Patch: Updates API request to send API key via HTTP only. Deprecates API key via parameters.

[dapineyro]

Overview

This PR changes all the APIkey via parameters to use only HTTP headers. This is a change required to support the upcoming deprecation of APIkey via parameters in cloudos.

Jira

https://lifebit.atlassian.net/browse/LIF-1350

Changes

• Refactors all API requests in which API key was sent via parameters, to use only HTTP headers.
• Updates Pytests

Tests

Using docker image:

docker run --rm -it quay.io/lifebitaiorg/cloudos-cli:v2.11.2

Global variables:

MY_API_KEY="xxxx"
CLOUDOS="https://dev.sdlc.lifebit.ai"
WORKSPACE_ID="xxxx"
PROJECT_NAME="davidp_testing"
WORKFLOW_NAME="Cufflinks"
JOB_PARAMS="/cloudos/examples/rnatoy.config"
JOB_NAME="cloudos-cli_QA"

Launch job

cloudos job run \
    --cloudos-url $CLOUDOS \
    --apikey $MY_API_KEY \
    --workspace-id $WORKSPACE_ID \
    --project-name "$PROJECT_NAME" \
    --workflow-name $WORKFLOW_NAME \
    --job-config $JOB_PARAMS \
    --job-name $JOB_NAME \
    --resumable  | tee job_status.txt

CloudOS python package: a package for interacting with CloudOS.

Version: 2.11.2

CloudOS job functionality: run and check jobs in CloudOS.

Executing run...
	No job_queue was specified, using the CloudOS default queue: Default_1.
	Job successfully launched to CloudOS, please check the following link: https://dev.sdlc.lifebit.ai/app/jobs/672ca06fcf949b9103547609
	Your assigned job id is: 672ca06fcf949b9103547609

	Your current job status is: initializing
	To further check your job status you can either go to https://dev.sdlc.lifebit.ai/app/jobs/672ca06fcf949b9103547609 or use the following command:
	cloudos job status \
		--apikey $MY_API_KEY \
		--cloudos-url https://dev.sdlc.lifebit.ai \
		--job-id 672ca06fcf949b9103547609

Check job status

job_id=$(grep -e '--job-id'  job_status.txt | rev | cut -f1 -d " " | rev)
cloudos job status \
    --apikey $MY_API_KEY \
    --cloudos-url $CLOUDOS \
    --job-id $job_id

CloudOS python package: a package for interacting with CloudOS.

Version: 2.11.2

CloudOS job functionality: run and check jobs in CloudOS.

Executing status...
	Your current job status is: initializing

	To further check your job status you can either go to https://dev.sdlc.lifebit.ai/app/jobs/672ca06fcf949b9103547609 or repeat the command you just used.

Get Job list CSV

cloudos job list \
    --cloudos-url $CLOUDOS \
    --apikey $MY_API_KEY \
    --workspace-id $WORKSPACE_ID

CloudOS python package: a package for interacting with CloudOS.

Version: 2.11.2

CloudOS job functionality: run and check jobs in CloudOS.

Executing list...
	Job list collected with a total of 30 jobs.
	Job list saved to joblist.csv

Get workflow list CSV

cloudos workflow list \
    --cloudos-url $CLOUDOS \
    --apikey $MY_API_KEY \
    --workspace-id $WORKSPACE_ID

CloudOS python package: a package for interacting with CloudOS.

Version: 2.11.2

CloudOS workflow functionality: list and import workflows.

Executing list...
	Workflow list collected with a total of 2623 workflows.
	Workflow list saved to workflow_list.csv

Get projects list

cloudos project list \
    --cloudos-url $CLOUDOS \
    --apikey $MY_API_KEY \
    --workspace-id $WORKSPACE_ID

CloudOS python package: a package for interacting with CloudOS.

Version: 2.11.2

CloudOS project functionality: list projects in CloudOS.

Executing list...
	Project list collected with a total of 976 projects.
	Project list saved to project_list.csv

Import a workflow

cloudos workflow import \
    --cloudos-url $CLOUDOS \
    --apikey $MY_API_KEY \
    --workspace-id $WORKSPACE_ID \
    --workflow-url "https://github.com/lifebit-ai/lifebit-platform-gwas" \
    --workflow-name "test_import_github_7" \
    --repository-project-id "30871219" \
    --repository-id "122059362"

CloudOS python package: a package for interacting with CloudOS.

Version: 2.11.2

CloudOS workflow functionality: list and import workflows.

Executing workflow import...

	[Message] Only Nextflow workflows are currently supported.

	Workflow test_import_github_7 was imported successfully with the following ID: 672ca4e63b9051e15ad34dc5

[l-mansouri]

LGTM!