This is an automated email from the ASF dual-hosted git repository.
lahirujayathilake pushed a change to branch master
in repository https://gitbox.apache.org/repos/asf/airavata.git
from a1d24895dd Deploying BayesPrism gateway in a new Jetstream VM
add 0099a40652 CyberFaCES docker file
add a8db55d86b add file ops to jupyter magics, cleanup code, update
agent.sh
add 07c59a245c temp commit to get cyberfaces meeting poc
add fcffabac45 update data tar and analysis script
add 1baf653252 add airavata magics to dev-tools/, make airavata-agent/
build generic
add 6e5c556960 reorganize agent-framework related code. make
airavata-magics a python package.
add 5a1ce93b2e revise jupyterhub spawned notebooks, add makefiles
add 14badc1e98 initial experiment sdk implementation
add 1dcb49a8e7 improve auth flow, add python code invocation, add plan
crud apis and file ul/dl apis, reduce settings.ini deps, fix bugs
add cd2d2a9d7e venv support for agent, update notebooks, show tables as
pandas df, update dir refs, fix bugs.
add 919bfd1d9d make settings.ini lean, add runtime picker {by cluster,
category}. change agent base dir.
add 88541dede6 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 c09d8235e3 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 276a64ec1d bump version to 0.0.16 add AlphaFold2 and Gaussian
applications update realm from 10000000 -> default add GROMACS and AMBER to MD
SDK
add 5deda3fa7a choose group/project from API, silent plan launch,
add_replica() -> create_task(), display task state, planid and taskid, improve
messaging
add 84e5ebf7ed add back kernel launcher to agent
add 36694d02b4 refine Makefiles, move app-scripts to agent-framework/, fix
bugs in agent.go and sample Dockerfile
add f58c097ab5 regenerate thrift specs
add 7147066445 cleanup airavata_sdk wrappers, error-handling in
airavata_experiments
add b5015274a9 add type-hinting imports to __init__ files
add b7f8a2b3a2 cleanup imports, fix bugs found by type checker
add 9a02f2faf3 enabled micromamba base when starting the kernel
add 5ab0aaff6a fix bugs in airavata-jupyter-magic package
add 496fcd84f6 fix dependency issue in cyberfaces agent
add 2cc7c666cd organize code, add other deployment files, partially redo
airavata_jupyter_magic for runtime switching
add 63f8ff76c7 refine code flow in airavata_jupyter_magic. bump version to
1.0.5, update notebook, fix bugs
add 3debcbcc4b updated notebooks
add 9d696d9d4b rename platform x86_64 -> amd64. fix issues in cyberfaces
dockerfile. update notebooks. move environment files.
add 53710ee6ee updated the agent dependencies
add a3785536c7 gkeyll agent image and notebook sample
add 5097dd7196 updated the gkeyll notebook script
add 1c45397dcd bump version zookeeper and kafka
add b4046f6f9a excluded logback from file service
add 45243c04e4 jobmanager configs and included registry server properties
for real-time monitor
add 12435359d0 initial research framework
add 214908200f add research portal
add 7958736384 entity classes and structure for research framework
add cadfa1637c research hub configurations and compose files
add 0ace0dfd58 relative dataset path for the spawner
add 9d4b8c68f4 global exception handler and boiler template for spinning
up a new JL cloning a git repo and mounting ro volume
add 20745efd0e authz token filtering and extracting username for the hub
add a3949229ce Setup complete
add 12fff47528 Basic API implementation working
add 8d19d88878 Add support for ModelResource
add 1ce60a6253 Pull multiple resources
add 40f48c9906 session entity impl and entity modifications
add 94e814e843 jupyterhub instance to show sample notebooks
add b22b4a2588 clone the repo in to the work directory and grant the right
permissions
add 852645b3fe disable authz token verification in dev mode
add 33d320c144 rhub session impl and some refactoring
add 226d9629c3 initialize user and changes to rhub service classes
add c8c3b21492 spawn containers with the given project, reattach to
existing sessions, service updates, and data initializations
add c0dbc72dc1 dev authz token filter for development
add 4fe26670f3 backend integration with portal code
add 6288ddf04a Backend integration with portal
add adee56c567 File tree added to ProjectDetails.tsx
add 27eb9e84f0 Use StoragePath from Properties in AgentManagementHandler
add 1de31a7352 Allow file tree exploring & handle rate limit error
add 5b6b1ffcc7 reused airavata user profile in research service, updated
the authz token filter
add b4084d7932 update the default data in DevDataInitializer and
application.yml. update package-lock.json
add d2da68cb1c bring airavata-python-sdk updates from cybershuttle-dev
add d746ebde84 Address CORS
add 913a62e28b fixed the thrift client issue, cannot reuse the client
connection for multiple calls
add 8e4be3aa85 configurable allowed origin for research service
add cd8d67670f Authentication for Research Portal (#481)
add e77eab862b renamed the file to fix npm run build
add 2e3ea8dfbf point to same agent-communication.proto
add 8939f0ced4 update /api/v1/agent endpoints, modify protos for env
creation, update agent go script with env creation code.
add 9c38135d6c refine agent.go, fix bugs
add 38b64e7c38 add kernel restart functionality to agent service and agent
add 70261d1818 update Makefiles and bump airavata python sdk to 2.0.5
add a476d0fef9 fix bugs in python sdk after base image / api changes
add 13cfa7d320 update sdk and agent service to accep yml file and
dependencies.
add 512012175e update notebooks
add c15d39f67f bump python sdk version to 2.0.5.post2
add fcb0c50670 make remote cell execution responsive. bump version to 2.0.6
add ab35f65796 refactoring UI and responsive changes
add 6ea5fe1329 Add auth to swagger
add ab6eaae418 Support logout
add 646f5f9e0b Homepage + redirecting logins
add 8d7e4c439b Condense to single resource page + allow unauthenticated
routes
add b212d69258 Cybershuttle.org homepage copy
add f52ab56f6a Changed the uploading file size in enveomics gateway
add 8169534a1b ide-integration docker-compose changes
add bfd2774ac8 update agent to accept libraries, pip, and mounts as input.
add 71bac95f5a update AgentManagementHandler to send libraries, pip, and
mounts in the Agent launch request.
add 7fbc376a9b handle empty lists correctly in the cybershuttle.yml reader.
add 21d1de0226 add overlay fs to agent for rw access. update makefile
scripts, add stderr logging to agent
add e3d14df161 fix issues in agent/sdk for creating custom environments.
update agent deployment scripts
add 919e119cf1 move mktemp from agent.sh into airavata-agent
add 7a0dfbf594 handle empty conda/pip deps, fix agent issues
add abcce2a8b8 fix sdk bugs and agent bugs
add 4952fadca2 update projects in research-service DevDataInitializer.
add 993eec02ce refactoring UI and responsive changes
add bd68aee7b5 Add auth to swagger
add ab8abcdfe7 Support logout
add a694026f1d Homepage + redirecting logins
add 453c694e8c Condense to single resource page + allow unauthenticated
routes
add b425cbc342 Cybershuttle.org homepage copy
add 6ec11ac557 Show project cards for repos + datasets
add f9ab83b639 Merge branch 'cybershuttle-staging' of
https://github.com/apache/airavata into new-features
add 29e70d9790 Fix userset
add eeb4027c1f Workshop changes
add f6251e9b34 Merge pull request #485 from ganning127/new-features
add 5acea912cf update DevDataInitializer projects/paths, update the
application.yml bundled with research-service.
add 60022055fc display version when loading airavata_jupyter_magic. add
--use parameter to pass allowed resources. move default variables around. add
%restart_runtime to magic detector, show %stat_runtime command in the display
message.
add ff7ce33a49 display version when loading airavata_jupyter_magic. add
--use parameter to pass allowed resources. move default variables around. add
%restart_runtime to magic detector, show %stat_runtime command in the display
message.
add 240d166f2e included ipywidgets for hub user containers
add 9fcfc066b5 update catalog data in DevDataInitiializer
add 6e5d934534 updated the hub data folder and included pip packages
add 6acef072af Support for HTML and JS support for magic output
add e90cb7b30f Merge pull request #487 from apache/Agent-HTML-Support
add f3e47ce2d7 bump python sdk version to 2.0.9
add 3069b06b8b Meta scheduling behavior for agent launch
add d0aca3312e ui/ux experience fixes
add dc81e7f2b1 add events
add f95f2a916e Merge pull request #486 from ganning127/fixes-for-wed
add ee2ca801d0 add separate --environ input to agent. add js2 targets to
makefile. update sdk to pass environ
add 1fb8450b81 move env_name generation to AgentManagementHandler
add 79eb6594e0 User error handling
add 9308a2423c Merge pull request #488 from ganning127/fixes-for-thurs
add 6e4d4074ee add chatter link
add 96e9689ae5 Merge pull request #489 from ganning127/agenda-change
add 43dab315f9 resolve cell id not incrementing in remote exec mode
add f063461cd6 Enable agent to keep alive the stream with server
add df26dd3e92 Support session termination & deletion on jupyter
add 2d101eda26 Allow terminated & stopped sessions from being blocked
add 8797fb309b Minor logging improvements
add 80b95ee772 Enabling audio like widjets in magic extension
add 8bae7e74a6 update DevDataInitializer
add 3e45510108 update DevDataInitializer
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 361544c204 Merge branch 'master' into cybershuttle-staging
add 497b86d76e update agent.sh to initialize scratch
add cfc00e5159 updated jupyterhub_config.py
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
add 34abbfb222 Merge branch 'master' into cybershuttle-staging
add e8f73d7a51 move old deployments into examples/, and app scripts into
dev-tools/app-scripts
add 50b71a954e move cybershuttle examples to cyber-shuttle org and add
links instead
add 2eb180795d included missing license headers
add 0b5cf3a523 research framework formatting and included missing license
headers
add 2eb089f5a2 Merge pull request #500 from apache/cybershuttle-staging
No new revisions were added by this update.
Summary of changes:
.gitignore | 2 +
.../airavata-python-sdk/.gitignore | 5 +-
.../airavata-python-sdk/README.md | 447 +-
.../airavata-python-sdk}/__init__.py | 0
.../airavata_experiments/airavata.py | 133 +-
.../neuro}/__init__.py | 6 +
.../airavata_experiments/neuro/applications.py | 87 +
.../airavata_jupyter_magic/__init__.py | 1772 +
.../airavata_jupyter_magic/device_auth.py | 63 +
.../airavata-python-sdk/docs/index.md | 39 +
.../docs/reference/airavata_experiments.md | 3 +
.../docs/reference/airavata_jupyter_magic.md | 3 +
.../docs/reference/airavata_sdk.md | 3 +
.../airavata-python-sdk/mkdocs.yml | 19 +
.../airavata-python-sdk/pyproject.toml | 12 +-
.../templates/email-monitor/email-config.yaml.j2 | 7 +-
dev-tools/ansible/roles/kafka/defaults/main.yml | 2 +-
dev-tools/ansible/roles/zookeeper/vars/main.yml | 2 +-
.../app-scripts/expanse_af2.sh | 0
.../app-scripts/expanse_namd.sh | 0
examples/projects_using_airavata.md | 35 +
examples/python_sdk_experiment_tracking.md | 2 +
examples/python_sdk_jupyter_notebooks.md | 2 +
modules/agent-framework/agent-service/pom.xml | 19 +
.../service/AgentServiceApplication.java | 18 +
.../agent/connection/service/UserContext.java | 18 +
.../service/config/AuthzTokenFilter.java | 18 +
.../service/config/ClusterApplicationConfig.java | 18 +
.../service/controllers/AgentController.java | 186 +-
.../service/controllers/ExperimentController.java | 57 +-
.../service/controllers/PlanController.java | 18 +
.../service/db/entity/AgentDeploymentInfo.java | 18 +
.../service/db/entity/AgentExecution.java | 18 +
.../service/db/entity/AgentExecutionStatus.java | 18 +
.../agent/connection/service/db/entity/Plan.java | 18 +
.../service/db/repo/AgentDeploymentInfoRepo.java | 18 +
.../service/db/repo/AgentExecutionRepo.java | 18 +
.../service/db/repo/AgentExecutionStatusRepo.java | 18 +
.../agent/connection/service/db/repo/PlanRepo.java | 18 +
.../service/handlers/AgentConnectionHandler.java | 561 +-
.../service/handlers/AgentManagementHandler.java | 122 +-
.../connection/service/handlers/FuseFSHandler.java | 18 +
.../connection/service/handlers/PlanHandler.java | 18 +
.../models/AgentAsyncCommandExecutionRequest.java | 61 +
.../models/AgentAsyncCommandExecutionResponse.java | 49 +
.../models/AgentAsyncCommandListRequest.java} | 30 +-
.../models/AgentAsyncCommandListResponse.java | 51 +
.../models/AgentAsyncCommandTerminateRequest.java | 35 +-
.../models/AgentAsyncCommandTerminateResponse.java | 36 +-
.../connection/service/models/AgentCommandAck.java | 22 -
.../service/models/AgentCommandExecutionAck.java} | 33 +-
.../models/AgentCommandExecutionRequest.java | 62 +
.../models/AgentCommandExecutionResponse.java | 49 +
.../service/models/AgentCommandRequest.java | 34 -
.../service/models/AgentCommandResponse.java | 31 -
.../service/models/AgentEnvSetupAck.java} | 33 +-
.../service/models/AgentEnvSetupRequest.java | 63 +
.../service/models/AgentEnvSetupResponse.java | 49 +
.../service/models/AgentInfoResponse.java | 18 +
.../service/models/AgentJupyterExecutionAck.java | 14 +-
.../models/AgentJupyterExecutionRequest.java | 49 +
.../models/AgentJupyterExecutionResponse.java | 50 +
.../service/models/AgentKernelRestartAck.java | 14 +-
.../service/models/AgentKernelRestartRequest.java | 36 +-
.../service/models/AgentKernelRestartResponse.java | 50 +
...chAgentRequest.java => AgentLaunchRequest.java} | 59 +-
.../service/models/AgentLaunchResponse.java | 64 +
.../service/models/AgentPythonExecutionAck.java | 14 +-
.../models/AgentPythonExecutionRequest.java | 59 +
.../models/AgentPythonExecutionResponse.java | 50 +
.../service/models/AgentPythonRunAck.java | 4 -
.../service/models/AgentPythonRunRequest.java | 61 -
.../service/models/AgentPythonRunResponse.java | 41 -
.../service/models/AgentTerminateResponse.java | 45 +
.../connection/service/models/AgentTunnelAck.java | 27 +
.../service/models/AgentTunnelCreateRequest.java | 49 +
.../service/models/AgentTunnelCreateResponse.java | 68 +
.../service/models/AgentTunnelCreationRequest.java | 67 -
.../models/AgentTunnelTerminateRequest.java | 35 +-
.../models/AgentTunnelTerminateResponse.java | 14 +-
.../connection/service/models/AsyncCommand.java | 37 +-
.../connection/service/models/DirectoryInfo.java | 18 +
.../service/models/ExperimentStorageResponse.java | 18 +
.../agent/connection/service/models/FileInfo.java | 18 +
.../service/models/JupyterExecutionAck.java | 4 -
.../service/models/JupyterExecutionRequest.java | 40 -
.../service/models/JupyterExecutionResponse.java | 41 -
.../service/models/LaunchAgentResponse.java | 36 -
.../service/models/TerminateAgentResponse.java | 27 -
.../service/services/AiravataFileService.java | 38 +-
.../service/services/AiravataService.java | 75 +-
.../src/main/resources/application.yml | 24 +
.../resources/distribution/conf/application.yml | 16 +
modules/agent-framework/airavata-agent/.gitignore | 1 +
modules/agent-framework/airavata-agent/Dockerfile | 19 +
modules/agent-framework/airavata-agent/Makefile | 148 +
modules/agent-framework/airavata-agent/README.md | 180 +-
.../airavata-agent/agent-communication.proto | 128 +-
modules/agent-framework/airavata-agent/agent.go | 637 +-
modules/agent-framework/airavata-agent/agent.sh | 123 +
modules/agent-framework/airavata-agent/go.mod | 68 +-
modules/agent-framework/airavata-agent/kernel.py | 22 +-
.../agent-framework/airavata-agent/pkg/jupyter.go | 251 +
.../agent-framework/airavata-agent/pkg/python.go | 54 +
.../agent-framework/airavata-agent/pkg/shell.go | 213 +
.../agent-framework/airavata-agent/pkg/tunnel.go | 115 +
.../agent-framework/airavata-agent/pkg/types.go | 25 +
.../protos/agent-communication.pb.go | 2770 +-
.../protos/agent-communication_grpc.pb.go | 102 +-
modules/agent-framework/airavata-fuse/Makefile | 17 +
modules/agent-framework/airavata-fuse/README.md | 19 +
.../airavata-jupyter-magic/.gitignore | 3 -
.../airavata-jupyter-magic/README.md | 28 -
.../airavata_jupyter_magic.py | 751 -
.../airavata-jupyter-magic/device_auth.py | 59 -
.../airavata-jupyter-magic/pyproject.toml | 30 -
.../deployments/agent-cerebrum/Dockerfile | 36 -
.../deployments/agent-cerebrum/Makefile | 10 -
.../deployments/agent-cerebrum/README.md | 13 -
.../deployments/agent-cyberfaces/Dockerfile | 53 -
.../deployments/agent-cyberfaces/Makefile | 17 -
.../deployments/agent-cyberfaces/README.md | 13 -
.../deployments/agent-cyberfaces/envs/aiml.yml | 44 -
.../deployments/agent-cyberfaces/envs/fair.yml | 82 -
.../agent-cyberfaces/envs/justiceindata.yml | 9 -
.../deployments/agent-cyberfaces/envs/rs.yml | 23 -
.../deployments/agent-gkeyll/Dockerfile | 6 -
.../deployments/agent-gkeyll/Makefile | 17 -
.../deployments/agent-gkeyll/README.md | 13 -
.../deployments/agent-i-guide/Dockerfile | 15 -
.../deployments/agent-i-guide/Makefile | 10 -
.../deployments/agent-i-guide/README.md | 13 -
.../deployments/agent-md/Dockerfile | 12 -
.../agent-framework/deployments/agent-md/Makefile | 10 -
.../agent-framework/deployments/agent-md/README.md | 13 -
.../deployments/agent-sample/Dockerfile | 9 -
.../deployments/agent-sample/Makefile | 10 -
.../deployments/agent-sample/README.md | 13 -
.../deployments/app-scripts/anvil_agent.sh | 41 -
.../deployments/app-scripts/expanse_agent.sh | 40 -
.../deployments/jupyterhub/Dockerfile | 13 -
.../deployments/jupyterhub/Dockerfile-jl-base | 28 -
.../deployments/jupyterhub/Dockerfile-jl-iguide | 30 -
.../deployments/jupyterhub/Makefile | 13 -
.../deployments/jupyterhub/README.md | 1 -
.../data/cerebrum/bkg/bkg_spikes_250Hz_3s.h5 | Bin 133346 -> 0 bytes
.../jupyterhub/data/cerebrum/config_nest.json | 54 -
.../data/cerebrum/description/config.json | 537 -
.../data/cerebrum/description/config_template.json | 283 -
.../data/cerebrum/description/custom_mod.json | 5858 -
.../cerebrum/description/db_connect_output.json | 70675 ---------
.../cyberfaces/Solution_DA3_DEM_Access_v4.ipynb | 601 -
.../Solution_DP6_DEM_Processing_v2.ipynb | 882 -
.../data/experiment_sdk/1_experiment_sdk.ipynb | 401 -
.../jupyterhub/data/gkeyll/plotE_z.ipynb | 164 -
.../data/iguide/NID_FIM_MH_F/MH_F_CA10022.tiff | Bin 365941 -> 0 bytes
.../data/iguide/NID_FIM_NH_F/NH_F_CA10022.tiff | Bin 27506 -> 0 bytes
.../data/iguide/NID_FIM_TAS_F/TAS_F_CA10022.tiff | Bin 232386 -> 0 bytes
.../data/iguide/census_geometry/census_data.csv | 83510 ----------
.../census_geometry/census_tract_from_api.geojson | 9115 --
.../census_geometry/tl_2020_06_tabblock20.geojson | 12896 --
.../jupyterhub/data/iguide/cyberfaces.ipynb | 868 -
.../jupyterhub/data/iguide/dam_list.csv | 346 -
.../md_demo/data/alphafold2/Abeta42_Dimer.fasta | 4 -
.../data/md_demo/data/amber/RAMP1.prmtop | 52609 -------
.../data/md_demo/data/amber/RAMP1_equil.rst7 | Bin 1129976 -> 0 bytes
.../jupyterhub/data/md_demo/data/amber/md.in | 9 -
.../md_demo/data/gaussian/NOR0N-RAD21-freq.gjf | 89 -
.../jupyterhub/data/md_demo/data/gromacs/md.mdp | 46 -
.../jupyterhub/data/md_demo/data/gromacs/npt.gro | 93291 -----------
.../jupyterhub/data/md_demo/data/gromacs/npt.tpr | Bin 4716544 -> 0 bytes
.../jupyterhub/data/md_demo/data/namd/b4pull.pdb | 97198 ------------
.../data/md_demo/data/namd/b4pull.restart.coor | Bin 2332708 -> 0 bytes
.../data/md_demo/data/namd/b4pull.restart.vel | Bin 2332708 -> 0 bytes
.../data/md_demo/data/namd/b4pull.restart.xsc | 3 -
.../data/md_demo/data/namd/par_all36_water.prm | 115 -
.../data/md_demo/data/namd/par_all36m_prot.prm | 3435 -
.../data/md_demo/data/namd/pull_cpu.conf | 100 -
.../data/md_demo/data/namd/pull_gpu.conf | 100 -
.../data/md_demo/data/namd/structure.pdb | 97198 ------------
.../data/md_demo/data/namd/structure.psf | 147335 ------------------
.../data/md_demo/molecular_dynamics.ipynb | 1706 -
.../jupyterhub/data/md_demo/settings.ini | 13 -
.../jupyterhub/data/namd_workshop/data/b4pull.pdb | 97198 ------------
.../data/namd_workshop/data/b4pull.restart.coor | Bin 2332708 -> 0 bytes
.../data/namd_workshop/data/b4pull.restart.vel | Bin 2332708 -> 0 bytes
.../data/namd_workshop/data/b4pull.restart.xsc | 3 -
.../data/namd_workshop/data/par_all36_water.prm | 115 -
.../data/namd_workshop/data/par_all36m_prot.prm | 3435 -
.../data/namd_workshop/data/pull_cpu.conf | 100 -
.../data/namd_workshop/data/pull_gpu.conf | 100 -
.../data/namd_workshop/data/structure.pdb | 97198 ------------
.../data/namd_workshop/data/structure.psf | 147335 ------------------
.../jupyterhub/data/namd_workshop/settings.ini | 17 -
.../jupyterhub/data/namd_workshop/smd_cpu.ipynb | 401 -
.../jupyterhub/data/namd_workshop/smd_gpu.ipynb | 401 -
.../deployments/jupyterhub/jupyterhub_config.py | 71 -
.../deployments/jupyterhub/nginx-conf | 36 -
modules/agent-framework/pom.xml | 19 +
.../proto/agent-communication.proto | 247 +-
.../apache/airavata/agents/api/FileMetadata.java | 9 +
.../airavata/helix/adaptor/SSHJAgentAdaptor.java | 2 +
modules/distribution/pom.xml | 11 +
.../resources/email-monitor/conf/email-config.yaml | 8 +-
.../conf/airavata-server.properties | 8 +-
modules/file-server/pom.xml | 14 +-
.../file/server/controller/FileController.java | 55 +-
.../file/server/model/AiravataDirectory.java | 19 +-
.../airavata/file/server/model/AiravataFile.java | 25 +
.../file/server/service/AirvataFileService.java | 108 +-
.../src/main/containers/docker-compose.yml | 4 +-
.../src/main/resources/email-config.yaml | 6 +-
.../src/main/resources/email-config.yaml | 10 +-
.../src/main/resources/airavata-server.properties | 8 +-
modules/research-framework/pom.xml | 42 +
modules/research-framework/portal/.gitignore | 24 +
modules/research-framework/portal/README.md | 54 +
modules/research-framework/portal/eslint.config.js | 28 +
modules/research-framework/portal/index.html | 16 +
.../research-framework/portal/package-lock.json | 4203 +
modules/research-framework/portal/package.json | 49 +
.../portal/public/cybershuttle_logo.png | Bin 0 -> 2627 bytes
.../images/Frame_14_FgnQDaE.original.original.png | Bin 0 -> 2627 bytes
modules/research-framework/portal/src/App.tsx | 116 +
.../portal/src/assets/AllenLogo.png | Bin 0 -> 11565 bytes
.../portal/src/assets/GTLogo.png | Bin 0 -> 53417 bytes
.../portal/src/assets/Hero.original.png | Bin 0 -> 3208051 bytes
.../portal/src/assets/IUFullLogo.png | Bin 0 -> 10163 bytes
.../portal/src/assets/IULogo.png | Bin 0 -> 2333 bytes
.../portal/src/assets/MolecularDynamics.png | Bin 0 -> 37240 bytes
.../portal/src/assets/NSFLogo.png | Bin 0 -> 42375 bytes
.../portal/src/assets/NeuroScience.png | Bin 0 -> 37427 bytes
.../portal/src/assets/PoweredByApache.png | Bin 0 -> 12850 bytes
.../portal/src/assets/UCSDLogo.png | Bin 0 -> 52605 bytes
.../portal/src/assets/UIUCLogo.png | Bin 0 -> 3490 bytes
.../portal/src/assets/XSEDELogo.png | Bin 0 -> 14094 bytes
.../portal/src/assets/access-logo-footer.svg | 1 +
.../portal/src/assets/airavata-logo.png | Bin 0 -> 14892 bytes
.../portal/src/assets/extensibleIcon.png | Bin 0 -> 7467 bytes
.../research-framework/portal/src/assets/react.svg | 1 +
.../portal/src/assets/reproIcon.png | Bin 0 -> 4275 bytes
.../portal/src/assets/thirdPartyIcon.png | Bin 0 -> 9044 bytes
.../portal/src/assets/userClockIcon.png | Bin 0 -> 6939 bytes
.../portal/src/components/GridContainer.tsx | 17 +
.../portal/src/components/Metadata.tsx | 66 +
.../portal/src/components/PageHeader.tsx | 28 +
.../portal/src/components/add/AddGitUrl.tsx | 92 +
.../portal/src/components/add/AddProjectMaster.tsx | 138 +
.../portal/src/components/add/AddRepoMaster.tsx | 67 +
.../src/components/add/ConfirmRepoDetails.tsx | 152 +
.../portal/src/components/add/DatasetSearch.tsx | 165 +
.../portal/src/components/add/RepoSearch.tsx | 157 +
.../portal/src/components/add/index.tsx | 35 +
.../src/components/auth/ProtectedComponent.tsx | 23 +
.../portal/src/components/auth/TokenHandler.tsx | 37 +
.../portal/src/components/auth/UserLoginPage.tsx | 62 +
.../portal/src/components/auth/UserMenu.tsx | 84 +
.../portal/src/components/auth/UserSet.tsx | 16 +
.../components/datasets/DatasetSpecificDetails.tsx | 20 +
.../portal/src/components/datasets/index.tsx | 70 +
.../portal/src/components/events/Apr11Workshop.tsx | 192 +
.../portal/src/components/events/May7Workshop.tsx | 197 +
.../portal/src/components/events/index.tsx | 40 +
.../src/components/home/AddRepositoryButton.tsx | 124 +
.../portal/src/components/home/AddZipButton.tsx | 113 +
.../portal/src/components/home/ButtonWithIcon.tsx | 22 +
.../src/components/home/CybershuttleLanding.tsx | 290 +
.../portal/src/components/home/ProjectCard.tsx | 34 +
.../portal/src/components/home/ProjectsSection.tsx | 47 +
.../portal/src/components/home/ResourceCard.tsx | 123 +
.../portal/src/components/home/SessionCard.tsx | 148 +
.../src/components/home/SessionCardControls.tsx | 141 +
.../portal/src/components/home/SessionsSection.tsx | 95 +
.../home/StartSessionFromProjectButton.tsx | 152 +
.../portal/src/components/home/index.tsx | 73 +
.../src/components/models/ModelCardButton.tsx | 17 +
.../src/components/models/ModelSpecificBox.tsx | 22 +
.../portal/src/components/models/index.tsx | 67 +
.../notebooks/NotebookSpecificDetails.tsx | 19 +
.../portal/src/components/notebooks/index.tsx | 72 +
.../projects/AssociatedProejctsSection.tsx | 40 +
.../src/components/repositories/GitHubFileTree.tsx | 274 +
.../repositories/RepositorySpecificDetails.tsx | 26 +
.../portal/src/components/repositories/index.tsx | 60 +
.../src/components/resources/ResourceDetails.tsx | 178 +
.../components/resources/ResourceSyncButton.tsx | 216 +
.../src/components/resources/ResourceTypeBadge.tsx | 26 +
.../portal/src/components/resources/TagInput.css | 103 +
.../portal/src/components/resources/index.tsx | 333 +
.../portal/src/components/typography/KeyPair.tsx | 34 +
.../src/components/typography/SectionHeading.tsx | 21 +
.../portal/src/components/ui/color-mode.tsx | 107 +
.../portal/src/components/ui/input-group.tsx | 53 +
.../portal/src/components/ui/provider.tsx | 12 +
.../portal/src/components/ui/toaster.tsx | 43 +
.../portal/src/components/ui/tooltip.tsx | 46 +
.../portal/src/data/MOCK_DATA.js | 555 +
.../portal/src/images/airavata_logo.png | Bin 0 -> 14892 bytes
.../portal/src/interfaces/AuthorType.tsx | 5 +
.../portal/src/interfaces/DatasetType.tsx | 7 +
.../portal/src/interfaces/MetadataType.tsx | 14 +
.../portal/src/interfaces/ModelType.tsx | 10 +
.../portal/src/interfaces/PrivacyEnum.ts | 4 +
.../portal/src/interfaces/ProjectType.tsx | 17 +
.../interfaces/Requests/CreateProjectRequest.tsx | 6 +
.../interfaces/Requests/CreateResourceRequest.tsx | 10 +
.../portal/src/interfaces/ResourceType.ts | 34 +
.../portal/src/interfaces/ResourceTypeEnum.ts | 6 +
.../portal/src/interfaces/SessionStatusEnum.ts | 7 +
.../portal/src/interfaces/SessionType.tsx | 13 +
.../portal/src/interfaces/StatusEnum.ts | 6 +
.../portal/src/interfaces/TagType.tsx | 4 +
.../portal/src/interfaces/UserType.ts | 10 +
.../portal/src/layouts/NavBar.tsx | 155 +
.../portal/src/layouts/NavBarFooterLayout.tsx | 14 +
modules/research-framework/portal/src/lib/api.ts | 48 +
.../research-framework/portal/src/lib/constants.ts | 17 +
.../portal/src/lib/controller.ts | 6 +
modules/research-framework/portal/src/lib/util.ts | 32 +
modules/research-framework/portal/src/main.tsx | 19 +
.../research-framework/portal/src/vite-env.d.ts | 1 +
.../research-framework/portal/tsconfig.app.json | 29 +
modules/research-framework/portal/tsconfig.json | 7 +
.../research-framework/portal/tsconfig.node.json | 24 +
modules/research-framework/portal/vite.config.ts | 8 +
.../research-hub/compose/Dockerfile | 21 +
.../compose/custom_templates/login.html | 52 +
.../research-hub/compose}/docker-compose.yaml | 8 +-
.../research-hub/compose/jupyterhub_config.py | 143 +
.../research-hub/compose/user-container/Dockerfile | 13 +
.../compose/user-container/bootstrap.sh | 1 +
.../compose/user-container/build-container.sh | 2 +
.../research-hub/compose/user-container/init.sh | 28 +
.../research-framework/research-service/README.md | 26 +-
.../research-service}/pom.xml | 56 +-
.../assembly/research-service-bin-assembly.xml} | 2 +-
.../src/main/compose/dbinit/01-init-db.sql | 8 +
.../src/main/compose/docker-compose.yaml | 41 +-
.../airavata/research/service/AiravataService.java | 72 +
.../service/ResearchServiceApplication.java | 36 +-
.../research/service/config/AuthzTokenFilter.java | 120 +
.../service/config/DevDataInitializer.java | 222 +
.../research/service/config/OpenApiConfig.java | 90 +
.../research/service/config/WebMvcConfig.java | 39 +
.../controller/GlobalExceptionController.java | 63 +
.../service/controller/ProjectController.java | 58 +
.../service/controller/ResearchHubController.java | 68 +
.../service/controller/ResourceController.java | 177 +
.../service/controller/SessionController.java | 80 +
.../research/service/dto/CreateProjectRequest.java | 61 +
.../service/dto/CreateResourceRequest.java | 81 +
.../service/dto/ModifyResourceRequest.java} | 29 +-
.../research/service/dto/RedirectResponse.java | 30 +-
.../research/service/dto/ResourceResponse.java | 45 +
.../research/service/enums/PrivacyEnum.java | 16 +-
.../research/service/enums/ResourceTypeEnum.java} | 34 +-
.../research/service/enums/SessionStatusEnum.java | 34 +-
.../research/service/enums/StatusEnum.java | 18 +-
.../research/service/exception/ErrorResponse.java | 66 +
.../service/exception/GlobalExceptionHandler.java | 42 +
.../research/service/handlers/ProjectHandler.java | 121 +
.../service/handlers/ResearchHubHandler.java | 163 +
.../research/service/handlers/ResourceHandler.java | 194 +
.../research/service/handlers/SessionHandler.java | 117 +
.../research/service/model/UserContext.java | 52 +
.../service/model/entity/DatasetResource.java | 45 +
.../service/model/entity/ModelResource.java | 56 +
.../service/model/entity/NotebookResource.java | 45 +
.../research/service/model/entity/Project.java | 135 +
.../service/model/entity/RepositoryResource.java | 45 +
.../research/service/model/entity/Resource.java | 184 +
.../research/service/model/entity/Session.java | 137 +
.../research/service/model/entity/Tag.java | 56 +
.../service/model/repo/ProjectRepository.java | 42 +
.../service/model/repo/ResourceRepository.java | 63 +
.../service/model/repo/SessionRepository.java | 43 +
.../research/service/model/repo/TagRepository.java | 30 +-
.../src/main/proto/research-service.proto | 33 +-
.../src/main/resources/application.yml | 72 +
.../distribution/bin/research-service-daemon.sh} | 8 +-
.../distribution/bin/research-service.sh} | 6 +-
.../src/main/resources/distribution/bin/setenv.sh | 0
.../resources/distribution/conf/application.yml | 71 +
.../main/resources/distribution}/conf/log4j2.xml | 4 +-
pom.xml | 4 +-
sandbox/simstream/README.md | 19 +
sandbox/simstream/example/README.md | 19 +
.../simstream/example/logfile_checker/README.md | 19 +
.../example/logfile_checker/remote_log.slurm | 17 +
sandbox/simstream/example/mem_streamer/README.md | 19 +
sandbox/simstream/example/openmm_example/README.md | 19 +
391 files changed, 21986 insertions(+), 1030676 deletions(-)
rename {modules/agent-framework/airavata-jupyter-magic =>
airavata-api/airavata-client-sdks/airavata-python-sdk}/__init__.py (100%)
copy
airavata-api/airavata-client-sdks/airavata-python-sdk/{airavata_sdk/clients/utils
=> airavata_experiments/neuro}/__init__.py (90%)
create mode 100644
airavata-api/airavata-client-sdks/airavata-python-sdk/airavata_experiments/neuro/applications.py
create mode 100644
airavata-api/airavata-client-sdks/airavata-python-sdk/airavata_jupyter_magic/__init__.py
create mode 100644
airavata-api/airavata-client-sdks/airavata-python-sdk/airavata_jupyter_magic/device_auth.py
create mode 100644
airavata-api/airavata-client-sdks/airavata-python-sdk/docs/index.md
create mode 100644
airavata-api/airavata-client-sdks/airavata-python-sdk/docs/reference/airavata_experiments.md
create mode 100644
airavata-api/airavata-client-sdks/airavata-python-sdk/docs/reference/airavata_jupyter_magic.md
create mode 100644
airavata-api/airavata-client-sdks/airavata-python-sdk/docs/reference/airavata_sdk.md
create mode 100644
airavata-api/airavata-client-sdks/airavata-python-sdk/mkdocs.yml
rename {modules/agent-framework/deployments =>
dev-tools}/app-scripts/expanse_af2.sh (100%)
rename {modules/agent-framework/deployments =>
dev-tools}/app-scripts/expanse_namd.sh (100%)
create mode 100644 examples/projects_using_airavata.md
create mode 100644 examples/python_sdk_experiment_tracking.md
create mode 100644 examples/python_sdk_jupyter_notebooks.md
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentAsyncCommandExecutionRequest.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentAsyncCommandExecutionResponse.java
copy
modules/{ide-integration/src/main/containers/pga/airavata-php-gateway/app/libraries/Thrift/Protocol/JSON/BaseContext.php
=>
agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentAsyncCommandListRequest.java}
(63%)
mode change 100755 => 100644
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentAsyncCommandListResponse.java
copy
airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/lib/Thrift/Protocol/JSON/BaseContext.php
=>
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentAsyncCommandTerminateRequest.java
(54%)
copy
airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/lib/Thrift/Protocol/JSON/BaseContext.php
=>
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentAsyncCommandTerminateResponse.java
(53%)
delete mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentCommandAck.java
copy
modules/{ide-integration/src/main/containers/pga/airavata-php-gateway/app/libraries/Thrift/Protocol/JSON/BaseContext.php
=>
agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentCommandExecutionAck.java}
(54%)
mode change 100755 => 100644
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentCommandExecutionRequest.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentCommandExecutionResponse.java
delete mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentCommandRequest.java
delete mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentCommandResponse.java
copy
modules/{ide-integration/src/main/containers/pga/airavata-php-gateway/app/libraries/Thrift/Protocol/JSON/BaseContext.php
=>
agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentEnvSetupAck.java}
(55%)
mode change 100755 => 100644
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentEnvSetupRequest.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentEnvSetupResponse.java
copy
airavata-api/airavata-client-sdks/airavata-cpp-sdk/src/main/resources/lib/thrift/thrift-config.h
=>
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentJupyterExecutionAck.java
(71%)
mode change 100755 => 100644
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentJupyterExecutionRequest.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentJupyterExecutionResponse.java
copy
airavata-api/airavata-client-sdks/airavata-cpp-sdk/src/main/resources/lib/thrift/thrift-config.h
=>
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentKernelRestartAck.java
(72%)
mode change 100755 => 100644
copy
airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/lib/Thrift/Protocol/JSON/BaseContext.php
=>
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentKernelRestartRequest.java
(55%)
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentKernelRestartResponse.java
rename
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/{LaunchAgentRequest.java
=> AgentLaunchRequest.java} (50%)
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentLaunchResponse.java
copy
airavata-api/airavata-client-sdks/airavata-cpp-sdk/src/main/resources/lib/thrift/thrift-config.h
=>
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentPythonExecutionAck.java
(71%)
mode change 100755 => 100644
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentPythonExecutionRequest.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentPythonExecutionResponse.java
delete mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentPythonRunAck.java
delete mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentPythonRunRequest.java
delete mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentPythonRunResponse.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentTerminateResponse.java
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/AgentTunnelCreationRequest.java
copy
airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/lib/Thrift/Protocol/JSON/BaseContext.php
=>
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentTunnelTerminateRequest.java
(54%)
copy
airavata-api/airavata-client-sdks/airavata-cpp-sdk/src/main/resources/lib/thrift/thrift-config.h
=>
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentTunnelTerminateResponse.java
(74%)
mode change 100755 => 100644
copy
airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/lib/Thrift/Protocol/JSON/BaseContext.php
=>
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AsyncCommand.java
(53%)
delete mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/JupyterExecutionAck.java
delete mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/JupyterExecutionRequest.java
delete mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/JupyterExecutionResponse.java
delete mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/LaunchAgentResponse.java
delete mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/TerminateAgentResponse.java
mode change 100644 => 120000
modules/agent-framework/airavata-agent/agent-communication.proto
create mode 100755 modules/agent-framework/airavata-agent/agent.sh
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/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
delete mode 100644
modules/agent-framework/deployments/agent-cerebrum/Dockerfile
delete mode 100644 modules/agent-framework/deployments/agent-cerebrum/Makefile
delete mode 100644 modules/agent-framework/deployments/agent-cerebrum/README.md
delete mode 100644
modules/agent-framework/deployments/agent-cyberfaces/Dockerfile
delete mode 100644
modules/agent-framework/deployments/agent-cyberfaces/Makefile
delete mode 100644
modules/agent-framework/deployments/agent-cyberfaces/README.md
delete mode 100644
modules/agent-framework/deployments/agent-cyberfaces/envs/aiml.yml
delete mode 100644
modules/agent-framework/deployments/agent-cyberfaces/envs/fair.yml
delete mode 100644
modules/agent-framework/deployments/agent-cyberfaces/envs/justiceindata.yml
delete mode 100644
modules/agent-framework/deployments/agent-cyberfaces/envs/rs.yml
delete mode 100644 modules/agent-framework/deployments/agent-gkeyll/Dockerfile
delete mode 100644 modules/agent-framework/deployments/agent-gkeyll/Makefile
delete mode 100644 modules/agent-framework/deployments/agent-gkeyll/README.md
delete mode 100644 modules/agent-framework/deployments/agent-i-guide/Dockerfile
delete mode 100644 modules/agent-framework/deployments/agent-i-guide/Makefile
delete mode 100644 modules/agent-framework/deployments/agent-i-guide/README.md
delete mode 100644 modules/agent-framework/deployments/agent-md/Dockerfile
delete mode 100644 modules/agent-framework/deployments/agent-md/Makefile
delete mode 100644 modules/agent-framework/deployments/agent-md/README.md
delete mode 100644 modules/agent-framework/deployments/agent-sample/Dockerfile
delete mode 100644 modules/agent-framework/deployments/agent-sample/Makefile
delete mode 100644 modules/agent-framework/deployments/agent-sample/README.md
delete mode 100644
modules/agent-framework/deployments/app-scripts/anvil_agent.sh
delete mode 100644
modules/agent-framework/deployments/app-scripts/expanse_agent.sh
delete mode 100644 modules/agent-framework/deployments/jupyterhub/Dockerfile
delete mode 100644
modules/agent-framework/deployments/jupyterhub/Dockerfile-jl-base
delete mode 100644
modules/agent-framework/deployments/jupyterhub/Dockerfile-jl-iguide
delete mode 100644 modules/agent-framework/deployments/jupyterhub/Makefile
delete mode 100644 modules/agent-framework/deployments/jupyterhub/README.md
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/cerebrum/bkg/bkg_spikes_250Hz_3s.h5
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/cerebrum/config_nest.json
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/cerebrum/description/config.json
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/cerebrum/description/config_template.json
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/cerebrum/description/custom_mod.json
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/cerebrum/description/db_connect_output.json
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/cyberfaces/Solution_DA3_DEM_Access_v4.ipynb
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/cyberfaces/Solution_DP6_DEM_Processing_v2.ipynb
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/experiment_sdk/1_experiment_sdk.ipynb
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/gkeyll/plotE_z.ipynb
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/iguide/NID_FIM_MH_F/MH_F_CA10022.tiff
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/iguide/NID_FIM_NH_F/NH_F_CA10022.tiff
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/iguide/NID_FIM_TAS_F/TAS_F_CA10022.tiff
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/iguide/census_geometry/census_data.csv
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/iguide/census_geometry/census_tract_from_api.geojson
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/iguide/census_geometry/tl_2020_06_tabblock20.geojson
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/iguide/cyberfaces.ipynb
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/iguide/dam_list.csv
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/alphafold2/Abeta42_Dimer.fasta
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/amber/RAMP1.prmtop
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/amber/RAMP1_equil.rst7
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/amber/md.in
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/gaussian/NOR0N-RAD21-freq.gjf
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/gromacs/md.mdp
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/gromacs/npt.gro
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/gromacs/npt.tpr
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/namd/b4pull.pdb
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/namd/b4pull.restart.coor
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/namd/b4pull.restart.vel
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/namd/b4pull.restart.xsc
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/namd/par_all36_water.prm
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/namd/par_all36m_prot.prm
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/namd/pull_cpu.conf
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/namd/pull_gpu.conf
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/namd/structure.pdb
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/namd/structure.psf
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/molecular_dynamics.ipynb
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/settings.ini
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/namd_workshop/data/b4pull.pdb
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/namd_workshop/data/b4pull.restart.coor
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/namd_workshop/data/b4pull.restart.vel
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/namd_workshop/data/b4pull.restart.xsc
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/namd_workshop/data/par_all36_water.prm
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/namd_workshop/data/par_all36m_prot.prm
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/namd_workshop/data/pull_cpu.conf
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/namd_workshop/data/pull_gpu.conf
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/namd_workshop/data/structure.pdb
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/namd_workshop/data/structure.psf
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/namd_workshop/settings.ini
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/namd_workshop/smd_cpu.ipynb
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/namd_workshop/smd_gpu.ipynb
delete mode 100644
modules/agent-framework/deployments/jupyterhub/jupyterhub_config.py
delete mode 100644 modules/agent-framework/deployments/jupyterhub/nginx-conf
create mode 100644 modules/research-framework/pom.xml
create mode 100644 modules/research-framework/portal/.gitignore
create mode 100644 modules/research-framework/portal/README.md
create mode 100644 modules/research-framework/portal/eslint.config.js
create mode 100644 modules/research-framework/portal/index.html
create mode 100644 modules/research-framework/portal/package-lock.json
create mode 100644 modules/research-framework/portal/package.json
create mode 100644
modules/research-framework/portal/public/cybershuttle_logo.png
create mode 100644
modules/research-framework/portal/public/media/images/Frame_14_FgnQDaE.original.original.png
create mode 100644 modules/research-framework/portal/src/App.tsx
create mode 100644 modules/research-framework/portal/src/assets/AllenLogo.png
create mode 100644 modules/research-framework/portal/src/assets/GTLogo.png
create mode 100644
modules/research-framework/portal/src/assets/Hero.original.png
create mode 100644 modules/research-framework/portal/src/assets/IUFullLogo.png
create mode 100644 modules/research-framework/portal/src/assets/IULogo.png
create mode 100644
modules/research-framework/portal/src/assets/MolecularDynamics.png
create mode 100644 modules/research-framework/portal/src/assets/NSFLogo.png
create mode 100644
modules/research-framework/portal/src/assets/NeuroScience.png
create mode 100644
modules/research-framework/portal/src/assets/PoweredByApache.png
create mode 100644 modules/research-framework/portal/src/assets/UCSDLogo.png
create mode 100644 modules/research-framework/portal/src/assets/UIUCLogo.png
create mode 100644 modules/research-framework/portal/src/assets/XSEDELogo.png
create mode 100644
modules/research-framework/portal/src/assets/access-logo-footer.svg
create mode 100644
modules/research-framework/portal/src/assets/airavata-logo.png
create mode 100644
modules/research-framework/portal/src/assets/extensibleIcon.png
create mode 100644 modules/research-framework/portal/src/assets/react.svg
create mode 100644 modules/research-framework/portal/src/assets/reproIcon.png
create mode 100644
modules/research-framework/portal/src/assets/thirdPartyIcon.png
create mode 100644
modules/research-framework/portal/src/assets/userClockIcon.png
create mode 100644
modules/research-framework/portal/src/components/GridContainer.tsx
create mode 100644
modules/research-framework/portal/src/components/Metadata.tsx
create mode 100644
modules/research-framework/portal/src/components/PageHeader.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
create mode 100644
modules/research-framework/portal/src/components/auth/ProtectedComponent.tsx
create mode 100644
modules/research-framework/portal/src/components/auth/TokenHandler.tsx
create mode 100644
modules/research-framework/portal/src/components/auth/UserLoginPage.tsx
create mode 100644
modules/research-framework/portal/src/components/auth/UserMenu.tsx
create mode 100644
modules/research-framework/portal/src/components/auth/UserSet.tsx
create mode 100644
modules/research-framework/portal/src/components/datasets/DatasetSpecificDetails.tsx
create mode 100644
modules/research-framework/portal/src/components/datasets/index.tsx
create mode 100644
modules/research-framework/portal/src/components/events/Apr11Workshop.tsx
create mode 100644
modules/research-framework/portal/src/components/events/May7Workshop.tsx
create mode 100644
modules/research-framework/portal/src/components/events/index.tsx
create mode 100644
modules/research-framework/portal/src/components/home/AddRepositoryButton.tsx
create mode 100644
modules/research-framework/portal/src/components/home/AddZipButton.tsx
create mode 100644
modules/research-framework/portal/src/components/home/ButtonWithIcon.tsx
create mode 100644
modules/research-framework/portal/src/components/home/CybershuttleLanding.tsx
create mode 100644
modules/research-framework/portal/src/components/home/ProjectCard.tsx
create mode 100644
modules/research-framework/portal/src/components/home/ProjectsSection.tsx
create mode 100644
modules/research-framework/portal/src/components/home/ResourceCard.tsx
create mode 100644
modules/research-framework/portal/src/components/home/SessionCard.tsx
create mode 100644
modules/research-framework/portal/src/components/home/SessionCardControls.tsx
create mode 100644
modules/research-framework/portal/src/components/home/SessionsSection.tsx
create mode 100644
modules/research-framework/portal/src/components/home/StartSessionFromProjectButton.tsx
create mode 100644
modules/research-framework/portal/src/components/home/index.tsx
create mode 100644
modules/research-framework/portal/src/components/models/ModelCardButton.tsx
create mode 100644
modules/research-framework/portal/src/components/models/ModelSpecificBox.tsx
create mode 100644
modules/research-framework/portal/src/components/models/index.tsx
create mode 100644
modules/research-framework/portal/src/components/notebooks/NotebookSpecificDetails.tsx
create mode 100644
modules/research-framework/portal/src/components/notebooks/index.tsx
create mode 100644
modules/research-framework/portal/src/components/projects/AssociatedProejctsSection.tsx
create mode 100644
modules/research-framework/portal/src/components/repositories/GitHubFileTree.tsx
create mode 100644
modules/research-framework/portal/src/components/repositories/RepositorySpecificDetails.tsx
create mode 100644
modules/research-framework/portal/src/components/repositories/index.tsx
create mode 100644
modules/research-framework/portal/src/components/resources/ResourceDetails.tsx
create mode 100644
modules/research-framework/portal/src/components/resources/ResourceSyncButton.tsx
create mode 100644
modules/research-framework/portal/src/components/resources/ResourceTypeBadge.tsx
create mode 100644
modules/research-framework/portal/src/components/resources/TagInput.css
create mode 100644
modules/research-framework/portal/src/components/resources/index.tsx
create mode 100644
modules/research-framework/portal/src/components/typography/KeyPair.tsx
create mode 100644
modules/research-framework/portal/src/components/typography/SectionHeading.tsx
create mode 100644
modules/research-framework/portal/src/components/ui/color-mode.tsx
create mode 100644
modules/research-framework/portal/src/components/ui/input-group.tsx
create mode 100644
modules/research-framework/portal/src/components/ui/provider.tsx
create mode 100644
modules/research-framework/portal/src/components/ui/toaster.tsx
create mode 100644
modules/research-framework/portal/src/components/ui/tooltip.tsx
create mode 100644 modules/research-framework/portal/src/data/MOCK_DATA.js
create mode 100644
modules/research-framework/portal/src/images/airavata_logo.png
create mode 100644
modules/research-framework/portal/src/interfaces/AuthorType.tsx
create mode 100644
modules/research-framework/portal/src/interfaces/DatasetType.tsx
create mode 100644
modules/research-framework/portal/src/interfaces/MetadataType.tsx
create mode 100644
modules/research-framework/portal/src/interfaces/ModelType.tsx
create mode 100644
modules/research-framework/portal/src/interfaces/PrivacyEnum.ts
create mode 100644
modules/research-framework/portal/src/interfaces/ProjectType.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
create mode 100644
modules/research-framework/portal/src/interfaces/ResourceType.ts
create mode 100644
modules/research-framework/portal/src/interfaces/ResourceTypeEnum.ts
create mode 100644
modules/research-framework/portal/src/interfaces/SessionStatusEnum.ts
create mode 100644
modules/research-framework/portal/src/interfaces/SessionType.tsx
create mode 100644
modules/research-framework/portal/src/interfaces/StatusEnum.ts
create mode 100644 modules/research-framework/portal/src/interfaces/TagType.tsx
create mode 100644 modules/research-framework/portal/src/interfaces/UserType.ts
create mode 100644 modules/research-framework/portal/src/layouts/NavBar.tsx
create mode 100644
modules/research-framework/portal/src/layouts/NavBarFooterLayout.tsx
create mode 100644 modules/research-framework/portal/src/lib/api.ts
create mode 100644 modules/research-framework/portal/src/lib/constants.ts
create mode 100644 modules/research-framework/portal/src/lib/controller.ts
create mode 100644 modules/research-framework/portal/src/lib/util.ts
create mode 100644 modules/research-framework/portal/src/main.tsx
create mode 100644 modules/research-framework/portal/src/vite-env.d.ts
create mode 100644 modules/research-framework/portal/tsconfig.app.json
create mode 100644 modules/research-framework/portal/tsconfig.json
create mode 100644 modules/research-framework/portal/tsconfig.node.json
create mode 100644 modules/research-framework/portal/vite.config.ts
create mode 100644 modules/research-framework/research-hub/compose/Dockerfile
create mode 100644
modules/research-framework/research-hub/compose/custom_templates/login.html
rename modules/{agent-framework/deployments/jupyterhub =>
research-framework/research-hub/compose}/docker-compose.yaml (71%)
create mode 100644
modules/research-framework/research-hub/compose/jupyterhub_config.py
create mode 100644
modules/research-framework/research-hub/compose/user-container/Dockerfile
create mode 100644
modules/research-framework/research-hub/compose/user-container/bootstrap.sh
create mode 100755
modules/research-framework/research-hub/compose/user-container/build-container.sh
create mode 100755
modules/research-framework/research-hub/compose/user-container/init.sh
copy sandbox/simstream/example/openmm_example/test.txt =>
modules/research-framework/research-service/README.md (58%)
copy modules/{agent-framework/agent-service =>
research-framework/research-service}/pom.xml (76%)
copy
modules/{agent-framework/agent-service/src/main/assembly/agent-service-bin-assembly.xml
=>
research-framework/research-service/src/main/assembly/research-service-bin-assembly.xml}
(97%)
create mode 100644
modules/research-framework/research-service/src/main/compose/dbinit/01-init-db.sql
copy dev-tools/ansible/roles/env_setup/tasks/redhat.yml =>
modules/research-framework/research-service/src/main/compose/docker-compose.yaml
(53%)
create mode 100644
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/AiravataService.java
copy
airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/lib/Thrift/Factory/TJSONProtocolFactory.php
=>
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/ResearchServiceApplication.java
(50%)
create mode 100644
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/config/AuthzTokenFilter.java
create mode 100644
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/config/DevDataInitializer.java
create mode 100644
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/config/OpenApiConfig.java
create mode 100644
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/config/WebMvcConfig.java
create mode 100644
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/controller/GlobalExceptionController.java
create mode 100644
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/controller/ProjectController.java
create mode 100644
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/controller/ResearchHubController.java
create mode 100644
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/controller/ResourceController.java
create mode 100644
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/controller/SessionController.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
copy
modules/{ide-integration/src/main/containers/pga/airavata-php-gateway/app/libraries/Thrift/Protocol/JSON/BaseContext.php
=>
research-framework/research-service/src/main/java/org/apache/airavata/research/service/dto/ModifyResourceRequest.java}
(64%)
mode change 100755 => 100644
copy
airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/lib/Thrift/Protocol/JSON/BaseContext.php
=>
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/dto/RedirectResponse.java
(58%)
create mode 100644
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/dto/ResourceResponse.java
copy
airavata-api/airavata-client-sdks/airavata-cpp-sdk/src/main/resources/lib/thrift/thrift-config.h
=>
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/enums/PrivacyEnum.java
(74%)
mode change 100755 => 100644
copy
modules/{ide-integration/src/main/containers/pga/airavata-php-gateway/app/libraries/Thrift/Protocol/JSON/BaseContext.php
=>
research-framework/research-service/src/main/java/org/apache/airavata/research/service/enums/ResourceTypeEnum.java}
(60%)
mode change 100755 => 100644
copy
airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/lib/Thrift/Protocol/JSON/BaseContext.php
=>
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/enums/SessionStatusEnum.java
(59%)
copy
airavata-api/airavata-client-sdks/airavata-cpp-sdk/src/main/resources/lib/thrift/thrift-config.h
=>
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/enums/StatusEnum.java
(72%)
mode change 100755 => 100644
create mode 100644
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/exception/ErrorResponse.java
create mode 100644
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/exception/GlobalExceptionHandler.java
create mode 100644
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/handlers/ProjectHandler.java
create mode 100644
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/handlers/ResearchHubHandler.java
create mode 100644
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/handlers/ResourceHandler.java
create mode 100644
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/handlers/SessionHandler.java
create mode 100644
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/model/UserContext.java
create mode 100644
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/model/entity/DatasetResource.java
create mode 100644
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/model/entity/ModelResource.java
create mode 100644
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/model/entity/NotebookResource.java
create mode 100644
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/model/entity/Project.java
create mode 100644
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/model/entity/RepositoryResource.java
create mode 100644
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/model/entity/Resource.java
create mode 100644
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/model/entity/Session.java
create mode 100644
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/model/entity/Tag.java
create mode 100644
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/model/repo/ProjectRepository.java
create mode 100644
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/model/repo/ResourceRepository.java
create mode 100644
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/model/repo/SessionRepository.java
copy
airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/lib/Thrift/Protocol/JSON/BaseContext.php
=>
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/model/repo/TagRepository.java
(62%)
copy
airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/lib/Thrift/Factory/TJSONProtocolFactory.php
=>
modules/research-framework/research-service/src/main/proto/research-service.proto
(67%)
create mode 100644
modules/research-framework/research-service/src/main/resources/application.yml
copy
modules/{agent-framework/agent-service/src/main/resources/distribution/bin/agent-service-daemon.sh
=>
research-framework/research-service/src/main/resources/distribution/bin/research-service-daemon.sh}
(92%)
copy
modules/{agent-framework/agent-service/src/main/resources/distribution/bin/agent-service.sh
=>
research-framework/research-service/src/main/resources/distribution/bin/research-service.sh}
(90%)
copy modules/{agent-framework/agent-service =>
research-framework/research-service}/src/main/resources/distribution/bin/setenv.sh
(100%)
create mode 100644
modules/research-framework/research-service/src/main/resources/distribution/conf/application.yml
copy modules/{distribution/src/main/resources/controller =>
research-framework/research-service/src/main/resources/distribution}/conf/log4j2.xml
(93%)
