Note The EBI Cloud Portal has been retired and its code base is no longer updated. This includes all tooling for the VM-related features of the BioExcel Portal.
If you would like to contact the Cloud Portal authors, please leave us feedback via the EBI contact form mentioning the EBI Cloud Portal in the Subject.
As of March 2023 the BioExcel project itself is ongoing and you can find more information here
Bioexcel portal client is a command line tool for end to end testing of Bioexcel portal. The objective is to test performance of Bioexcel portal backend which is actually EBI cloud portal API server. The testing is focused on Cloud Portal's deployment with multiple concurrent user sessions and destruction process.
python 3.6
ecp-cli module
install from github:
pip3 install git+https://github.com/EMBL-EBI-TSI/ecp-cli/
pip3 install git+https://github.com/EMBL-EBI-TSI/bioexcel-cli/
json Directory contains necessary json files for running of Bioexcel portal client.
deploy.json Describes What & how many applications should be deployed through which launcher.
We have four type of launchers for Bioexcel portal's deployment of an application.
bioexcel, nfsclient, ecpimage, ecpapplication
JSON structure:
{ "deployments" : [{
"application_name":"NAFlex",
"launcher":"bioexcel",
"config_name":"bioexcel config",
"team_name":"Bioexcel"
}]}
application - biotools application to be deployed
launcher - one of the four launchers
config_name - configuration to be used for deployment
team_name - team in which application is shared
we can provide n number of deployment object inside deployments array block. Deployment will be done one by one.
destroy.json Describe what are all the deployments to be destroyed.
JSON structure:
{"deployments":[
{"reference":"TSI1583323328233"}
]}
reference - deployment reference to be destroyed
we can provide n number of reference object inside deployments array block.
user.json Describes user accounts to be used and number concurrent sessions to be created
while doing deployment.There are two ways that user sessions can be created.
One is from given JWT token. The other way is through HTTP login from credentials specified on user.json.
You can give JWT token by arugument.--token #JWT token saved file path relative#.
If user is not member of the BioExcel Embassy team, user will be added to before deployment
by supplying team owner's JWT token with --owner argument.
JSON structure:
{
"user-sessions":1,
"users": [{
"username":"bioexcel1",
"password":"bioexcel123"
}
}
user-sessions - number of concurrent user sessions to be created from the account of JWT token specified. this attributed will be ignored if --token argument is not specified.
username - username for session creation through HTTP login
password - password for session creation through HTTP login
You can specify n number of user objects inside users array. This type of session creation will happen only if --token is not specified.
Application name Launcher
PyMDSetup bioexcel
Chromatin Dynamics bioexcel
COMPSs bioexcel
NAFlex nfsclient
PyMDSetup nfsclient
Chromatin Dynamics nfsclient
CWL VM environment ecpapplication
Jupyter Server Instance ecpapplication
For bioexcel and nfsclient launcher team_name is not required. config_name
is used if specified.It will use default value if config_name is not specified.
For ecpimage launcher team_name is not required. application_name and config_name
are mandatorily specified on deploy.json
For config_name application_name, config_name and team_name are mandatory and must be specified in deploy.json.
bioexcel-cli *argument* [*action*]
Actions :
deploy
destroy
arguments
--token: Optional argument. Relative path of the text file content which is JWT token from AAP authentication server. Credentials on user.json will be looked if this is specified.
--owner: Optional argument. Relative path of the text file content which is JWT token of BioExcel Embassy team owner's account. Owner token is required in case of user not member of the team and User will be added to team automatically.
1.Deploy PyMDSetup application through BioExcel launcher with 5 concurrent user sessions
Get the JWT of a user who is a member of BioExcel Embassy team. Copy the content to file called token.txt.
Use following contents with json files.
user.json :-
{
"user-sessions":5,
"users": [{
"username":"",
"password":""
}]
}
deploy.json :-
{
"deployments": [
{
"application_name":"PyMDSetup",
"launcher":"bioexcel",
"config_name":"",
"team_name":""
}
]
}
Execute :-
bioexcel-cli –-token token.txt deploy
2.Deploy NAFlex application through NFS Client launcher with given 3 user accounts of concurrent sessions.
Assuming 3 users are member of BioExcel Embassy team.
user.json :-
{
"user-sessions":1,
"users": [{
"username":"bioexcel1",
"password": "password"
},{
"username":"bioexcel2",
"password": "password"
},{
"username":"bioexcel3",
"password": "password"
}]
}
deploy.json :-
{
"deployments": [
{
"application_name": "NAFlex",
"launcher": "nfsclient",
"config_name": "",
"team_name": ""
}
]
}
Execute:-
bioexcel-cli deploy
3.Deploy Jupyter Server Instance application through ECP application launcher with a user who is not member of the team.
Get the JWT of the user account and copy the content to file called token.txt.
Get the JWT of the team owner's and copy the content to file called owner.txt.
user.json :-
{
"user-sessions":1,
"users" : [{
"username":"",
"password":""
}]
}
deploy.json :-
{
"deployments" : [
{
"application_name": "Jupyter Server Instance",
"launcher": "ecpapplication",
"config_name": "Jupyter biobb_wf_md_setup",
"team_name": "BioExcel Embassy"
}
]
}
Execute:-
bioexcel-cli –-token token.txt --owner owner.txt deploy
Once user added to team, you can execute the same without giving --owner argument.
4.Destroy some deployments by giving deployment references.
user.json :-
{
"user-sessions":1,
"users": [{
"username":"bioexcel1",
"password": "password"
}]
}
destroy.json :-
{
"deployments": [
{
"reference":"TSI1583323328233"
},
{
"reference":"TSI1583323325989"
},
{
"reference":"TSI1583323325989"
}
]
}
Execute:
bioexcel-cli destroy