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 f42bf98491 move portal to research-framework
omit cca00762dc initial research framework
omit 4f2f07f112 Initial research-framework portal
omit 22be98dcd9 cleanup code. add placeholders for job monitor email/pw in
airavata-server.properties
omit 3c2b9397bb fix issues with helix participant and job engine starter
omit b13e81da33 get hibernate orm to validate against test db. manually
specify catalog for conflicting entities.
omit eb9b50b12e migrate openjpa to hibernate, update pool and dbcp deps to
pool2 and dbcp2.
omit e44acc9da5 parametrize pom versions. add maven-enforcer rule for
dependency convergence and fix version issues.
omit c6fc644ad8 regenerated thrift stubs with version 0.21.0 and fix issues
omit 8b9ca6c94e migrate javax.mail to jakarta.mail to fix email-monitor
bug. exclude conflicting angus-mail dependency. add missing @Deprecated tags.
omit eaa1b7fd07 simplify devcontainer. unify maven-compiler plugin version.
omit e10321af33 migrate openjpa to 4.0.1. update javax.persistence to
jakarta.persistence.
omit a5f2a0d1a1 fix pom issues when running in devcontainer
omit 25e2fcc752 fix generated protos unused issue
omit 9c700c7b0b update rabbitmq and proto versions, fix proto path in
agent-service
omit 54f9d1d951 change protobuf plugin to a maintained one
omit aeba381891 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
omit bd94c98f80 move docker-compose file to .devcontainer
omit 13f4e46336 rename devcontainer to Airavata
omit 56f28c3639 add AF2Complex notebook
omit 27d2ba06d0 updated devcontainer and compose for easy use in vscode
omit fb4155084f create devcontainer.json and integrate with docker-compose
file. fix bugs.
omit 99504c30ab move self-signed certs to a single location
omit 829bd328c7 partial solution for keycloak update in ide-integration
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
new 2d17099ce5 partial solution for keycloak update in ide-integration
new dda0b48d49 move self-signed certs to a single location
new 33402f2a6c create devcontainer.json and integrate with docker-compose
file. fix bugs.
new 4c8d9db1b4 updated devcontainer and compose for easy use in vscode
new 5882ed9e50 add AF2Complex notebook
new 1fa520acbb rename devcontainer to Airavata
new bed9c6ac83 move docker-compose file to .devcontainer
new 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
new 550df6a64b change protobuf plugin to a maintained one
new b4f5e8d14a update rabbitmq and proto versions, fix proto path in
agent-service
new 722beff41e fix generated protos unused issue
new 25ca66b871 fix pom issues when running in devcontainer
new 05e63d7a3f migrate openjpa to 4.0.1. update javax.persistence to
jakarta.persistence.
new 7dbeb40772 simplify devcontainer. unify maven-compiler plugin version.
new feaee51f77 migrate javax.mail to jakarta.mail to fix email-monitor
bug. exclude conflicting angus-mail dependency. add missing @Deprecated tags.
new acf6937ec1 regenerated thrift stubs with version 0.21.0 and fix issues
new 51feea9d4a parametrize pom versions. add maven-enforcer rule for
dependency convergence and fix version issues.
new abc7bfd0ef migrate openjpa to hibernate, update pool and dbcp deps to
pool2 and dbcp2.
new 8a750ed8aa get hibernate orm to validate against test db. manually
specify catalog for conflicting entities.
new d0dd7633c7 fix issues with helix participant and job engine starter
new ad2d1c367f cleanup code. add placeholders for job monitor email/pw in
airavata-server.properties
new bf8d62291d Initial research-framework portal
new c9012d4007 initial research framework
new 23c31506cc move portal to research-framework
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 (f42bf98491)
\
N -- N -- N refs/heads/cybershuttle-dev (23c31506cc)
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 24 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-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 | 557 +-
.../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 +-
.../scigap/production/host_vars/enveomics/vars.yml | 4 +-
.../service/controllers/AgentController.java | 103 +-
.../service/controllers/ExperimentController.java | 38 +-
.../service/handlers/AgentConnectionHandler.java | 367 +-
.../service/handlers/AgentManagementHandler.java | 104 +-
...mmandAck.java => AgentCommandExecutionAck.java} | 2 +-
...uest.java => AgentCommandExecutionRequest.java} | 32 +-
...nse.java => AgentCommandExecutionResponse.java} | 20 +-
...{AgentCommandAck.java => AgentEnvSetupAck.java} | 2 +-
.../service/models/AgentEnvSetupRequest.java | 45 +
.../service/models/AgentEnvSetupResponse.java | 31 +
.../service/models/AgentJupyterExecutionAck.java | 4 +
...uest.java => AgentJupyterExecutionRequest.java} | 31 +-
...nse.java => AgentJupyterExecutionResponse.java} | 21 +-
.../service/models/AgentKernelRestartAck.java | 4 +
.../service/models/AgentKernelRestartRequest.java | 23 +
.../service/models/AgentKernelRestartResponse.java | 32 +
...chAgentRequest.java => AgentLaunchRequest.java} | 41 +-
...AgentResponse.java => AgentLaunchResponse.java} | 14 +-
.../service/models/AgentPythonExecutionAck.java | 4 +
...quest.java => AgentPythonExecutionRequest.java} | 41 +-
...onse.java => AgentPythonExecutionResponse.java} | 23 +-
.../service/models/AgentPythonRunAck.java | 4 -
.../service/models/AgentPythonRunRequest.java | 61 -
...ntResponse.java => AgentTerminateResponse.java} | 4 +-
...reationRequest.java => AgentTunnelRequest.java} | 2 +-
...entCommandAck.java => AgentTunnelResponse.java} | 15 +-
.../service/models/JupyterExecutionAck.java | 4 -
.../service/models/JupyterExecutionResponse.java | 41 -
.../service/services/AiravataFileService.java | 20 +-
.../service/services/AiravataService.java | 57 +-
.../src/main/resources/application.yml | 2 +
modules/agent-framework/airavata-agent/.gitignore | 1 +
modules/agent-framework/airavata-agent/Makefile | 63 +
modules/agent-framework/airavata-agent/README.md | 8 +-
.../airavata-agent/agent-communication.proto | 128 +-
modules/agent-framework/airavata-agent/agent.go | 855 +-
modules/agent-framework/airavata-agent/agent.sh | 86 +
modules/agent-framework/airavata-agent/kernel.py | 6 +-
.../protos/agent-communication.pb.go | 1991 +--
.../protos/agent-communication_grpc.pb.go | 85 +-
.../airavata-jupyter-magic/.gitignore | 3 -
.../airavata-jupyter-magic/README.md | 28 -
.../airavata-jupyter-magic/device_auth.py | 59 -
.../airavata-jupyter-magic/pyproject.toml | 30 -
.../deployments/agent-cerebrum/Makefile | 7 +
.../deployments/agent-cyberfaces/Makefile | 4 +-
.../deployments/agent-gkeyll/Makefile | 4 +-
.../deployments/jupyterhub/data/allen-v1 | 1 +
.../cosyne_tutorial_part_1.ipynb} | 12897 +------------------
.../data/cosyne/cosyne_tutorial_part_2.ipynb | 2470 ++++
.../jupyterhub/data/cosyne/cybershuttle.yml | 64 +
.../deployments/jupyterhub/data/functional-network | 1 +
.../jupyterhub/data/gkeyll/plotE_z.ipynb | 6 +-
.../deployments/jupyterhub/data/md_demo/.gitignore | 2 +
.../proto/agent-communication.proto | 195 +-
modules/research-framework/portal/.gitignore | 2 +-
modules/research-framework/portal/eslint.config.js | 12 +-
modules/research-framework/portal/index.html | 23 +-
.../research-framework/portal/package-lock.json | 6672 ++++++----
modules/research-framework/portal/package.json | 8 +-
.../portal/public/cybershuttle_logo.png | Bin 0 -> 2627 bytes
modules/research-framework/portal/src/App.tsx | 109 +-
.../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/extensibleIcon.png | Bin 0 -> 7467 bytes
.../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/PageHeader.tsx | 4 +-
.../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 | 76 +
.../portal/src/components/auth/UserSet.tsx | 16 +
.../components/datasets/DatasetSpecificDetails.tsx | 20 +
.../portal/src/components/datasets/index.tsx | 54 +-
.../portal/src/components/events/index.tsx | 229 +
.../src/components/home/AddRepositoryButton.tsx | 1 -
.../src/components/home/CybershuttleLanding.tsx | 290 +
.../portal/src/components/home/ProjectCard.tsx | 102 +-
.../portal/src/components/home/ProjectsSection.tsx | 50 +-
.../portal/src/components/home/ResourceCard.tsx | 115 +
.../portal/src/components/home/SessionCard.tsx | 173 +-
.../src/components/home/SessionCardControls.tsx | 141 +
.../portal/src/components/home/SessionsSection.tsx | 92 +-
.../home/StartSessionFromProjectButton.tsx | 150 +
.../portal/src/components/home/index.tsx | 53 +-
.../src/components/models/ModelCardButton.tsx | 17 +
.../src/components/models/ModelSpecificBox.tsx | 22 +
.../portal/src/components/models/index.tsx | 47 +-
.../notebooks/NotebookSpecificDetails.tsx | 19 +
.../portal/src/components/notebooks/index.tsx | 69 +-
.../projects/AssociatedProejctsSection.tsx | 40 +
.../src/components/repositories/GitHubFileTree.tsx | 264 +
.../repositories/RepositorySpecificDetails.tsx | 29 +
.../portal/src/components/repositories/index.tsx | 67 +-
.../src/components/resources/ResourceDetails.tsx | 175 +
.../src/components/resources/ResourceTypeBadge.tsx | 26 +
.../portal/src/components/resources/TagInput.css | 103 +
.../portal/src/components/resources/index.tsx | 244 +
.../src/components/typography/SectionHeading.tsx | 21 +
.../portal/src/components/ui/toaster.tsx | 43 +
.../portal/src/components/ui/tooltip.tsx | 46 +
.../airavata-logo.png => images/airavata_logo.png} | Bin
.../portal/src/interfaces/PrivacyEnum.ts | 4 +
.../portal/src/interfaces/ProjectType.tsx | 11 +-
.../portal/src/interfaces/ResourceType.ts | 34 +
.../portal/src/interfaces/ResourceTypeEnum.ts | 6 +
.../portal/src/interfaces/SessionStatusEnum.ts | 7 +
.../portal/src/interfaces/SessionType.tsx | 20 +-
.../portal/src/interfaces/StatusEnum.ts | 6 +
.../portal/src/interfaces/TagType.tsx | 4 +
.../portal/src/interfaces/UserType.ts | 10 +
.../portal/src/layouts/NavBar.tsx | 150 +
.../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 | 21 +-
.../research-hub/compose/Dockerfile | 21 +
.../compose/custom_templates/login.html | 52 +
.../research-hub/compose}/docker-compose.yaml | 8 +-
.../research-hub/compose/jupyterhub_config.py | 140 +
.../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 | 21 +
.../research-framework/research-service/pom.xml | 34 +-
.../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} | 33 +-
.../service/ResponseTypes/RedirectResponse.java | 17 +
.../service/ResponseTypes/ResourceResponse.java | 26 +
.../research/service/config/AuthzTokenFilter.java | 115 +
.../service/config/DevDataInitializer.java | 203 +
.../research/service/config/OpenApiConfig.java | 54 +
.../research/service/config/WebMvcConfig.java} | 31 +-
.../controller/GlobalExceptionController.java | 63 +
.../service/controller/ProjectController.java | 28 +
.../service/controller/ResearchHubController.java | 79 +
.../service/controller/ResourceController.java | 140 +
.../service/controller/SessionController.java | 59 +
.../research/service/enums/PrivacyEnum.java | 6 +
.../research/service/enums/ResourceTypeEnum.java | 17 +
.../research/service/enums/SessionStatusEnum.java | 17 +
.../research/service/enums/StatusEnum.java | 8 +
.../research/service/exception/ErrorResponse.java | 47 +
.../service/exception/GlobalExceptionHandler.java | 24 +
.../research/service/handlers/ProjectHandler.java | 73 +
.../service/handlers/ResearchHubHandler.java | 146 +
.../research/service/handlers/ResourceHandler.java | 127 +
.../research/service/handlers/SessionHandler.java | 117 +
.../research/service/model/UserContext.java | 52 +
.../service/model/entity/DatasetResource.java} | 38 +-
.../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} | 52 +-
.../service/model/repo/ProjectRepository.java | 38 +
.../service/model/repo/ResourceRepository.java | 52 +
.../service/model/repo/SessionRepository.java | 43 +
.../service/model/repo/TagRepository.java} | 21 +-
.../src/main}/proto/research-service.proto | 11 +-
.../src/main/resources/application.yml | 56 +
.../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 | 55 +
.../main/resources/distribution}/conf/log4j2.xml | 4 +-
202 files changed, 16377 insertions(+), 18238 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
rename
modules/agent-framework/airavata-jupyter-magic/airavata_jupyter_magic.py =>
airavata-api/airavata-client-sdks/airavata-python-sdk/airavata_jupyter_magic/__init__.py
(55%)
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
copy
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/{AgentCommandAck.java
=> AgentCommandExecutionAck.java} (91%)
rename
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/{AgentCommandRequest.java
=> AgentCommandExecutionRequest.java} (76%)
copy
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/{AgentCommandResponse.java
=> AgentCommandExecutionResponse.java} (70%)
copy
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/{AgentCommandAck.java
=> AgentEnvSetupAck.java} (92%)
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
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentJupyterExecutionAck.java
copy
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/{JupyterExecutionRequest.java
=> AgentJupyterExecutionRequest.java} (50%)
rename
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/{AgentPythonRunResponse.java
=> AgentJupyterExecutionResponse.java} (55%)
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentKernelRestartAck.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentKernelRestartRequest.java
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} (65%)
rename
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/{LaunchAgentResponse.java
=> AgentLaunchResponse.java} (68%)
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentPythonExecutionAck.java
rename
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/{JupyterExecutionRequest.java
=> AgentPythonExecutionRequest.java} (51%)
rename
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/{AgentCommandResponse.java
=> AgentPythonExecutionResponse.java} (60%)
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
rename
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/{TerminateAgentResponse.java
=> AgentTerminateResponse.java} (84%)
rename
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/{AgentTunnelCreationRequest.java
=> AgentTunnelRequest.java} (97%)
rename
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/{AgentCommandAck.java
=> AgentTunnelResponse.java} (57%)
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/JupyterExecutionResponse.java
mode change 100644 => 120000
modules/agent-framework/airavata-agent/agent-communication.proto
create mode 100755 modules/agent-framework/airavata-agent/agent.sh
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/device_auth.py
delete mode 100644
modules/agent-framework/airavata-jupyter-magic/pyproject.toml
create mode 160000 modules/agent-framework/deployments/jupyterhub/data/allen-v1
copy
modules/agent-framework/deployments/jupyterhub/data/{iguide/census_geometry/tl_2020_06_tabblock20.geojson
=> cosyne/cosyne_tutorial_part_1.ipynb} (55%)
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/cosyne/cosyne_tutorial_part_2.ipynb
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/cosyne/cybershuttle.yml
create mode 160000
modules/agent-framework/deployments/jupyterhub/data/functional-network
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/.gitignore
create mode 100644
modules/research-framework/portal/public/cybershuttle_logo.png
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/extensibleIcon.png
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/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/events/index.tsx
create mode 100644
modules/research-framework/portal/src/components/home/CybershuttleLanding.tsx
create mode 100644
modules/research-framework/portal/src/components/home/ResourceCard.tsx
create mode 100644
modules/research-framework/portal/src/components/home/SessionCardControls.tsx
create mode 100644
modules/research-framework/portal/src/components/home/StartSessionFromProjectButton.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/notebooks/NotebookSpecificDetails.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/resources/ResourceDetails.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/SectionHeading.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
copy modules/research-framework/portal/src/{assets/airavata-logo.png =>
images/airavata_logo.png} (100%)
create mode 100644
modules/research-framework/portal/src/interfaces/PrivacyEnum.ts
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/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/research-hub/compose/Dockerfile
create mode 100644
modules/research-framework/research-hub/compose/custom_templates/login.html
copy 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
create mode 100644 modules/research-framework/research-service/README.md
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
modules/{airavata-helix/task-core/src/main/java/org/apache/airavata/helix/core/support/TaskHelperImpl.java
=>
research-framework/research-service/src/main/java/org/apache/airavata/research/service/ResearchServiceApplication.java}
(56%)
create mode 100644
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/ResponseTypes/RedirectResponse.java
create mode 100644
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/ResponseTypes/ResourceResponse.java
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
copy
modules/{ide-integration/src/main/containers/pga/airavata-php-gateway/app/libraries/Thrift/Factory/TJSONProtocolFactory.php
=>
research-framework/research-service/src/main/java/org/apache/airavata/research/service/config/WebMvcConfig.java}
(52%)
mode change 100755 => 100644
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/enums/PrivacyEnum.java
create mode 100644
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/enums/ResourceTypeEnum.java
create mode 100644
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/enums/SessionStatusEnum.java
create mode 100644
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/enums/StatusEnum.java
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
copy
modules/{credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/store/impl/util/CredentialStoreDBInitConfig.java
=>
research-framework/research-service/src/main/java/org/apache/airavata/research/service/model/entity/DatasetResource.java}
(53%)
copy
modules/{registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/LocalDataMovementEntity.java
=>
research-framework/research-service/src/main/java/org/apache/airavata/research/service/model/entity/ModelResource.java}
(50%)
copy
modules/{registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/LocalDataMovementEntity.java
=>
research-framework/research-service/src/main/java/org/apache/airavata/research/service/model/entity/NotebookResource.java}
(53%)
create mode 100644
modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/model/entity/Project.java
copy
modules/{registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/LocalDataMovementEntity.java
=>
research-framework/research-service/src/main/java/org/apache/airavata/research/service/model/entity/RepositoryResource.java}
(53%)
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
copy
modules/{registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/LocalDataMovementEntity.java
=>
research-framework/research-service/src/main/java/org/apache/airavata/research/service/model/entity/Tag.java}
(55%)
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
modules/{db-event-manager/src/main/java/org/apache/airavata/db/event/manager/utils/Constants.java
=>
research-framework/research-service/src/main/java/org/apache/airavata/research/service/model/repo/TagRepository.java}
(68%)
copy modules/research-framework/{ =>
research-service/src/main}/proto/research-service.proto (63%)
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%)