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"""CLI experiment command and sub-commands."""
import json
import os
import shutil
import zipfile
from pathlib import Path
from typing import List, Optional
import requests
import typer
from rich import print # pylint:disable=redefined-builtin
from rich.console import Console
from rich.table import Table
from typing_extensions import Annotated
from folding_studio.config import API_URL, REQUEST_TIMEOUT
from folding_studio.utils.headers import get_auth_headers
app = typer.Typer(
no_args_is_help=True,
help=(
"Get experiment information and metadata, like its status, "
"results or the generated features (msa, templates, etc.).\n"
"Read more at https://int-bio-foldingstudio-gcp.nw.r.appspot.com/how-to-guides/af2_openfold/fetch_folding_job_status/."
),
)
experiment_ID_argument = typer.Argument(help="ID of the experiment.")
def _download_file_from_signed_url(
exp_id: str,
endpoint: str,
output: Path,
force: bool,
unzip: bool = False,
) -> None:
"""Download a zip file from an experiment id.
Args:
exp_id (str): Experiment id.
endpoint (str): API endpoint to call.
output (Path): Output file path.
force (bool): Force file writing if it already exists.
unzip (bool): Unzip the zip file after downloading.
Raises:
typer.Exit: If output file path exists but force set to false.
typer.Exit: If unzip set to true but the directory already exists and force set to false.
typer.Exit: If an error occurred during the initial API call.
"""
if output.exists() and not force:
print(
f"Warning: The file '{output}' already exists. Use the --force flag to overwrite it."
)
raise typer.Exit(code=1)
if unzip:
if not output.suffix == ".zip":
print(
"Error: The downloaded file is not a .zip file. Please ensure the correct file format."
)
raise typer.Exit(code=1)
dir_path = output.with_suffix("")
if dir_path.exists() and not force:
print(
f"Warning: The --unzip flag is raised but the directory '{dir_path}' "
"already exists. Use the --force flag to overwrite it."
)
raise typer.Exit(code=1)
headers = get_auth_headers()
url = API_URL + endpoint
response = requests.get(
url,
params={"experiment_id": exp_id},
headers=headers,
timeout=REQUEST_TIMEOUT,
)
if not response.ok:
print(f"Failed to download the file: {response.content.decode()}.")
raise typer.Exit(code=1)
file_response = requests.get(
response.json()["signed_url"],
stream=True,
timeout=REQUEST_TIMEOUT,
)
with output.open("wb") as f:
file_response.raw.decode_content = True
shutil.copyfileobj(file_response.raw, f)
print(f"File downloaded successfully to {output}.")
if unzip:
dir_path.mkdir(parents=True, exist_ok=True)
with zipfile.ZipFile(output, "r") as zip_ref:
zip_ref.extractall(dir_path)
print(f"Extracted all files to {dir_path}.")
@app.command()
def status(
exp_id: Annotated[str, experiment_ID_argument],
):
"""Get an experiment status."""
headers = get_auth_headers()
url = API_URL + "getExperimentStatus"
response = requests.get(
url,
params={"experiment_id": exp_id},
headers=headers,
timeout=REQUEST_TIMEOUT,
)
if not response.ok:
print(f"An error occurred : {response.content.decode()}")
raise typer.Exit(code=1)
message = response.json()
print(message["status"])
@app.command()
def list(
limit: Annotated[
int,
typer.Option(
help=("Max number of experiment to display in the terminal."),
),
] = 100,
output: Annotated[
Optional[Path],
typer.Option(
"--output",
"-o",
help=(
"Path to the file where the job metadata returned by the server are written."
),
),
] = None,
): # pylint:disable=redefined-builtin
"""Get all your done and pending experiment ids. The IDs are provided in the order of submission, starting with the most recent."""
headers = get_auth_headers()
url = API_URL + "getDoneAndPendingExperiments"
response = requests.get(
url,
headers=headers,
timeout=REQUEST_TIMEOUT,
)
if not response.ok:
print(f"An error occurred : {response.content.decode()}")
raise typer.Exit(code=1)
response_json = response.json()
if output:
with open(output, "w") as f:
json.dump(response_json, f, indent=4)
print(f"Done and pending experiments list written to [bold]{output}[/bold]")
table = Table(title="Done and pending experiments")
table.add_column("Experiment ID", justify="right", style="cyan", no_wrap=True)
table.add_column("Status", style="magenta")
total_exp_nb = 0
for status, exp_list in response_json.items():
total_exp_nb += len(exp_list)
for exp in exp_list:
table.add_row(exp, status)
if limit < total_exp_nb:
print(
f"The table below is truncated to the last [bold]{limit}[/bold] submitted experiments. Increase '--limit' to see more."
)
if not output:
print("Use '--output' to get the full list in file format.")
else:
print(f"See the full list in file format at [bold]{output}[/bold]")
break
console = Console()
console.print(table)
@app.command()
def features(
exp_id: Annotated[str, experiment_ID_argument],
output: Annotated[
Optional[Path],
typer.Option(
help="Local path to download the zip to. Default to '<exp_id>_features.zip'."
),
] = None,
force: Annotated[
bool,
typer.Option(
help=(
"Forces the download to overwrite any existing file "
"with the same name in the specified location."
)
),
] = False,
unzip: Annotated[
bool, typer.Option(help="Automatically unzip the file after its download.")
] = False,
):
"""Get an experiment features."""
if output is None:
output = Path(f"{exp_id}_features.zip")
_download_file_from_signed_url(
exp_id=exp_id,
endpoint="getZippedExperimentFeatures",
output=output,
force=force,
unzip=unzip,
)
@app.command()
def results(
exp_id: Annotated[str, experiment_ID_argument],
output: Annotated[
Optional[Path],
typer.Option(
help="Local path to download the zip to. Default to '<exp_id>_results.zip'."
),
] = None,
force: Annotated[
bool,
typer.Option(
help=(
"Forces the download to overwrite any existing file "
"with the same name in the specified location."
)
),
] = False,
unzip: Annotated[
bool, typer.Option(help="Automatically unzip the file after its download.")
] = False,
):
"""Get an experiment results."""
if output is None:
output = Path(f"{exp_id}_results.zip")
_download_file_from_signed_url(
exp_id=exp_id,
endpoint="getZippedExperimentResults",
output=output,
force=force,
unzip=unzip,
)
@app.command()
def cancel(
exp_id: Annotated[List[str], experiment_ID_argument],
):
"""Cancel experiments job executions.
You can pass one or more experiment id
"""
headers = get_auth_headers()
url = API_URL + "cancelJob"
response = requests.post(
url,
data={"experiment_ids": exp_id},
headers=headers,
timeout=REQUEST_TIMEOUT,
)
if not response.ok:
print(f"An error occurred : {response.content.decode()}")
raise typer.Exit(code=1)
message = response.json()
print(message)
@app.command()
def logs(
exp_id: Annotated[str, experiment_ID_argument],
output: Annotated[
Optional[Path],
typer.Option(
help="Local path to download the logs to. Default to '<exp_id>_logs.txt'."
),
] = None,
force: Annotated[
bool,
typer.Option(
help=(
"Forces the download to overwrite any existing file "
"with the same name in the specified location."
)
),
] = False,
):
"""Get an experiment logs."""
if output is None:
output = Path(f"{exp_id}_logs.txt")
_download_file_from_signed_url(
exp_id=exp_id,
endpoint="getExperimentLogs",
output=output,
force=force,
)
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