tsx Events page
add a01e9199d2 add magics to spawn/kill subprocess and tunnels
add 647893efc0 fix sdk bugs in tunneling, logging, and subprocess
management.
add 6e7b300dcf fix terminate_shell bug
add 522a8ed505 switch to port-forwarding kernel clients. connect all zmq
channels for interactive operation.
add 6cc061836e recolor --live logs, add web terminal, install ttyd by
default (required)
add d509c54c02 bump version to 2.1.2
add f5c4c3f3a7 fix bug
add a5a775f1ab fix bug in shell command parsing
add a5ca8ba4ab Updating mimetype decoding for new run cell
add cd541dcd2c bump version to 2.1.3.post2
add b7c93b6045 Minor bug fixes and adding clear output to message type
add 4324145a67 bump version to 2.1.3.post3
add 01fe5ef88d pass display_data and execute_result to native display
handler
add d08c2aaaae fix shell command parsing issue in %run_subprocess
add 3c7a3db583 add hostname arg to run_subprocess_inner and
launch_remote_kernel
add f2d32f43f6 fix bug
add e93f83232e show terminal via link (workaround for https iframe issue)
add e2462747a9 fix data directory creation issue
add 4b8a056dac add cleanup logic to agent.sh, update Makefile to scp
agent.sh sequentially
new a417d4ac8c 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 efe6fcb751 regenerated thrift stubs with version 0.21.0 and fix issues
new c5fe7a33c2 parametrize pom versions. add maven-enforcer rule for
dependency convergence and fix version issues.
new 639ded3860 migrate openjpa to hibernate, update pool and dbcp deps to
pool2 and dbcp2.
new 31d15360d6 get hibernate orm to validate against test db. manually
specify catalog for conflicting entities.
new 76244f5a02 fix issues with helix participant and job engine starter
new 4daf7e5672 fix deprecations, cleanup code. add placeholders for job
monitor email/pw in airavata-server.properties
new 8943a9dd70 update airavata distribution module to match deployment
structure
new 05d0105105 gather all dependency versions to /pom.xml. fix bugs.
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Summary of changes:
.../airavata_jupyter_magic/__init__.py | 1014 ++++++++--
.../airavata_jupyter_magic/device_auth.py | 2 +-
.../airavata-python-sdk/pyproject.toml | 4 +-
.../service/controllers/AgentController.java | 81 +-
.../service/handlers/AgentConnectionHandler.java | 264 ++-
...java => AgentAsyncCommandExecutionRequest.java} | 3 +-
.../models/AgentAsyncCommandExecutionResponse.java | 31 +
...uest.java => AgentAsyncCommandListRequest.java} | 12 +-
...Ack.java => AgentAsyncCommandListResponse.java} | 15 +-
...java => AgentAsyncCommandTerminateRequest.java} | 13 +-
...ava => AgentAsyncCommandTerminateResponse.java} | 12 +-
.../connection/service/models/AgentTunnelAck.java | 9 +
.../service/models/AgentTunnelCreateRequest.java | 31 +
.../service/models/AgentTunnelCreateResponse.java | 50 +
.../service/models/AgentTunnelRequest.java | 67 -
...quest.java => AgentTunnelTerminateRequest.java} | 13 +-
.../models/AgentTunnelTerminateResponse.java | 4 +
.../connection/service/models/AsyncCommand.java | 24 +
.../src/main/resources/application.yml | 6 +
modules/agent-framework/airavata-agent/Makefile | 96 +-
modules/agent-framework/airavata-agent/README.md | 153 +-
modules/agent-framework/airavata-agent/agent.go | 425 +---
modules/agent-framework/airavata-agent/agent.sh | 52 +-
modules/agent-framework/airavata-agent/go.mod | 68 +-
.../agent-framework/airavata-agent/pkg/jupyter.go | 234 +++
.../agent-framework/airavata-agent/pkg/python.go | 37 +
.../agent-framework/airavata-agent/pkg/shell.go | 196 ++
.../agent-framework/airavata-agent/pkg/tunnel.go | 98 +
.../agent-framework/airavata-agent/pkg/types.go | 8 +
.../protos/agent-communication.pb.go | 2030 ++++++++++----------
.../protos/agent-communication_grpc.pb.go | 2 +-
.../airavata-jupyter-magic/.gitignore | 3 -
.../airavata-jupyter-magic/README.md | 28 -
.../airavata-jupyter-magic/__init__.py | 0
.../airavata_jupyter_magic.py | 751 --------
.../airavata-jupyter-magic/device_auth.py | 59 -
.../airavata-jupyter-magic/pyproject.toml | 30 -
.../proto/agent-communication.proto | 66 +-
.../apache/airavata/agents/api/FileMetadata.java | 9 +
.../airavata/helix/adaptor/SSHJAgentAdaptor.java | 2 +
.../file/server/controller/FileController.java | 54 +-
.../file/server/model/AiravataDirectory.java | 19 +-
.../airavata/file/server/model/AiravataFile.java | 7 +
.../file/server/service/AirvataFileService.java | 108 +-
.../images/Frame_14_FgnQDaE.original.original.png} | Bin
.../portal/src/components/add/AddProjectMaster.tsx | 1 -
.../src/components/add/ConfirmRepoDetails.tsx | 6 +-
.../portal/src/components/auth/UserMenu.tsx | 22 +-
.../events/{index.tsx => Apr11Workshop.tsx} | 49 +-
.../portal/src/components/events/May7Workshop.tsx | 197 ++
.../portal/src/components/events/index.tsx | 251 +--
.../home/StartSessionFromProjectButton.tsx | 12 +-
.../portal/src/components/resources/index.tsx | 151 +-
.../portal/src/components/typography/KeyPair.tsx | 34 +
.../portal/src/layouts/NavBar.tsx | 2 +-
.../research-framework/research-service/pom.xml | 2 +-
pom.xml | 26 +
57 files changed, 4035 insertions(+), 2908 deletions(-)
copy
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/{AgentCommandExecutionRequest.java
=> AgentAsyncCommandExecutionRequest.java} (94%)
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentAsyncCommandExecutionResponse.java
copy
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/{AgentKernelRestartRequest.java
=> AgentAsyncCommandListRequest.java} (52%)
copy
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/{AgentEnvSetupAck.java
=> AgentAsyncCommandListResponse.java} (59%)
copy
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/{AgentKernelRestartRequest.java
=> AgentAsyncCommandTerminateRequest.java} (54%)
rename
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/{AgentTunnelResponse.java
=> AgentAsyncCommandTerminateResponse.java} (57%)
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentTunnelCreateRequest.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentTunnelCreateResponse.java
delete mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentTunnelRequest.java
copy
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/{AgentKernelRestartRequest.java
=> AgentTunnelTerminateRequest.java} (54%)
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentTunnelTerminateResponse.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AsyncCommand.java
create mode 100644 modules/agent-framework/airavata-agent/pkg/jupyter.go
create mode 100644 modules/agent-framework/airavata-agent/pkg/python.go
create mode 100644 modules/agent-framework/airavata-agent/pkg/shell.go
create mode 100644 modules/agent-framework/airavata-agent/pkg/tunnel.go
create mode 100644 modules/agent-framework/airavata-agent/pkg/types.go
delete mode 100644 modules/agent-framework/airavata-jupyter-magic/.gitignore
delete mode 100644 modules/agent-framework/airavata-jupyter-magic/README.md
delete mode 100644 modules/agent-framework/airavata-jupyter-magic/__init__.py
delete mode 100644
modules/agent-framework/airavata-jupyter-magic/airavata_jupyter_magic.py
delete mode 100644
modules/agent-framework/airavata-jupyter-magic/device_auth.py
delete mode 100644
modules/agent-framework/airavata-jupyter-magic/pyproject.toml
copy modules/research-framework/portal/public/{cybershuttle_logo.png =>
media/images/Frame_14_FgnQDaE.original.original.png} (100%)
copy modules/research-framework/portal/src/components/events/{index.tsx =>
Apr11Workshop.tsx} (88%)
create mode 100644
modules/research-framework/portal/src/components/events/May7Workshop.tsx
create mode 100644
modules/research-framework/portal/src/components/typography/KeyPair.tsx
