This is an automated email from the ASF dual-hosted git repository.
github-bot pushed a change to branch
dependabot/maven/modules/airavata-metascheduler/metadata-analyzer/org.quartz-scheduler-quartz-2.3.2
in repository https://gitbox.apache.org/repos/asf/airavata.git
omit 8c4732dacc Bump quartz in
/modules/airavata-metascheduler/metadata-analyzer
add 7a91399b97 Ansible: prod metascheduler config for ultrascan
add a5ba0ca77f Ansible: add public hostname for api server
add ff6ebdffa0 Log error message if db init fails
add d1f439491e changing check table to CONFIGURATION
add 709493625c Ansible: fixes for haproxy configuration
add ca9d5155ba AIRAVATA-3694 Fix comparison when var is a string
add 161dd0a21b AIRAVATA-3694 Fix comparison when var is a string
add 4acfa4aa84 fix hardcorded ipaddress
add 0b1880f8b7 Merge pull request #428 from isururanawaka/metaschedular
add 7daac92d61 Ansible: updating google analytics tracking id to GA4 one
add 244a1fa235 Ansible: smiles django app config
add 1caad3ecc2 Ansible: add gzip/cache support for svg
add fbc9e7cc7b Ansible: switch to manual install/update of smiles django
app
add 56ece454e5 Ansible: load cilogon userinfo and display to admins
add 1d9710d8bd Ansible: enable tus and increase upload limit in
md.cybershuttle.org
add ee036e22cf Adding Carbonate to the SimCCS maptool as default resource
and Jun Wang new PI to get notification
add 5a22abf9f3 Removing unused code
add 6fcefb2c47 AIRAVATA-3697 Switching to column level utf8 character set
add 71bc7c3d30 AIRAVATA-3697 Set lang and locale on WSGIDaemonProcess
add b3d68364c3 Merge branch 'AIRAVATA-3697'
add 1b1d9c9b57 Ansible: tus upload directory cleanup script
add e862948576 Adding shared directory and workspace redirection to SMILES
gateway
add 5df32f41da Adding shared data directory for the Molecular Dynamics
gateway
add 1d8fdabd5c Increased the input file size
add 43ae0d4fd9 Adding Diego and Sudhakar's GT mail to get new user
notifications.
add a63b9c0946 Updating the emails to receive new user account
notifications.
add a7976518f7 Updated PI Sudhakar's new email to receive new user
notifications
add 2e294e153a Updated administrator email to receive new user notification
add 0e4baa3225 Adding new administrators to the gateway new user
notification
add b3f09dc00a Adding new administrators to covid-geoact
add 540c594d97 Adding new administrator emails for new user notifications
for dreg
add 49fb1b06e1 Adding new emails for new user notifications to EHT portal
add 577cbfeba1 Adding emails for new user notifications in future water
portal
add 8c00deb38c Updating new user notification emails of administrators
add 533d2d1124 Updated the admin emails for new user notifications
add cfe90a8615 updating emails for new user notification
add 08356e5249 Updating admin emails for new user notifications
add 767248be31 Updated the admin emails for new user notifications
add 372d8be03a Udated admin emails in Lrose gateway for new user
notifications
add 96c3eb6551 Updated admin emails for new user notifications in
InterACTWEL
add 52a4c6d3ce Updating admin emails for new user notifications
add 404e20b971 Updating the admin emails for new user notifications
add dafbe00f3d Updating admin emails for new user notifications
add 5d23fe90f5 Updating admin emails for new user notifications
add 2688023d99 Adding admin emails for new user notifications
add 4ce1e5b918 Adding admin emails for new user notifications
add 235c126403 updating admin emails for new user notifications
add a80b45999f Updating admin emails for new user notifications
add d3d69ad2d2 Updating admin emails for new user notifications
add 795b8ba463 Updated admin emails for new user notification
add 695bec0647 Updating admin emails for new user notifications
add 429a619d4b Updated emails for new user notifications
add 8eb7779722 Updated admin emails for new user notifications
add 56c0f78f92 updated admin emails for new user notifications
add f7fa1069ab Updated admin emails for new user notifications
add 7e3deb8197 Updated admin emails for new user notifications
add c993c1d03e Updated admin emails for new user notifications
add 00a8b8396b Updated admin emails for new user notifications
add 8ac4f7c838 Updated admin emails for new user notifications
add 468bde56f3 Updated admin emails for new user notifications
add 52b02e59f5 Updated admin emails for new user notifications
add 1c1d4aa491 Updated admin emails for new user notifications
add 863d3d6dcd Updated admin emails for new user notifications
add c081c102cb Commented south dakota gateway
add 9e077f9385 Updating SMILES admin emails
add b1ecb6e4b8 Adding development SMILES gateway
add 34033cef58 Adding new dev SMILES gateway
add 4bb746cd34 Adding new SMILES gateway
add 8a285813e9 Adding new dev SMILES gateway
add e4ce834524 Adding new dev SMILES gateway
add fc28ae9417 Added new gateway key to dev SMILES
add aca1ebdbf5 Updated admin notification email list.
add b6ff0477a2 Adding new BSR app to AMOS gateway
add 50ebcc30de Adding Enveomics gateway
add 0137429bbf Added new admin email for scigap notifications
add 29310c2c26 Updating the CILogon and gateway key for new Enveomics
gateway
add b2e96f300a Adding new DT4H gateway
add 7975840275 Commented the BSR deployment in AMOS gateway through
Ansible.
add 61686443db Added gateway key and CILogon to DT4H gateway
add 96ece8265e first working version
add 13d6e4d522 remove connection information screen
add 8c18fab4b8 stop proxy when application quits
add 4ba0f4bf6d support for publishing
add 9a8430bd47 update gitignore for publishing
add d0b5e68abb setup list experiments
add 19ae5b3561 template for pagination
add 735310696b tab view works
add 6ad88659d4 added support for logo
add 6188e9bb71 added redirect back for login
add 0a6ed88c73 open blank jupyterlab when clicking jupyter
add 44c42003b0 clean up code
add 71369aba74 setup for pagination
add 63a0934277 login changes
add 3f1252041c added cilogon code
add 5c181a2077 trying to do cilogon
add 87e19f37dc added parsing for final URL
add cc47670013 login code
add 182a5be5c4 working version for data
add 7cfbdb14f7 working pagination
add 61ef2c7c9a change to table view
add d1b8d54dc8 refresh token works
add 33651d12b9 added support for type
add f37eed3235 addded header
add 27eae55b59 header
add f6221ee523 quality of life enhancements
add 4a56b01ae8 NAMD create ui (backup)
add ef03e2630e updating naming
add 211a554f4f login fixes and specific user
add 9b60fd46c1 make contribute on github link work
add 28439566a8 update readme
add 7e10ee4388 display you if experiment is yours
add 653924205a add in navbar
add 75db60afa4 ui fixes
add 35d573a704 cleanup code
add b34123d58c added cookie?
add 930985204a working create namd
add cd454c0fd1 added toast
add c630c77aee bug fixes
add 15cce12b60 change urls to deployed
add 4cd43d075b packaging changes
add 28c4c37700 refactor working 1
add 92d45c9ae8 refactoring code
add 84a4dae2a2 queues, compute, all works now
add c0a008069d work on the proxy
add 6ae1e8a265 working on vnc
add 5049221b11 fixed multiple vmd
add bcb894c388 remove logs
add 2da4a7b8d6 logging
add 8d3fb6870e working logging
add 1a6052029e vmd support
add fd6e174448 added code
add 526a1a277b reset fix
add 288f1050b4 fixes
add 9d0f80b61d code
add cfaf418792 added code for VMD
add 2778299f30 more vmd
add 95f0bbf58d new user bug still exists
add d82c388cd0 login
add c129b84399 fixed experiment
add 3e29045783 exp details
add 78a401c2c4 working version currently
add 49a425be22 demo changes
add 2e3b7eba9c demo changes more
add 0a7f682dab fix bug with re-rendering and closing tabs
add 070ff826dc output files
add c8d148b8dc remove all the proxy code
add 983bdcad4c added
add 7fde0312e9 switch to experiment inputs and refactoring
add 6c80df3516 change naming
add e5a4cb9e6b add user profile
add 408a0051a5 homepage wording & user experiment acecss change
add 86d9d43aec remove jn and vmd from jn and vmd exp
add 13fff65a3f fixes to experiment modal
add 9312c650bf added
add 6faeddeac4 add page navigation warnings
add c46435c9e5 login bug solved
add 4d3ae60814 vnc ref got
add 161470e83b added
add f0017cec49 user can now save
add 6bc8d64485 simple bug fixes
add 367282ffab added code
add 7fe7b2318a added default filtering for NAMD
add d9975a1688 added failure handling for create experiment
add 4b6ed7e036 trying...
add 42ec94f846 added latest changes
add a4c1980b11 fixing things
add f4d5c3f032 trying to do refresh
add 36cb895e96 added latest changes
add f4529864c0 refactoring
add 97575b03ae moved list experiments to its own component
add 5a222e1699 added docker
add 3dcdc03a17 testing
add 87a9fee224 added docker changes
add 1b8d274a07 code cleanup
add 4e853e4c43 added changes to ui
add b54ad5c5e7 add contianerId
add 495668f57a support for pause/unpause
add 57006f52c7 added renaming
add adbda86df2 added images
add 815fbc4092 change docker
add 0dda361dbb added avaliable programs
add 7fac7b89e0 added port mappings & cache
add 16c5305a0c added
add e971a2c5fd added latest changes working"
add 5cec951a05 added opening from url
add db23b427de added callbacks
add 3780f03e32 remove dialog
add ddff53e445 fixes
add 2eb9d826aa show only cs
add 7a28f8b1d6 added
add 8628511b81 saving tabs
add c94a942fc6 redesign
add 329138a7bd added
add e1e6695d86 benchmark
add 89038bd818 revert electron forge
add ab385b7dcb added device oauth flow
add 66f407e9d0 added read and write file functions
add 21d6ac88e4 fixed for home dir
add fbb15af4ab temp fix'
add d211dd9941 added login code flow works now
add b22c84eef8 publishing changes
add 48b76d0b83 major ui changes and refactoring
add d482300a19 added major changes
add da41c3e1fd added testing versions
add 3a39de0ef9 change home key location
add 3dadcb0440 added fixes
add 1d3b24b635 2.0.4
add 999cbf2aee 2.0.5
add 0b05c18af7 2.1.0
add 9b68ec0629 2.0.6
add cdb799bb7c update readme
add 407772ae2a add asf src headers
add b7ab318b72 Resurrecting DELTA topology gateway
add 90c8d85b5c Adding the gateway key to resurrected DELTA topology gateway
add deca91bc0d Added new admins for user notifications
add bbcecfd24f Adding new gateway, Cybershuttle testdrive
add 0fe7e21333 Adding the new Cybershuttle gateway
add 0f61b8247f Adding new email for notifications in SMILES gateway
add 27512ab50f Adding CILogon and gateway key to Cybershuttle testdrive
add 82c0a903a5 Adding new admin email for notifications in AMOS gateway
add b9fcdfcf4b Fix jar plugin version issue
add ff2668f985 Adding the shared file directory in to AI confluence gateway
add 25bfaa29ca Agent framework initial commit
add 9ccf69a350 Emitting agent execution response
add 5c6563131d Adding ipython kernel wrapper
add ee3920e7a3 Supporting streamed outputs in kernel execution
add a7d3d1f52e Enabling jupyter cell execution support
add 657897d2b4 Initial magic extension bundle
add 5b276ad615 initial airavata service integration with agent framework
add 0c1f609ecd implemented services to get, create and launch experiments
for agent-framework
add cb44d8f75d Adding container configurations to jupyter and airavata
agent
add c50760df01 Showing image data in cell output
add 6c4fdcde76 add airavata-fuse starter implementation
add 9728b62711 update README
add b768da924c add license headers
add 4a2f16f056 extract configurations when launching experiment and agent
script
add dbafd24c3a initial implementation for airavata fuse service
integration with experiments
add 4febeff575 Adding the distribution for connection service
add 667b4ef3c2 Adding agent management apis
add 0972d9adeb Merge branch 'master' into master
add 97a8b79e06 Merge pull request #440 from lahirujayathilake/master
add 4c9c7262f3 Agent FS initial change
add f7fc547d1b Jupyter image changes
add e73b706824 Update redme with jupyter container build
add 6442f4e771 Merge branch 'master' into master
add b30310a37a Merge branch 'master' of
https://github.com/ganning127/airavata
add aee4513e80 Merge pull request #435 from ganning127/master
add 6c2085db1b removed the duplicated module definition:
'org.apache.airavata:connection-service' to fix the build issue
add b6887e1338 Merge pull request #441 from lahirujayathilake/master
add 1b61e62603 Changed the gateway domain in cybershuttle testdrive to
cybershuttle.org
add b2c55c468d Changed the gateway domain in cybershuttle testdrive to
cybershuttle.org
add a19ac85b6f Changed the gateway domain in cybershuttle testdrive to
cybershuttle.org
add eb9173b09c increased the file archive period for neuroscience portal
add a046088fae increased the file archive period for neuroscience portal
add 0ea1aa7fce Improving error path handling of agent
add 106d5f6dee Refactoring parent pom
add 223480ac5c Upgrading keycloak to v24
add 6117e50498 Removing older dependencies
add e1fc3d5735 Upgrading outdated dependencies
add 5dfbc2f230 Adding openid scope for password auth in pga
add 0930cf3a6b Adding auth.cybershuttle.org certificate to trust store
add 7781882abc Refactoring agent service and adding db connection
add d6bc669d97 Adding spring db properties to distribution
add 138fb60e19 Removing incompatible libraries from the agent service
add ce82e61a43 Setting trust store paths as vm arguments
add 030e80aeb8 i-guide templates
add d87e4b2362 Adding missing dependencies
add e4f03e5368 docker file to build airavata cerebrum agent
add 65c0892873 updated the dependencies for v1l4 agent docker
add 3f846601f7 configurations for the cerebrum agent
add da5a94dd38 run an agent and jl locally for development
add 0ce3789403 introduced logs for agent executions
add 9d67702cd8 Merge pull request #445 from
lahirujayathilake/agent-framewok-refactoring
add 3d3996c318 Adding support to device auth for jupyter agent
add f5be99618b remove incompatible httpclient version to align with
resteasy-client
add 4397056bda Fix run_remote magic and update kernel to properly render
outputs and display errors in airavata_magics.py
add ee9c67cdc0 included error outputs and enhanced agent log messages
add addcefe317 included cs_login python extension
add 76667ed4bf included the data for iguide agent
add b9d7420d85 updated the sshj library version
add e4f0d0586f updated the httpclient and bouncy castle library versions
add 68774548c0 JupyterHub docker deployment configuration
add 93421fa5bf Terminate idle notebook containers
add 1e64aab248 enable ssl for jupyterhub
add 3b78b2640b MD-based user container for notebook
add 9367451409 Adding python execution support for agent
add 6ea4b678f8 Fetching python libraries from agent
add 0eeffef158 support airavata experiment plan services
add c9b38971c7 included the gateway when fetching plans relevant for a user
add a7da883b69 updated the groovy library version and slurm groovy script
add f0b550615e included the required libraries for the distributions
add 83eb5a3d1c md notebook and cs settings file changes
add 1eb3e010e9 updated the config files
add 6093d54a8e changes to the jupyter notebook
add 0b67b3cfbf Fix dependency issues by replacing org.codehaus.jackson
with com.fasterxml.jackson
add 3de0edda3e removed log4j-slf4j-impl dependencies
add ea0a19a9ae included codehaus jackson dependency for helix
add efa5548bac updated the docker repo name
add bdb538e151 upgraded the sfl4j version
add ec4a624ad2 application interface pulled by the group
add c8f7853fa3 File server initial implementation
add e29842fcc1 Support to upload files
add e1bcf29695 extract process id using exp id
add f29da04100 change gateway information
add 451e028d57 Adding shared file directory in the Cyberhsuttle gateway
add 97a8c33aa2 Enabling issues
add 4e7bce20fc upgrade sshj library version
add 605f66e73e Merge pull request #450 from lahirujayathilake/master
add 6659753cd0 install airavata-python-sdk with its dependencies
add 69121866cd change requires to install_requires
add 0b8eee9fb6 add pyproject.toml for newer python versions. relax
requirements.txt versions
add 5968af93fd Merge pull request #449 from
yasithdev/airavata-python-sdk-deps
add 985642ed94 Upgrade to log4j-slf4j2-impl for SLF4J 2.x compatibility
add d8bcee8ece Changed the domain of Cybershuttle dev/staging gateway
add 776a6af7fa Merge branch 'master' into agent-framewok-refactoring
add 0a540fd60f pick the right group compute resource preference to launch
the airavata agent
add 201fe322b3 included airavata magics and auto-import them in user level
notebooks
add c965eb82e5 Merge pull request #455 from
apache/agent-framewok-refactoring
add 95b508db6d CyberFaCES docker file
add 397f1cdaf6 add file ops to jupyter magics, cleanup code, update
agent.sh
add 741815f673 temp commit to get cyberfaces meeting poc
add 896f11c016 update data tar and analysis script
add 684711d180 add airavata magics to dev-tools/, make airavata-agent/
build generic
add 9394c945fd reorganize agent-framework related code. make
airavata-magics a python package.
add 17012d556b revise jupyterhub spawned notebooks, add makefiles
add 3560c00c2d initial experiment sdk implementation
add 8b9cacf758 improve auth flow, add python code invocation, add plan
crud apis and file ul/dl apis, reduce settings.ini deps, fix bugs
add a9594b965b venv support for agent, update notebooks, show tables as
pandas df, update dir refs, fix bugs.
add 1046150be6 make settings.ini lean, add runtime picker {by cluster,
category}. change agent base dir.
add 47d882e396 add pre-submission validator, update storage dir, take
CONNECTION_SVC_URL and FILEMGR_SVC_URL from settings.ini, cleanup runtime.py,
add fallback apis to airavata.py, rearrange files, setup file ul/dl apis,
improve ux, update notebooks, add agent scripts, refine code, fix bugs
add 599fba45fd fix bug in code execution, remove jupyter kernel start from
agent add support to cold-start analysis agents reset changes to
sftp_file_handling_client update notebooks remove verbose log from remote code
execution separate python env creation and code execution steps. always return
stdout+err for command/script executions lock agent to python 3.12 and update
pyproject.toml update file listing and python execution cmds
add fa6a4207a0 bump version to 0.0.16 add AlphaFold2 and Gaussian
applications update realm from 10000000 -> default add GROMACS and AMBER to MD
SDK
add 83052b074d choose group/project from API, silent plan launch,
add_replica() -> create_task(), display task state, planid and taskid, improve
messaging
add 8061e070b5 add back kernel launcher to agent
add ca369fc700 refine Makefiles, move app-scripts to agent-framework/, fix
bugs in agent.go and sample Dockerfile
add d7d5275990 regenerate thrift specs
add 251edd3890 cleanup airavata_sdk wrappers, error-handling in
airavata_experiments
add c3273418ba add type-hinting imports to __init__ files
add 86425b63dd cleanup imports, fix bugs found by type checker
add 118b1dcc18 enabled micromamba base when starting the kernel
add de6c7f04af fix bugs in airavata-jupyter-magic package
add 9776da5d14 fix dependency issue in cyberfaces agent
add 8b9cfeae02 organize code, add other deployment files, partially redo
airavata_jupyter_magic for runtime switching
add 56bee085dc refine code flow in airavata_jupyter_magic. bump version to
1.0.5, update notebook, fix bugs
add 94319b5951 updated notebooks
add 7716162705 rename platform x86_64 -> amd64. fix issues in cyberfaces
dockerfile. update notebooks. move environment files.
add c96c793730 updated the agent dependencies
add d3c191c8f3 gkeyll agent image and notebook sample
add 5f42822a16 updated the gkeyll notebook script
add 238b9d1ab5 Changed the uploading file size in enveomics gateway
add 3420f70e16 ide-integration docker-compose changes
add 7a7a4715bc Added keycloak.conf, Updated docker-compose.yml, Updated
airavata.jks
add cea66cb840 Replaced airavata.jks with an updated version
add 148a93ea73 modified keycloak.conf
add f884cb1914 removed duplicate keycloak volume
add 619578bf19 Merge pull request #468 from riccog/master
add 1833e74d7d Bump quartz in
/modules/airavata-metascheduler/metadata-analyzer
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 (8c4732dacc)
\
N -- N -- N
refs/heads/dependabot/maven/modules/airavata-metascheduler/metadata-analyzer/org.quartz-scheduler-quartz-2.3.2
(1833e74d7d)
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.
No new revisions were added by this update.
Summary of changes:
.asf.yaml | 5 +
.gitignore | 9 +
airavata-api/airavata-api-server/pom.xml | 10 +-
.../airavata/api/client/AiravataClientFactory.java | 27 +
.../airavata-cpp-sdk/src/main/resources/LICENSE | 4 +-
.../airavata-python-sdk/.gitignore | 8 +
.../airavata-python-sdk/airavata/__init__.py | 4 +
.../airavata/api/Airavata-remote | 4 +-
.../airavata-python-sdk/airavata/api/Airavata.py | 6252 +-
.../airavata-python-sdk/airavata/api/__init__.py | 5 +
.../airavata-python-sdk/airavata/api/constants.py | 8 +-
.../airavata/api/credential/__init__.py | 4 +
.../credential/store/CredentialStoreService-remote | 4 +-
.../api/credential/store/CredentialStoreService.py | 349 +-
.../airavata/api/credential/store/__init__.py | 5 +
.../airavata/api/credential/store/constants.py | 8 +-
.../api/credential/store/error/__init__.py | 5 +
.../api/credential/store/error/constants.py | 8 +-
.../airavata/api/credential/store/error/ttypes.py | 12 +-
.../airavata/api/credential/store/ttypes.py | 8 +-
.../airavata/api/error/__init__.py | 5 +
.../airavata/api/error/constants.py | 8 +-
.../airavata/api/error/ttypes.py | 97 +-
.../api/sharing/SharingRegistryService-remote | 4 +-
.../airavata/api/sharing/SharingRegistryService.py | 1424 +-
.../airavata/api/sharing/__init__.py | 5 +
.../airavata/api/sharing/constants.py | 8 +-
.../airavata/api/sharing/ttypes.py | 8 +-
.../airavata-python-sdk/airavata/api/ttypes.py | 8 +-
.../airavata-python-sdk/airavata/base/__init__.py | 4 +
.../airavata/base/api/BaseAPI-remote | 4 +-
.../airavata/base/api/BaseAPI.py | 22 +-
.../airavata/base/api/__init__.py | 5 +
.../airavata/base/api/constants.py | 8 +-
.../airavata/base/api/ttypes.py | 8 +-
.../airavata-python-sdk/airavata/model/__init__.py | 5 +
.../airavata/model/appcatalog/__init__.py | 4 +
.../appcatalog/accountprovisioning/__init__.py | 5 +
.../appcatalog/accountprovisioning/constants.py | 8 +-
.../model/appcatalog/accountprovisioning/ttypes.py | 56 +-
.../model/appcatalog/appdeployment/__init__.py | 5 +
.../model/appcatalog/appdeployment/constants.py | 8 +-
.../model/appcatalog/appdeployment/ttypes.py | 91 +-
.../model/appcatalog/appinterface/__init__.py | 5 +
.../model/appcatalog/appinterface/constants.py | 8 +-
.../model/appcatalog/appinterface/ttypes.py | 28 +-
.../model/appcatalog/computeresource/__init__.py | 5 +
.../model/appcatalog/computeresource/constants.py | 8 +-
.../model/appcatalog/computeresource/ttypes.py | 426 +-
.../model/appcatalog/gatewaygroups/__init__.py | 5 +
.../model/appcatalog/gatewaygroups/constants.py | 8 +-
.../model/appcatalog/gatewaygroups/ttypes.py | 20 +-
.../model/appcatalog/gatewayprofile/__init__.py | 5 +
.../model/appcatalog/gatewayprofile/constants.py | 8 +-
.../model/appcatalog/gatewayprofile/ttypes.py | 94 +-
.../appcatalog/groupresourceprofile/__init__.py | 5 +
.../appcatalog/groupresourceprofile/constants.py | 8 +-
.../appcatalog/groupresourceprofile/ttypes.py | 142 +-
.../model/appcatalog/parallelism/__init__.py | 5 +
.../model/appcatalog/parallelism/constants.py | 8 +-
.../model/appcatalog/parallelism/ttypes.py | 27 +-
.../airavata/model/appcatalog/parser/__init__.py | 5 +
.../airavata/model/appcatalog/parser/constants.py | 8 +-
.../airavata/model/appcatalog/parser/ttypes.py | 145 +-
.../model/appcatalog/storageresource/__init__.py | 5 +
.../model/appcatalog/storageresource/constants.py | 8 +-
.../model/appcatalog/storageresource/ttypes.py | 26 +-
.../appcatalog/userresourceprofile/__init__.py | 5 +
.../appcatalog/userresourceprofile/constants.py | 8 +-
.../model/appcatalog/userresourceprofile/ttypes.py | 68 +-
.../airavata/model/application/__init__.py | 4 +
.../airavata/model/application/io/__init__.py | 5 +
.../airavata/model/application/io/constants.py | 8 +-
.../airavata/model/application/io/ttypes.py | 115 +-
.../airavata/model/commons/__init__.py | 5 +
.../airavata/model/commons/constants.py | 8 +-
.../airavata/model/commons/ttypes.py | 40 +-
.../airavata/model/constants.py | 8 +-
.../airavata/model/credential/__init__.py | 4 +
.../airavata/model/credential/store/__init__.py | 5 +
.../airavata/model/credential/store/constants.py | 8 +-
.../airavata/model/credential/store/ttypes.py | 118 +-
.../airavata/model/data/__init__.py | 4 +
.../airavata/model/data/movement/__init__.py | 5 +
.../airavata/model/data/movement/constants.py | 8 +-
.../airavata/model/data/movement/ttypes.py | 157 +-
.../airavata/model/data/replica/__init__.py | 5 +
.../airavata/model/data/replica/constants.py | 8 +-
.../airavata/model/data/replica/ttypes.py | 134 +-
.../airavata/model/dbevent/__init__.py | 5 +
.../airavata/model/dbevent/constants.py | 8 +-
.../airavata/model/dbevent/ttypes.py | 130 +-
.../airavata/model/experiment/__init__.py | 5 +
.../airavata/model/experiment/constants.py | 8 +-
.../airavata/model/experiment/ttypes.py | 212 +-
.../airavata/model/group/__init__.py | 5 +
.../airavata/model/group/constants.py | 8 +-
.../airavata/model/group/ttypes.py | 64 +-
.../airavata/model/job/__init__.py | 5 +
.../airavata/model/job/constants.py | 8 +-
.../airavata/model/job/ttypes.py | 36 +-
.../airavata/model/messaging/__init__.py | 4 +
.../airavata/model/messaging/event/__init__.py | 5 +
.../airavata/model/messaging/event/constants.py | 8 +-
.../airavata/model/messaging/event/ttypes.py | 301 +-
.../airavata/model/process/__init__.py | 5 +
.../airavata/model/process/constants.py | 8 +-
.../airavata/model/process/ttypes.py | 76 +-
.../airavata/model/scheduling/__init__.py | 5 +
.../airavata/model/scheduling/constants.py | 8 +-
.../airavata/model/scheduling/ttypes.py | 42 +-
.../airavata/model/security/__init__.py | 5 +
.../airavata/model/security/constants.py | 8 +-
.../airavata/model/security/ttypes.py | 16 +-
.../airavata/model/sharing/__init__.py | 5 +
.../airavata/model/sharing/constants.py | 8 +-
.../airavata/model/sharing/ttypes.py | 362 +-
.../airavata/model/status/__init__.py | 5 +
.../airavata/model/status/constants.py | 8 +-
.../airavata/model/status/ttypes.py | 234 +-
.../airavata/model/task/__init__.py | 5 +
.../airavata/model/task/constants.py | 8 +-
.../airavata/model/task/ttypes.py | 182 +-
.../airavata/model/tenant/__init__.py | 5 +
.../airavata/model/tenant/constants.py | 8 +-
.../airavata/model/tenant/ttypes.py | 94 +-
.../airavata-python-sdk/airavata/model/ttypes.py | 8 +-
.../airavata/model/user/__init__.py | 5 +
.../airavata/model/user/constants.py | 8 +-
.../airavata/model/user/ttypes.py | 269 +-
.../airavata/model/workflow/__init__.py | 5 +
.../airavata/model/workflow/constants.py | 8 +-
.../airavata/model/workflow/ttypes.py | 348 +-
.../airavata/model/workspace/__init__.py | 5 +
.../airavata/model/workspace/constants.py | 8 +-
.../airavata/model/workspace/ttypes.py | 192 +-
.../airavata/service/__init__.py | 4 +
.../airavata/service/profile/__init__.py | 5 +
.../airavata/service/profile/constants.py | 8 +-
.../service/profile/groupmanager/__init__.py | 4 +
.../groupmanager/cpi/GroupManagerService-remote | 4 +-
.../groupmanager/cpi/GroupManagerService.py | 360 +-
.../service/profile/groupmanager/cpi/__init__.py | 5 +
.../service/profile/groupmanager/cpi/constants.py | 8 +-
.../profile/groupmanager/cpi/error/__init__.py | 5 +
.../profile/groupmanager/cpi/error/constants.py | 8 +-
.../profile/groupmanager/cpi/error/ttypes.py | 12 +-
.../service/profile/groupmanager/cpi/ttypes.py | 8 +-
.../airavata/service/profile/iam/__init__.py | 4 +
.../airavata/service/profile/iam/admin/__init__.py | 4 +
.../service/profile/iam/admin/services/__init__.py | 4 +
.../iam/admin/services/cpi/IamAdminServices-remote | 4 +-
.../iam/admin/services/cpi/IamAdminServices.py | 416 +-
.../profile/iam/admin/services/cpi/__init__.py | 5 +
.../profile/iam/admin/services/cpi/constants.py | 8 +-
.../iam/admin/services/cpi/error/__init__.py | 5 +
.../iam/admin/services/cpi/error/constants.py | 8 +-
.../profile/iam/admin/services/cpi/error/ttypes.py | 12 +-
.../profile/iam/admin/services/cpi/ttypes.py | 8 +-
.../airavata/service/profile/tenant/__init__.py | 4 +
.../profile/tenant/cpi/TenantProfileService-remote | 4 +-
.../profile/tenant/cpi/TenantProfileService.py | 190 +-
.../service/profile/tenant/cpi/__init__.py | 5 +
.../service/profile/tenant/cpi/constants.py | 8 +-
.../service/profile/tenant/cpi/error/__init__.py | 5 +
.../service/profile/tenant/cpi/error/constants.py | 8 +-
.../service/profile/tenant/cpi/error/ttypes.py | 12 +-
.../airavata/service/profile/tenant/cpi/ttypes.py | 8 +-
.../airavata/service/profile/ttypes.py | 8 +-
.../airavata/service/profile/user/__init__.py | 4 +
.../profile/user/cpi/UserProfileService-remote | 4 +-
.../service/profile/user/cpi/UserProfileService.py | 198 +-
.../airavata/service/profile/user/cpi/__init__.py | 5 +
.../airavata/service/profile/user/cpi/constants.py | 8 +-
.../service/profile/user/cpi/error/__init__.py | 5 +
.../service/profile/user/cpi/error/constants.py | 8 +-
.../service/profile/user/cpi/error/ttypes.py | 12 +-
.../airavata/service/profile/user/cpi/ttypes.py | 8 +-
.../airavata_experiments/__init__.py | 180 +
.../airavata_experiments/airavata.py | 800 +
.../auth}/__init__.py | 15 +
.../airavata_experiments/auth/device_auth.py | 186 +
.../airavata_experiments/base.py | 133 +
.../utils => airavata_experiments/md}/__init__.py | 10 +
.../airavata_experiments/md/applications.py | 258 +
.../airavata_experiments/plan.py | 199 +
.../airavata_experiments/runtime.py | 274 +
.../airavata_experiments/scripter.py | 144 +
.../airavata_experiments/sftp.py | 122 +
.../airavata_experiments/task.py | 106 +
.../airavata_sdk/clients/api_server_client.py | 7231 +-
.../clients/credential_store_client.py | 47 +-
.../airavata_sdk/clients/file_handling_client.py | 18 +-
.../airavata_sdk/clients/group_manager_client.py | 216 +-
.../airavata_sdk/clients/iam_admin_client.py | 239 +-
.../airavata_sdk/clients/keycloak_token_fetcher.py | 100 +-
.../clients/sftp_file_handling_client.py | 23 +-
.../clients/sharing_registry_client.py | 916 +-
.../airavata_sdk/clients/tenant_profile_client.py | 126 +-
.../airavata_sdk/clients/user_profile_client.py | 137 +-
.../clients/utils/api_server_client_util.py | 41 +-
.../clients/utils/data_model_creation_util.py | 93 +-
.../clients/utils/experiment_handler_util.py | 79 +-
.../samples/api_server_client_samples.py | 17 +-
.../samples/create_launch_echo_experiment.py | 43 +-
.../samples/create_launch_gaussian_experiment.py | 50 +-
.../airavata_sdk/samples/file_utils.py | 1 +
.../samples/group_manager_client_samples.py | 8 +-
.../samples/iam_admin_client_samples.py | 5 +-
.../airavata_sdk/samples/metadata_fetcher.py | 16 +-
.../samples/sharing_registry_client_samples.py | 6 +-
.../samples/tenant_profile_client_samples.py | 5 +-
.../samples/user_profile_client_samples.py | 8 +-
.../airavata_sdk/transport/settings.py | 56 +-
.../airavata_sdk/transport/utils.py | 317 +-
.../airavata-python-sdk/pyproject.toml | 38 +
.../airavata-python-sdk/requirements.txt | 11 -
.../airavata-python-sdk/setup.cfg | 26 -
.../airavata-python-sdk/setup.py | 21 -
.../java-client-samples/pom.xml | 2 +-
airavata-local-agent/README.md | 42 +
.../electron-builder.yml | 18 +-
airavata-local-agent/main/background.js | 798 +
airavata-local-agent/main/helpers/create-window.js | 100 +
airavata-local-agent/main/helpers/index.js | 22 +
airavata-local-agent/main/preload.js | 97 +
airavata-local-agent/package-lock.json | 7863 +
airavata-local-agent/package.json | 52 +
.../DockerComponents/AvaliablePrograms.jsx | 90 +
.../DockerComponents/DockerContainersList.jsx | 407 +
.../DockerComponents/DockerImagesList.jsx | 87 +
.../DockerComponents/DockerInspectModal.jsx | 173 +
.../DockerComponents/Programs/JupyterProgram.jsx | 194 +
.../renderer/components/ExperimentModal.jsx | 594 +
.../renderer/components/ExperimentsList.jsx | 164 +
.../renderer/components/Footer.jsx | 93 +
.../renderer/components/HeaderBox.jsx | 124 +
.../renderer/components/JupyterLab.jsx | 175 +
.../renderer/components/LinkIconBox.jsx | 66 +
.../renderer/components/LocalFuncs.jsx | 27 +
.../renderer/components/NavBar.jsx | 49 +
.../renderer/components/NavContainer.jsx | 78 +
.../renderer/components/PanelBody.jsx | 38 +
.../renderer/components/TextWithBoldKey.jsx | 30 +
.../renderer/components/UserModal.jsx | 124 +
.../renderer/components/VNCItem.jsx | 48 +
.../renderer/components/VNCViewer.jsx | 324 +
.../renderer/components/temp/VNCTest.jsx | 37 +
airavata-local-agent/renderer/lib/Contexts.js | 101 +
airavata-local-agent/renderer/lib/constants.js | 25 +
airavata-local-agent/renderer/lib/logger.js | 70 +
airavata-local-agent/renderer/lib/utilityFuncs.js | 159 +
airavata-local-agent/renderer/next.config.js | 32 +
airavata-local-agent/renderer/pages/_app.jsx | 37 +
.../renderer/pages/create-namd-experiment.jsx | 1261 +
.../renderer/pages/docker-home.jsx | 203 +
.../renderer/pages/experiment/[experimentId].js | 72 +
airavata-local-agent/renderer/pages/home.jsx | 136 +
.../renderer/pages/login-callback.jsx | 63 +
airavata-local-agent/renderer/pages/login.jsx | 226 +
airavata-local-agent/renderer/pages/tabs-view.jsx | 759 +
.../renderer/pages/temp/docker-page.jsx | 453 +
.../renderer/pages/temp/page-with-vnc-test.jsx | 35 +
.../renderer/pages/temp/vnc-client.jsx | 179 +
.../renderer/public/images/cs-logo.png | Bin 0 -> 34102 bytes
.../renderer/public/images/jupyter_logo.png | Bin 0 -> 53006 bytes
.../renderer/public/images/logo.png | Bin 0 -> 120101 bytes
airavata-local-agent/resources/icon.icns | Bin 0 -> 154042 bytes
airavata-local-agent/resources/icon.ico | Bin 0 -> 189104 bytes
.../iam-admin-services-core/pom.xml | 25 +-
.../core/impl/TenantManagementKeycloakImpl.java | 5 +-
.../profile-service-commons/pom.xml | 6 +
airavata-services/services-security/pom.xml | 8 +-
.../simccs/files/django-ssl-vhost.conf.j2 | 12 +-
.../scigap/production/group_vars/all/vars.yml | 5 +-
.../production/host_vars/ai-confluence/vars.yml | 8 +-
.../production/host_vars/ampgateway/vars.yml | 4 +-
.../production/host_vars/bayesprism/vars.yml | 2 +-
.../scigap/production/host_vars/bcbportal/vars.yml | 2 +-
.../production/host_vars/covid-geoact/vars.yml | 2 +-
.../scigap/production/host_vars/delta/vars.yml | 27 +-
.../production/host_vars/dev-smiles/vars.yml | 75 +
.../production/host_vars/dev-smiles/vault.yml | 12 +
.../host_vars/dreg/files/django-ssl-vhost.conf.j2 | 12 +-
.../scigap/production/host_vars/dreg/vars.yml | 2 +-
.../host_vars/{nasa-veda => dt4h}/vars.yml | 18 +-
.../scigap/production/host_vars/dt4h/vault.yml | 12 +
.../production/host_vars/ehtgateway/vars.yml | 2 +-
.../{molecular-dynamics => enveomics}/vars.yml | 22 +-
.../production/host_vars/enveomics/vault.yml | 12 +
.../production/host_vars/futurewater/vars.yml | 2 +-
.../scigap/production/host_vars/geo/vars.yml | 2 +-
.../production/host_vars/georgiastate/vars.yml | 2 +-
.../production/host_vars/global-flood/vars.yml | 2 +-
.../scigap/production/host_vars/immune/vars.yml | 2 +-
.../production/host_vars/interactwel/vars.yml | 2 +-
.../scigap/production/host_vars/lrose/vars.yml | 2 +-
.../host_vars/microbial-genomes/vars.yml | 2 +-
.../host_vars/molecular-dynamics/vars.yml | 14 +-
.../scigap/production/host_vars/nasa-veda/vars.yml | 2 +-
.../host_vars/neuroscience-cybershuttle/vars.yml | 4 +-
.../scigap/production/host_vars/nexttdb/vars.yml | 2 +-
.../production/host_vars/pace-gatech/vars.yml | 4 +-
.../production/host_vars/pathogenomics/vars.yml | 2 +-
.../scigap/production/host_vars/physicell/vars.yml | 2 +-
.../scigap/production/host_vars/regsnps/vars.yml | 2 +-
.../scigap/production/host_vars/sdstate/vars.yml | 2 +-
.../scigap/production/host_vars/seagrid/vars.yml | 2 +-
.../scigap/production/host_vars/searchsra/vars.yml | 2 +-
.../simccs/files/django-ssl-vhost.conf.j2 | 12 +-
.../scigap/production/host_vars/simccs/vars.yml | 5 +-
.../production/host_vars/simvascular/vars.yml | 2 +-
.../production/host_vars/simvascular_old/vars.yml | 2 +-
.../scigap/production/host_vars/smiles/vars.yml | 19 +-
.../production/host_vars/snowvision/vars.yml | 2 +-
.../{ai-confluence => testdrive-cs}/vars.yml | 30 +-
.../production/host_vars/testdrive-cs/vault.yml | 12 +
.../scigap/production/host_vars/testdrive/vars.yml | 2 +-
.../scigap/production/host_vars/tsunami/vars.yml | 2 +-
.../scigap/production/host_vars/ultrascan/vars.yml | 2 +-
.../host_vars/vlab-plasmascience/vars.yml | 2 +-
.../ansible/inventories/scigap/production/hosts | 9 +-
.../scigap/production/pga_config/scigap/vars.yml | 2 +-
.../simccs/files/django-ssl-vhost.conf.j2 | 12 +-
.../common/vars/main.yml => kafka-rest-proxy.yml} | 5 +-
dev-tools/ansible/roles/api-orch/defaults/main.yml | 7 +-
.../files/prepareLetsEncryptCertificates.sh | 1 +
dev-tools/ansible/roles/api-orch/handlers/main.yml | 3 +-
.../tasks/haproxy/install_deps_Centos_7.yml | 1 +
dev-tools/ansible/roles/api-orch/tasks/main.yml | 15 +-
.../roles/api-orch/templates/haproxy.cfg.j2 | 4 +-
dev-tools/ansible/roles/django/tasks/main.yml | 2 +-
.../django/templates/django-ssl-vhost.conf.j2 | 4 +-
.../roles/django/templates/django-vhost.conf.j2 | 12 +-
.../roles/django/templates/settings_local.py.j2 | 2 +-
dev-tools/ansible/roles/tusd/tasks/main.yml | 8 +
.../tusd/templates/tus-temp-dir-cleanup.cron.j2 | 4 +
.../{roles/common/vars/main.yml => zookeeper.yml} | 5 +-
modules/agent-framework/agent-service/.gitignore | 1 +
modules/agent-framework/agent-service/pom.xml | 192 +
.../main/assembly/agent-service-bin-assembly.xml | 35 +-
.../service/AgentServiceApplication.java | 13 +
.../agent/connection/service/UserContext.java | 34 +
.../service/config/AuthzTokenFilter.java | 48 +
.../service/config/ClusterApplicationConfig.java | 26 +
.../service/controllers/AgentController.java | 90 +
.../service/controllers/ExperimentController.java | 50 +
.../service/controllers/PlanController.java | 90 +
.../service/db/entity/AgentDeploymentInfo.java | 59 +
.../service/db/entity/AgentExecution.java | 48 +
.../service/db/entity/AgentExecutionStatus.java | 76 +
.../agent/connection/service/db/entity/Plan.java | 55 +
.../service/db/repo/AgentDeploymentInfoRepo.java | 9 +
.../service/db/repo/AgentExecutionRepo.java | 9 +
.../service/db/repo/AgentExecutionStatusRepo.java | 9 +
.../agent/connection/service/db/repo/PlanRepo.java | 13 +
.../service/handlers/AgentConnectionHandler.java | 307 +
.../service/handlers/AgentManagementHandler.java | 179 +
.../connection/service/handlers/FuseFSHandler.java | 112 +
.../connection/service/handlers/PlanHandler.java | 35 +
.../connection/service/models/AgentCommandAck.java | 22 +
.../service/models/AgentCommandRequest.java | 34 +
.../service/models/AgentCommandResponse.java | 31 +
.../service/models/AgentInfoResponse.java | 27 +
.../service/models/AgentPythonRunAck.java | 4 +
.../service/models/AgentPythonRunRequest.java | 61 +
.../service/models/AgentPythonRunResponse.java | 41 +
.../connection/service/models/AgentTunnelAck.java | 22 +
.../service/models/AgentTunnelCreationRequest.java | 67 +
.../connection/service/models/DirectoryInfo.java | 23 +
.../service/models/ExperimentStorageResponse.java | 43 +
.../agent/connection/service/models/FileInfo.java | 88 +
.../service/models/JupyterExecutionAck.java | 4 +
.../service/models/JupyterExecutionRequest.java | 40 +
.../service/models/JupyterExecutionResponse.java | 41 +
.../service/models/LaunchAgentRequest.java | 84 +
.../service/models/LaunchAgentResponse.java} | 29 +-
.../service/models/TerminateAgentResponse.java | 27 +
.../service/services/AiravataFileService.java | 163 +
.../service/services/AiravataService.java | 110 +
.../agent-framework/agent-service/src/main/proto | 1 +
.../src/main/resources/application.yml | 37 +
.../distribution/bin/agent-service-daemon.sh} | 15 +-
.../resources/distribution/bin/agent-service.sh} | 9 +-
.../src/main/resources/distribution}/bin/setenv.sh | 2 +-
.../resources/distribution/conf/application.yml | 37 +
.../main/resources/distribution/conf}/log4j2.xml | 0
.../resources/distribution/conf/truststore.jks | Bin 0 -> 1654 bytes
.../src/main/resources/truststore.jks | Bin 0 -> 1654 bytes
modules/agent-framework/airavata-agent/.gitignore | 5 +
modules/agent-framework/airavata-agent/Dockerfile | 15 +
modules/agent-framework/airavata-agent/Makefile | 11 +
modules/agent-framework/airavata-agent/README.md | 89 +
.../airavata-agent/agent-communication.proto | 127 +
modules/agent-framework/airavata-agent/agent.go | 481 +
modules/agent-framework/airavata-agent/go.mod | 16 +
modules/agent-framework/airavata-agent/kernel.py | 145 +
.../protos/agent-communication.pb.go | 1831 +
.../protos/agent-communication_grpc.pb.go | 143 +
modules/agent-framework/airavata-fuse/.gitignore | 4 +
modules/agent-framework/airavata-fuse/Makefile | 25 +
modules/agent-framework/airavata-fuse/README.md | 18 +
.../agent-framework/airavata-fuse/data/foo/bar.txt | 1 +
.../agent-framework/airavata-fuse/data/hello.txt | 1 +
.../airavata-fuse/src/grpcfs/adapters.go | 81 +
.../agent-framework/airavata-fuse/src/grpcfs/fs.go | 249 +
.../airavata-fuse/src/grpcfs/go.mod | 16 +
.../airavata-fuse/src/grpcfs/go.sum | 18 +
.../airavata-fuse/src/grpcfs/grpc.go | 129 +
.../airavata-fuse/src/grpcfs/inode.go | 166 +
.../airavata-fuse/src/grpcfs/pb/grpcfs.pb.go | 2319 +
.../airavata-fuse/src/grpcfs/pb/grpcfs_grpc.pb.go | 396 +
.../airavata-fuse/src/grpcfs_client/go.mod | 19 +
.../airavata-fuse/src/grpcfs_client/go.sum | 18 +
.../airavata-fuse/src/grpcfs_client/main.go | 82 +
.../airavata-fuse/src/grpcfs_server/go.mod | 18 +
.../airavata-fuse/src/grpcfs_server/go.sum | 14 +
.../airavata-fuse/src/grpcfs_server/main.go | 239 +
.../airavata-fuse/src/proto/grpcfs.proto | 137 +
.../airavata-jupyter-magic/.gitignore | 3 +
.../airavata-jupyter-magic/README.md | 28 +
.../airavata-jupyter-magic}/__init__.py | 0
.../airavata_jupyter_magic.py | 751 +
.../airavata-jupyter-magic/device_auth.py | 59 +
.../airavata-jupyter-magic/pyproject.toml | 30 +
.../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_af2.sh | 133 +
.../deployments/app-scripts/expanse_agent.sh | 40 +
.../deployments/app-scripts/expanse_namd.sh | 231 +
.../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 0 -> 133346 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 0 -> 365941 bytes
.../data/iguide/NID_FIM_NH_F/NH_F_CA10022.tiff | Bin 0 -> 27506 bytes
.../data/iguide/NID_FIM_TAS_F/TAS_F_CA10022.tiff | Bin 0 -> 232386 bytes
.../data/iguide/census_geometry/census_data.csv | 83510 ++++++++++
.../census_geometry/census_tract_from_api.geojson | Bin 14479360 ->
14094084 bytes
.../census_geometry/tl_2020_06_tabblock20.geojson | Bin 14479360 ->
19018197 bytes
.../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 0 -> 1129976 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 0 -> 4716544 bytes
.../jupyterhub/data/md_demo/data/namd/b4pull.pdb | 97198 ++++++++++++
.../data/md_demo/data/namd/b4pull.restart.coor | Bin 0 -> 2332708 bytes
.../data/md_demo/data/namd/b4pull.restart.vel | Bin 0 -> 2332708 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 0 -> 2332708 bytes
.../data/namd_workshop/data/b4pull.restart.vel | Bin 0 -> 2332708 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/docker-compose.yaml | 24 +
.../deployments/jupyterhub/jupyterhub_config.py | 71 +
.../deployments/jupyterhub/nginx-conf | 36 +
.../pom.xml | 13 +-
.../proto/agent-communication.proto | 147 +
modules/agent-framework/proto/airavata-fuse.proto | 183 +
modules/airavata-helix/agent-api/pom.xml | 11 +-
.../apache/airavata/agents/api/AdaptorParams.java | 3 +-
.../airavata-helix/agent-impl/sshj-agent/pom.xml | 2 +-
.../airavata/helix/adaptor/SSHJAgentAdaptor.java | 26 +-
.../adaptor/wrapper/SCPFileTransferWrapper.java | 20 +
modules/airavata-helix/helix-spectator/pom.xml | 2 +-
.../airavata/helix/impl/task/AiravataTask.java | 2 +-
modules/airavata-helix/task-api/pom.xml | 4 +
.../airavata/metascheduler/core/utils/Utils.java | 6 +-
modules/commons/pom.xml | 5 +-
.../airavata/common/utils/DBInitializer.java | 4 +-
.../src/main/resources/SLURM_Groovy.template | 6 +-
.../impl/ssh/SSHCredentialGenerator.java | 101 -
modules/distribution/pom.xml | 67 +-
.../src/main/assembly/controller-bin-assembly.xml | 6 +-
.../main/assembly/email-monitor-bin-assembly.xml | 4 +-
.../src/main/assembly/parser-wm-bin-assembly.xml | 3 +-
.../src/main/assembly/participant-bin-assembly.xml | 6 +-
.../src/main/assembly/post-wm-bin-assembly.xml | 5 +-
.../src/main/assembly/pre-wm-bin-assembly.xml | 5 +-
.../assembly/realtime-monitor-bin-assembly.xml | 4 +-
.../src/main/resources/api-server/LICENSE | 4 +-
modules/file-server/pom.xml | 81 +
.../main/assembly/file-service-bin-assembly.xml | 34 +-
.../file/server/FileServerApplication.java | 16 +
.../file/server/FileServerConfiguration.java | 47 +
.../file/server/controller/FileController.java | 89 +
.../file/server/model/AiravataDirectory.java | 49 +
.../airavata/file/server/model/AiravataFile.java | 47 +
.../file/server/model/FileUploadResponse.java | 47 +
.../file/server/service/AirvataFileService.java | 113 +
.../file/server/service/ProcessDataManager.java | 57 +
.../src/main/resources/application.properties | 12 +
.../distribution/bin/file-service-daemon.sh} | 13 +-
.../resources/distribution/bin/file-service.sh} | 9 +-
.../src/main/resources/distribution}/bin/setenv.sh | 2 +-
.../distribution/conf/application.properties | 12 +
.../main/resources/distribution/conf}/log4j2.xml | 0
modules/ide-integration/README.md | 3 +
.../init/05-replica-catalog-migrations.sql | 32 +-
.../src/main/containers/docker-compose.yml | 24 +-
.../main/containers/keycloak/Default-export.json | 3448 +-
.../src/main/containers/keycloak/keycloak.conf | 37 +
.../app/libraries/Keycloak/Keycloak.php | 2 +-
.../app/tests/selenium/pom.xml | 7 +-
.../src/main/resources/keystores/airavata.jks | Bin 2679 -> 2848 bytes
.../main/resources/keystores/client_truststore.jks | Bin 1258 -> 2282 bytes
.../core/utils/ReplicaCatalogDBInitConfig.java | 2 +-
.../src/main/resources/replicacatalog-mysql.sql | 22 +-
.../registry/registry-tools/registry-tool/pom.xml | 1 -
.../DeltaScripts/replicaCatalog_schema_delta.sql | 33 +-
.../sharing-registry-distribution/pom.xml | 6 +
pom.xml | 772 +-
.../component-cpis/generate-cpi-stubs.sh | 2 +-
.../generate-thrift-stubs.sh | 10 +-
.../service-cpis/generate-service-cpi-stubs.sh | 2 +-
tools/load-client/pom.xml | 4 +-
570 files changed, 1046030 insertions(+), 17737 deletions(-)
create mode 100644
airavata-api/airavata-client-sdks/airavata-python-sdk/airavata_experiments/__init__.py
create mode 100644
airavata-api/airavata-client-sdks/airavata-python-sdk/airavata_experiments/airavata.py
copy
airavata-api/airavata-client-sdks/airavata-python-sdk/{airavata_sdk/clients/utils
=> airavata_experiments/auth}/__init__.py (75%)
create mode 100644
airavata-api/airavata-client-sdks/airavata-python-sdk/airavata_experiments/auth/device_auth.py
create mode 100644
airavata-api/airavata-client-sdks/airavata-python-sdk/airavata_experiments/base.py
copy
airavata-api/airavata-client-sdks/airavata-python-sdk/{airavata_sdk/clients/utils
=> airavata_experiments/md}/__init__.py (82%)
create mode 100644
airavata-api/airavata-client-sdks/airavata-python-sdk/airavata_experiments/md/applications.py
create mode 100644
airavata-api/airavata-client-sdks/airavata-python-sdk/airavata_experiments/plan.py
create mode 100644
airavata-api/airavata-client-sdks/airavata-python-sdk/airavata_experiments/runtime.py
create mode 100644
airavata-api/airavata-client-sdks/airavata-python-sdk/airavata_experiments/scripter.py
create mode 100644
airavata-api/airavata-client-sdks/airavata-python-sdk/airavata_experiments/sftp.py
create mode 100644
airavata-api/airavata-client-sdks/airavata-python-sdk/airavata_experiments/task.py
create mode 100644
airavata-api/airavata-client-sdks/airavata-python-sdk/pyproject.toml
delete mode 100644
airavata-api/airavata-client-sdks/airavata-python-sdk/requirements.txt
delete mode 100644
airavata-api/airavata-client-sdks/airavata-python-sdk/setup.cfg
delete mode 100644
airavata-api/airavata-client-sdks/airavata-python-sdk/setup.py
create mode 100644 airavata-local-agent/README.md
copy
modules/configuration/server/src/main/resources/enableLegacyTLS.properties =>
airavata-local-agent/electron-builder.yml (76%)
create mode 100644 airavata-local-agent/main/background.js
create mode 100644 airavata-local-agent/main/helpers/create-window.js
create mode 100644 airavata-local-agent/main/helpers/index.js
create mode 100644 airavata-local-agent/main/preload.js
create mode 100644 airavata-local-agent/package-lock.json
create mode 100644 airavata-local-agent/package.json
create mode 100644
airavata-local-agent/renderer/components/DockerComponents/AvaliablePrograms.jsx
create mode 100644
airavata-local-agent/renderer/components/DockerComponents/DockerContainersList.jsx
create mode 100644
airavata-local-agent/renderer/components/DockerComponents/DockerImagesList.jsx
create mode 100644
airavata-local-agent/renderer/components/DockerComponents/DockerInspectModal.jsx
create mode 100644
airavata-local-agent/renderer/components/DockerComponents/Programs/JupyterProgram.jsx
create mode 100644 airavata-local-agent/renderer/components/ExperimentModal.jsx
create mode 100644 airavata-local-agent/renderer/components/ExperimentsList.jsx
create mode 100644 airavata-local-agent/renderer/components/Footer.jsx
create mode 100644 airavata-local-agent/renderer/components/HeaderBox.jsx
create mode 100644 airavata-local-agent/renderer/components/JupyterLab.jsx
create mode 100644 airavata-local-agent/renderer/components/LinkIconBox.jsx
create mode 100644 airavata-local-agent/renderer/components/LocalFuncs.jsx
create mode 100644 airavata-local-agent/renderer/components/NavBar.jsx
create mode 100644 airavata-local-agent/renderer/components/NavContainer.jsx
create mode 100644 airavata-local-agent/renderer/components/PanelBody.jsx
create mode 100644 airavata-local-agent/renderer/components/TextWithBoldKey.jsx
create mode 100644 airavata-local-agent/renderer/components/UserModal.jsx
create mode 100644 airavata-local-agent/renderer/components/VNCItem.jsx
create mode 100644 airavata-local-agent/renderer/components/VNCViewer.jsx
create mode 100644 airavata-local-agent/renderer/components/temp/VNCTest.jsx
create mode 100644 airavata-local-agent/renderer/lib/Contexts.js
create mode 100644 airavata-local-agent/renderer/lib/constants.js
create mode 100644 airavata-local-agent/renderer/lib/logger.js
create mode 100644 airavata-local-agent/renderer/lib/utilityFuncs.js
create mode 100644 airavata-local-agent/renderer/next.config.js
create mode 100644 airavata-local-agent/renderer/pages/_app.jsx
create mode 100644
airavata-local-agent/renderer/pages/create-namd-experiment.jsx
create mode 100644 airavata-local-agent/renderer/pages/docker-home.jsx
create mode 100644
airavata-local-agent/renderer/pages/experiment/[experimentId].js
create mode 100644 airavata-local-agent/renderer/pages/home.jsx
create mode 100644 airavata-local-agent/renderer/pages/login-callback.jsx
create mode 100644 airavata-local-agent/renderer/pages/login.jsx
create mode 100644 airavata-local-agent/renderer/pages/tabs-view.jsx
create mode 100644 airavata-local-agent/renderer/pages/temp/docker-page.jsx
create mode 100644
airavata-local-agent/renderer/pages/temp/page-with-vnc-test.jsx
create mode 100644 airavata-local-agent/renderer/pages/temp/vnc-client.jsx
create mode 100644 airavata-local-agent/renderer/public/images/cs-logo.png
create mode 100644 airavata-local-agent/renderer/public/images/jupyter_logo.png
create mode 100644 airavata-local-agent/renderer/public/images/logo.png
create mode 100644 airavata-local-agent/resources/icon.icns
create mode 100644 airavata-local-agent/resources/icon.ico
create mode 100644
dev-tools/ansible/inventories/scigap/production/host_vars/dev-smiles/vars.yml
create mode 100644
dev-tools/ansible/inventories/scigap/production/host_vars/dev-smiles/vault.yml
copy dev-tools/ansible/inventories/scigap/production/host_vars/{nasa-veda =>
dt4h}/vars.yml (70%)
create mode 100644
dev-tools/ansible/inventories/scigap/production/host_vars/dt4h/vault.yml
copy
dev-tools/ansible/inventories/scigap/production/host_vars/{molecular-dynamics
=> enveomics}/vars.yml (65%)
create mode 100644
dev-tools/ansible/inventories/scigap/production/host_vars/enveomics/vault.yml
copy dev-tools/ansible/inventories/scigap/production/host_vars/{ai-confluence
=> testdrive-cs}/vars.yml (54%)
create mode 100644
dev-tools/ansible/inventories/scigap/production/host_vars/testdrive-cs/vault.yml
copy dev-tools/ansible/{roles/common/vars/main.yml => kafka-rest-proxy.yml}
(94%)
create mode 100644
dev-tools/ansible/roles/tusd/templates/tus-temp-dir-cleanup.cron.j2
copy dev-tools/ansible/{roles/common/vars/main.yml => zookeeper.yml} (93%)
create mode 100644 modules/agent-framework/agent-service/.gitignore
create mode 100644 modules/agent-framework/agent-service/pom.xml
copy tools/load-client/src/main/assembly/load-client-bin-assembly.xml =>
modules/agent-framework/agent-service/src/main/assembly/agent-service-bin-assembly.xml
(73%)
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/AgentServiceApplication.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/UserContext.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/config/AuthzTokenFilter.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/config/ClusterApplicationConfig.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/controllers/AgentController.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/controllers/ExperimentController.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/controllers/PlanController.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/db/entity/AgentDeploymentInfo.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/db/entity/AgentExecution.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/db/entity/AgentExecutionStatus.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/db/entity/Plan.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/db/repo/AgentDeploymentInfoRepo.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/db/repo/AgentExecutionRepo.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/db/repo/AgentExecutionStatusRepo.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/db/repo/PlanRepo.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/handlers/AgentConnectionHandler.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/handlers/AgentManagementHandler.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/handlers/FuseFSHandler.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/handlers/PlanHandler.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentCommandAck.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentCommandRequest.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentCommandResponse.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentInfoResponse.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentPythonRunAck.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentPythonRunRequest.java
create 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/AgentTunnelAck.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentTunnelCreationRequest.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/DirectoryInfo.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/ExperimentStorageResponse.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/FileInfo.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/JupyterExecutionAck.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/JupyterExecutionRequest.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/JupyterExecutionResponse.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/LaunchAgentRequest.java
copy
modules/{airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/parsing/ProcessCompletionMessage.java
=>
agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/LaunchAgentResponse.java}
(50%)
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/TerminateAgentResponse.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/services/AiravataFileService.java
create mode 100644
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/services/AiravataService.java
create mode 120000 modules/agent-framework/agent-service/src/main/proto
create mode 100644
modules/agent-framework/agent-service/src/main/resources/application.yml
copy
modules/{distribution/src/main/resources/controller/bin/controller-daemon.sh =>
agent-framework/agent-service/src/main/resources/distribution/bin/agent-service-daemon.sh}
(85%)
mode change 100644 => 100755
copy modules/{distribution/src/main/resources/controller/bin/controller.sh =>
agent-framework/agent-service/src/main/resources/distribution/bin/agent-service.sh}
(81%)
mode change 100644 => 100755
copy modules/{distribution/src/main/resources/parser-wm =>
agent-framework/agent-service/src/main/resources/distribution}/bin/setenv.sh
(98%)
mode change 100644 => 100755
create mode 100644
modules/agent-framework/agent-service/src/main/resources/distribution/conf/application.yml
copy modules/{airavata-helix/helix-spectator/src/main/resources =>
agent-framework/agent-service/src/main/resources/distribution/conf}/log4j2.xml
(100%)
create mode 100644
modules/agent-framework/agent-service/src/main/resources/distribution/conf/truststore.jks
create mode 100644
modules/agent-framework/agent-service/src/main/resources/truststore.jks
create mode 100644 modules/agent-framework/airavata-agent/.gitignore
create mode 100644 modules/agent-framework/airavata-agent/Dockerfile
create mode 100644 modules/agent-framework/airavata-agent/Makefile
create mode 100644 modules/agent-framework/airavata-agent/README.md
create mode 100644
modules/agent-framework/airavata-agent/agent-communication.proto
create mode 100644 modules/agent-framework/airavata-agent/agent.go
create mode 100644 modules/agent-framework/airavata-agent/go.mod
create mode 100644 modules/agent-framework/airavata-agent/kernel.py
create mode 100644
modules/agent-framework/airavata-agent/protos/agent-communication.pb.go
create mode 100644
modules/agent-framework/airavata-agent/protos/agent-communication_grpc.pb.go
create mode 100644 modules/agent-framework/airavata-fuse/.gitignore
create mode 100644 modules/agent-framework/airavata-fuse/Makefile
create mode 100644 modules/agent-framework/airavata-fuse/README.md
create mode 100644 modules/agent-framework/airavata-fuse/data/foo/bar.txt
create mode 100644 modules/agent-framework/airavata-fuse/data/hello.txt
create mode 100644 modules/agent-framework/airavata-fuse/src/grpcfs/adapters.go
create mode 100644 modules/agent-framework/airavata-fuse/src/grpcfs/fs.go
create mode 100644 modules/agent-framework/airavata-fuse/src/grpcfs/go.mod
create mode 100644 modules/agent-framework/airavata-fuse/src/grpcfs/go.sum
create mode 100644 modules/agent-framework/airavata-fuse/src/grpcfs/grpc.go
create mode 100644 modules/agent-framework/airavata-fuse/src/grpcfs/inode.go
create mode 100644
modules/agent-framework/airavata-fuse/src/grpcfs/pb/grpcfs.pb.go
create mode 100644
modules/agent-framework/airavata-fuse/src/grpcfs/pb/grpcfs_grpc.pb.go
create mode 100644
modules/agent-framework/airavata-fuse/src/grpcfs_client/go.mod
create mode 100644
modules/agent-framework/airavata-fuse/src/grpcfs_client/go.sum
create mode 100644
modules/agent-framework/airavata-fuse/src/grpcfs_client/main.go
create mode 100644
modules/agent-framework/airavata-fuse/src/grpcfs_server/go.mod
create mode 100644
modules/agent-framework/airavata-fuse/src/grpcfs_server/go.sum
create mode 100644
modules/agent-framework/airavata-fuse/src/grpcfs_server/main.go
create mode 100644 modules/agent-framework/airavata-fuse/src/proto/grpcfs.proto
create mode 100644 modules/agent-framework/airavata-jupyter-magic/.gitignore
create mode 100644 modules/agent-framework/airavata-jupyter-magic/README.md
copy {airavata-api/airavata-client-sdks/airavata-python-sdk/airavata =>
modules/agent-framework/airavata-jupyter-magic}/__init__.py (100%)
create mode 100644
modules/agent-framework/airavata-jupyter-magic/airavata_jupyter_magic.py
create mode 100644
modules/agent-framework/airavata-jupyter-magic/device_auth.py
create mode 100644
modules/agent-framework/airavata-jupyter-magic/pyproject.toml
create mode 100644
modules/agent-framework/deployments/agent-cerebrum/Dockerfile
create mode 100644 modules/agent-framework/deployments/agent-cerebrum/Makefile
create mode 100644 modules/agent-framework/deployments/agent-cerebrum/README.md
create mode 100644
modules/agent-framework/deployments/agent-cyberfaces/Dockerfile
create mode 100644
modules/agent-framework/deployments/agent-cyberfaces/Makefile
create mode 100644
modules/agent-framework/deployments/agent-cyberfaces/README.md
create mode 100644
modules/agent-framework/deployments/agent-cyberfaces/envs/aiml.yml
create mode 100644
modules/agent-framework/deployments/agent-cyberfaces/envs/fair.yml
create mode 100644
modules/agent-framework/deployments/agent-cyberfaces/envs/justiceindata.yml
create mode 100644
modules/agent-framework/deployments/agent-cyberfaces/envs/rs.yml
create mode 100644 modules/agent-framework/deployments/agent-gkeyll/Dockerfile
create mode 100644 modules/agent-framework/deployments/agent-gkeyll/Makefile
create mode 100644 modules/agent-framework/deployments/agent-gkeyll/README.md
create mode 100644 modules/agent-framework/deployments/agent-i-guide/Dockerfile
create mode 100644 modules/agent-framework/deployments/agent-i-guide/Makefile
create mode 100644 modules/agent-framework/deployments/agent-i-guide/README.md
create mode 100644 modules/agent-framework/deployments/agent-md/Dockerfile
create mode 100644 modules/agent-framework/deployments/agent-md/Makefile
create mode 100644 modules/agent-framework/deployments/agent-md/README.md
create mode 100644 modules/agent-framework/deployments/agent-sample/Dockerfile
create mode 100644 modules/agent-framework/deployments/agent-sample/Makefile
create mode 100644 modules/agent-framework/deployments/agent-sample/README.md
create mode 100644
modules/agent-framework/deployments/app-scripts/anvil_agent.sh
create mode 100755
modules/agent-framework/deployments/app-scripts/expanse_af2.sh
create mode 100644
modules/agent-framework/deployments/app-scripts/expanse_agent.sh
create mode 100755
modules/agent-framework/deployments/app-scripts/expanse_namd.sh
create mode 100644 modules/agent-framework/deployments/jupyterhub/Dockerfile
create mode 100644
modules/agent-framework/deployments/jupyterhub/Dockerfile-jl-base
create mode 100644
modules/agent-framework/deployments/jupyterhub/Dockerfile-jl-iguide
create mode 100644 modules/agent-framework/deployments/jupyterhub/Makefile
create mode 100644 modules/agent-framework/deployments/jupyterhub/README.md
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/cerebrum/bkg/bkg_spikes_250Hz_3s.h5
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/cerebrum/config_nest.json
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/cerebrum/description/config.json
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/cerebrum/description/config_template.json
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/cerebrum/description/custom_mod.json
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/cerebrum/description/db_connect_output.json
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/cyberfaces/Solution_DA3_DEM_Access_v4.ipynb
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/cyberfaces/Solution_DP6_DEM_Processing_v2.ipynb
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/experiment_sdk/1_experiment_sdk.ipynb
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/gkeyll/plotE_z.ipynb
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/iguide/NID_FIM_MH_F/MH_F_CA10022.tiff
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/iguide/NID_FIM_NH_F/NH_F_CA10022.tiff
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/iguide/NID_FIM_TAS_F/TAS_F_CA10022.tiff
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/iguide/census_geometry/census_data.csv
copy AWSCLIV2.pkg =>
modules/agent-framework/deployments/jupyterhub/data/iguide/census_geometry/census_tract_from_api.geojson
(55%)
copy AWSCLIV2.pkg =>
modules/agent-framework/deployments/jupyterhub/data/iguide/census_geometry/tl_2020_06_tabblock20.geojson
(51%)
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/iguide/cyberfaces.ipynb
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/iguide/dam_list.csv
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/alphafold2/Abeta42_Dimer.fasta
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/amber/RAMP1.prmtop
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/amber/RAMP1_equil.rst7
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/amber/md.in
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/gaussian/NOR0N-RAD21-freq.gjf
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/gromacs/md.mdp
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/gromacs/npt.gro
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/gromacs/npt.tpr
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/namd/b4pull.pdb
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/namd/b4pull.restart.coor
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/namd/b4pull.restart.vel
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/namd/b4pull.restart.xsc
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/namd/par_all36_water.prm
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/namd/par_all36m_prot.prm
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/namd/pull_cpu.conf
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/namd/pull_gpu.conf
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/namd/structure.pdb
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/namd/structure.psf
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/molecular_dynamics.ipynb
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/settings.ini
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/namd_workshop/data/b4pull.pdb
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/namd_workshop/data/b4pull.restart.coor
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/namd_workshop/data/b4pull.restart.vel
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/namd_workshop/data/b4pull.restart.xsc
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/namd_workshop/data/par_all36_water.prm
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/namd_workshop/data/par_all36m_prot.prm
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/namd_workshop/data/pull_cpu.conf
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/namd_workshop/data/pull_gpu.conf
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/namd_workshop/data/structure.pdb
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/namd_workshop/data/structure.psf
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/namd_workshop/settings.ini
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/namd_workshop/smd_cpu.ipynb
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/namd_workshop/smd_gpu.ipynb
create mode 100644
modules/agent-framework/deployments/jupyterhub/docker-compose.yaml
create mode 100644
modules/agent-framework/deployments/jupyterhub/jupyterhub_config.py
create mode 100644 modules/agent-framework/deployments/jupyterhub/nginx-conf
copy modules/{airavata-metascheduler => agent-framework}/pom.xml (74%)
create mode 100644 modules/agent-framework/proto/agent-communication.proto
create mode 100644 modules/agent-framework/proto/airavata-fuse.proto
delete mode 100644
modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/credential/impl/ssh/SSHCredentialGenerator.java
create mode 100644 modules/file-server/pom.xml
copy tools/load-client/src/main/assembly/load-client-bin-assembly.xml =>
modules/file-server/src/main/assembly/file-service-bin-assembly.xml (74%)
create mode 100644
modules/file-server/src/main/java/org/apache/airavata/file/server/FileServerApplication.java
create mode 100644
modules/file-server/src/main/java/org/apache/airavata/file/server/FileServerConfiguration.java
create mode 100644
modules/file-server/src/main/java/org/apache/airavata/file/server/controller/FileController.java
create mode 100644
modules/file-server/src/main/java/org/apache/airavata/file/server/model/AiravataDirectory.java
create mode 100644
modules/file-server/src/main/java/org/apache/airavata/file/server/model/AiravataFile.java
create mode 100644
modules/file-server/src/main/java/org/apache/airavata/file/server/model/FileUploadResponse.java
create mode 100644
modules/file-server/src/main/java/org/apache/airavata/file/server/service/AirvataFileService.java
create mode 100644
modules/file-server/src/main/java/org/apache/airavata/file/server/service/ProcessDataManager.java
create mode 100644
modules/file-server/src/main/resources/application.properties
copy
modules/{distribution/src/main/resources/email-monitor/bin/email-monitor-daemon.sh
=> file-server/src/main/resources/distribution/bin/file-service-daemon.sh}
(87%)
copy modules/{distribution/src/main/resources/controller/bin/controller.sh =>
file-server/src/main/resources/distribution/bin/file-service.sh} (84%)
copy modules/{distribution/src/main/resources/parser-wm =>
file-server/src/main/resources/distribution}/bin/setenv.sh (98%)
create mode 100644
modules/file-server/src/main/resources/distribution/conf/application.properties
copy modules/{airavata-helix/helix-spectator/src/main/resources =>
file-server/src/main/resources/distribution/conf}/log4j2.xml (100%)
create mode 100644
modules/ide-integration/src/main/containers/keycloak/keycloak.conf