import json
import typing
import argparse
from datetime import datetime
from typing import Any, Tuple, List, Dict
from firecloud import fiss
from terra_notebook_utils import workflows
from terra_notebook_utils.cli import Config, dispatch
workflow_cli = dispatch.group("workflows", help=workflows.__doc__)
workspace_args: Dict[str, Dict[str, Any]] = {
"--workspace": dict(
type=str,
default=None,
help="workspace name. If not provided, the configured CLI workspace will be used"
),
"--workspace-namespace": dict(
type=str,
required=False,
default=Config.info['workspace_namespace'],
help=("The billing project for GS requests. "
"If omitted, the CLI configured `workspace_namespace` will be used. "
"Note that DRS URLs also involve a GS request.")
)
}
@workflow_cli.command("list-submissions", arguments={**workspace_args})
import json
import argparse
from terra_notebook_utils import vcf, WORKSPACE_GOOGLE_PROJECT
from terra_notebook_utils.cli import dispatch
from terra_notebook_utils.drs import blob_for_url
vcf_cli = dispatch.group(
"vcf",
help=vcf.__doc__,
arguments={
"path":
dict(help="local path, gs://, or drs://"),
"--billing-project":
dict(type=str,
required=False,
default=WORKSPACE_GOOGLE_PROJECT,
help=("The billing project for GS requests. "
"If omitted, the environment variables GOOGLE_PROJECT, "
"GCP_PROJECT, AND GCLOUD_PROJECT will be in that order.")),
})
@vcf_cli.command("head")
def head(args: argparse.Namespace):
"""
Output VCF header.
"""
blob = blob_for_url(args.path, args.billing_project)
info = vcf.VCFInfo.with_blob(blob)
info.print_header()
import argparse
from terra_notebook_utils import vcf
from terra_notebook_utils.cli import dispatch, Config
import google.cloud.storage.blob
vcf_cli = dispatch.group("vcf", help=vcf.__doc__, arguments={
"path": dict(
help="local path, gs://, or drs://"
),
"--workspace": dict(
type=str,
default=None,
help="Workspace name. If not provided, the configured CLI workspace will be used."
),
"--workspace-namespace": dict(
type=str,
required=False,
default=Config.info['workspace_namespace'],
help=("The billing project for GS requests. "
"If omitted, the CLI configured `workspace_google_project` will be used. "
"Note that DRS URLs also involve a GS request.")
),
})
@vcf_cli.command("head")
def head(args: argparse.Namespace):
"""
Output VCF header.
"""
import json
import typing
import argparse
from firecloud import fiss
from terra_notebook_utils import workspace
from terra_notebook_utils.cli import Config, dispatch
workspace_cli = dispatch.group("workspace", help=workspace.__doc__)
@workspace_cli.command("list")
def list_workspaces(args: argparse.Namespace):
"""
List workspaces available to the current usuer
"""
list_workspaces.__doc__ = workspace.list_workspaces.__doc__
data = workspace.list_workspaces()
info_keys = ["name", "createdBy", "bucketName", "namespace"]
workspaces = [{key: ws['workspace'][key] for key in info_keys}
for ws in data]
print(json.dumps(workspaces, indent=2))
@workspace_cli.command("get", arguments={
"--workspace": dict(type=str, required=True, help="workspace name"),
"--workspace-namespace": dict(type=str, required=False, default=None, help="workspace namespace"),
})
def get_workspace(args: argparse.Namespace):
"""
import json
import argparse
from uuid import uuid4
from terra_notebook_utils import table as tnu_table
from terra_notebook_utils.cli import dispatch, CLIConfig
table_cli = dispatch.group("table", help=tnu_table.__doc__, arguments={
"--workspace": dict(
type=str,
default=None,
help="workspace name. If not provided, the configured CLI workspace will be used"
),
"--workspace-namespace": dict(
type=str,
default=None,
help=("The workspace namespace represents the parent containing the workspace "
"(the Terra billing project) "
"If omitted, the CLI configured `workspace_namespace` will be used. ")
),
})
@table_cli.command("list")
def list_tables(args: argparse.Namespace):
"""
List all tables in the workspace
"""
args.workspace, args.workspace_namespace = CLIConfig.resolve(args.workspace, args.workspace_namespace)
for table in tnu_table.list_tables(args.workspace, args.workspace_namespace):
print(table)
"""
Configure the CLI
"""
import typing
import argparse
from terra_notebook_utils.cli import Config, dispatch
config_cli = dispatch.group("config", help=__doc__)
@config_cli.command("set-workspace", arguments={"workspace": dict()})
def set_config_workspace(args: argparse.Namespace):
"""
Set workspace for cli commands
"""
Config.info["workspace"] = args.workspace
Config.write()
@config_cli.command("set-workspace-namespace",
arguments={"workspace_namespace": dict(type=str)})
def set_config_workspace_namespace(args: argparse.Namespace):
"""
Set workspace namespace for cli commands
"""
Config.info["workspace_namespace"] = args.workspace_namespace
Config.write()
@config_cli.command("print")
