Index

Symbols

--accelerate-file-staging cloudos-job-clone-resume command line option, [1] cloudos-job-run command line option --all-fields cloudos-job-list command line option cloudos-project-list command line option cloudos-queue-list command line option cloudos-workflow-list command line option --apikey cloudos-bash-array-job command line option cloudos-bash-job command line option cloudos-cromwell-start command line option cloudos-cromwell-status command line option cloudos-cromwell-stop command line option cloudos-datasets-cp command line option cloudos-datasets-link command line option cloudos-datasets-ls command line option cloudos-datasets-mkdir command line option cloudos-datasets-mv command line option cloudos-datasets-rename command line option cloudos-datasets-rm command line option cloudos-job-abort command line option cloudos-job-clone-resume command line option, [1] cloudos-job-details command line option cloudos-job-list command line option cloudos-job-logs command line option cloudos-job-results command line option cloudos-job-run command line option cloudos-job-status command line option cloudos-job-workdir command line option cloudos-procurement-images-ls command line option cloudos-procurement-images-reset command line option cloudos-procurement-images-set command line option cloudos-project-create command line option cloudos-project-list command line option cloudos-queue-list command line option cloudos-workflow-import command line option cloudos-workflow-list command line option --archived cloudos-job-list command line option --array-file cloudos-bash-array-job command line option --array-file-project cloudos-bash-array-job command line option --array-parameter cloudos-bash-array-job command line option --azure-worker-instance-disk cloudos-job-run command line option --azure-worker-instance-spot cloudos-job-run command line option --azure-worker-instance-type cloudos-job-run command line option --cloudos-url cloudos-bash-array-job command line option cloudos-bash-job command line option cloudos-cromwell-start command line option cloudos-cromwell-status command line option cloudos-cromwell-stop command line option cloudos-datasets-cp command line option cloudos-datasets-link command line option cloudos-datasets-ls command line option cloudos-datasets-mkdir command line option cloudos-datasets-mv command line option cloudos-datasets-rename command line option cloudos-datasets-rm command line option cloudos-job-abort command line option cloudos-job-clone-resume command line option, [1] cloudos-job-details command line option cloudos-job-list command line option cloudos-job-logs command line option cloudos-job-results command line option cloudos-job-run command line option cloudos-job-status command line option cloudos-job-workdir command line option cloudos-procurement-images-ls command line option cloudos-procurement-images-reset command line option cloudos-procurement-images-set command line option cloudos-project-create command line option cloudos-project-list command line option cloudos-queue-list command line option cloudos-workflow-import command line option cloudos-workflow-list command line option --command cloudos-bash-array-job command line option cloudos-bash-job command line option --cost-limit cloudos-bash-array-job command line option cloudos-bash-job command line option cloudos-job-clone-resume command line option, [1] cloudos-job-run command line option cloudos-workflow-import command line option --cpus cloudos-bash-array-job command line option cloudos-bash-job command line option --cromwell-token cloudos-cromwell-start command line option cloudos-cromwell-status command line option cloudos-cromwell-stop command line option cloudos-job-run command line option --custom-script-path cloudos-bash-array-job command line option --custom-script-project cloudos-bash-array-job command line option --debug cloudos command line option --destination-project-name cloudos-datasets-cp command line option cloudos-datasets-mv command line option --details cloudos-datasets-ls command line option --disable-column-check cloudos-bash-array-job command line option --disable-ssl-verification cloudos-bash-array-job command line option cloudos-bash-job command line option cloudos-cromwell-start command line option cloudos-cromwell-status command line option cloudos-cromwell-stop command line option cloudos-datasets-cp command line option cloudos-datasets-link command line option cloudos-datasets-ls command line option cloudos-datasets-mkdir command line option cloudos-datasets-mv command line option cloudos-datasets-rename command line option cloudos-datasets-rm command line option cloudos-job-abort command line option cloudos-job-clone-resume command line option, [1] cloudos-job-details command line option cloudos-job-list command line option cloudos-job-logs command line option cloudos-job-results command line option cloudos-job-run command line option cloudos-job-status command line option cloudos-job-workdir command line option cloudos-procurement-images-ls command line option cloudos-procurement-images-reset command line option cloudos-procurement-images-set command line option cloudos-project-create command line option cloudos-project-list command line option cloudos-queue-list command line option cloudos-workflow-import command line option cloudos-workflow-list command line option --do-not-save-logs cloudos-bash-array-job command line option cloudos-bash-job command line option cloudos-job-clone-resume command line option, [1] cloudos-job-run command line option --execution-platform cloudos-bash-array-job command line option cloudos-bash-job command line option cloudos-job-run command line option --filter-job-id cloudos-job-list command line option --filter-job-name cloudos-job-list command line option --filter-only-mine cloudos-job-list command line option --filter-owner cloudos-job-list command line option --filter-project cloudos-job-list command line option --filter-queue cloudos-job-list command line option --filter-status cloudos-job-list command line option --filter-workflow cloudos-job-list command line option --force cloudos-datasets-rm command line option --git-branch cloudos-job-clone-resume command line option, [1] cloudos-job-run command line option --git-commit cloudos-job-run command line option --git-tag cloudos-job-run command line option --hpc-id cloudos-job-run command line option --image-id cloudos-procurement-images-set command line option --image-name cloudos-procurement-images-set command line option --image-type cloudos-procurement-images-reset command line option cloudos-procurement-images-set command line option --instance-disk cloudos-bash-array-job command line option cloudos-bash-job command line option cloudos-job-run command line option --instance-type cloudos-bash-array-job command line option cloudos-bash-job command line option cloudos-job-clone-resume command line option, [1] cloudos-job-run command line option --job-config cloudos-job-run command line option --job-id cloudos-job-clone-resume command line option, [1] cloudos-job-details command line option cloudos-job-logs command line option cloudos-job-results command line option cloudos-job-status command line option cloudos-job-workdir command line option --job-ids cloudos-job-abort command line option --job-name cloudos-bash-array-job command line option cloudos-bash-job command line option cloudos-job-clone-resume command line option, [1] cloudos-job-run command line option --job-queue cloudos-bash-array-job command line option cloudos-bash-job command line option cloudos-job-clone-resume command line option, [1] cloudos-job-run command line option --last cloudos-bash-array-job command line option cloudos-bash-job command line option cloudos-job-list command line option cloudos-job-run command line option --last-n-jobs cloudos-job-list command line option --limit cloudos-procurement-images-ls command line option --list-columns cloudos-bash-array-job command line option --lustre-size cloudos-bash-array-job command line option cloudos-bash-job command line option cloudos-job-run command line option --make-default cloudos-configure command line option --memory cloudos-bash-array-job command line option cloudos-bash-job command line option --new-project cloudos-project-create command line option --nextflow-profile cloudos-job-clone-resume command line option, [1] cloudos-job-run command line option --nextflow-version cloudos-job-clone-resume command line option, [1] cloudos-job-run command line option --organisation-id cloudos-procurement-images-reset command line option cloudos-procurement-images-set command line option --output-basename cloudos-job-details command line option cloudos-job-list command line option cloudos-project-list command line option cloudos-queue-list command line option cloudos-workflow-list command line option --output-format cloudos-job-details command line option cloudos-job-list command line option cloudos-project-list command line option cloudos-queue-list command line option cloudos-workflow-list command line option --page cloudos-job-list command line option cloudos-procurement-images-ls command line option cloudos-project-list command line option

--parameter cloudos-bash-array-job command line option cloudos-bash-job command line option cloudos-job-clone-resume command line option, [1] cloudos-job-run command line option --parameters cloudos-job-details command line option --procurement-id cloudos-procurement-images-ls command line option cloudos-procurement-images-reset command line option cloudos-procurement-images-set command line option --profile cloudos-bash-array-job command line option cloudos-bash-job command line option cloudos-configure command line option cloudos-configure-remove-profile command line option cloudos-cromwell-start command line option cloudos-cromwell-status command line option cloudos-cromwell-stop command line option cloudos-datasets-cp command line option cloudos-datasets-link command line option cloudos-datasets-ls command line option cloudos-datasets-mkdir command line option cloudos-datasets-mv command line option cloudos-datasets-rename command line option cloudos-datasets-rm command line option cloudos-job-abort command line option cloudos-job-clone-resume command line option, [1] cloudos-job-details command line option cloudos-job-list command line option cloudos-job-logs command line option cloudos-job-results command line option cloudos-job-run command line option cloudos-job-status command line option cloudos-job-workdir command line option cloudos-procurement-images-ls command line option cloudos-procurement-images-reset command line option cloudos-procurement-images-set command line option cloudos-project-create command line option cloudos-project-list command line option cloudos-queue-list command line option cloudos-workflow-import command line option cloudos-workflow-list command line option --project-name cloudos-bash-array-job command line option cloudos-bash-job command line option cloudos-datasets-cp command line option cloudos-datasets-link command line option cloudos-datasets-ls command line option cloudos-datasets-mkdir command line option cloudos-datasets-mv command line option cloudos-datasets-rename command line option cloudos-datasets-rm command line option cloudos-job-clone-resume command line option, [1] cloudos-job-run command line option --provider cloudos-procurement-images-reset command line option cloudos-procurement-images-set command line option --region cloudos-procurement-images-reset command line option cloudos-procurement-images-set command line option --repository-platform cloudos-bash-array-job command line option cloudos-bash-job command line option cloudos-job-run command line option cloudos-workflow-import command line option --request-interval cloudos-bash-array-job command line option cloudos-bash-job command line option cloudos-job-run command line option --resumable cloudos-job-clone-resume command line option, [1] cloudos-job-run command line option --separator cloudos-bash-array-job command line option --session-id cloudos-datasets-link command line option --ssl-cert cloudos-bash-array-job command line option cloudos-bash-job command line option cloudos-cromwell-start command line option cloudos-cromwell-status command line option cloudos-cromwell-stop command line option cloudos-datasets-cp command line option cloudos-datasets-link command line option cloudos-datasets-ls command line option cloudos-datasets-mkdir command line option cloudos-datasets-mv command line option cloudos-datasets-rename command line option cloudos-datasets-rm command line option cloudos-job-abort command line option cloudos-job-clone-resume command line option, [1] cloudos-job-details command line option cloudos-job-list command line option cloudos-job-logs command line option cloudos-job-results command line option cloudos-job-run command line option cloudos-job-status command line option cloudos-job-workdir command line option cloudos-procurement-images-ls command line option cloudos-procurement-images-reset command line option cloudos-procurement-images-set command line option cloudos-project-create command line option cloudos-project-list command line option cloudos-queue-list command line option cloudos-workflow-import command line option cloudos-workflow-list command line option --storage-mode cloudos-bash-array-job command line option cloudos-bash-job command line option cloudos-job-run command line option --use-private-docker-repository cloudos-job-run command line option --verbose cloudos-cromwell-start command line option cloudos-cromwell-status command line option cloudos-cromwell-stop command line option cloudos-job-abort command line option cloudos-job-clone-resume command line option, [1] cloudos-job-details command line option cloudos-job-list command line option cloudos-job-logs command line option cloudos-job-results command line option cloudos-job-run command line option cloudos-job-status command line option cloudos-job-workdir command line option cloudos-project-create command line option cloudos-project-list command line option cloudos-workflow-list command line option --version cloudos command line option cloudos-cromwell-start command line option cloudos-cromwell-status command line option cloudos-cromwell-stop command line option --wait-completion cloudos-bash-array-job command line option cloudos-bash-job command line option cloudos-job-run command line option --wait-time cloudos-bash-array-job command line option cloudos-bash-job command line option cloudos-cromwell-start command line option cloudos-job-run command line option --wdl-importsfile cloudos-job-run command line option --wdl-mainfile cloudos-job-run command line option --workflow-description cloudos-workflow-import command line option --workflow-docs-link cloudos-workflow-import command line option --workflow-name cloudos-bash-array-job command line option cloudos-bash-job command line option cloudos-job-run command line option cloudos-workflow-import command line option --workflow-url cloudos-workflow-import command line option --workspace-id cloudos-bash-array-job command line option cloudos-bash-job command line option cloudos-cromwell-start command line option cloudos-cromwell-status command line option cloudos-cromwell-stop command line option cloudos-datasets-cp command line option cloudos-datasets-link command line option cloudos-datasets-ls command line option cloudos-datasets-mkdir command line option cloudos-datasets-mv command line option cloudos-datasets-rename command line option cloudos-datasets-rm command line option cloudos-job-abort command line option cloudos-job-clone-resume command line option, [1] cloudos-job-list command line option cloudos-job-logs command line option cloudos-job-results command line option cloudos-job-run command line option cloudos-job-workdir command line option cloudos-project-create command line option cloudos-project-list command line option cloudos-queue-list command line option cloudos-workflow-import command line option cloudos-workflow-list command line option -a cloudos-bash-array-job command line option -c cloudos-bash-array-job command line option cloudos-bash-job command line option cloudos-cromwell-start command line option cloudos-cromwell-status command line option cloudos-cromwell-stop command line option cloudos-datasets-cp command line option cloudos-datasets-link command line option cloudos-datasets-ls command line option cloudos-datasets-mkdir command line option cloudos-datasets-mv command line option cloudos-datasets-rename command line option cloudos-datasets-rm command line option cloudos-job-abort command line option cloudos-job-clone-resume command line option, [1] cloudos-job-details command line option cloudos-job-list command line option cloudos-job-logs command line option cloudos-job-results command line option cloudos-job-run command line option cloudos-job-status command line option cloudos-job-workdir command line option cloudos-procurement-images-ls command line option cloudos-procurement-images-reset command line option cloudos-procurement-images-set command line option cloudos-project-create command line option cloudos-project-list command line option cloudos-queue-list command line option cloudos-workflow-import command line option cloudos-workflow-list command line option -d cloudos-workflow-import command line option -k cloudos-bash-array-job command line option cloudos-bash-job command line option cloudos-cromwell-start command line option cloudos-cromwell-status command line option cloudos-cromwell-stop command line option cloudos-datasets-cp command line option cloudos-datasets-link command line option cloudos-datasets-ls command line option cloudos-datasets-mkdir command line option cloudos-datasets-mv command line option cloudos-datasets-rename command line option cloudos-datasets-rm command line option cloudos-job-abort command line option cloudos-job-clone-resume command line option, [1] cloudos-job-details command line option cloudos-job-list command line option cloudos-job-logs command line option cloudos-job-results command line option cloudos-job-run command line option cloudos-job-status command line option cloudos-job-workdir command line option cloudos-procurement-images-ls command line option cloudos-procurement-images-reset command line option cloudos-procurement-images-set command line option cloudos-project-create command line option cloudos-project-list command line option cloudos-queue-list command line option cloudos-workflow-import command line option cloudos-workflow-list command line option -p cloudos-bash-array-job command line option cloudos-bash-job command line option cloudos-job-clone-resume command line option, [1] cloudos-job-run command line option -t cloudos-cromwell-start command line option cloudos-cromwell-status command line option cloudos-cromwell-stop command line option cloudos-job-run command line option -w cloudos-workflow-import command line option

A

abort_job() (cloudos_cli.clos.Cloudos method) (cloudos_cli.datasets.datasets.Datasets method) (cloudos_cli.jobs.job.Job method) (cloudos_cli.link.link.Link method) (cloudos_cli.procurement.images.Images method) (cloudos_cli.queue.queue.Queue method) AccountNotLinkedException add_note() (cloudos_cli.utils.errors.AccountNotLinkedException method) (cloudos_cli.utils.errors.BadRequestException method) (cloudos_cli.utils.errors.JobAccessDeniedException method) (cloudos_cli.utils.errors.JoBNotCompletedException method) (cloudos_cli.utils.errors.NoCloudForWorkspaceException method) (cloudos_cli.utils.errors.NotAuthorisedException method) (cloudos_cli.utils.errors.TimeOutException method)

apikey (cloudos_cli.clos.Cloudos attribute) (cloudos_cli.datasets.datasets.Datasets attribute) (cloudos_cli.jobs.job.Job attribute) (cloudos_cli.link.link.Link attribute) (cloudos_cli.procurement.images.Images attribute) (cloudos_cli.queue.queue.Queue attribute) args (cloudos_cli.utils.errors.AccountNotLinkedException attribute) (cloudos_cli.utils.errors.BadRequestException attribute) (cloudos_cli.utils.errors.JobAccessDeniedException attribute) (cloudos_cli.utils.errors.JoBNotCompletedException attribute) (cloudos_cli.utils.errors.NoCloudForWorkspaceException attribute) (cloudos_cli.utils.errors.NotAuthorisedException attribute) (cloudos_cli.utils.errors.TimeOutException attribute)

B

BadRequestException

C

check_if_profile_exists() (cloudos_cli.configure.configure.ConfigurationProfile method) check_payload() (cloudos_cli.import_wf.import_wf.ImportWorflow method) (cloudos_cli.import_wf.import_wf.WFImport method) classify_pattern() (in module cloudos_cli.utils.array_job) clone_or_resume_job() (cloudos_cli.jobs.job.Job method) Cloudos (class in cloudos_cli.clos) cloudos command line option --debug --version cloudos-bash-array-job command line option --apikey --array-file --array-file-project --array-parameter --cloudos-url --command --cost-limit --cpus --custom-script-path --custom-script-project --disable-column-check --disable-ssl-verification --do-not-save-logs --execution-platform --instance-disk --instance-type --job-name --job-queue --last --list-columns --lustre-size --memory --parameter --profile --project-name --repository-platform --request-interval --separator --ssl-cert --storage-mode --wait-completion --wait-time --workflow-name --workspace-id -a -c -k -p cloudos-bash-job command line option --apikey --cloudos-url --command --cost-limit --cpus --disable-ssl-verification --do-not-save-logs --execution-platform --instance-disk --instance-type --job-name --job-queue --last --lustre-size --memory --parameter --profile --project-name --repository-platform --request-interval --ssl-cert --storage-mode --wait-completion --wait-time --workflow-name --workspace-id -c -k -p cloudos-configure command line option --make-default --profile cloudos-configure-remove-profile command line option --profile cloudos-cromwell-start command line option --apikey --cloudos-url --cromwell-token --disable-ssl-verification --profile --ssl-cert --verbose --version --wait-time --workspace-id -c -k -t cloudos-cromwell-status command line option --apikey --cloudos-url --cromwell-token --disable-ssl-verification --profile --ssl-cert --verbose --version --workspace-id -c -k -t cloudos-cromwell-stop command line option --apikey --cloudos-url --cromwell-token --disable-ssl-verification --profile --ssl-cert --verbose --version --workspace-id -c -k -t cloudos-datasets-cp command line option --apikey --cloudos-url --destination-project-name --disable-ssl-verification --profile --project-name --ssl-cert --workspace-id -c -k DESTINATION_PATH SOURCE_PATH cloudos-datasets-link command line option --apikey --cloudos-url --disable-ssl-verification --profile --project-name --session-id --ssl-cert --workspace-id -c -k PATH cloudos-datasets-ls command line option --apikey --cloudos-url --details --disable-ssl-verification --profile --project-name --ssl-cert --workspace-id -c -k PATH cloudos-datasets-mkdir command line option --apikey --cloudos-url --disable-ssl-verification --profile --project-name --ssl-cert --workspace-id -c -k NEW_FOLDER_PATH cloudos-datasets-mv command line option --apikey --cloudos-url --destination-project-name --disable-ssl-verification --profile --project-name --ssl-cert --workspace-id -c -k DESTINATION_PATH SOURCE_PATH cloudos-datasets-rename command line option --apikey --cloudos-url --disable-ssl-verification --profile --project-name --ssl-cert --workspace-id -c -k NEW_NAME SOURCE_PATH cloudos-datasets-rm command line option --apikey --cloudos-url --disable-ssl-verification --force --profile --project-name --ssl-cert --workspace-id -c -k TARGET_PATH cloudos-job-abort command line option --apikey --cloudos-url --disable-ssl-verification --job-ids --profile --ssl-cert --verbose --workspace-id -c -k cloudos-job-clone-resume command line option --accelerate-file-staging, [1] --apikey, [1] --cloudos-url, [1] --cost-limit, [1] --disable-ssl-verification, [1] --do-not-save-logs, [1] --git-branch, [1] --instance-type, [1] --job-id, [1] --job-name, [1] --job-queue, [1] --nextflow-profile, [1] --nextflow-version, [1] --parameter, [1] --profile, [1] --project-name, [1] --resumable, [1] --ssl-cert, [1] --verbose, [1] --workspace-id, [1] -c, [1] -k, [1] -p, [1] cloudos-job-details command line option --apikey --cloudos-url --disable-ssl-verification --job-id --output-basename --output-format --parameters --profile --ssl-cert --verbose -c -k cloudos-job-list command line option --all-fields --apikey --archived --cloudos-url --disable-ssl-verification --filter-job-id --filter-job-name --filter-only-mine --filter-owner --filter-project --filter-queue --filter-status --filter-workflow --last --last-n-jobs --output-basename --output-format --page --profile --ssl-cert --verbose --workspace-id -c -k

cloudos-job-logs command line option --apikey --cloudos-url --disable-ssl-verification --job-id --profile --ssl-cert --verbose --workspace-id -c -k cloudos-job-results command line option --apikey --cloudos-url --disable-ssl-verification --job-id --profile --ssl-cert --verbose --workspace-id -c -k cloudos-job-run command line option --accelerate-file-staging --apikey --azure-worker-instance-disk --azure-worker-instance-spot --azure-worker-instance-type --cloudos-url --cost-limit --cromwell-token --disable-ssl-verification --do-not-save-logs --execution-platform --git-branch --git-commit --git-tag --hpc-id --instance-disk --instance-type --job-config --job-name --job-queue --last --lustre-size --nextflow-profile --nextflow-version --parameter --profile --project-name --repository-platform --request-interval --resumable --ssl-cert --storage-mode --use-private-docker-repository --verbose --wait-completion --wait-time --wdl-importsfile --wdl-mainfile --workflow-name --workspace-id -c -k -p -t cloudos-job-status command line option --apikey --cloudos-url --disable-ssl-verification --job-id --profile --ssl-cert --verbose -c -k cloudos-job-workdir command line option --apikey --cloudos-url --disable-ssl-verification --job-id --profile --ssl-cert --verbose --workspace-id -c -k cloudos-procurement-images-ls command line option --apikey --cloudos-url --disable-ssl-verification --limit --page --procurement-id --profile --ssl-cert -c -k cloudos-procurement-images-reset command line option --apikey --cloudos-url --disable-ssl-verification --image-type --organisation-id --procurement-id --profile --provider --region --ssl-cert -c -k cloudos-procurement-images-set command line option --apikey --cloudos-url --disable-ssl-verification --image-id --image-name --image-type --organisation-id --procurement-id --profile --provider --region --ssl-cert -c -k cloudos-project-create command line option --apikey --cloudos-url --disable-ssl-verification --new-project --profile --ssl-cert --verbose --workspace-id -c -k cloudos-project-list command line option --all-fields --apikey --cloudos-url --disable-ssl-verification --output-basename --output-format --page --profile --ssl-cert --verbose --workspace-id -c -k cloudos-queue-list command line option --all-fields --apikey --cloudos-url --disable-ssl-verification --output-basename --output-format --profile --ssl-cert --workspace-id -c -k cloudos-workflow-import command line option --apikey --cloudos-url --cost-limit --disable-ssl-verification --profile --repository-platform --ssl-cert --workflow-description --workflow-docs-link --workflow-name --workflow-url --workspace-id -c -d -k -w cloudos-workflow-list command line option --all-fields --apikey --cloudos-url --disable-ssl-verification --output-basename --output-format --profile --ssl-cert --verbose --workspace-id -c -k cloudos_cli module cloudos_cli._version module cloudos_cli.clos module cloudos_cli.configure module cloudos_cli.configure.configure module cloudos_cli.datasets module cloudos_cli.datasets.datasets module cloudos_cli.import_wf module cloudos_cli.import_wf.import_wf module cloudos_cli.jobs module cloudos_cli.jobs.job module cloudos_cli.link module cloudos_cli.link.link module cloudos_cli.logging module cloudos_cli.logging.logger module cloudos_cli.procurement module cloudos_cli.procurement.images module cloudos_cli.queue module cloudos_cli.queue.queue module cloudos_cli.utils module cloudos_cli.utils.array_job module cloudos_cli.utils.cloud module cloudos_cli.utils.details module cloudos_cli.utils.errors module cloudos_cli.utils.last_wf module cloudos_cli.utils.requests module cloudos_cli.utils.resources module cloudos_url (cloudos_cli.clos.Cloudos attribute) (cloudos_cli.datasets.datasets.Datasets attribute) (cloudos_cli.jobs.job.Job attribute) (cloudos_cli.link.link.Link attribute) (cloudos_cli.procurement.images.Images attribute) (cloudos_cli.queue.queue.Queue attribute) CommandContextFilter (class in cloudos_cli.logging.logger) config_file (cloudos_cli.configure.configure.ConfigurationProfile attribute) ConfigurationProfile (class in cloudos_cli.configure.configure) convert_nextflow_to_json() (cloudos_cli.jobs.job.Job method) converter() (cloudos_cli.logging.logger.LogFormatter method) copy_item() (cloudos_cli.datasets.datasets.Datasets method) create_profile_from_input() (cloudos_cli.configure.configure.ConfigurationProfile method) create_project() (cloudos_cli.clos.Cloudos method) (cloudos_cli.datasets.datasets.Datasets method) (cloudos_cli.jobs.job.Job method) (cloudos_cli.link.link.Link method) (cloudos_cli.procurement.images.Images method) (cloudos_cli.queue.queue.Queue method) create_virtual_folder() (cloudos_cli.datasets.datasets.Datasets method) credentials_file (cloudos_cli.configure.configure.ConfigurationProfile attribute) cromwell_switch() (cloudos_cli.clos.Cloudos method) (cloudos_cli.datasets.datasets.Datasets method) (cloudos_cli.jobs.job.Job method) (cloudos_cli.link.link.Link method) (cloudos_cli.procurement.images.Images method) (cloudos_cli.queue.queue.Queue method) cromwell_token (cloudos_cli.clos.Cloudos attribute) (cloudos_cli.datasets.datasets.Datasets attribute) (cloudos_cli.jobs.job.Job attribute) (cloudos_cli.link.link.Link attribute) (cloudos_cli.procurement.images.Images attribute) (cloudos_cli.queue.queue.Queue attribute)

D

Datasets (class in cloudos_cli.datasets.datasets) default_msec_format (cloudos_cli.logging.logger.LogFormatter attribute) default_time_format (cloudos_cli.logging.logger.LogFormatter attribute) delete_item() (cloudos_cli.datasets.datasets.Datasets method) DESTINATION_PATH cloudos-datasets-cp command line option cloudos-datasets-mv command line option

detect_workflow() (cloudos_cli.clos.Cloudos method) (cloudos_cli.datasets.datasets.Datasets method) (cloudos_cli.jobs.job.Job method) (cloudos_cli.link.link.Link method) (cloudos_cli.procurement.images.Images method) (cloudos_cli.queue.queue.Queue method) determine_default_profile() (cloudos_cli.configure.configure.ConfigurationProfile method) docker_workflow_param_processing() (cloudos_cli.jobs.job.Job method)

E

extract_project() (in module cloudos_cli.utils.array_job)

F

fetch_cloudos_id() (cloudos_cli.jobs.job.Job method) fetch_job_queue_id() (cloudos_cli.queue.queue.Queue method) fetch_project_id() (cloudos_cli.datasets.datasets.Datasets method) filter() (cloudos_cli.logging.logger.CommandContextFilter method) find_cloud() (in module cloudos_cli.utils.cloud)

format() (cloudos_cli.logging.logger.LogFormatter method) format_bytes() (in module cloudos_cli.utils.resources) formatException() (cloudos_cli.logging.logger.LogFormatter method) formatMessage() (cloudos_cli.logging.logger.LogFormatter method) formatStack() (cloudos_cli.logging.logger.LogFormatter method) formatTime() (cloudos_cli.logging.logger.LogFormatter method)

G

generate_datasets_for_project() (in module cloudos_cli.utils.array_job) get_cromwell_status() (cloudos_cli.clos.Cloudos method) (cloudos_cli.datasets.datasets.Datasets method) (cloudos_cli.jobs.job.Job method) (cloudos_cli.link.link.Link method) (cloudos_cli.procurement.images.Images method) (cloudos_cli.queue.queue.Queue method) get_field_from_jobs_endpoint() (cloudos_cli.jobs.job.Job method) get_file_or_folder_id() (in module cloudos_cli.utils.array_job) get_job_list() (cloudos_cli.clos.Cloudos method) (cloudos_cli.datasets.datasets.Datasets method) (cloudos_cli.jobs.job.Job method) (cloudos_cli.link.link.Link method) (cloudos_cli.procurement.images.Images method) (cloudos_cli.queue.queue.Queue method) get_job_logs() (cloudos_cli.clos.Cloudos method) (cloudos_cli.datasets.datasets.Datasets method) (cloudos_cli.jobs.job.Job method) (cloudos_cli.link.link.Link method) (cloudos_cli.procurement.images.Images method) (cloudos_cli.queue.queue.Queue method) get_job_queues() (cloudos_cli.queue.queue.Queue method) get_job_request_payload() (cloudos_cli.jobs.job.Job method) get_job_results() (cloudos_cli.clos.Cloudos method) (cloudos_cli.datasets.datasets.Datasets method) (cloudos_cli.jobs.job.Job method) (cloudos_cli.link.link.Link method) (cloudos_cli.procurement.images.Images method) (cloudos_cli.queue.queue.Queue method) get_job_status() (cloudos_cli.clos.Cloudos method) (cloudos_cli.datasets.datasets.Datasets method) (cloudos_cli.jobs.job.Job method) (cloudos_cli.link.link.Link method) (cloudos_cli.procurement.images.Images method) (cloudos_cli.queue.queue.Queue method) get_job_workdir() (cloudos_cli.clos.Cloudos method) (cloudos_cli.datasets.datasets.Datasets method) (cloudos_cli.jobs.job.Job method) (cloudos_cli.link.link.Link method) (cloudos_cli.procurement.images.Images method) (cloudos_cli.queue.queue.Queue method) get_param_value() (cloudos_cli.configure.configure.ConfigurationProfile static method) get_path() (in module cloudos_cli.utils.details) get_project_id_from_name() (cloudos_cli.clos.Cloudos method) (cloudos_cli.datasets.datasets.Datasets method) (cloudos_cli.jobs.job.Job method) (cloudos_cli.link.link.Link method) (cloudos_cli.procurement.images.Images method) (cloudos_cli.queue.queue.Queue method)

get_project_list() (cloudos_cli.clos.Cloudos method) (cloudos_cli.datasets.datasets.Datasets method) (cloudos_cli.jobs.job.Job method) (cloudos_cli.link.link.Link method) (cloudos_cli.procurement.images.Images method) (cloudos_cli.queue.queue.Queue method) get_repo() (cloudos_cli.import_wf.import_wf.ImportWorflow method) (cloudos_cli.import_wf.import_wf.WFImport method) get_repo_main_file() (cloudos_cli.import_wf.import_wf.ImportWorflow method) (cloudos_cli.import_wf.import_wf.WFImport method) get_storage_contents() (cloudos_cli.clos.Cloudos method) (cloudos_cli.datasets.datasets.Datasets method) (cloudos_cli.jobs.job.Job method) (cloudos_cli.link.link.Link method) (cloudos_cli.procurement.images.Images method) (cloudos_cli.queue.queue.Queue method) get_user_info() (cloudos_cli.clos.Cloudos method) (cloudos_cli.datasets.datasets.Datasets method) (cloudos_cli.jobs.job.Job method) (cloudos_cli.link.link.Link method) (cloudos_cli.procurement.images.Images method) (cloudos_cli.queue.queue.Queue method) get_workflow_content() (cloudos_cli.clos.Cloudos method) (cloudos_cli.datasets.datasets.Datasets method) (cloudos_cli.jobs.job.Job method) (cloudos_cli.link.link.Link method) (cloudos_cli.procurement.images.Images method) (cloudos_cli.queue.queue.Queue method) get_workflow_list() (cloudos_cli.clos.Cloudos method) (cloudos_cli.datasets.datasets.Datasets method) (cloudos_cli.jobs.job.Job method) (cloudos_cli.link.link.Link method) (cloudos_cli.procurement.images.Images method) (cloudos_cli.queue.queue.Queue method) get_workflow_max_pagination() (cloudos_cli.clos.Cloudos method) (cloudos_cli.datasets.datasets.Datasets method) (cloudos_cli.jobs.job.Job method) (cloudos_cli.link.link.Link method) (cloudos_cli.procurement.images.Images method) (cloudos_cli.queue.queue.Queue method)

I

Images (class in cloudos_cli.procurement.images) import_workflow() (cloudos_cli.import_wf.import_wf.ImportWorflow method) (cloudos_cli.import_wf.import_wf.WFImport method) importsfile (cloudos_cli.jobs.job.Job attribute) ImportWorflow (class in cloudos_cli.import_wf.import_wf) is_glob_pattern() (in module cloudos_cli.utils.array_job) is_module() (cloudos_cli.clos.Cloudos method) (cloudos_cli.datasets.datasets.Datasets method) (cloudos_cli.jobs.job.Job method) (cloudos_cli.link.link.Link method) (cloudos_cli.procurement.images.Images method) (cloudos_cli.queue.queue.Queue method)

is_probably_regex() (in module cloudos_cli.utils.array_job) is_valid_regex() (in module cloudos_cli.utils.array_job)

J

Job (class in cloudos_cli.jobs.job)

JobAccessDeniedException JoBNotCompletedException

L

last (cloudos_cli.jobs.job.Job attribute) limit (cloudos_cli.procurement.images.Images attribute) Link (class in cloudos_cli.link.link) link_folder() (cloudos_cli.link.link.Link method) list_azure_container_content() (cloudos_cli.datasets.datasets.Datasets method) list_datasets_content() (cloudos_cli.datasets.datasets.Datasets method) list_folder_content() (cloudos_cli.datasets.datasets.Datasets method)

list_procurement_images() (cloudos_cli.procurement.images.Images method) list_profiles() (cloudos_cli.configure.configure.ConfigurationProfile method) list_project_content() (cloudos_cli.datasets.datasets.Datasets method) list_s3_folder_content() (cloudos_cli.datasets.datasets.Datasets method) list_virtual_folder_content() (cloudos_cli.datasets.datasets.Datasets method) load_profile() (cloudos_cli.configure.configure.ConfigurationProfile method) load_profile_and_validate_data() (cloudos_cli.configure.configure.ConfigurationProfile method) LogFormatter (class in cloudos_cli.logging.logger)

M

mainfile (cloudos_cli.jobs.job.Job attribute) make_default_profile() (cloudos_cli.configure.configure.ConfigurationProfile method) module cloudos_cli cloudos_cli._version cloudos_cli.clos cloudos_cli.configure cloudos_cli.configure.configure cloudos_cli.datasets cloudos_cli.datasets.datasets cloudos_cli.import_wf cloudos_cli.import_wf.import_wf cloudos_cli.jobs cloudos_cli.jobs.job cloudos_cli.link cloudos_cli.link.link cloudos_cli.logging cloudos_cli.logging.logger cloudos_cli.procurement cloudos_cli.procurement.images cloudos_cli.queue cloudos_cli.queue.queue cloudos_cli.utils cloudos_cli.utils.array_job cloudos_cli.utils.cloud cloudos_cli.utils.details cloudos_cli.utils.errors cloudos_cli.utils.last_wf cloudos_cli.utils.requests cloudos_cli.utils.resources

move_files_and_folders() (cloudos_cli.datasets.datasets.Datasets method)

N

NEW_FOLDER_PATH cloudos-datasets-mkdir command line option NEW_NAME cloudos-datasets-rename command line option

NoCloudForWorkspaceException NotAuthorisedException

P

page (cloudos_cli.procurement.images.Images attribute) parse_file_explorer_path() (cloudos_cli.link.link.Link method) parse_s3_path() (cloudos_cli.link.link.Link method) PATH cloudos-datasets-link command line option cloudos-datasets-ls command line option process_job_list() (cloudos_cli.clos.Cloudos static method) (cloudos_cli.datasets.datasets.Datasets static method) (cloudos_cli.jobs.job.Job static method) (cloudos_cli.link.link.Link static method) (cloudos_cli.procurement.images.Images static method) (cloudos_cli.queue.queue.Queue static method) process_project_list() (cloudos_cli.clos.Cloudos static method) (cloudos_cli.datasets.datasets.Datasets static method) (cloudos_cli.jobs.job.Job static method) (cloudos_cli.link.link.Link static method) (cloudos_cli.procurement.images.Images static method) (cloudos_cli.queue.queue.Queue static method)

process_queue_list() (cloudos_cli.queue.queue.Queue static method) process_workflow_list() (cloudos_cli.clos.Cloudos static method) (cloudos_cli.datasets.datasets.Datasets static method) (cloudos_cli.jobs.job.Job static method) (cloudos_cli.link.link.Link static method) (cloudos_cli.procurement.images.Images static method) (cloudos_cli.queue.queue.Queue static method) procurement_id (cloudos_cli.procurement.images.Images attribute) project_id (cloudos_cli.datasets.datasets.Datasets property) (cloudos_cli.jobs.job.Job property) project_name (cloudos_cli.datasets.datasets.Datasets attribute) (cloudos_cli.jobs.job.Job attribute) (cloudos_cli.link.link.Link attribute)

Q

Queue (class in cloudos_cli.queue.queue)

R

remove_profile() (cloudos_cli.configure.configure.ConfigurationProfile method) rename_item() (cloudos_cli.datasets.datasets.Datasets method) reorder_job_list() (cloudos_cli.clos.Cloudos method) (cloudos_cli.datasets.datasets.Datasets method) (cloudos_cli.jobs.job.Job method) (cloudos_cli.link.link.Link method) (cloudos_cli.procurement.images.Images method) (cloudos_cli.queue.queue.Queue method) repository_platform (cloudos_cli.jobs.job.Job attribute) reset_procurement_organisation_image() (cloudos_cli.procurement.images.Images method)

resolve_user_id() (cloudos_cli.clos.Cloudos method) (cloudos_cli.datasets.datasets.Datasets method) (cloudos_cli.jobs.job.Job method) (cloudos_cli.link.link.Link method) (cloudos_cli.procurement.images.Images method) (cloudos_cli.queue.queue.Queue method) retrieve_cols_from_array_file() (cloudos_cli.jobs.job.Job method) retry_requests_delete() (in module cloudos_cli.utils.requests) retry_requests_get() (in module cloudos_cli.utils.requests) retry_requests_post() (in module cloudos_cli.utils.requests) retry_requests_put() (in module cloudos_cli.utils.requests)

S

save_job_list_to_csv() (cloudos_cli.clos.Cloudos method) (cloudos_cli.datasets.datasets.Datasets method) (cloudos_cli.jobs.job.Job method) (cloudos_cli.link.link.Link method) (cloudos_cli.procurement.images.Images method) (cloudos_cli.queue.queue.Queue method) send_job() (cloudos_cli.jobs.job.Job method) set_from_click_ctx() (cloudos_cli.logging.logger.CommandContextFilter method) set_procurement_organisation_image() (cloudos_cli.procurement.images.Images method)

set_seed_from_argv() (cloudos_cli.logging.logger.CommandContextFilter method) setup_logging() (in module cloudos_cli.logging.logger) setup_params_array_file() (cloudos_cli.jobs.job.Job method) SOURCE_PATH cloudos-datasets-cp command line option cloudos-datasets-mv command line option cloudos-datasets-rename command line option split_array_file_params() (cloudos_cli.jobs.job.Job static method) ssl_selector() (in module cloudos_cli.utils.resources)

T

TARGET_PATH cloudos-datasets-rm command line option

TimeOutException

U

update_command_context_from_click() (in module cloudos_cli.logging.logger)

update_parameter_value() (cloudos_cli.jobs.job.Job method) usesTime() (cloudos_cli.logging.logger.LogFormatter method)

V

verify (cloudos_cli.datasets.datasets.Datasets attribute) (cloudos_cli.jobs.job.Job attribute) (cloudos_cli.link.link.Link attribute) (cloudos_cli.procurement.images.Images attribute) (cloudos_cli.queue.queue.Queue attribute)

W

wait_job_completion() (cloudos_cli.clos.Cloudos method) (cloudos_cli.datasets.datasets.Datasets method) (cloudos_cli.jobs.job.Job method) (cloudos_cli.link.link.Link method) (cloudos_cli.procurement.images.Images method) (cloudos_cli.queue.queue.Queue method) WFImport (class in cloudos_cli.import_wf.import_wf) with_traceback() (cloudos_cli.utils.errors.AccountNotLinkedException method) (cloudos_cli.utils.errors.BadRequestException method) (cloudos_cli.utils.errors.JobAccessDeniedException method) (cloudos_cli.utils.errors.JoBNotCompletedException method) (cloudos_cli.utils.errors.NoCloudForWorkspaceException method) (cloudos_cli.utils.errors.NotAuthorisedException method) (cloudos_cli.utils.errors.TimeOutException method) workflow_content_query() (cloudos_cli.clos.Cloudos method) (cloudos_cli.datasets.datasets.Datasets method) (cloudos_cli.jobs.job.Job method) (cloudos_cli.link.link.Link method) (cloudos_cli.procurement.images.Images method) (cloudos_cli.queue.queue.Queue method)

workflow_id (cloudos_cli.jobs.job.Job property) workflow_import() (cloudos_cli.clos.Cloudos method) (cloudos_cli.datasets.datasets.Datasets method) (cloudos_cli.jobs.job.Job method) (cloudos_cli.link.link.Link method) (cloudos_cli.procurement.images.Images method) (cloudos_cli.queue.queue.Queue method) workflow_name (cloudos_cli.jobs.job.Job attribute) workspace_id (cloudos_cli.datasets.datasets.Datasets attribute) (cloudos_cli.jobs.job.Job attribute) (cloudos_cli.link.link.Link attribute) (cloudos_cli.queue.queue.Queue attribute)

Y

youngest_workflow_id_by_name() (in module cloudos_cli.utils.last_wf)