"""
endpoint = endpoint_from_token(api_key["api_key"])
# attempt to get a token from Fence
- auth_url = "{}/user/credentials/cdis/access_token".format(endpoint)
+ auth_url = "{}/user/credentials/api/access_token".format(endpoint)
resp = requests.post(auth_url, json=api_key)
token_key = "access_token"
return _handle_access_token_response(resp, token_key)
@@ -486,6 +486,19 @@ Source code for gen3.auth
return self._access_token
+
+[docs]
+ def get_api_key(self):
+ """
+ Returns the actual API key loaded, or None if the loaded credentials
+ do not contain one (for example a raw access token).
+ """
+ if not self._refresh_token:
+ return None
+
+ return self._refresh_token.get("api_key")
+
+
def _get_auth_value(self):
"""Returns the Authorization header value for the request
diff --git a/docs/_build/html/auth.html b/docs/_build/html/auth.html
index ccccddc25..df6616189 100644
--- a/docs/_build/html/auth.html
+++ b/docs/_build/html/auth.html
@@ -124,6 +124,13 @@ Gen3 Auth Helper
+
+get_api_key()[source]¶
+Returns the actual API key loaded, or None if the loaded credentials
+do not contain one (for example a raw access token).
+Gen3Auth.curl()Gen3Auth.get_access_token()Gen3Auth.get_access_token_from_wts()Gen3Auth.get_api_key()Gen3Auth.refresh_access_token()G
get_aliases() (gen3.metadata.Gen3Metadata method)
get_all_records() (gen3.index.Gen3Index method)
+
+ get_api_key() (gen3.auth.Gen3Auth method)
get_dictionary_all() (gen3.submission.Gen3Submission method)
diff --git a/docs/_build/html/index.html b/docs/_build/html/index.html
index d329e8bcb..8137650a4 100644
--- a/docs/_build/html/index.html
+++ b/docs/_build/html/index.html
@@ -43,6 +43,7 @@ Welcome to Gen3 SDK’s documentation!Gen3Auth.curl()
Gen3Auth.get_access_token()Gen3Auth.get_access_token_from_wts()Gen3Auth.get_api_key()Gen3Auth.refresh_access_token()`. On the S3 route it does not: Gen3's S3 endpoint
+reads the task token out of the SigV4 `Credential=/...` field of the header
+Nextflow signed, so that header is forwarded untouched and the proof travels in `DPoP`
+alone.
+
+Nothing else is proxied. Any other path — and any path that uses `..` to climb out of the
+prefix it matched — gets a local `404` and is never sent anywhere. Everything the proxy
+does forward carries the task token, so an unrecognized path is refused rather than
+guessed at.
+
+## Prerequisites
+
+- The SDK with the `dpop` extra: `pip install 'gen3[dpop]'`
+- `nextflow` on your `PATH`
+- Gen3 credentials — an API key at `~/.gen3/credentials.json` (see
+ [the CLI guide](howto/cli.md) for the other forms `--auth` accepts)
+
+## Configuring your pipeline
+
+Keep the config you already use with Gen3 Workflow — the one that points straight at your
+commons. `gen3 nextflow run` does not edit it. It writes a small override to a temporary
+file and passes it as the last `-c`, and Nextflow merges `-c` files over the existing
+config rather than replacing them, so only the keys the proxy forces change. A normal
+`nextflow.config`:
+
+```groovy
+plugins {
+ id 'nf-ga4gh'
+}
+process {
+ executor = 'tes'
+ container = 'quay.io/nextflow/bash'
+}
+tes {
+ endpoint = 'https:///ga4gh/tes'
+ oauthToken = env('GEN3_TOKEN')
+ timeout = 60
+}
+aws {
+ accessKey = env('GEN3_TOKEN')
+ secretKey = 'N/A' # pragma: allowlist secret
+ region = 'us-east-1'
+ client {
+ endpoint = 'https:///workflows/s3'
+ s3PathStyleAccess = true
+ maxErrorRetry = 1
+ }
+}
+// As reported by GET https:///workflows/storage/setup
+workDir = 's3:///'
+```
+
+Run that with `gen3 nextflow run main.nf` and the generated override changes five keys:
+`tes.endpoint` and `aws.client.endpoint` become the local proxy, `tes.oauthToken` and
+`aws.accessKey` become the task token, and `aws.client.s3PathStyleAccess` is forced on.
+`workDir`, `region`, `timeout`, `maxErrorRetry`, `plugins` and `process` are yours and are
+left as they are. `gen3 -vv nextflow run` logs the generated file's contents; `nextflow -c config` prints the merged result.
+
+Two details explain why those five:
+
+- **`accessKey` has to be the task token, and `secretKey` is unused.** Gen3's S3 endpoint
+ reads the token out of the SigV4 `Credential=/...` field of the header Nextflow
+ signs. The signature itself is never verified — Gen3 re-signs with its own AWS
+ credentials — which is why `secretKey` can be any non-empty string.
+- **Path-style S3 access is required.** Gen3's S3 endpoint reads the bucket name from the
+ first segment of the request path, and refuses a request whose first segment is not your
+ own bucket. Virtual-host-style addressing puts the bucket in the `Host` header instead,
+ which the proxy has to overwrite with the upstream host — leaving the endpoint to read a
+ key prefix as the bucket name and answer `403`.
+
+### Wiring it up yourself
+
+`--no-generated-config` suppresses the override, at which point your config has to reach
+the proxy on its own using the two environment variables:
+
+```groovy
+tes {
+ endpoint = "http://127.0.0.1:${env('GEN3_DPOP_PROXY_PORT')}/ga4gh/tes"
+ oauthToken = env('GEN3_DPOP_BOUND_TASK_TOKEN')
+}
+aws {
+ accessKey = env('GEN3_DPOP_BOUND_TASK_TOKEN')
+ secretKey = 'N/A' # pragma: allowlist secret
+ client {
+ endpoint = "http://127.0.0.1:${env('GEN3_DPOP_PROXY_PORT')}/s3"
+ s3PathStyleAccess = true
+ }
+}
+```
+
+Two things to watch for when writing it by hand:
+
+- **The S3 endpoint must include `/s3`.** The proxy routes only `/ga4gh/tes` and `/s3`;
+ pointing the S3 client at the proxy root gets a `404` for every object request.
+- **Do not use `def` in a Nextflow config.** The parser rejects variable declarations
+ alongside config statements (`Variable declarations cannot be mixed with config
+ statements`), so interpolate the port inline in each endpoint as above. `env()` and
+ `System.getenv()` both work.
+
+## Running a pipeline
+
+```bash
+# Basic run (add -v for INFO logs, -vv for DEBUG)
+gen3 -v nextflow run main.nf
+
+# Nextflow's own flags pass straight through
+gen3 -v nextflow run main.nf -profile gen3 -resume
+
+# Ask for a specific task token lifetime, in seconds
+gen3 -v nextflow run main.nf --task-token-expiration 3600
+
+# Override the proxy's own settings (same options as `gen3 dpop proxy start`)
+gen3 -v nextflow run main.nf --port 8000 \
+ --tes-endpoint https://gen3.example.com/ga4gh/tes \
+ --s3-endpoint https://gen3.example.com/workflows/s3
+```
+
+The command exits with Nextflow's exit code, so it can be used in scripts and CI.
+
+Every flag `gen3 nextflow run` does not recognize is forwarded to `nextflow run`, so
+Nextflow's own options and your pipeline's params work as usual. The one exception is a
+pipeline param that happens to share a name with an option in `gen3 nextflow run --help`
+(`--port` is the plausible one) — put `--` before it and everything after is handed to
+Nextflow untouched:
+
+```bash
+gen3 -v nextflow run main.nf -- --port 8080
+```
+
+## Running the proxy on its own
+
+Useful for debugging, or for driving several Nextflow commands against one proxy:
+
+```bash
+# Prints the port it bound to; Ctrl+C to stop
+gen3 -v dpop proxy start
+
+# Pin the port, and/or override discovery of the endpoints
+gen3 -v dpop proxy start --port 8000 \
+ --tes-endpoint https://gen3.example.com/ga4gh/tes \
+ --s3-endpoint https://gen3.example.com/workflows/s3
+```
+
+Full option list: `gen3 dpop proxy start --help`. Note that this command only starts the
+proxy — it does not export `GEN3_DPOP_PROXY_PORT` or `GEN3_DPOP_BOUND_TASK_TOKEN` into
+your shell, so a plain `nextflow run` afterwards has to be given the port some other way.
+The simplest is to set the port yourself before starting the proxy, since both sides read
+the same variable:
+
+```bash
+export GEN3_DPOP_PROXY_PORT=8000
+gen3 -v dpop proxy start # binds 8000
+nextflow run main.nf # config reads 8000 from the environment
+```
+
+The task token still has to be supplied separately; only the port is shared this way.
+
+## Using it from Python
+
+```python
+from gen3.auth import Gen3Auth
+from gen3.dpop import dpop_proxy_context
+
+auth = Gen3Auth()
+
+with dpop_proxy_context(auth=auth) as (task_token, proxy_port):
+ # Anything sent to 127.0.0.1:{proxy_port} is signed and forwarded.
+ ...
+```
+
+`gen3.dpop_nextflow.run_gen3_nextflow()` is the same thing plus the `nextflow run` child
+process.
+
+## Security properties
+
+- **The private key never leaves the process.** It is generated in memory per run and is
+ never written to disk.
+- **Proofs are per-request.** Each proxied request gets a fresh proof with a unique
+ `jti`, bound to the request's method (`htm`) and URL (`htu`) and to the task token
+ (`ath`).
+- **Nonces are server-driven.** When a server answers with `use_dpop_nonce`, the proxy
+ caches the nonce from the `DPoP-Nonce` response header, re-signs, and retries — up to
+ two retries per request. It does not manage nonce lifetimes itself; the server decides
+ when a nonce is stale.
+- **Task tokens are scoped.** `--task-token-type` (default `WORKFLOW`) asks Gen3 for a
+ token limited to that purpose.
+- **The proxy only serves the task token holder.** It listens on `127.0.0.1`, which is
+ not a boundary on its own: every process on the host can connect to that port, and so
+ can a page open in your browser. So the proxy requires each request to present the task
+ token, the way Nextflow already does - as the TES `oauthToken` and as the S3 access key
+ ID - and refuses anything else with a 401 before it routes the request. The token is
+ passed to Nextflow in `GEN3_DPOP_BOUND_TASK_TOKEN`, so it is readable by other processes
+ running as *you*; it is not readable by other users, and a drive-by request from a
+ browser cannot guess it.
+- **Only TES and S3 are proxied.** `/ga4gh/tes` and `/s3` are the only paths forwarded,
+ and only to the commons that issued your credentials, so the task token is never sent
+ to another host.
+
+Two limits worth knowing about:
+
+- **The task token is not renewed.** It is fetched once at startup. A pipeline that runs
+ longer than the token's lifetime will start seeing 401s; use `--task-token-expiration`
+ to request a lifetime that covers the run.
+- **The task token cannot outlive your API key.** Gen3 refuses to issue one that would,
+ so `--task-token-expiration` is capped by whatever is left of the API key. For a long
+ pipeline, download a fresh API key first. The SDK checks this before it makes the
+ request and tells you the maximum you can ask for.
+
+## Troubleshooting
+
+Every failure below is reported as an `Error: ...` line, not a traceback. A traceback
+means an SDK bug — please file it. A missing `nextflow` binary also logs an `ERROR` line
+above it explaining the fix.
+
+| Symptom | What it means |
+| ---------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------- |
+| `Requested a task token lifetime of N seconds, but your API key expires in ...` | `--task-token-expiration` exceeds what is left of your API key. Ask for the stated maximum, or download a new API key. |
+| `Your API key expired at ...` | Download a new API key from the Gen3 profile page. |
+| `Could not get a WORKFLOW task token from ...: [400] ...` | Gen3 rejected the exchange. The text after the status code comes straight from Gen3 and is the actual reason. |
+| `Could not find an API key for the DPoP token exchange.` | No API key was found. Check `~/.gen3/credentials.json` or pass `--auth`. |
+| `No Gen3 endpoint is configured.` | The credentials do not name a commons. Download a fresh API key. |
+| `--tes-endpoint ... is not on - the commons that issued your credentials.` | An endpoint override points at a different host than your API key. Gen3 serves TES and S3 from the same host as the commons, and the task token is only valid there, so the proxy refuses to start rather than send it elsewhere. |
+| `Something is already listening on 127.0.0.1:PORT` | Another proxy (or anything else) holds that port. Drop `--port` to get a free one automatically. |
+| `Server did not provide a nonce in DPoP-Nonce header.` (HTTP 502) | The server demanded a nonce but sent none. It is a server-side bug; check the Gen3 deployment's DPoP configuration. |
+| `502 Upstream request failed` | The proxy could not reach the TES or S3 endpoint. Verify the endpoints with `--tes-endpoint` / `--s3-endpoint`. |
+| `504 Upstream timeout` | No progress from the upstream for five minutes, or no connection within 30 seconds. |
+| Repeated `401` from TES or S3 | Check the `WWW-Authenticate` value the proxy logs with each rejection: `invalid_token` usually means an expired task token, `invalid_dpop_proof` a proof the server would not accept. |
+| Nextflow talks to the commons directly instead of the proxy | With `--no-generated-config` the config has to point at the proxy itself; see [Wiring it up yourself](#wiring-it-up-yourself). Otherwise run with `-vv` and check the generated override — a later `-c` on your own command line would win over it. |
+| `404 Not Found` from the proxy on every object request | `aws.client.endpoint` is missing the `/s3` suffix. The proxy routes only `/ga4gh/tes` and `/s3`. See [Wiring it up yourself](#wiring-it-up-yourself). |
+| `Bucket misconfigured. Hit the `GET /storage/setup` endpoint and try again.` (400 on the first upload) | Your workflow bucket and its encryption key have not been provisioned yet. Call `GET {commons}/workflows/storage/setup` once, then rerun. The SDK does not call it for you, because it creates cloud resources. |
+| `... (bucket '...') not allowed. You can make calls to your personal bucket, '...'` (403) | The first path segment of the S3 request is not your bucket. Either `workDir` names the wrong bucket — the setup endpoint above reports the right one — or `aws.client.s3PathStyleAccess` is not `true`. |
+| `Could not find `nextflow` on your PATH.` (with `Error: [Errno 2] ...` after it) | Install Nextflow, or run `gen3 dpop proxy start` and drive Nextflow yourself. |
+| `The DPoP proxy needs uvicorn` | Install the extra: `pip install 'gen3[dpop]'`. |
+
+To see more, run with `-vv`: each proxied request logs its resolved upstream URL, the
+response status, any nonce retries, and the full response body of a failed token
+exchange.
+
+## Worker pods
+
+Task containers launched by Gen3 Workflow do not use this proxy. They authenticate with
+their own mechanism (OAuth 2 client credentials) and send no DPoP header. The DPoP-bound
+task token and the proxy are strictly client-side.
\ No newline at end of file
diff --git a/gen3/auth.py b/gen3/auth.py
index cc0fbed87..8715c9582 100755
--- a/gen3/auth.py
+++ b/gen3/auth.py
@@ -71,7 +71,7 @@ def get_access_token_with_key(api_key):
"""
endpoint = endpoint_from_token(api_key["api_key"])
# attempt to get a token from Fence
- auth_url = "{}/user/credentials/cdis/access_token".format(endpoint)
+ auth_url = "{}/user/credentials/api/access_token".format(endpoint)
resp = requests.post(auth_url, json=api_key)
token_key = "access_token"
return _handle_access_token_response(resp, token_key)
@@ -445,6 +445,16 @@ def get_access_token(self):
# use cache
return self._access_token
+ def get_api_key(self):
+ """
+ Returns the actual API key loaded, or None if the loaded credentials
+ do not contain one (for example a raw access token).
+ """
+ if not self._refresh_token:
+ return None
+
+ return self._refresh_token.get("api_key")
+
def _get_auth_value(self):
"""Returns the Authorization header value for the request
diff --git a/gen3/cli/__main__.py b/gen3/cli/__main__.py
index 995bfda62..d4f475feb 100644
--- a/gen3/cli/__main__.py
+++ b/gen3/cli/__main__.py
@@ -13,11 +13,13 @@
import gen3.cli.objects as objects
import gen3.cli.file as file
import gen3.cli.drs_pull as drs_pull
+import gen3.cli.dpop as dpop
import gen3.cli.users as users
import gen3.cli.wrap as wrap
import gen3
from gen3 import logging as sdklogging
from gen3.cli import nih
+from gen3.cli import nextflow
class AuthFactory:
@@ -143,6 +145,8 @@ def main(
main.add_command(drs_pull.drs_pull)
main.add_command(file.file)
main.add_command(nih.nih)
+main.add_command(dpop.dpop)
main.add_command(users.users)
main.add_command(wrap.run)
+main.add_command(nextflow.nextflow)
main()
diff --git a/gen3/cli/dpop.py b/gen3/cli/dpop.py
new file mode 100644
index 000000000..1afb8b726
--- /dev/null
+++ b/gen3/cli/dpop.py
@@ -0,0 +1,98 @@
+"""CLI commands for DPoP proxy management."""
+
+import threading
+
+import click
+from cdislogging import get_logger
+
+from gen3.auth import Gen3Auth
+from gen3.dpop import dpop_proxy_context, USER_FACING_ERRORS
+
+logging = get_logger(__name__)
+
+
+@click.group()
+def dpop() -> None:
+ """DPoP proxy management commands."""
+ pass
+
+
+@dpop.group()
+def proxy() -> None:
+ """Manage the DPoP proxy server."""
+ pass
+
+
+@proxy.command(name="start")
+@click.option(
+ "--port",
+ type=int,
+ default=0,
+ envvar="GEN3_DPOP_PROXY_PORT",
+ show_envvar=True,
+ help="Port to run proxy on. Set ENV VAR, otherwise defaults to an OS-assigned free port.",
+)
+@click.option(
+ "--task-token-type",
+ type=str,
+ default="WORKFLOW",
+ show_default=True,
+ help="Type of task token to request.",
+)
+@click.option(
+ "--task-token-expiration",
+ type=int,
+ default=None,
+ help="Task token expiration time in seconds. Server default if omitted.",
+)
+@click.option(
+ "--tes-endpoint",
+ type=str,
+ default=None,
+ help="Will default to standard location in the Gen3 instance of your API key.",
+)
+@click.option(
+ "--s3-endpoint",
+ type=str,
+ default=None,
+ help="Will default to standard location in the Gen3 instance of your API key.",
+)
+@click.pass_context
+def proxy_start_command(
+ ctx: click.Context,
+ port: int,
+ task_token_type: str,
+ task_token_expiration: int | None,
+ tes_endpoint: str | None,
+ s3_endpoint: str | None,
+) -> None:
+ """
+ Start the DPoP proxy server in the foreground.
+
+ Point Nextflow (or another client) at the port and stop the proxy
+ with Ctrl+C. See docs/nextflow.md for the Nextflow configuration.
+ """
+ stop_event = threading.Event()
+ try:
+ auth: Gen3Auth = ctx.obj.get("auth_factory").get()
+
+ with dpop_proxy_context(
+ auth=auth,
+ port=port or None,
+ task_token_type=task_token_type,
+ task_token_expiration=task_token_expiration,
+ tes_endpoint=tes_endpoint,
+ s3_endpoint=s3_endpoint,
+ ) as (_, proxy_port):
+ logging.warning(
+ f"*** Starting Gen3 DPoP proxy on http://127.0.0.1:{proxy_port} (Press Ctrl+C to stop)... ***"
+ )
+ try:
+ stop_event.wait()
+ except KeyboardInterrupt:
+ pass
+ finally:
+ logging.info("*** Stopped Gen3 DPoP proxy. ***")
+ except USER_FACING_ERRORS as exc:
+ # These say what the user should do
+ raise click.ClickException(str(exc)) from exc
diff --git a/gen3/cli/nextflow.py b/gen3/cli/nextflow.py
new file mode 100644
index 000000000..e0017cc52
--- /dev/null
+++ b/gen3/cli/nextflow.py
@@ -0,0 +1,122 @@
+"""
+CLI commands for running Nextflow workflows with DPoP-bound task tokens.
+"""
+
+import click
+from cdislogging import get_logger
+
+from gen3.auth import Gen3Auth
+from gen3.dpop import USER_FACING_ERRORS
+from gen3.dpop_nextflow import run_gen3_nextflow
+
+logging = get_logger(__name__)
+
+
+@click.group()
+def nextflow():
+ """Nextflow usage in Gen3"""
+ pass
+
+
+@nextflow.command(
+ name="run",
+ context_settings={"ignore_unknown_options": True, "allow_extra_args": True},
+)
+@click.argument("nextflow_args", nargs=-1, type=click.UNPROCESSED)
+# The following options mirror `gen3 dpop proxy start`; both hand them to dpop_proxy_context().
+@click.option(
+ "--port",
+ type=int,
+ default=0,
+ envvar="GEN3_DPOP_PROXY_PORT",
+ show_envvar=True,
+ help="Port to run proxy on. Set ENV VAR, otherwise defaults to an OS-assigned free port.",
+)
+@click.option(
+ "--task-token-type",
+ type=str,
+ default="WORKFLOW",
+ show_default=True,
+ help="Type of task token to request.",
+)
+@click.option(
+ "--task-token-expiration",
+ type=int,
+ default=None,
+ help="Task token expiration time in seconds. Server default if omitted.",
+)
+@click.option(
+ "--tes-endpoint",
+ type=str,
+ default=None,
+ help="Will default to standard location in the Gen3 instance of your API key.",
+)
+@click.option(
+ "--s3-endpoint",
+ type=str,
+ default=None,
+ help="Will default to standard location in the Gen3 instance of your API key.",
+)
+@click.option(
+ "--no-generated-config",
+ is_flag=True,
+ help="Do not generate the config that redirects Nextflow to the proxy. Your own "
+ "config then has to point tes.endpoint and aws.client.endpoint at "
+ "127.0.0.1:$GEN3_DPOP_PROXY_PORT itself, and use $GEN3_DPOP_BOUND_TASK_TOKEN as "
+ "tes.oauthToken and aws.accessKey; see the Nextflow guide in the docs.",
+)
+@click.pass_context
+def nextflow_run(
+ ctx: click.Context,
+ nextflow_args: tuple,
+ port: int,
+ task_token_type: str,
+ task_token_expiration: int | None,
+ tes_endpoint: str | None,
+ s3_endpoint: str | None,
+ no_generated_config: bool,
+) -> None:
+ """
+ Run Nextflow with a Gen3 DPoP proxy.
+
+ Requires Gen3Auth credentials (API key or refresh token) configured. TES and
+ S3 endpoints are determined from the credentials.
+
+ Keep your normal Gen3 Nextflow config, the one pointing at your commons. A
+ small override redirecting TES and S3 to the proxy is generated and passed with
+ `-c` last, so nothing else in your config changes.
+
+ Anything not listed below is passed through to `nextflow run`. If your
+ pipeline takes a parameter named like one of these options, put `--` first:
+ everything after it goes to Nextflow untouched.
+
+ Examples: `gen3 -v nextflow run hello.nf`, `gen3 -v nextflow run main.nf -resume`,
+ `gen3 -v nextflow run main.nf -- --port 8080`
+ """
+ logging.info("Running Nextflow with DPoP proxy...")
+
+ try:
+ auth: Gen3Auth = ctx.obj.get("auth_factory").get()
+ return_code = run_gen3_nextflow(
+ nf_args=list(nextflow_args),
+ auth=auth,
+ port=port or None,
+ task_token_type=task_token_type,
+ task_token_expiration=task_token_expiration,
+ tes_endpoint=tes_endpoint,
+ s3_endpoint=s3_endpoint,
+ generate_config=not no_generated_config,
+ )
+ except (*USER_FACING_ERRORS, FileNotFoundError) as exc:
+ # These say what the user should do
+ raise click.ClickException(str(exc)) from exc
+
+ if return_code != 0:
+ logging.error(
+ f"!!! Nextflow errored. It exited with a non-zero exit code: {return_code}. "
+ f"See above logs for more error info from Nextflow. !!!"
+ )
+
+ # Click discards whatever a command returns, so the exit code has to be set
+ # explicitly or a failed pipeline would look successful to the caller.
+ ctx.exit(return_code)
diff --git a/gen3/dpop.py b/gen3/dpop.py
new file mode 100644
index 000000000..d61fe30a3
--- /dev/null
+++ b/gen3/dpop.py
@@ -0,0 +1,1079 @@
+"""
+DPoP utilities for token exchange and local proxy.
+"""
+
+import asyncio
+from contextlib import contextmanager
+from datetime import datetime, timezone
+import hmac
+import json
+import socket
+import tempfile
+import threading
+import time
+from typing import (
+ AbstractSet,
+ Any,
+ AsyncIterator,
+ Dict,
+ Generator,
+ Literal,
+ Tuple,
+ TYPE_CHECKING,
+)
+
+import httpx2
+import humanfriendly
+import requests
+from authutils.dpop import generate_dpop_proof
+from cdislogging import get_logger
+from joserfc import jwk
+
+from gen3.auth import decode_token, Gen3Auth, Gen3AuthError
+
+# uvicorn is optional (the `dpop` extra), but gen3.cli.__main__ imports this module
+# unconditionally, so it can only be imported lazily inside start_proxy_server. This
+# import exists solely so type checkers can resolve that function's return annotation.
+if TYPE_CHECKING:
+ import uvicorn
+
+logging = get_logger(__name__)
+
+# httpx2 logs one line per request under its own top-level logger. Reparenting it
+# here puts it under `gen3`, so the CLI's -v/-vv flags govern it like everything
+# else; `start_proxy_server` does the same for uvicorn's logger.
+get_logger("httpx2").parent = logging
+
+# Proxy should not forward all headers - these are the ones to skip.
+#
+# Connection-specific fields describe the client's connection to us, not
+# ours to the upstream, so an intermediary strips them (RFC 9110 7.6.1).
+#
+# Framing fields have to be recomputed: uvicorn has already de-chunked the body, so
+# forwarding the client's `transfer-encoding` or `content-length` would describe a
+# body we are no longer sending (RFC 9112 6.1 and 6.2).
+#
+# `dpop` is dropped because this proxy mints its own proof. `authorization` is not:
+# the S3 route needs the client's SigV4 header to arrive intact, and the TES route
+# overwrites it later.
+_HEADERS_NOT_FORWARDED = frozenset(
+ {
+ b"connection",
+ b"content-length",
+ b"dpop",
+ b"host",
+ b"keep-alive",
+ b"proxy-authenticate",
+ b"proxy-authorization",
+ b"te",
+ b"trailer",
+ b"transfer-encoding",
+ b"upgrade",
+ }
+)
+
+# The two services the proxy will route to. Broken out here
+# to allow expansion in the typing easily if we add more services/endpoints.
+_SERVICE_TES = "tes"
+_SERVICE_S3 = "s3"
+Service = Literal["tes", "s3"]
+
+# Same idea for the response direction. Content headers are kept, because the
+# response body is forwarded raw (still compressed, if it arrived that way).
+_RESPONSE_HEADERS_NOT_FORWARDED = frozenset(
+ {
+ "connection",
+ "keep-alive",
+ "proxy-authenticate",
+ "trailer",
+ "transfer-encoding",
+ "upgrade",
+ }
+)
+
+# Request bodies are held so a nonce retry can replay them. Anything larger than
+# this spills to a temp file instead of sitting in RAM: workflow inputs staged
+# through the S3 endpoint can be arbitrarily large.
+_MAX_BODY_SIZE_IN_MEMORY = 8 * 1024 * 1024
+
+# httpx2 defaults every phase to 5s, which breaks any transfer or task listing
+# slower than that. The read/write budgets below are per socket operation rather
+# than per request, so a large-but-progressing staging transfer never trips them.
+_UPSTREAM_TIMEOUT = httpx2.Timeout(connect=30.0, read=300.0, write=300.0, pool=None)
+
+_MAX_NONCE_RETRIES = 2
+
+# Authorization schemes that carry the access token directly, lowercased for a
+# case-insensitive match. An S3 client sends an AWS signature instead, with the token as the
+# access key ID.
+_SCHEMES_CARRYING_THE_TOKEN = ("bearer ", "dpop ")
+
+# Chunk size for replaying a buffered request body upstream.
+_BODY_CHUNK_BYTES = 1024 * 1024
+
+
+class MissingDPoPNonceError(RuntimeError):
+ """Raised when a server demands a DPoP nonce without supplying one."""
+
+
+class ProxyStartupError(RuntimeError):
+ """Raised when the background DPoP proxy server cannot be started."""
+
+
+# Failures the user can do something about. Callers that present errors to people
+# (the CLI) report these as a message rather than a traceback; anything else is a
+# bug and should keep its traceback.
+USER_FACING_ERRORS = (
+ Gen3AuthError,
+ ImportError,
+ MissingDPoPNonceError,
+ ProxyStartupError,
+ requests.RequestException,
+)
+
+
+def resolve_service_endpoints(
+ auth: Gen3Auth,
+ tes_endpoint: str | None = None,
+ s3_endpoint: str | None = None,
+) -> Tuple[str, str]:
+ """
+ Work out which TES and S3 endpoints the proxy should forward to.
+
+ Args:
+ auth (Gen3Auth): Authenticated Gen3Auth instance.
+ tes_endpoint (str | None): Override, or None for {endpoint}/ga4gh/tes.
+ s3_endpoint (str | None): Override, or None for {endpoint}/workflows/s3.
+
+ Returns:
+ Tuple[str, str]: The TES and S3 endpoints.
+
+ Raises:
+ Gen3AuthError: If the credentials do not name a commons, or an override
+ points at a different host than the commons that issued them.
+ """
+ if not auth.endpoint:
+ raise Gen3AuthError(
+ "No Gen3 endpoint is configured. Use credentials that name their "
+ "commons, such as an API key with an `iss` claim."
+ )
+
+ tes_endpoint = tes_endpoint or f"{auth.endpoint}/ga4gh/tes"
+ s3_endpoint = s3_endpoint or f"{auth.endpoint}/workflows/s3"
+
+ # The task token is issued by the commons the credentials name, and Gen3 always
+ # serves TES and S3 from that same host, so an endpoint anywhere else can only
+ # be a mistake - and sending the token there would leak it to another domain.
+ #
+ # Future NOTE: If we ever support separate hosts for task execution vs storage,
+ # we'll need to rethink this. For now, this protects the user
+ # against accidentally sending a task token from Commons A to Commons B
+ commons_host = httpx2.URL(auth.endpoint).host
+ for option, endpoint in (
+ ("--tes-endpoint", tes_endpoint),
+ ("--s3-endpoint", s3_endpoint),
+ ):
+ if httpx2.URL(endpoint).host != commons_host:
+ raise Gen3AuthError(
+ f"{option} is {endpoint}, which is not on {commons_host} - the "
+ "commons that issued your credentials. The task token is only "
+ "valid there, so it will not be sent anywhere else."
+ )
+
+ return tes_endpoint, s3_endpoint
+
+
+@contextmanager
+def dpop_proxy_context(
+ auth: Gen3Auth,
+ task_token_type: str = "WORKFLOW",
+ task_token_expiration: int | None = None,
+ tes_endpoint: str | None = None,
+ s3_endpoint: str | None = None,
+ port: int | None = None,
+) -> Generator[Tuple[str, int], None, None]:
+ """
+ Context manager to initialize, run, and cleanly shut down a background DPoP proxy server.
+
+ Handles JWK key generation, API key task token exchange, AsyncDPoPProxy instantiation,
+ and background server lifecycle cleanup.
+
+ Args:
+ auth (Gen3Auth): Authenticated Gen3Auth instance.
+ task_token_type (str): Type of task token to request. Defaults to "WORKFLOW".
+ task_token_expiration (int | None): Expiration time in seconds for the task token.
+ tes_endpoint (str | None): GA4GH TES endpoint URL. Defaults to {endpoint}/ga4gh/tes.
+ s3_endpoint (str | None): S3 service endpoint URL. Defaults to
+ {endpoint}/workflows/s3.
+ port (int | None): Specific port to bind to, or None to let the OS assign one.
+
+ Yields:
+ Tuple[str, int]: A tuple containing (task_token, proxy_port).
+
+ Raises:
+ Gen3AuthError: If no API key is available, or the token endpoint rejects
+ the exchange.
+ ProxyStartupError: If the proxy server cannot be started.
+ MissingDPoPNonceError: If the token endpoint demands a nonce without
+ providing one.
+ requests.RequestException: If the commons cannot be reached.
+ """
+ tes_endpoint, s3_endpoint = resolve_service_endpoints(
+ auth, tes_endpoint, s3_endpoint
+ )
+ token_endpoint = f"{auth.endpoint}/user/credentials/api/access_token"
+
+ key = jwk.generate_key("EC", "P-256", private=True)
+
+ api_key = auth.get_api_key()
+ if not api_key:
+ raise Gen3AuthError(
+ "Could not find an API key for the DPoP token exchange. Download one from "
+ "the Gen3 profile page to ~/.gen3/credentials.json, or pass --auth."
+ )
+
+ logging.info(f"Found API key! Using endpoint: {auth.endpoint}")
+
+ access_token = auth.get_access_token()
+
+ logging.info(
+ f"Exchanging API key for task token (type: {task_token_type}, expiration: {task_token_expiration or 'server default'})..."
+ )
+ task_token, nonce = exchange_api_key_for_task_token(
+ key=key,
+ token_endpoint=token_endpoint,
+ api_key=api_key,
+ task_token_type=task_token_type,
+ task_token_expiration=task_token_expiration,
+ additional_headers={"Authorization": f"Bearer {access_token}"},
+ )
+ logging.info(f"Got task token (type: {task_token_type}) successfully!")
+
+ config = {
+ "KEY": key,
+ "TASK_TOKEN": task_token,
+ "TES_ENDPOINT": tes_endpoint,
+ "S3_ENDPOINT": s3_endpoint,
+ "CACHED_NONCE": nonce,
+ }
+
+ logging.info("Finding port and starting Gen3 DPoP Proxy...")
+ app = AsyncDPoPProxy(config)
+ server, thread, proxy_port = start_proxy_server(
+ app, host="127.0.0.1", port=port, log_level="warning"
+ )
+
+ try:
+ yield task_token, proxy_port
+ finally:
+ server.should_exit = True
+ # The thread runs the shutdown itself; without joining, the listening
+ # socket can outlive this context manager and leak the port.
+ thread.join(timeout=10)
+ if thread.is_alive():
+ logging.warning(
+ "Gen3 DPoP proxy did not shut down within 10 seconds; "
+ f"port {proxy_port} may stay bound until this process exits."
+ )
+
+
+class AsyncDPoPProxy:
+ """Async ASGI proxy that adds DPoP proof headers to outgoing requests."""
+
+ def __init__(self, config: dict[str, Any]) -> None:
+ self._config = config
+ self._client = httpx2.AsyncClient(
+ limits=httpx2.Limits(max_connections=None, max_keepalive_connections=100),
+ timeout=_UPSTREAM_TIMEOUT,
+ verify=True,
+ )
+
+ async def __call__(self, scope: dict[str, Any], receive, send) -> None:
+ """ASGI application entry point."""
+ if scope["type"] == "lifespan":
+ # Nothing to set up or tear down here. Returning nothing
+ # to unblock uvicorn startup/shutdown events
+ return
+
+ if scope["type"] != "http":
+ await self._send_error(send, 404, "Not Found")
+ return
+
+ # Before routing, so an unauthorized caller cannot learn which paths exist either.
+ if not self._caller_holds_the_task_token(scope.get("headers", [])):
+ logging.warning(
+ "Refusing a request that did not present the task token. This proxy signs "
+ "what it forwards, so only the process it was started for may use it."
+ )
+ await self._send_error(send, 401, "Unauthorized")
+ return
+
+ method = scope["method"]
+ path = scope["path"]
+ query_string = scope.get("query_string", b"").decode("utf-8")
+
+ route = self._resolve_upstream_url(path, query_string)
+ if route is None:
+ await self._send_error(send, 404, "Not Found")
+ return
+
+ upstream_url, service = route
+ logging.info(f"upstream_url: {upstream_url}")
+
+ headers = self._build_headers(
+ method, upstream_url, scope.get("headers", []), service
+ )
+
+ with tempfile.SpooledTemporaryFile(max_size=_MAX_BODY_SIZE_IN_MEMORY) as body:
+ await self._read_body(receive, body)
+
+ try:
+ response = await self._send_with_nonce_retry(
+ method, upstream_url, headers, body
+ )
+ except httpx2.TimeoutException as exc:
+ logging.error(f"Timed out talking to {upstream_url}: {exc}")
+ await self._send_error(send, 504, f"Upstream timeout: {exc}")
+ return
+ except httpx2.HTTPError as exc:
+ logging.error(f"Could not reach {upstream_url}: {exc}")
+ await self._send_error(send, 502, f"Upstream request failed: {exc}")
+ return
+ except MissingDPoPNonceError as exc:
+ # this happens if the server doesn't actually give us a nonce -
+ # it's a server-side error
+ logging.error(str(exc))
+ await self._send_error(send, 502, str(exc))
+ return
+
+ await self._send_response(send, response)
+
+ async def aclose(self) -> None:
+ """Close the shared upstream HTTP client."""
+ await self._client.aclose()
+
+ def _caller_holds_the_task_token(
+ self, request_headers: list[tuple[bytes, bytes]]
+ ) -> bool:
+ """
+ Check that a request came from the process this proxy was started for.
+
+ The proxy signs whatever it forwards with the DPoP key, so anything that can reach it
+ can act as the user for the life of the run.
+
+ Holding the task token is what authorizes a caller. Nextflow already sends it on both
+ routes - as the TES `oauthToken` and as the S3 access key ID - so requiring it costs
+ the pipeline nothing.
+
+ Args:
+ request_headers (list[tuple[bytes, bytes]]): Raw headers from the ASGI scope.
+
+ Returns:
+ bool: True if the caller presented the task token.
+ """
+ presented = _presented_access_token(
+ _header_value(request_headers, b"authorization")
+ )
+ if not presented:
+ return False
+ # Constant time: the comparison is against a live credential.
+ return hmac.compare_digest(
+ presented.encode("utf-8"), str(self._config["TASK_TOKEN"]).encode("utf-8")
+ )
+
+ def _resolve_upstream_url(
+ self, path: str, query_string: str
+ ) -> tuple[str, Service] | None:
+ """
+ Route a path to its upstream base, or refuse to route it at all.
+
+ Only TES and S3 traffic belongs on this proxy, so the two prefixes are
+ matched explicitly rather than treating everything else as S3. The
+ endpoints already end in their prefix, so it is stripped here to avoid
+ doubling it.
+
+ Args:
+ path (str): Request path from the ASGI scope, already URL-decoded.
+ query_string (str): Raw query string, or "" if there was none.
+
+ Returns:
+ tuple[str, Service] | None: The upstream URL and the service it
+ belongs to, which decides how the request is authenticated. None
+ if the path is neither a TES nor an S3 path, or if it escapes the
+ base it was routed to.
+ """
+ service: Service
+ if path.startswith("/ga4gh/tes"):
+ service = _SERVICE_TES
+ base = self._config["TES_ENDPOINT"].rstrip("/")
+ subpath = path.removeprefix("/ga4gh/tes")
+ elif path.startswith("/s3"):
+ service = _SERVICE_S3
+ base = self._config["S3_ENDPOINT"].rstrip("/")
+ subpath = path.removeprefix("/s3")
+ else:
+ logging.warning(
+ f"Refusing to proxy {path}: only /ga4gh/tes and /s3 paths are "
+ "proxied. Check the endpoints your pipeline is configured with."
+ )
+ return None
+
+ # httpx2 resolves dot segments when it builds the request, so `/s3/../user`
+ # would leave the base chosen above and reach an arbitrary commons endpoint
+ # carrying the task token. Normalize here and confirm it stayed put.
+ url = httpx2.URL(f"{base}{subpath}")
+ if not str(url).startswith(base):
+ logging.warning(
+ f"Refusing to proxy {path}: it resolves to {url}, which is outside "
+ f"{base}. The task token is only sent to the TES and S3 endpoints."
+ )
+ return None
+
+ upstream_url = f"{url}?{query_string}" if query_string else str(url)
+ return upstream_url, service
+
+ def _build_headers(
+ self,
+ method: str,
+ url: str,
+ request_headers: list[tuple[bytes, bytes]],
+ service: Service,
+ ) -> dict[str, str]:
+ """
+ Build request headers with DPoP credentials.
+
+ Both services get a fresh proof in the `DPoP` header. They differ in how
+ the token itself is carried: TES wants `Authorization: DPoP `,
+ while Gen3's S3 endpoint reads the token out of the SigV4 `Credential=`
+ field, so the client's signed `Authorization` is passed through as-is.
+
+ Args:
+ method (str): The request method, signed into the proof as `htm`.
+ url (str): The upstream URL, signed into the proof as `htu`.
+ request_headers (list[tuple[bytes, bytes]]): Raw headers from the
+ ASGI scope.
+ service (Service): Which upstream this is going to, from
+ `_resolve_upstream_url`.
+
+ Returns:
+ dict[str, str]: Headers to send upstream.
+ """
+ headers = {
+ k.decode("utf-8"): v.decode("utf-8")
+ for k, v in request_headers
+ if k.lower() not in _HEADERS_NOT_FORWARDED
+ }
+
+ if service != _SERVICE_S3:
+ # Lowercase to overwrite the client's header rather than sit beside it:
+ # ASGI header names arrive lowercased
+ headers["authorization"] = f"DPoP {self._config['TASK_TOKEN']}"
+ headers["DPoP"] = self._generate_proof(method, url)
+ # The Authorization value is a live credential and `-vv` output ends up in
+ # bug reports, so log the proof (useful, single-use) but never the token.
+ logging.debug(f"DPoP proof for {method} {url}: {headers['DPoP']}")
+
+ return headers
+
+ def _generate_proof(self, method: str, url: str) -> str:
+ """Generate a fresh DPoP proof JWT for the given method and URL."""
+ return generate_dpop_proof(
+ key=self._config["KEY"],
+ method=method,
+ url=url,
+ access_token=self._config.get("TASK_TOKEN"),
+ nonce=self._config.get("CACHED_NONCE"),
+ )
+
+ async def _send_with_nonce_retry(
+ self,
+ method: str,
+ url: str,
+ headers: dict[str, str],
+ body: tempfile.SpooledTemporaryFile,
+ ) -> httpx2.Response:
+ """
+ Send the buffered request upstream, retrying nonce rejections.
+
+ Args:
+ method (str): HTTP method of the incoming request.
+ url (str): Resolved upstream URL.
+ headers (dict[str, str]): Headers to send upstream, including the DPoP proof.
+ body (tempfile.SpooledTemporaryFile): Buffered request body, replayed on retry.
+
+ Returns:
+ httpx2.Response: Upstream response, still streaming unless its body was
+ read to classify a nonce error.
+
+ Raises:
+ MissingDPoPNonceError: If the server asks for a nonce without providing one.
+ httpx2.HTTPError: If the upstream request cannot be completed.
+ """
+ # Framing has to be explicit: given an iterator body and no content-length,
+ # httpx2 sends `transfer-encoding: chunked`, which S3-compatible backends
+ # reject for uploads. Bodyless requests skip the iterator entirely, so they
+ # go out with no framing headers at all.
+ body.seek(0, 2)
+ body_length = body.tell()
+ if body_length:
+ headers["content-length"] = str(body_length)
+
+ for attempt in range(_MAX_NONCE_RETRIES + 1):
+ body.seek(0)
+ request = self._client.build_request(
+ method,
+ url,
+ content=_aiter_file(body) if body_length else b"",
+ headers=headers,
+ )
+ response = await self._client.send(request, stream=True)
+ logging.info(f"Got response. Status Code: {response.status_code}")
+ if response.status_code >= 400:
+ # WWW-Authenticate carries the DPoP failure reason (invalid_dpop_proof,
+ # invalid_token, ...), which is the only clue for a rejected proof.
+ logging.warning(
+ f"{method} {url} was rejected with {response.status_code}. "
+ f"WWW-Authenticate: "
+ f"{response.headers.get('WWW-Authenticate', '')}"
+ )
+
+ if attempt == _MAX_NONCE_RETRIES or not await _is_dpop_nonce_error_async(
+ response
+ ):
+ return response
+
+ logging.info(f"Nonce rejection attempt {attempt + 1}...")
+ logging.debug(f"Response headers: {response.headers}")
+ await response.aclose()
+
+ if not response.headers.get("DPoP-Nonce"):
+ raise MissingDPoPNonceError(
+ "Server did not provide a nonce in DPoP-Nonce header. "
+ "It is required to do so for DPoP to work."
+ )
+
+ self._config["CACHED_NONCE"] = response.headers["DPoP-Nonce"]
+ logging.info("updated CACHED_NONCE w/ server-provided nonce")
+
+ headers["DPoP"] = self._generate_proof(method, url)
+ await asyncio.sleep(0.1 * (attempt + 1))
+
+ async def _send_response(self, send, response: httpx2.Response) -> None:
+ """Stream the upstream response back to the ASGI client."""
+ try:
+ if response.is_stream_consumed:
+ # Classifying a nonce error read and decoded the body, so the
+ # upstream content headers no longer describe what is forwarded.
+ await self._send_buffered_response(send, response)
+ return
+
+ await send(
+ {
+ "type": "http.response.start",
+ "status": response.status_code,
+ "headers": _forwardable_response_headers(response),
+ }
+ )
+ async for chunk in response.aiter_raw():
+ await send(
+ {"type": "http.response.body", "body": chunk, "more_body": True}
+ )
+ await send({"type": "http.response.body", "body": b""})
+ finally:
+ await response.aclose()
+
+ async def _send_buffered_response(self, send, response: httpx2.Response) -> None:
+ """Forward an already-read response, recomputing its content headers."""
+ body = response.content
+ headers = _forwardable_response_headers(
+ response, drop={"content-encoding", "content-length"}
+ )
+ headers.append((b"content-length", str(len(body)).encode("utf-8")))
+
+ await send(
+ {
+ "type": "http.response.start",
+ "status": response.status_code,
+ "headers": headers,
+ }
+ )
+ await send({"type": "http.response.body", "body": body})
+
+ async def _send_error(self, send, status: int, message: str) -> None:
+ """Send a plain-text error response to the ASGI client."""
+ body = message.encode("utf-8")
+ await send(
+ {
+ "type": "http.response.start",
+ "status": status,
+ "headers": [
+ (b"content-type", b"text/plain; charset=utf-8"),
+ (b"content-length", str(len(body)).encode("utf-8")),
+ ],
+ }
+ )
+ await send({"type": "http.response.body", "body": body})
+
+ @staticmethod
+ async def _read_body(receive, buffer: tempfile.SpooledTemporaryFile) -> None:
+ """Read the full request body from the ASGI receive queue into a buffer."""
+ more_body = True
+ while more_body:
+ message = await receive()
+ buffer.write(message.get("body", b""))
+ more_body = message.get("more_body", False)
+
+
+def exchange_api_key_for_task_token(
+ key: jwk.Key,
+ token_endpoint: str,
+ api_key: str,
+ task_token_type: str,
+ task_token_expiration: int | None = None,
+ additional_headers: Dict[str, str] | None = None,
+ timeout: float | Tuple[float, float] = (10, 60),
+) -> Tuple[str, str | None]:
+ """
+ Exchange API key for DPoP-bound task token.
+
+ Args:
+ key (jwk.Key): Private JWK instance for signing DPoP proof.
+ token_endpoint (str): Target token endpoint URL.
+ api_key (str): Gen3 user API key string.
+ task_token_type (str): Task token scope/type (e.g., "WORKFLOW").
+ task_token_expiration (int | None): Requested token expiration in seconds.
+ additional_headers (Dict[str, str] | None): Additional headers to include.
+ timeout (float | Tuple[float, float]): requests timeout, as seconds or
+ (connect, read) seconds.
+
+ Returns:
+ Tuple[str, str | None]: A tuple containing (access_token, cached_nonce).
+
+ Raises:
+ Gen3AuthError: If the requested lifetime cannot outlive the API key, if the
+ token endpoint returns an error status, or if the response carries no
+ access token.
+ MissingDPoPNonceError: If the endpoint demands a nonce without providing one.
+ requests.RequestException: If the token endpoint cannot be reached.
+ """
+ _check_expiration_fits_api_key(api_key, task_token_expiration)
+
+ headers = {"DPoP": generate_dpop_proof(key=key, method="POST", url=token_endpoint)}
+ logging.debug(f"Generated DPoP Headers: {headers}")
+ if additional_headers:
+ headers.update(additional_headers)
+
+ params: Dict[str, str | int] = {"task_token": task_token_type}
+ if task_token_expiration is not None:
+ params["expires_in"] = task_token_expiration
+
+ nonce = None
+ for attempt in range(_MAX_NONCE_RETRIES + 1):
+ response = requests.post(
+ token_endpoint,
+ json={"api_key": api_key},
+ params=params,
+ headers=headers,
+ timeout=timeout,
+ )
+
+ if not _is_dpop_nonce_error(response):
+ break
+
+ logging.info(
+ f"Got invalid nonce error (attempt {attempt + 1} of "
+ f"{_MAX_NONCE_RETRIES + 1}). Trying with server-provided nonce..."
+ )
+ if not response.headers.get("DPoP-Nonce"):
+ raise MissingDPoPNonceError(
+ "Token endpoint asked for a DPoP nonce without providing one in a "
+ "DPoP-Nonce header. It is required to do so for DPoP to work."
+ )
+ nonce = response.headers["DPoP-Nonce"]
+ headers["DPoP"] = generate_dpop_proof(
+ key=key, method="POST", url=token_endpoint, nonce=nonce
+ )
+
+ if not response.ok:
+ logging.debug(f"Token endpoint response body: {response.text}")
+ raise Gen3AuthError(
+ f"Could not get a {task_token_type} task token from {response.url}: "
+ f"[{response.status_code}] {_server_error_message(response)}"
+ )
+
+ try:
+ access_token = response.json()["access_token"]
+ except (ValueError, KeyError, TypeError):
+ raise Gen3AuthError(
+ f"Token endpoint {token_endpoint} returned no access_token for a "
+ f"{task_token_type} task token. Response body: "
+ f"{response.text}"
+ )
+
+ return access_token, nonce
+
+
+def _header_value(request_headers: list[tuple[bytes, bytes]], name: bytes) -> str:
+ """
+ Read one header out of the raw ASGI header list.
+
+ Args:
+ request_headers (list[tuple[bytes, bytes]]): Raw headers from the ASGI scope.
+ name (bytes): Lowercased header name to look for.
+
+ Returns:
+ str: The header value, or "" if it is absent.
+ """
+ for key, value in request_headers:
+ if key.lower() == name:
+ return value.decode("utf-8", "replace")
+ return ""
+
+
+def _presented_access_token(auth_header: str) -> str | None:
+ """
+ Read the access token out of an Authorization header, whichever way it was presented.
+
+ Understands the same shapes Gen3's S3 endpoint does, so that a header this proxy accepts
+ is one the upstream would read the same token out of.
+
+ Args:
+ auth_header (str): Value of the incoming Authorization header.
+
+ Returns:
+ str | None: The token, or None if the header carries none.
+ """
+ if not auth_header:
+ return None
+
+ stripped = auth_header.strip()
+ if stripped.lower().startswith(_SCHEMES_CARRYING_THE_TOKEN):
+ parts = stripped.split(maxsplit=1)
+ candidate = parts[1].strip() if len(parts) == 2 else ""
+ elif "Credential=" in stripped:
+ candidate = stripped.split("Credential=")[1].split("/")[0]
+ elif "AWS " in stripped:
+ candidate = stripped.split("AWS ")[1].split(":")[0]
+ else:
+ return None
+
+ # A client acting on behalf of a user appends the user ID to its token.
+ return candidate.split(";userId=")[0] or None
+
+
+def is_proxy_running(port: int, host: str = "127.0.0.1") -> bool:
+ """
+ Check if a proxy server is running on the given port.
+
+ Args:
+ port (int): Port number to test.
+ host (str): Host address to connect to. Defaults to "127.0.0.1".
+
+ Returns:
+ bool: True if connection succeeded, False otherwise.
+ """
+ try:
+ with socket.create_connection((host, port), timeout=1):
+ return True
+ except (socket.timeout, ConnectionRefusedError, OSError):
+ return False
+
+
+def start_proxy_server(
+ app: object,
+ host: str = "127.0.0.1",
+ port: int | None = None,
+ log_level: str = "warning",
+ timeout: float = 10,
+) -> Tuple["uvicorn.Server", threading.Thread, int]:
+ """
+ Start proxy server in a background thread.
+
+ Args:
+ app (object): ASGI application instance. If it exposes an async
+ ``aclose()``, it is awaited during shutdown.
+ host (str): Host address to bind to. Defaults to "127.0.0.1".
+ port (int | None): Port to bind to, or None to let the OS assign one.
+ log_level (str): Uvicorn log level. Defaults to "warning".
+ timeout (float): Startup wait timeout in seconds. Defaults to 10.
+
+ Returns:
+ Tuple[uvicorn.Server, threading.Thread, int]: A tuple containing
+ (uvicorn_server, background_thread, actual_bound_port).
+
+ Raises:
+ ProxyStartupError: If the port is taken, or the server does not come up
+ within the timeout period.
+ ImportError: If the `dpop` extra is not installed.
+ """
+ try:
+ import uvicorn
+ except ImportError as exc:
+ raise ImportError(
+ "The DPoP proxy needs uvicorn, which ships in the `dpop` extra. "
+ "Install it with: pip install 'gen3[dpop]'"
+ ) from exc
+
+ # Checked up front because uvicorn reports a bind failure by exiting the thread,
+ # which reaches the caller as a much vaguer startup error.
+ if port and is_proxy_running(port, host):
+ raise ProxyStartupError(
+ f"Something is already listening on {host}:{port}. Pick another port "
+ "with --port, or omit it to get an OS-assigned one."
+ )
+
+ uvicorn_logger = get_logger("uvicorn")
+ uvicorn_logger.parent = logging
+
+ server = uvicorn.Server(
+ uvicorn.Config(
+ app,
+ # Port 0 lets the kernel pick a free port atomically; probing for a
+ # free port first and binding second is a race.
+ host=host,
+ port=port or 0,
+ log_level=log_level,
+ log_config=None,
+ )
+ )
+
+ proxy_started = threading.Event()
+ actual_port: int | None = None
+ startup_error: BaseException | None = None
+
+ def _run_server() -> None:
+ nonlocal actual_port, startup_error
+ loop = asyncio.new_event_loop()
+ asyncio.set_event_loop(loop)
+ try:
+ server.config.load()
+ server.lifespan = server.config.lifespan_class(server.config)
+ loop.run_until_complete(server.startup())
+
+ for sock in server.servers:
+ actual_port = sock.sockets[0].getsockname()[1]
+ break
+
+ proxy_started.set()
+ loop.run_until_complete(server.main_loop())
+ except BaseException as exc: # SystemExit if uvicorn cannot bind
+ startup_error = exc
+ finally:
+ proxy_started.set()
+ try:
+ # uvicorn only closes its listening sockets in shutdown(); skipping
+ # it leaks the bound port for the life of the process.
+ loop.run_until_complete(server.shutdown())
+ if hasattr(app, "aclose"):
+ loop.run_until_complete(app.aclose())
+ finally:
+ loop.close()
+
+ thread = threading.Thread(target=_run_server, daemon=True)
+ thread.start()
+ proxy_started.wait(timeout=timeout)
+
+ if actual_port is None:
+ target = f"{host}:{port}" if port else f"{host} on an OS-assigned port"
+ reason = (
+ f"{type(startup_error).__name__}: {startup_error}"
+ if startup_error
+ else f"it did not come up within {timeout} seconds"
+ )
+ raise ProxyStartupError(
+ f"Could not start the DPoP proxy server on {target} - {reason}. "
+ "Any uvicorn errors above have the details."
+ ) from startup_error
+
+ return server, thread, actual_port
+
+
+async def _aiter_file(
+ buffer: tempfile.SpooledTemporaryFile,
+) -> AsyncIterator[bytes]:
+ """Yield a buffered body in chunks, off the event loop thread."""
+ while True:
+ chunk = await asyncio.to_thread(buffer.read, _BODY_CHUNK_BYTES)
+ if not chunk:
+ return
+ yield chunk
+
+
+def _check_expiration_fits_api_key(
+ api_key: str, task_token_expiration: int | None
+) -> None:
+ """
+ Refuse a task token lifetime the API key cannot cover.
+
+ Gen3 will not issue a token that outlives the API key it was requested with, and
+ its rejection does not say what lifetime would have worked. The API key is a JWT,
+ so the answer can be worked out locally before spending a round trip.
+
+ Args:
+ api_key (str): The Gen3 API key (a JWT) being exchanged.
+ task_token_expiration (int | None): Requested lifetime in seconds, if any.
+
+ Raises:
+ Gen3AuthError: If the API key has expired, or expires before the requested
+ lifetime would.
+ """
+ if not task_token_expiration:
+ return
+
+ try:
+ api_key_expiration = decode_token(api_key).get("exp")
+ except Exception as exc:
+ # decode_token raises a bare Exception for anything it cannot split or parse.
+ # An unreadable key is the token endpoint's business, not this check's.
+ logging.debug(f"Could not read the API key's expiration, skipping check: {exc}")
+ return
+
+ if not api_key_expiration:
+ logging.debug("API key carries no `exp` claim, skipping expiration check.")
+ return
+
+ remaining_seconds = int(api_key_expiration - time.time())
+ expires_at = datetime.fromtimestamp(api_key_expiration, tz=timezone.utc)
+
+ if remaining_seconds <= 0:
+ raise Gen3AuthError(
+ f"Your API key expired at {expires_at:%Y-%m-%d %H:%M UTC}. "
+ "Create a new one on the Gen3 profile page and try again."
+ )
+
+ if task_token_expiration > remaining_seconds:
+ raise Gen3AuthError(
+ f"Requested a task token lifetime of {task_token_expiration} seconds "
+ f"({humanfriendly.format_timespan(task_token_expiration)}), but your API "
+ f"key expires in {humanfriendly.format_timespan(remaining_seconds)} "
+ f"(at {expires_at:%Y-%m-%d %H:%M UTC}). Gen3 will not issue a task token "
+ f"that outlives the API key: request at most {remaining_seconds} seconds, "
+ "or create a new API key."
+ )
+
+
+def _server_error_message(response: requests.Response) -> str:
+ """
+ Extract the most useful human-readable message from an error response.
+
+ Args:
+ response (requests.Response): The error response.
+
+ Returns:
+ str: A server-provided explanation, or the response body if it has no
+ recognizable error field.
+ """
+ try:
+ body = response.json()
+ except ValueError:
+ return response.text or ""
+
+ if isinstance(body, dict):
+ for key in ("error_description", "message", "detail", "error"):
+ value = body.get(key)
+ if isinstance(value, str) and value:
+ return value
+
+ return json.dumps(body)
+
+
+def _forwardable_response_headers(
+ response: httpx2.Response, drop: AbstractSet[str] = frozenset()
+) -> list[tuple[bytes, bytes]]:
+ """
+ Encode upstream response headers, dropping ones a proxy must not forward.
+
+ Args:
+ response (httpx2.Response): Upstream response.
+ drop (AbstractSet[str]): Extra lowercase header names to omit.
+
+ Returns:
+ list[tuple[bytes, bytes]]: Header pairs in ASGI form.
+ """
+ return [
+ (k.encode("utf-8"), v.encode("utf-8"))
+ for k, v in response.headers.multi_items()
+ if k.lower() not in _RESPONSE_HEADERS_NOT_FORWARDED and k.lower() not in drop
+ ]
+
+
+async def _is_dpop_nonce_error_async(response: httpx2.Response) -> bool:
+ """
+ Check if a streamed response is requesting a DPoP nonce retry.
+
+ Args:
+ response (httpx2.Response): Streaming HTTP response instance.
+
+ Returns:
+ bool: True if server requested DPoP nonce retry, False otherwise.
+ """
+ if response.status_code not in (400, 401):
+ return False
+
+ # The body is only needed for the auth-server style error, and error bodies
+ # are small; reading it makes the streamed response replayable below.
+ await response.aread()
+ return _is_dpop_nonce_error(response)
+
+
+def _is_dpop_nonce_error(
+ response: httpx2.Response | requests.Response,
+) -> bool:
+ """
+ Check if a 400 or 401 response is requesting a DPoP nonce retry.
+
+ Args:
+ response (httpx2.Response | requests.Response): HTTP response instance.
+
+ Returns:
+ bool: True if server requested DPoP nonce retry, False otherwise.
+ """
+ if response.status_code not in (400, 401):
+ return False
+
+ # Check Resource Server (RS) style: WWW-Authenticate header
+ www_auth = response.headers.get("WWW-Authenticate", "")
+ if 'error="use_dpop_nonce"' in www_auth or "error='use_dpop_nonce'" in www_auth:
+ logging.debug(
+ "DPoP Nonce error found in www-authenticate header (resource server response)"
+ )
+ return True
+
+ # Check Authorization Server (AS) style: Safe JSON body parse
+ body_error = None
+ try:
+ data = response.json()
+ if isinstance(data, dict):
+ body_error = next(
+ (
+ data[key]
+ for key in ("error", "error_description", "message")
+ if isinstance(data.get(key), str) and data[key]
+ ),
+ None,
+ )
+ except (
+ ValueError,
+ httpx2.DecodingError,
+ requests.exceptions.RequestException,
+ ):
+ # Body is empty, non-JSON, or raised a library-specific decoding error
+ pass
+
+ if body_error == "use_dpop_nonce":
+ logging.debug("DPoP Nonce error found in response JSON (auth server response)")
+ return True
+
+ if body_error:
+ # Servers may attach a DPoP-Nonce to every response on a DPoP endpoint, so the
+ # header alone cannot be trusted below. Retrying here would burn the retry
+ # budget and bury the explanation the server just gave.
+ logging.debug(f"Not a nonce error; server reported: {body_error}")
+ return False
+
+ # Fallback: Presence of DPoP-Nonce header on a 400/401 error
+ if "DPoP-Nonce" in response.headers:
+ logging.info("DPoP Nonce in headers and got a 40x.")
+ return True
+
+ return False
diff --git a/gen3/dpop_nextflow.py b/gen3/dpop_nextflow.py
new file mode 100644
index 000000000..f947a50f0
--- /dev/null
+++ b/gen3/dpop_nextflow.py
@@ -0,0 +1,188 @@
+"""
+Demonstrating Proof of Possesssion (DPoP)-bound Task Token and Async Proxy for Nextflow Workflows.
+
+This module provides client-side support for generating DPoP-bound task tokens
+and running a local proxy for Nextflow pipelines.
+
+Routes both TES and S3 traffic through DPoP.
+"""
+
+import contextlib
+import os
+from pathlib import Path
+import subprocess
+import tempfile
+from typing import List, Optional
+
+from cdislogging import get_logger
+
+from gen3.auth import Gen3Auth
+from gen3.dpop import dpop_proxy_context, resolve_service_endpoints
+
+logging = get_logger(__name__)
+
+# Written to a temp file and passed to `nextflow run` with `-c` last on every run.
+# Nextflow merges a `-c` file over the config the pipeline already has rather than
+# replacing it, and the last `-c` wins, so this redirects a config that points
+# straight at a commons to the local proxy instead, one key at a time. It sets only
+# the keys the proxy forces; workDir, region, executor and plugins stay the user's.
+#
+# The token is read from the environment rather than written here: a task token is
+# a bearer-equivalent credential, and a temp file holding one is readable by every
+# process on the host for the life of the run.
+_PROXY_CONFIG_TEMPLATE = """\
+// Generated by `gen3 nextflow run` - recreated every run, deleted when it ends.
+//
+// This overrides only what the DPoP proxy requires. Your own config still owns
+// everything else: plugins, executor, container, region, workDir.
+//
+// The endpoints below are the local proxy, which signs every request with a
+// short-lived key held only in memory and forwards it to your commons:
+//
+// TES {tes_endpoint}
+// S3 {s3_endpoint}
+//
+// To wire this up by hand instead, pass --no-generated-config; see the docs.
+tes {{
+ endpoint = 'http://127.0.0.1:{port}/ga4gh/tes'
+ oauthToken = env('GEN3_DPOP_BOUND_TASK_TOKEN')
+}}
+aws {{
+ // Gen3's S3 endpoint reads the token out of the SigV4 `Credential` field, so
+ // the task token is the access key and the secret is never used.
+ accessKey = env('GEN3_DPOP_BOUND_TASK_TOKEN')
+ secretKey = 'N/A'
+ client {{
+ endpoint = 'http://127.0.0.1:{port}/s3'
+ // Gen3's S3 endpoint reads the bucket name from the first segment of
+ // the request path. Virtual-host addressing puts it in `Host` instead,
+ // which the proxy has to overwrite, leaving the endpoint to read a key
+ // prefix as the bucket name and refuse the request.
+ s3PathStyleAccess = true
+ }}
+}}
+"""
+
+
+def run_gen3_nextflow(
+ nf_args: List[str],
+ auth: Gen3Auth,
+ task_token_type: str = "WORKFLOW",
+ task_token_expiration: Optional[int] = None,
+ tes_endpoint: Optional[str] = None,
+ s3_endpoint: Optional[str] = None,
+ port: Optional[int] = None,
+ generate_config: bool = True,
+) -> int:
+ """
+ Wrap Nextflow execution with DPoP-bound task token security.
+
+ Generates an ephemeral key, exchanges the user's credentials for a DPoP-bound
+ task token, starts a local proxy, then runs Nextflow with the task token and
+ proxy port in its environment as `GEN3_DPOP_BOUND_TASK_TOKEN` and
+ `GEN3_DPOP_PROXY_PORT`.
+
+ By default it also writes a temporary Nextflow config that redirects TES and S3
+ to the proxy and passes it with `-c` last, so a config pointing straight at a
+ commons runs through the proxy without being edited. Nextflow merges `-c` files
+ over the existing config, so only the keys the proxy forces change - workDir,
+ region, executor and plugins stay as the pipeline set them. Pass
+ `generate_config=False` to point the config at the proxy by hand instead; see
+ docs/nextflow.md.
+
+ Args:
+ nf_args (List[str]): Arguments to pass to `nextflow run`.
+ auth (Gen3Auth): Authenticated Gen3Auth instance with endpoint and credentials.
+ task_token_type (str): Type of task token to request. Defaults to "WORKFLOW".
+ task_token_expiration (Optional[int]): Expiration time in seconds for the
+ task token. The service default is used if omitted.
+ tes_endpoint (Optional[str]): GA4GH TES endpoint URL. Defaults to
+ {endpoint}/ga4gh/tes.
+ s3_endpoint (Optional[str]): S3 service endpoint URL. Defaults to
+ {endpoint}/workflows/s3.
+ port (Optional[int]): Port for the proxy, or None for an OS-assigned one.
+ generate_config (bool): Whether to generate a Nextflow config pointing at
+ the proxy and pass it with `-c`. Defaults to True.
+
+ Returns:
+ int: Nextflow process exit code.
+
+ Raises:
+ Gen3AuthError: If the DPoP-bound token exchange fails.
+ ProxyStartupError: If the local proxy cannot be started.
+ FileNotFoundError: If the `nextflow` executable is not on PATH.
+ """
+ # Resolved up front so the generated config can name the real upstreams in its
+ # header comment, and so a bad --tes-endpoint fails before the token exchange.
+ resolved_tes_endpoint, resolved_s3_endpoint = resolve_service_endpoints(
+ auth, tes_endpoint, s3_endpoint
+ )
+
+ with dpop_proxy_context(
+ auth=auth,
+ task_token_type=task_token_type,
+ task_token_expiration=task_token_expiration,
+ tes_endpoint=tes_endpoint,
+ s3_endpoint=s3_endpoint,
+ port=port,
+ ) as (task_token, proxy_port):
+ env = os.environ.copy()
+ env["GEN3_DPOP_BOUND_TASK_TOKEN"] = task_token
+ env["GEN3_DPOP_PROXY_PORT"] = str(proxy_port)
+
+ with contextlib.ExitStack() as stack:
+ args = list(nf_args)
+ if generate_config:
+ # The config outlives nothing: the directory goes away with the run.
+ directory = stack.enter_context(tempfile.TemporaryDirectory())
+ config_path = _write_proxy_config(
+ directory=directory,
+ proxy_port=proxy_port,
+ tes_endpoint=resolved_tes_endpoint,
+ s3_endpoint=resolved_s3_endpoint,
+ )
+ args += ["-c", config_path]
+ logging.info(f"Generated Nextflow config: {config_path}")
+
+ logging.info("*** Starting Nextflow run... ***")
+ try:
+ result = subprocess.run(
+ ["nextflow", "run"] + args, env=env, check=False
+ )
+ except FileNotFoundError:
+ logging.error(
+ "Could not find `nextflow` on your PATH. Install it and try again."
+ )
+ raise
+ logging.info("*** Completed Nextflow run! ***")
+ return result.returncode
+
+
+def _write_proxy_config(
+ directory: str,
+ proxy_port: int,
+ tes_endpoint: str,
+ s3_endpoint: str,
+) -> str:
+ """
+ Write the Nextflow config that redirects TES and S3 to the local proxy.
+
+ Args:
+ directory (str): Directory to write into; the caller owns its lifetime.
+ proxy_port (int): Port the DPoP proxy is listening on.
+ tes_endpoint (str): Upstream TES endpoint, for the comment header.
+ s3_endpoint (str): Upstream S3 endpoint, for the comment header.
+
+ Returns:
+ str: Path to the config file that was written.
+ """
+ contents = _PROXY_CONFIG_TEMPLATE.format(
+ port=proxy_port,
+ tes_endpoint=tes_endpoint,
+ s3_endpoint=s3_endpoint,
+ )
+
+ path = Path(directory) / "gen3-dpop.config"
+ path.write_text(contents)
+ logging.debug(f"Generated Nextflow config {path}:\n{contents}")
+ return str(path)
diff --git a/poetry.lock b/poetry.lock
index 6fd949415..7cc3551a5 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 2.1.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 2.3.1 and should not be changed by hand.
[[package]]
name = "aiofiles"
@@ -14,150 +14,148 @@ files = [
[[package]]
name = "aiohappyeyeballs"
-version = "2.6.1"
+version = "2.7.1"
description = "Happy Eyeballs for asyncio"
optional = false
-python-versions = ">=3.9"
+python-versions = ">=3.10"
groups = ["main"]
files = [
- {file = "aiohappyeyeballs-2.6.1-py3-none-any.whl", hash = "sha256:f349ba8f4b75cb25c99c5c2d84e997e485204d2902a9597802b0371f09331fb8"},
- {file = "aiohappyeyeballs-2.6.1.tar.gz", hash = "sha256:c3f9d0113123803ccadfdf3f0faa505bc78e6a72d1cc4806cbd719826e943558"},
+ {file = "aiohappyeyeballs-2.7.1-py3-none-any.whl", hash = "sha256:9243213661e29250eb41368e5daa826fc017156c3b8a11440826b2e3ed376472"},
+ {file = "aiohappyeyeballs-2.7.1.tar.gz", hash = "sha256:065665c041c42a5938ed220bdcd7230f22527fbec085e1853d2402c8a3615d9d"},
]
[[package]]
name = "aiohttp"
-version = "3.13.2"
+version = "3.14.3"
description = "Async http client/server framework (asyncio)"
optional = false
-python-versions = ">=3.9"
+python-versions = ">=3.10"
groups = ["main"]
files = [
- {file = "aiohttp-3.13.2-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:2372b15a5f62ed37789a6b383ff7344fc5b9f243999b0cd9b629d8bc5f5b4155"},
- {file = "aiohttp-3.13.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:e7f8659a48995edee7229522984bd1009c1213929c769c2daa80b40fe49a180c"},
- {file = "aiohttp-3.13.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:939ced4a7add92296b0ad38892ce62b98c619288a081170695c6babe4f50e636"},
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- {file = "aiohttp-3.13.2-cp310-cp310-manylinux2014_armv7l.manylinux_2_17_armv7l.manylinux_2_31_armv7l.whl", hash = "sha256:6e7352512f763f760baaed2637055c49134fd1d35b37c2dedfac35bfe5cf8725"},
- {file = "aiohttp-3.13.2-cp310-cp310-manylinux2014_ppc64le.manylinux_2_17_ppc64le.manylinux_2_28_ppc64le.whl", hash = "sha256:e09a0a06348a2dd73e7213353c90d709502d9786219f69b731f6caa0efeb46f5"},
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[[package]]
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-codecs = ["cramjam", "lz4", "zstandard"]
+codecs = ["backports.zstd ; python_version < \"3.14\"", "cramjam", "lz4"]
lz4 = ["lz4"]
snappy = ["cramjam"]
-zstandard = ["zstandard"]
+zstandard = ["backports.zstd ; python_version < \"3.14\""]
[[package]]
name = "fhirclient"
-version = "4.3.2"
+version = "4.4.0"
description = "A flexible client for FHIR servers supporting the SMART on FHIR protocol"
optional = true
-python-versions = ">=3.9"
+python-versions = ">=3.10"
groups = ["main"]
markers = "extra == \"fhir\""
files = [
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@@ -1268,30 +1036,6 @@ requests = ">=2.4"
[package.extras]
tests = ["pytest (>=2.5)", "pytest-cov", "responses"]
-[[package]]
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-groups = ["dev"]
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-itsdangerous = ">=2.1.2"
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-Werkzeug = ">=2.3.7"
-
-[package.extras]
-async = ["asgiref (>=3.2)"]
-dotenv = ["python-dotenv"]
-
[[package]]
name = "frozenlist"
version = "1.8.0"
@@ -1432,33 +1176,16 @@ files = [
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]
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-python-versions = ">=3.6,<4.0"
-groups = ["dev"]
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-[package.dependencies]
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-cdiserrors = "<2.0.0"
-httpx = ">=0.20.0,<1.0.0"
-six = ">=1.16.0,<2.0.0"
-
[[package]]
name = "gen3dictionary"
-version = "2.0.4"
+version = "3.0.0"
description = ""
optional = false
-python-versions = "<4.0,>=3.9"
+python-versions = "<4,>=3.13"
groups = ["main"]
files = [
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[package.dependencies]
@@ -1490,38 +1217,19 @@ version = "0.16.0"
description = "A pure-Python, bring-your-own-I/O implementation of HTTP/1.1"
optional = false
python-versions = ">=3.8"
-groups = ["main", "dev"]
+groups = ["main"]
files = [
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-name = "hsclient"
-version = "0.1"
-description = ""
-optional = false
-python-versions = "*"
-groups = ["dev"]
-files = []
-develop = false
-
-[package.dependencies]
-requests = ">=2.5.2,<3.0.0"
-
-[package.source]
-type = "git"
-url = "https://github.com/uc-cdis/hsclient"
-reference = "1.0.0"
-resolved_reference = "f122072ee245216da5e4260f718d6f886db81773"
-
[[package]]
name = "httpcore"
version = "1.0.9"
description = "A minimal low-level HTTP client."
optional = false
python-versions = ">=3.8"
-groups = ["main", "dev"]
+groups = ["main"]
files = [
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@@ -1537,13 +1245,36 @@ http2 = ["h2 (>=3,<5)"]
socks = ["socksio (==1.*)"]
trio = ["trio (>=0.22.0,<1.0)"]
+[[package]]
+name = "httpcore2"
+version = "2.10.0"
+description = "A minimal low-level HTTP client."
+optional = false
+python-versions = ">=3.10"
+groups = ["main"]
+markers = "sys_platform != \"emscripten\""
+files = [
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+
+[package.dependencies]
+h11 = ">=0.16"
+truststore = ">=0.10"
+
+[package.extras]
+asyncio = ["anyio (>=4.5.0,<5.0)"]
+http2 = ["h2 (>=3,<5)"]
+socks = ["socksio (==1.*)"]
+trio = ["trio (>=0.33.0,<1.0)"]
+
[[package]]
name = "httpx"
version = "0.28.1"
description = "The next generation HTTP client."
optional = false
python-versions = ">=3.8"
-groups = ["main", "dev"]
+groups = ["main"]
files = [
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@@ -1562,6 +1293,46 @@ http2 = ["h2 (>=3,<5)"]
socks = ["socksio (==1.*)"]
zstd = ["zstandard (>=0.18.0)"]
+[[package]]
+name = "httpx2"
+version = "2.10.0"
+description = "The next generation HTTP client."
+optional = false
+python-versions = ">=3.10"
+groups = ["main"]
+files = [
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+
+[package.dependencies]
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+httpcore2 = {version = "2.10.0", markers = "sys_platform != \"emscripten\""}
+httpx2-jsfetch = {version = "*", markers = "sys_platform == \"emscripten\" and python_version >= \"3.12\""}
+idna = ">=3.18"
+truststore = {version = ">=0.10", markers = "sys_platform != \"emscripten\""}
+
+[package.extras]
+brotli = ["brotli ; platform_python_implementation == \"CPython\"", "brotlicffi ; platform_python_implementation != \"CPython\""]
+cli = ["click (>=8.4.2)", "pygments (==2.*)", "rich (>=10,<16)"]
+http2 = ["h2 (>=3,<5)"]
+socks = ["socksio (==1.*)"]
+ws = ["wsproto (>=1.2)"]
+zstd = ["zstandard (>=0.18.0) ; python_version <= \"3.13\""]
+
+[[package]]
+name = "httpx2-jsfetch"
+version = "1.0"
+description = "httpx2 transports for Emscripten/Pyodide, backed by the JavaScript fetch API."
+optional = false
+python-versions = ">=3.12"
+groups = ["main"]
+markers = "sys_platform == \"emscripten\""
+files = [
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+]
+
[[package]]
name = "humanfriendly"
version = "10.0"
@@ -1579,102 +1350,53 @@ pyreadline3 = {version = "*", markers = "sys_platform == \"win32\" and python_ve
[[package]]
name = "idna"
-version = "3.11"
+version = "3.18"
description = "Internationalized Domain Names in Applications (IDNA)"
optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
groups = ["main", "dev"]
files = [
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]
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+all = ["mypy (>=1.11.2)", "pytest (>=8.3.2)", "ruff (>=0.6.2)"]
[[package]]
name = "importlib-metadata"
-version = "8.7.0"
+version = "8.9.0"
description = "Read metadata from Python packages"
optional = false
-python-versions = ">=3.9"
-groups = ["main", "dev"]
+python-versions = ">=3.10"
+groups = ["main"]
files = [
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zipp = ">=3.20"
[package.extras]
-check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""]
+check = ["pytest-checkdocs (>=2.14)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""]
cover = ["pytest-cov"]
doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-enabler = ["pytest-enabler (>=2.2)"]
+enabler = ["pytest-enabler (>=3.4)"]
perf = ["ipython"]
-test = ["flufl.flake8", "importlib_resources (>=1.3) ; python_version < \"3.9\"", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-perf (>=0.9.2)"]
-type = ["pytest-mypy"]
+test = ["packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-perf (>=0.9.2)"]
+type = ["pytest-mypy (>=1.0.1) ; platform_python_implementation != \"PyPy\""]
[[package]]
name = "indexclient"
-version = "2.3.1"
+version = "6.3.0"
description = ""
optional = false
-python-versions = "*"
-groups = ["main", "dev"]
-files = [
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-description = "Gen3 Indexing Service"
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-groups = ["dev"]
-files = []
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-
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-authutils = "^6.0.0"
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-cdislogging = "^1.0.0"
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-dosclient = {git = "https://github.com/uc-cdis/dosclient", rev = "1.1.0"}
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-gen3authz = "^1.0.4"
-hsclient = {git = "https://github.com/uc-cdis/hsclient", rev = "1.0.0"}
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-jsonschema = "^3.2"
-psycopg2 = "^2.7"
-PyYAML = ">=5.3,<7"
-sqlalchemy = "~1.3.3"
-sqlalchemy-utils = "^0.37.3"
-
-[package.source]
-type = "git"
-url = "https://github.com/uc-cdis/indexd.git"
-reference = "5.0.4"
-resolved_reference = "5d3e54c31edba946f92d6d9ddccb016a7520e668"
-
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-description = "brain-dead simple config-ini parsing"
-optional = false
-python-versions = ">=3.8"
-groups = ["dev"]
-markers = "python_version < \"3.11\""
+python-versions = "<4.0,>=3.13"
+groups = ["main"]
files = [
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]
[[package]]
@@ -1684,41 +1406,28 @@ description = "brain-dead simple config-ini parsing"
optional = false
python-versions = ">=3.10"
groups = ["dev"]
-markers = "python_version >= \"3.11\""
files = [
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]
[[package]]
-name = "itsdangerous"
-version = "2.2.0"
-description = "Safely pass data to untrusted environments and back."
+name = "joserfc"
+version = "1.7.4"
+description = "The ultimate Python library for JOSE RFCs, including JWS, JWE, JWK, JWA, JWT"
optional = false
-python-versions = ">=3.8"
-groups = ["dev"]
-files = [
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-name = "jinja2"
-version = "3.1.6"
-description = "A very fast and expressive template engine."
-optional = false
-python-versions = ">=3.7"
-groups = ["dev"]
+python-versions = ">=3.10"
+groups = ["main"]
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python-json-logger = ">=2.0.0"
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optional = false
python-versions = ">=3.8"
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description = "pytest: simple powerful testing with Python"
optional = false
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python-versions = ">=3.8"
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[[package]]
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+version = "4.1.0"
description = "Backport of pathlib-compatible object wrapper for zip files"
optional = false
-python-versions = ">=3.9"
-groups = ["main", "dev"]
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- {file = "zipp-3.23.0.tar.gz", hash = "sha256:a07157588a12518c9d4034df3fbbee09c814741a33ff63c05fa29d26a2404166"},
+ {file = "zipp-4.1.0-py3-none-any.whl", hash = "sha256:25ad4e16390cd314347dd8f1de67a2ac538ae658ed4ab9db16029c07c188e97f"},
+ {file = "zipp-4.1.0.tar.gz", hash = "sha256:4cb57381f544315db7688e976e922a2b18cdb513d21cc194eb42232ba2a3e602"},
]
-markers = {dev = "python_version < \"3.11\""}
[package.extras]
-check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""]
+check = ["pytest-checkdocs (>=2.14)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""]
cover = ["pytest-cov"]
doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-enabler = ["pytest-enabler (>=2.2)"]
+enabler = ["pytest-enabler (>=3.4)"]
test = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more_itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"]
-type = ["pytest-mypy"]
+type = ["pytest-mypy (>=1.0.1) ; platform_python_implementation != \"PyPy\""]
[extras]
+dpop = ["uvicorn"]
fhir = ["fhirclient"]
[metadata]
lock-version = "2.1"
-python-versions = ">=3.9, <4"
-content-hash = "0ef223739ee0f4e9faf3bf60aa2c6ca6ea2757f7b84023e93c838109379a6915"
+python-versions = ">=3.13, <4"
+content-hash = "4021e5294293b73b7e341d0f029afe3c2db21cbf106cb95fed42ac22c5512493"
diff --git a/pyproject.toml b/pyproject.toml
index 85368130d..0e41bc3c5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,7 +1,7 @@
[tool.poetry]
name = "gen3"
homepage = "https://gen3.org/"
-version = "4.28.3"
+version = "5.0.0"
description = "Gen3 CLI and Python SDK"
authors = ["Center for Translational Data Science at the University of Chicago "]
license = "Apache-2.0"
@@ -13,46 +13,54 @@ classifiers = [
"Intended Audience :: Science/Research",
"Intended Audience :: Developers",
"License :: OSI Approved :: Apache Software License",
- "Programming Language :: Python :: 3.9",
+ "Programming Language :: Python :: 3.13",
"Topic :: Scientific/Engineering",
]
[tool.poetry.dependencies]
-python = ">=3.9, <4"
+python = ">=3.13, <4"
requests = "*"
-indexclient = "^2.3.0"
+httpx2 = ">=2.9.1"
+indexclient = ">=2.3.0"
drsclient = ">=0.3.0"
aiohttp = "*"
backoff = "*"
-cdislogging = "^1.1.0"
+cdislogging = ">=1.1.0"
click = "*"
importlib_metadata = ">=8,<9"
jsonschema = "*"
# FIXME updating to >=0.6.0 breaks a few tests
dataclasses-json = "<=0.5.9"
pypfb = ">=0.6.2"
-tqdm = "^4.61.2"
+tqdm = ">=4.61.2"
humanfriendly ="*"
python-dateutil = "*"
aiofiles = "*"
pandas = ">=1.4.2"
-xmltodict = "^0.13.0"
+xmltodict = ">=0.13.0"
gen3users = "*"
+joserfc = ">=1.7.3"
+
+authutils = {git = "https://github.com/uc-cdis/authutils.git", rev = "feat/dpop"}
# A list of all of the optional dependencies, some of which are included in the
# below `extras`. They can be opted into by apps.
+# fhir
fhirclient = { version = "*", optional = true }
+# dpop
+uvicorn = { version = "*", optional = true }
+
[tool.poetry.extras]
fhir = ["fhirclient"]
+dpop = ["uvicorn"]
[tool.poetry.group.dev.dependencies]
-pytest = "^6.0.0"
+pytest = ">=6.0.0"
pytest-cov = "*"
+pytest-xdist = "*"
requests-mock = "*"
-cdisutilstest = { git = "https://github.com/uc-cdis/cdisutils-test.git", tag = "2.0.0" }
-indexd = { git = "https://github.com/uc-cdis/indexd.git", tag = "5.0.4" }
-deptry = "^0.23.1"
+deptry = ">=0.23.1"
[tool.poetry.scripts]
gen3 = "gen3.cli.__main__:main"
@@ -65,7 +73,27 @@ build-backend = "poetry.masonry.api"
[tool.pytest.ini_options]
minversion = "6.0"
-addopts = "-vv"
+# Run tests in parallel (as much as possible) by default.
+#
+# `load`, xdist's default, hands each test to whichever worker is free, so two tests
+# from the same module can run at once in different processes. `loadscope` instead
+# groups tests by class, or by module for tests outside one, and gives each whole
+# group to a single worker, so a module's tests stay in order in one process.
+#
+# `--dist loadscope` MUST accompany `-n`. Why? Some modules are not independent
+# test-by-test:
+# - the fixed TMP_FOLDER in gen3/tools/indexing/download_manifest.py, which the
+# library wipes on entry and then collects with a glob
+# - the ~/.cache/gen3 token cache, keyed by API key rather than by test
+# - download_tests/test_resolvers.py, where one test reads a DRS cache file that an
+# earlier test in the module wrote
+# - others? there might be...
+#
+# Under `load` these corrupt each other or go missing, and which tests fail moves
+# around from run to run. Thus, `loadscope` keeps things safe.
+#
+# Pass `-n0` to run serially if needed for debugging.
+addopts = "-vv --dist loadscope -n auto"
testpaths = [
"tests",
]
diff --git a/tests/conftest.py b/tests/conftest.py
index f118fe9f5..609011cac 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,22 +1,15 @@
"""
Conf Test for Gen3 test suite
"""
-from multiprocessing import Process
-import multiprocessing
+
+from collections.abc import Generator
from unittest.mock import patch
import os
import pytest
-import requests
from drsclient.client import DrsClient
-from cdisutilstest.code.indexd_fixture import (
- setup_database,
- clear_database,
- create_user,
-)
+
from gen3.cli.auth import endpoint
-from indexd import get_app
-from indexd.default_settings import settings
from gen3.file import Gen3File
from gen3.index import Gen3Index
@@ -25,6 +18,7 @@
from gen3.auth import Gen3Auth
from gen3.object import Gen3Object
+from tests.fake_indexd import FakeIndexd
os.makedirs("tests/outputs", exist_ok=True)
@@ -117,83 +111,37 @@ def supported_protocol(request):
return request.param
-@pytest.fixture(scope="session")
-def indexd_server():
- """
- Fixture copied from cdisutils-test and updated to mock Arborist
+@pytest.fixture
+def indexd_server() -> Generator[FakeIndexd, None, None]:
"""
+ An empty in-memory indexd, with every HTTP client routed to it.
- class MockServer(object):
- def __init__(self, port):
- self.port = port
- self.baseurl = "http://localhost:{}".format(port)
-
- def run_indexd(port):
- app = get_app()
- app.run(host="localhost", port=port, debug=False)
-
- def wait_for_indexd_alive(port):
- url = "http://localhost:{}".format(port)
- try:
- requests.get(url)
- except requests.ConnectionError:
- return wait_for_indexd_alive(port)
- else:
- return
-
- def wait_for_indexd_not_alive(port):
- url = "http://localhost:{}".format(port)
- try:
- requests.get(url)
- except requests.ConnectionError:
- return
- else:
- return wait_for_indexd_not_alive(port)
-
- class MockArboristClient(object):
- def auth_request(*args, **kwargs):
- return True
-
- port = 8001
- settings["auth"].arborist = MockArboristClient()
- indexd = Process(target=run_indexd, args=[port])
- # Add this line because OS X multiprocessing default is spawn which will cause pickling errors
- # NOTE: fork is unstable and not technically supported on OS X, forking is only supported on Unix
- # However explicitly setting default behavior to fork to pass unit test, only used for tests
- # https://docs.python.org/3/library/multiprocessing.html
- # https://github.com/pytest-dev/pytest-flask/issues/104
- multiprocessing.set_start_method("fork")
- indexd.start()
- wait_for_indexd_alive(port)
-
- yield MockServer(port=port)
-
- indexd.terminate()
+ Each test gets its own store, so there is no database to clear between them.
+ """
+ fake_indexd = FakeIndexd()
+ with fake_indexd.serving_in_process():
+ yield fake_indexd
@pytest.fixture
-def index_client(indexd_server):
+def index_client(indexd_server: FakeIndexd) -> Gen3Index:
"""
- Handles getting all the docs from an
- indexing endpoint. Currently this is changing from
- signpost to indexd, so we'll use just indexd_client now.
- I.E. test to a common interface this could be multiply our
- tests:
- https://docs.pytest.org/en/latest/fixture.html#parametrizing-fixtures
+ Gen3Index pointed at the fake indexd.
"""
- setup_database()
+ return Gen3Index(indexd_server.baseurl, ("admin", "admin"), service_location="")
- try:
- user = create_user("admin", "admin")
- except Exception:
- # assume user already exists, try using username and password for admin
- user = ("admin", "admin")
- client = Gen3Index(indexd_server.baseurl, user, service_location="")
-
- yield client
+@pytest.fixture
+def gen3_index_over_http() -> Generator[Gen3Index, None, None]:
+ """
+ Gen3Index pointed at a fake indexd listening on a real socket.
- clear_database()
+ For tools that shell out: a subprocess cannot see the in-process patching that
+ `indexd_server` relies on, so it needs a server it can actually connect to.
+ """
+ fake = FakeIndexd()
+ with fake.serving_over_http():
+ yield Gen3Index(fake.baseurl, ("admin", "admin"), service_location="")
@pytest.fixture
@@ -213,21 +161,11 @@ def gen3_query(gen3_auth):
@pytest.fixture(scope="function")
-def drs_client(indexd_server):
- """
- Returns a DrsClient. This will delete any documents,
- aliases, or users made by this
- client after the test has completed.
- Currently the default user is the admin user
- Runs once per test.
- """
- try:
- user = create_user("user", "user")
- except Exception:
- user = ("user", "user")
- client = DrsClient(baseurl=indexd_server.baseurl, auth=user)
- yield client
- clear_database()
+def drs_client(indexd_server: FakeIndexd) -> DrsClient:
+ """
+ Returns a DrsClient pointed at the fake indexd.
+ """
+ return DrsClient(baseurl=indexd_server.baseurl, auth=("user", "user"))
@pytest.fixture(scope="function")
diff --git a/tests/download_tests/test_download.py b/tests/download_tests/test_download.py
index 7440c1f4c..315c62d30 100644
--- a/tests/download_tests/test_download.py
+++ b/tests/download_tests/test_download.py
@@ -246,7 +246,7 @@ def test_get_drs_object_type(drs_objects, index, expected):
assert get_drs_object_type(drs_objects[index]) == expected
-@pytest.mark.parametrize("hostname", [("test.datacommons.io")])
+@pytest.mark.parametrize("hostname", ["test.datacommons.io"])
def test_get_external_wts_oidc(wts_oidc, hostname):
with requests_mock.Mocker() as m:
m.get(f"https://{hostname}/wts/external_oidc/", json=wts_oidc[hostname])
@@ -670,7 +670,7 @@ def test_download_objects(
# test download object with no auth
m.post(
- f"http://{hostname}/user/credentials/cdis/access_token",
+ f"http://{hostname}/user/credentials/api/access_token",
json={},
status_code=404,
)
@@ -864,7 +864,7 @@ def test_no_gen3_auth():
with requests_mock.Mocker() as m:
m.post(
- f"http://{hostname}/user/credentials/cdis/access_token",
+ f"http://{hostname}/user/credentials/api/access_token",
json={},
status_code=501,
)
@@ -924,7 +924,7 @@ def test_list_no_auth(
with requests_mock.Mocker() as m:
m.get(f"https://{hostname}/wts/external_oidc/", json=wts_oidc[hostname])
m.post(
- f"http://{hostname}/user/credentials/cdis/access_token",
+ f"http://{hostname}/user/credentials/api/access_token",
json={"access_token": "test_access_token"},
)
for object_id, info in drs_object_info.items():
@@ -937,7 +937,7 @@ def test_list_no_auth(
# test getting auth error
# test no auth
m.post(
- f"http://{hostname}/user/credentials/cdis/access_token",
+ f"http://{hostname}/user/credentials/api/access_token",
json={"access_token": "test_access_token"},
status_code=401,
)
diff --git a/tests/dpop/__init__.py b/tests/dpop/__init__.py
new file mode 100644
index 000000000..e69de29bb
diff --git a/tests/dpop/conftest.py b/tests/dpop/conftest.py
new file mode 100644
index 000000000..af8622815
--- /dev/null
+++ b/tests/dpop/conftest.py
@@ -0,0 +1,9 @@
+"""
+Values shared by the DPoP tests: the fake commons and the token it hands out.
+
+Both the proxy tests and the Nextflow tests assert on these, so they live here to
+keep the two files describing the same commons.
+"""
+
+TASK_TOKEN = "test-task-token-abc123"
+COMMONS = "https://gen3.example.com"
diff --git a/tests/dpop/test_dpop.py b/tests/dpop/test_dpop.py
new file mode 100644
index 000000000..49482a8a8
--- /dev/null
+++ b/tests/dpop/test_dpop.py
@@ -0,0 +1,1322 @@
+"""
+Test the DPoP token exchange, local proxy, and `gen3 dpop` commands.
+
+The proxy is exercised over real HTTP: each test runs the ASGI app under uvicorn
+in front of a local echo server, so assertions are made on what the upstream
+actually received rather than on the proxy's internals.
+"""
+
+import asyncio
+import base64
+from contextlib import contextmanager
+from dataclasses import dataclass
+import gzip
+import hashlib
+import json
+import logging as stdlib_logging
+import socket
+import time
+from typing import Any, Generator, Iterator
+from unittest.mock import MagicMock, patch
+
+import httpx2
+import pytest
+import requests
+from click.testing import CliRunner, Result
+from joserfc import jwk
+
+from gen3.auth import Gen3AuthError
+from gen3.cli.dpop import dpop
+from gen3.dpop import (
+ AsyncDPoPProxy,
+ MissingDPoPNonceError,
+ ProxyStartupError,
+ dpop_proxy_context,
+ exchange_api_key_for_task_token,
+ is_proxy_running,
+ logging as dpop_logging,
+ resolve_service_endpoints,
+ start_proxy_server,
+)
+from tests.dpop.conftest import COMMONS, TASK_TOKEN
+
+TOKEN_ENDPOINT = f"{COMMONS}/user/credentials/api/access_token"
+TES_PATH = "/ga4gh/tes/v1/tasks"
+S3_PATH = "/s3/bucket/key.txt"
+
+
+class _StubAuth:
+ """Minimal stand-in for Gen3Auth covering what dpop_proxy_context reads."""
+
+ def __init__(
+ self,
+ api_key: str | None = "some-api-key",
+ endpoint: str = COMMONS,
+ ) -> None:
+ self.endpoint = endpoint
+ self._api_key = api_key
+
+ def get_api_key(self) -> str | None:
+ """Return the configured API key."""
+ return self._api_key
+
+ def get_access_token(self) -> str:
+ """Return a placeholder user access token."""
+ return "user-access-token"
+
+
+def _api_key_expiring_in(seconds: int | None) -> str:
+ """
+ Build an unsigned JWT shaped like a Gen3 API key with the given lifetime.
+
+ Args:
+ seconds (int | None): Lifetime from now, or None to omit `exp` entirely.
+
+ Returns:
+ str: The encoded, unsigned API key.
+ """
+
+ def encode(payload: dict) -> str:
+ raw = json.dumps(payload).encode()
+ return base64.urlsafe_b64encode(raw).rstrip(b"=").decode("ascii")
+
+ claims: dict[str, Any] = {"scope": ["fence"]}
+ if seconds is not None:
+ claims["exp"] = int(time.time()) + seconds
+
+ header = encode({"alg": "RS256", "typ": "JWT"})
+ return f"{header}.{encode(claims)}.signature-not-checked-by-decode_token"
+
+
+@pytest.fixture
+def ec_key() -> jwk.Key:
+ """Generate an ephemeral EC P-256 key like the proxy does at startup."""
+ return jwk.generate_key("EC", "P-256", private=True)
+
+
+@pytest.fixture
+def dpop_logs() -> Iterator[list[stdlib_logging.LogRecord]]:
+ """Collect every record gen3.dpop logs at DEBUG during the test."""
+ records: list[stdlib_logging.LogRecord] = []
+ handler = stdlib_logging.Handler()
+ handler.emit = records.append
+ previous_level = dpop_logging.level
+
+ dpop_logging.addHandler(handler)
+ dpop_logging.setLevel(stdlib_logging.DEBUG)
+ yield records
+ dpop_logging.removeHandler(handler)
+ dpop_logging.setLevel(previous_level)
+
+
+@pytest.fixture
+def proxy(ec_key) -> Iterator["_Proxy"]:
+ """Run AsyncDPoPProxy in front of the echo upstream, both on localhost."""
+ upstream = _Upstream()
+ with _running(upstream) as upstream_port:
+ config = {
+ "KEY": ec_key,
+ "TASK_TOKEN": TASK_TOKEN,
+ "TES_ENDPOINT": f"http://127.0.0.1:{upstream_port}/ga4gh/tes",
+ "S3_ENDPOINT": f"http://127.0.0.1:{upstream_port}/s3",
+ "CACHED_NONCE": None,
+ }
+ app = AsyncDPoPProxy(config)
+ with _running(app) as port:
+ yield _Proxy(
+ upstream=upstream,
+ upstream_port=upstream_port,
+ config=config,
+ app=app,
+ url=f"http://127.0.0.1:{port}",
+ )
+
+
+class TestTaskTokenExchange:
+ """exchange_api_key_for_task_token against a cooperating token endpoint."""
+
+ def test_returns_the_task_token(self, ec_key, requests_mock):
+ """A successful exchange returns the token and no nonce."""
+ requests_mock.post(TOKEN_ENDPOINT, json={"access_token": TASK_TOKEN})
+
+ assert _exchange(ec_key) == (TASK_TOKEN, None)
+
+ def test_sends_a_dpop_proof_for_the_token_endpoint(self, ec_key, requests_mock):
+ """The request carries a proof bound to POST and the token endpoint."""
+ requests_mock.post(TOKEN_ENDPOINT, json={"access_token": TASK_TOKEN})
+
+ _exchange(ec_key)
+
+ payload = _jwt_segment(requests_mock.last_request.headers["DPoP"], 1)
+ assert payload["htm"] == "POST"
+ assert payload["htu"] == TOKEN_ENDPOINT
+ # No access token exists yet, so there is nothing to hash into ath.
+ assert "ath" not in payload
+
+ def test_task_token_type_and_expiration_are_requested(self, ec_key, requests_mock):
+ """
+ Token type and requested lifetime are sent as query parameters.
+
+ Asserted against the raw URL because requests_mock's parsed `qs`
+ lowercases values, which would hide a change in the token type's case.
+ """
+ requests_mock.post(TOKEN_ENDPOINT, json={"access_token": TASK_TOKEN})
+
+ _exchange(ec_key, task_token_expiration=900)
+
+ url = requests_mock.last_request.url
+ assert "task_token=WORKFLOW" in url
+ assert "expires_in=900" in url
+
+ def test_expiration_is_omitted_when_not_requested(self, ec_key, requests_mock):
+ """Without an explicit expiration the server default is left alone."""
+ requests_mock.post(TOKEN_ENDPOINT, json={"access_token": TASK_TOKEN})
+
+ _exchange(ec_key)
+
+ assert "expires_in" not in requests_mock.last_request.url
+
+
+class TestTaskTokenExchangeNonceRetry:
+ """A token endpoint that demands a nonce before it will issue a token."""
+
+ def test_nonce_challenge_is_retried(self, ec_key, requests_mock):
+ """A use_dpop_nonce response is retried with the server-provided nonce."""
+ requests_mock.post(
+ TOKEN_ENDPOINT,
+ [
+ {
+ "status_code": 400,
+ "json": {"error": "use_dpop_nonce"},
+ "headers": {"DPoP-Nonce": "as-nonce-1"},
+ },
+ {"status_code": 200, "json": {"access_token": TASK_TOKEN}},
+ ],
+ )
+
+ assert _exchange(ec_key) == (TASK_TOKEN, "as-nonce-1")
+ payload = _jwt_segment(requests_mock.last_request.headers["DPoP"], 1)
+ assert payload["nonce"] == "as-nonce-1"
+
+ def test_challenge_carrying_only_a_nonce_header_is_retried(
+ self, ec_key, requests_mock
+ ):
+ """A refusal with a nonce but no explanation is still read as a nonce demand."""
+ requests_mock.post(
+ TOKEN_ENDPOINT,
+ [
+ {
+ "status_code": 401,
+ "text": "",
+ "headers": {"DPoP-Nonce": "as-nonce-2"},
+ },
+ {"status_code": 200, "json": {"access_token": TASK_TOKEN}},
+ ],
+ )
+
+ assert _exchange(ec_key) == (TASK_TOKEN, "as-nonce-2")
+
+ def test_endless_nonce_challenge_gives_up(self, ec_key, requests_mock):
+ """An endpoint that never accepts a nonce ends in an error, not a loop."""
+ requests_mock.post(
+ TOKEN_ENDPOINT,
+ status_code=400,
+ json={"error": "use_dpop_nonce"},
+ headers={"DPoP-Nonce": "as-nonce-1"},
+ )
+
+ _refusal(ec_key)
+
+ assert requests_mock.call_count == 3
+
+ def test_challenge_without_a_nonce_header_raises(self, ec_key, requests_mock):
+ """A nonce demand with no DPoP-Nonce header is a server protocol error."""
+ requests_mock.post(
+ TOKEN_ENDPOINT, status_code=400, json={"error": "use_dpop_nonce"}
+ )
+
+ with pytest.raises(MissingDPoPNonceError):
+ _exchange(ec_key)
+
+
+class TestTaskTokenExchangeFailures:
+ """
+ What the caller is told when the exchange fails.
+
+ These assert only on data the fake server put in the response, never on this
+ SDK's own wording, so rephrasing an error message cannot break them.
+ """
+
+ def test_missing_access_token_raises(self, ec_key, requests_mock):
+ """A 200 without an access_token fails instead of returning None."""
+ requests_mock.post(TOKEN_ENDPOINT, json={"unexpected": "shape"})
+
+ with pytest.raises(Gen3AuthError):
+ _exchange(ec_key)
+
+ def test_unreachable_commons_raises_a_request_error(self, ec_key, requests_mock):
+ """A connection failure surfaces as a requests error, not a bare traceback."""
+ requests_mock.post(TOKEN_ENDPOINT, exc=requests.ConnectionError("no route"))
+
+ with pytest.raises(requests.RequestException):
+ _exchange(ec_key)
+
+ def test_status_code_and_url_are_reported(self, ec_key, requests_mock):
+ """The error names the status and the endpoint that rejected the request."""
+ requests_mock.post(TOKEN_ENDPOINT, status_code=403, json={"error": "denied"})
+
+ error = str(_refusal(ec_key))
+
+ assert "403" in error
+ assert TOKEN_ENDPOINT in error
+
+ # `body` is passed straight to requests_mock as kwargs (json= or text=).
+
+ @pytest.mark.parametrize(
+ "body,expected",
+ [
+ # Whichever field fence puts its explanation in, it is quoted back.
+ pytest.param({"json": {"message": "no can do"}}, "no can do", id="message"),
+ pytest.param(
+ {"json": {"error_description": "no can do"}},
+ "no can do",
+ id="error_description",
+ ),
+ pytest.param({"json": {"detail": "no can do"}}, "no can do", id="detail"),
+ pytest.param({"json": {"error": "no can do"}}, "no can do", id="error"),
+ # An HTML or plain-text body is included rather than dropped.
+ pytest.param(
+ {"text": "bad gateway"}, "bad gateway", id="html"
+ ),
+ # A JSON error with no field this SDK knows about is reported as-is.
+ pytest.param({"json": {"weird": ["shape"]}}, '"weird"', id="unknown_shape"),
+ # JSON that is not an object at all still has to survive the trip.
+ pytest.param({"json": ["no can do"]}, "no can do", id="json_array"),
+ ],
+ )
+ def test_server_explanation_is_surfaced(
+ self, ec_key, requests_mock, body, expected
+ ):
+ """Whatever the server said reaches the caller."""
+ requests_mock.post(TOKEN_ENDPOINT, status_code=400, **body)
+
+ assert expected in str(_refusal(ec_key))
+
+ def test_empty_error_body_still_raises(self, ec_key, requests_mock):
+ """A refusal with no body at all is still an error, not a crash."""
+ requests_mock.post(TOKEN_ENDPOINT, status_code=500, text="")
+
+ _refusal(ec_key)
+
+ def test_unrelated_error_is_not_retried_as_a_nonce_problem(
+ self, ec_key, requests_mock
+ ):
+ """A 400 carrying a nonce header but explaining something else is not retried."""
+ requests_mock.post(
+ TOKEN_ENDPOINT,
+ status_code=400,
+ json={"message": "no can do"},
+ headers={"DPoP-Nonce": "nonce-attached-to-everything"},
+ )
+
+ error = str(_refusal(ec_key))
+
+ assert requests_mock.call_count == 1
+ assert "no can do" in error
+
+
+class TestApiKeyExpirationCheck:
+ """The lifetime a task token can be asked for is bounded by the API key."""
+
+ @pytest.fixture(autouse=True)
+ def token_endpoint(self, requests_mock) -> None:
+ """Answer any exchange that does reach the network with a task token."""
+ requests_mock.post(TOKEN_ENDPOINT, json={"access_token": TASK_TOKEN})
+
+ def test_lifetime_within_the_api_key_is_allowed(self, ec_key, requests_mock):
+ """A lifetime the key can cover goes through untouched."""
+ token, _ = _exchange(
+ ec_key, api_key=_api_key_expiring_in(7200), task_token_expiration=3600
+ )
+
+ assert token == TASK_TOKEN
+ assert "expires_in=3600" in requests_mock.last_request.url
+
+ @pytest.mark.parametrize(
+ "api_key_lifetime,requested_lifetime",
+ [
+ pytest.param(3600, 345600, id="request_outlives_api_key"),
+ pytest.param(-60, 60, id="api_key_already_expired"),
+ ],
+ )
+ def test_impossible_lifetime_is_refused_before_any_request(
+ self, ec_key, requests_mock, api_key_lifetime, requested_lifetime
+ ):
+ """A lifetime the API key cannot cover fails locally, with no round trip."""
+ with pytest.raises(Gen3AuthError):
+ _exchange(
+ ec_key,
+ api_key=_api_key_expiring_in(api_key_lifetime),
+ task_token_expiration=requested_lifetime,
+ )
+
+ assert not requests_mock.called
+
+ def test_no_requested_lifetime_skips_the_check(self, ec_key, requests_mock):
+ """Without an explicit lifetime the server picks one, so nothing is checked."""
+ token, _ = _exchange(ec_key, api_key=_api_key_expiring_in(-60))
+
+ assert token == TASK_TOKEN
+ assert requests_mock.called
+
+ @pytest.mark.parametrize(
+ "api_key",
+ [
+ pytest.param("not-a-jwt", id="not_a_jwt"),
+ pytest.param("a.b.c", id="undecodable_segments"),
+ pytest.param("", id="empty"),
+ pytest.param(_api_key_expiring_in(None), id="no_exp_claim"),
+ ],
+ )
+ def test_api_key_with_no_readable_expiration_defers_to_the_server(
+ self, ec_key, requests_mock, api_key
+ ):
+ """A key that cannot bound the lifetime is the token endpoint's problem."""
+ token, _ = _exchange(ec_key, api_key=api_key, task_token_expiration=345600)
+
+ assert token == TASK_TOKEN
+ assert requests_mock.called
+
+
+class TestServiceEndpointResolution:
+ """Which TES and S3 endpoints the proxy is allowed to forward to."""
+
+ def test_endpoints_default_to_the_commons_that_issued_the_credentials(self):
+ """With no overrides, both endpoints sit on the commons named by the API key."""
+ tes_endpoint, s3_endpoint = resolve_service_endpoints(_StubAuth())
+
+ assert tes_endpoint == f"{COMMONS}/ga4gh/tes"
+ assert s3_endpoint == f"{COMMONS}/workflows/s3"
+
+ def test_overrides_on_the_same_commons_are_used_as_given(self):
+ """A commons that serves these APIs from elsewhere can say so."""
+ endpoints = resolve_service_endpoints(
+ _StubAuth(),
+ tes_endpoint=f"{COMMONS}/ga4gh-tes/v2",
+ s3_endpoint=f"{COMMONS}/data/s3",
+ )
+
+ assert endpoints == (f"{COMMONS}/ga4gh-tes/v2", f"{COMMONS}/data/s3")
+
+ @pytest.mark.parametrize(
+ "override",
+ [
+ pytest.param(
+ {"tes_endpoint": "https://other.example.com/ga4gh/tes"}, id="tes"
+ ),
+ pytest.param({"s3_endpoint": "https://other.example.com/s3"}, id="s3"),
+ ],
+ )
+ def test_an_endpoint_on_another_host_is_refused(self, override):
+ """
+ The task token is only valid on the commons that issued it.
+
+ Forwarding to any other host would hand that host a working credential, so
+ a mistyped endpoint has to fail rather than be honored.
+ """
+ with pytest.raises(Gen3AuthError):
+ resolve_service_endpoints(_StubAuth(), **override)
+
+
+class TestProxyLifecycle:
+ """Starting and stopping the background proxy server."""
+
+ @staticmethod
+ def _app(ec_key) -> AsyncDPoPProxy:
+ """A proxy app with no upstreams configured, for tests that only bind a port."""
+ return AsyncDPoPProxy({"KEY": ec_key, "TASK_TOKEN": TASK_TOKEN})
+
+ def test_os_assigned_port_is_reported(self, ec_key):
+ """With no port requested, the bound port is returned to the caller."""
+ with _running(self._app(ec_key)) as port:
+ assert port > 0
+ assert is_proxy_running(port)
+
+ def test_requested_port_is_honored(self, ec_key):
+ """An explicit port is used as given."""
+ requested = _unused_port()
+
+ with _running(self._app(ec_key), port=requested) as port:
+ assert port == requested
+
+ def test_shutdown_releases_the_port(self, ec_key):
+ """Stopping the server closes its listening socket and ends the thread."""
+ server, thread, port = start_proxy_server(self._app(ec_key), log_level="error")
+ server.should_exit = True
+ thread.join(timeout=10)
+
+ assert not thread.is_alive()
+ assert not is_proxy_running(port)
+
+ def test_context_manager_starts_and_stops_the_proxy(self, requests_mock):
+ """dpop_proxy_context yields a live proxy and tears it down on exit."""
+ requests_mock.post(TOKEN_ENDPOINT, json={"access_token": TASK_TOKEN})
+
+ with dpop_proxy_context(auth=_StubAuth()) as (task_token, port):
+ assert task_token == TASK_TOKEN
+ assert is_proxy_running(port)
+
+ assert not is_proxy_running(port)
+
+ def test_taken_port_fails_fast(self, ec_key):
+ """
+ A port that is in use is caught up front, not after the startup timeout.
+
+ Without the pre-check this still raises ProxyStartupError, just ten seconds
+ later, so the elapsed time is the only thing that tells the two apart.
+ """
+ with _running(self._app(ec_key)) as port:
+ started = time.monotonic()
+
+ with pytest.raises(ProxyStartupError):
+ start_proxy_server(self._app(ec_key), port=port, log_level="error")
+
+ assert time.monotonic() - started < 1
+
+ @pytest.mark.parametrize(
+ "auth",
+ [
+ pytest.param(_StubAuth(api_key=None), id="no_api_key"),
+ pytest.param(_StubAuth(endpoint=""), id="no_endpoint"),
+ ],
+ )
+ def test_context_manager_requires_credentials(self, auth, requests_mock):
+ """Incomplete credentials fail before anything is sent to the commons."""
+ requests_mock.post(TOKEN_ENDPOINT, json={"access_token": TASK_TOKEN})
+
+ with pytest.raises(Gen3AuthError):
+ with dpop_proxy_context(auth=auth):
+ pass
+
+ assert not requests_mock.called
+
+
+class TestProxyRouting:
+ """Where the proxy forwards each incoming path."""
+
+ @pytest.mark.parametrize(
+ "incoming_path,upstream_path",
+ [
+ # The endpoints already end in the prefix, so it must not be doubled.
+ (TES_PATH, TES_PATH),
+ (S3_PATH, S3_PATH),
+ ],
+ )
+ def test_path_is_routed_without_doubling_the_prefix(
+ self, proxy, incoming_path, upstream_path
+ ):
+ """Each incoming path reaches the right upstream at the right path."""
+ response = proxy.get(incoming_path)
+
+ assert response.status_code == 200
+ assert proxy.upstream.last_request["path"] == upstream_path
+
+ def test_method_and_query_string_are_preserved(self, proxy):
+ """The upstream sees the client's method and query parameters unchanged."""
+ proxy.request("DELETE", TES_PATH, params={"page": "2"})
+
+ assert proxy.upstream.last_request["method"] == "DELETE"
+ assert proxy.upstream.last_request["query"] == "page=2"
+
+ @pytest.mark.parametrize(
+ "path",
+ [
+ pytest.param("/bucket/key.txt", id="root_is_not_a_shortcut_for_s3"),
+ pytest.param("/user/credentials/api/access_token", id="other_gen3_service"),
+ pytest.param("/ga4gh/drs/v1/objects/abc", id="other_ga4gh_api"),
+ pytest.param("/", id="root"),
+ ],
+ )
+ def test_paths_outside_tes_and_s3_are_refused(self, proxy, path, dpop_logs):
+ """
+ Only TES and S3 traffic belongs on this proxy; the rest never leaves.
+
+ The task token and a valid proof are attached to everything forwarded, so
+ an unrecognized path must not be guessed at.
+ """
+ response = proxy.get(path)
+
+ assert response.status_code == 404
+ assert proxy.upstream.requests == []
+ # A local 404 is indistinguishable from an upstream one without this.
+ assert len(_warnings(dpop_logs)) >= 1
+
+ @pytest.mark.parametrize(
+ "path",
+ [
+ pytest.param("/s3/../user/credentials/api/access_token", id="literal"),
+ pytest.param("/s3/%2e%2e/user/x", id="percent_encoded"),
+ pytest.param("/s3/bucket/../../user/x", id="nested"),
+ pytest.param("/ga4gh/tes/../../user/x", id="from_tes"),
+ ],
+ )
+ def test_paths_that_escape_their_upstream_base_are_refused(
+ self, proxy, path, dpop_logs
+ ):
+ """
+ A path may not use `..` to reach a commons endpoint outside its base.
+
+ uvicorn hands over the decoded path and httpx resolves dot segments when
+ it builds the request, so without this the proxy would sign a request to
+ any path on the commons with the task token.
+ """
+ assert proxy.raw_get_status(path) == 404
+ assert proxy.upstream.requests == []
+ # This one is worth noticing in a log: it means something is sending paths
+ # that try to leave the two endpoints the task token is meant for.
+ assert len(_warnings(dpop_logs)) >= 1
+
+
+class TestProxyHeaders:
+ """What the proxy sends upstream on behalf of the client."""
+
+ def test_only_the_task_token_holder_may_use_the_proxy(self, proxy):
+ """
+ A caller that does not hold the task token is refused.
+ """
+ for header in (None, "Bearer some-other-token", "Bearer", "Basic abc", ""):
+ headers = {} if header is None else {"Authorization": header}
+ # An empty dict would let the helper fill in the token, so ask for a header
+ # that carries no usable one.
+ response = proxy.get(
+ TES_PATH, headers=headers or {"Authorization": "Bearer wrong"}
+ )
+ assert response.status_code == 401, f"accepted {header!r}"
+ assert proxy.upstream.requests == [], "nothing should have been forwarded"
+
+ def test_the_task_token_is_accepted_however_it_is_presented(self, proxy):
+ """
+ Both routes authorize on the same token: TES sends it behind a scheme, and an S3
+ client sends it as the access key ID of an AWS signature.
+ """
+ assert proxy.get(TES_PATH).status_code == 200
+ assert (
+ proxy.get(
+ S3_PATH,
+ headers={
+ "Authorization": f"AWS4-HMAC-SHA256 Credential={TASK_TOKEN}"
+ "/20240101/us-east-1/s3/aws4_request"
+ },
+ ).status_code
+ == 200
+ )
+ assert (
+ proxy.get(
+ S3_PATH, headers={"Authorization": f"AWS {TASK_TOKEN}:signature"}
+ ).status_code
+ == 200
+ )
+
+ def test_tes_credentials_are_replaced(self, proxy):
+ """On the TES route the proxy supplies both credentials itself."""
+ proxy.get(
+ TES_PATH,
+ headers={
+ "Authorization": f"Bearer {TASK_TOKEN}",
+ "DPoP": "client-supplied-proof",
+ },
+ )
+
+ headers = proxy.upstream.last_request["headers"]
+ assert headers["authorization"] == f"DPoP {TASK_TOKEN}"
+ assert headers["dpop"] != "client-supplied-proof"
+
+ def test_tes_sends_one_authorization_header(self, proxy):
+ """
+ The client's `Authorization` is replaced on the TES route, not duplicated.
+ This validates there's no unintentional duplication due to header case.
+ """
+ proxy.get(TES_PATH, headers={"Authorization": f"Bearer {TASK_TOKEN}"})
+
+ names = proxy.upstream.last_request["header_names"]
+ assert names.count("authorization") == 1
+
+ def test_s3_signature_survives_the_hop(self, proxy):
+ """On the S3 route the client's signed `Authorization` is forwarded as-is."""
+ # Gen3's S3 endpoint reads the token out of the SigV4 `Credential` field, so
+ # replacing the header with the DPoP scheme leaves it no token to find.
+ signed = f"AWS4-HMAC-SHA256 Credential={TASK_TOKEN}/20240101/us-east-1/s3/aws4_request"
+ proxy.get(
+ S3_PATH,
+ headers={"Authorization": signed, "DPoP": "client-supplied-proof"},
+ )
+
+ headers = proxy.upstream.last_request["headers"]
+ assert headers["authorization"] == signed
+ assert headers["dpop"] != "client-supplied-proof"
+
+ def test_unrelated_headers_are_forwarded(self, proxy):
+ """Client headers the proxy has no opinion about are passed through."""
+ proxy.put(
+ S3_PATH,
+ headers={
+ "x-amz-content-sha256": "UNSIGNED-PAYLOAD",
+ "x-amz-date": "20240101T000000Z",
+ },
+ data=b"payload",
+ )
+
+ headers = proxy.upstream.last_request["headers"]
+ assert headers["x-amz-content-sha256"] == "UNSIGNED-PAYLOAD"
+ assert headers["x-amz-date"] == "20240101T000000Z"
+
+ def test_host_header_names_the_upstream(self, proxy):
+ """Host is rebuilt for the upstream rather than forwarded from the client."""
+ proxy.get(TES_PATH)
+
+ assert (
+ proxy.upstream.last_request["headers"]["host"]
+ == f"127.0.0.1:{proxy.upstream_port}"
+ )
+
+ def test_connection_specific_headers_are_not_forwarded(self, proxy):
+ """
+ Connection-specific fields describe the client's connection, not ours.
+
+ An intermediary strips them rather than passing them on (RFC 9110 7.6.1).
+ """
+ proxy.get(TES_PATH, headers={"te": "trailers", "upgrade": "h2c"})
+
+ headers = proxy.upstream.last_request["headers"]
+ assert "te" not in headers
+ assert "upgrade" not in headers
+
+ def test_task_token_is_never_logged(self, proxy, dpop_logs):
+ """`-vv` output could get pasted into bug reports, so it must carry no credential."""
+ proxy.get(TES_PATH)
+
+ logged = "\n".join(r.getMessage() for r in dpop_logs)
+ assert "DPoP proof" in logged, "debug logging did not run"
+ assert TASK_TOKEN not in logged
+
+
+class TestProxyDPoPProof:
+ """The proof the upstream receives with each proxied request."""
+
+ def test_proof_binds_the_request_and_the_task_token(self, proxy):
+ """htm, htu and ath describe the request the upstream actually got."""
+ proxy.request("POST", TES_PATH, params={"page": "2"}, json={"a": 1})
+
+ payload = proxy.proof()
+ assert payload["htm"] == "POST"
+ assert payload["htu"] == f"http://127.0.0.1:{proxy.upstream_port}{TES_PATH}"
+ # htu carries scheme, host and path only, per RFC 9449 4.2.
+ assert "?" not in payload["htu"]
+ assert payload["ath"] == _expected_ath(TASK_TOKEN)
+
+ def test_proof_header_advertises_the_public_key_only(self, proxy):
+ """The embedded JWK is an EC public key, never the private component."""
+ proxy.get(TES_PATH)
+
+ header = proxy.proof(index=0)
+ assert header["typ"] == "dpop+jwt"
+ assert header["alg"] == "ES256"
+ assert header["jwk"]["kty"] == "EC"
+ assert "d" not in header["jwk"]
+
+ def test_each_request_gets_a_fresh_proof(self, proxy):
+ """jti is unique per proxied request so proofs cannot be replayed."""
+ proxy.get(TES_PATH)
+ first_jti = proxy.proof()["jti"]
+ proxy.get(TES_PATH)
+
+ assert proxy.proof()["jti"] != first_jti
+
+ def test_cached_nonce_is_included_in_the_proof(self, proxy):
+ """A nonce already known at startup is carried in every proof."""
+ proxy.config["CACHED_NONCE"] = "nonce-from-token-exchange"
+ proxy.get(TES_PATH)
+
+ assert proxy.proof()["nonce"] == "nonce-from-token-exchange"
+
+
+class TestProxyBodies:
+ """Request and response bodies through the proxy."""
+
+ def test_chunked_upload_is_reframed_with_a_content_length(self, proxy):
+ """
+ A chunked upload from the client goes upstream with a content-length.
+
+ S3-compatible backends reject chunked PUTs, so the client's framing cannot
+ be passed through.
+ """
+
+ def chunks():
+ for _ in range(3):
+ yield b"y" * 100
+
+ response = proxy.put(S3_PATH, data=chunks())
+
+ assert response.status_code == 200
+ request = proxy.upstream.last_request
+ assert request["body_length"] == 300
+ assert request["headers"]["content-length"] == "300"
+ assert "transfer-encoding" not in request["headers"]
+
+ def test_bodyless_request_carries_no_framing_headers(self, proxy):
+ """A GET goes upstream without content-length or transfer-encoding."""
+ proxy.get(TES_PATH)
+
+ request = proxy.upstream.last_request
+ assert request["body_length"] == 0
+ assert "content-length" not in request["headers"]
+ assert "transfer-encoding" not in request["headers"]
+
+ def test_large_upload_arrives_intact(self, proxy):
+ """A body larger than the in-memory spool threshold is forwarded whole."""
+ size = 12 * 1024 * 1024
+
+ response = proxy.put("/s3/bucket/big", data=b"q" * size, timeout=120)
+
+ assert response.status_code == 200
+ assert proxy.upstream.last_request["body_length"] == size
+
+ def test_large_download_arrives_intact(self, proxy):
+ """A multi-megabyte response is streamed back with its content-length."""
+ proxy.upstream.response_megabytes = 8
+
+ with proxy.get("/s3/bucket/big", stream=True, timeout=120) as response:
+ content_length = response.headers["content-length"]
+ received = sum(len(chunk) for chunk in response.iter_content(65536))
+
+ assert received == 8 * 1024 * 1024
+ assert content_length == str(received)
+
+
+class TestProxyNonceRetry:
+ """How the proxy answers a use_dpop_nonce challenge."""
+
+ def test_challenge_is_retried_with_the_server_nonce(self, proxy):
+ """A nonce challenge is retried transparently and the client sees success."""
+ proxy.upstream.nonce_challenges_to_send = 1
+
+ response = proxy.get(TES_PATH)
+
+ assert response.status_code == 200
+ assert proxy.proof()["nonce"] == "server-nonce-1"
+
+ def test_body_is_replayed_on_retry(self, proxy):
+ """The retried request carries the same body as the original."""
+ proxy.upstream.nonce_challenges_to_send = 1
+
+ response = proxy.put(S3_PATH, data=b"x" * 4096)
+
+ assert response.status_code == 200
+ assert proxy.upstream.last_request["body_length"] == 4096
+
+ def test_persistent_challenge_is_returned_to_the_client(self, proxy):
+ """After the retry budget is spent, the upstream's 401 reaches the client."""
+ proxy.upstream.nonce_challenges_to_send = 99
+
+ response = proxy.get(TES_PATH)
+
+ assert response.status_code == 401
+ assert response.json() == {"error": "use_dpop_nonce"}
+ assert proxy.upstream.nonce_challenges_sent == 3
+
+ def test_challenge_without_a_usable_nonce_becomes_a_502(self, proxy):
+ """A server demanding a nonce but sending an empty one is a protocol error."""
+ proxy.upstream.nonce_challenges_to_send = 1
+ proxy.upstream.nonce_header = b""
+
+ response = proxy.get(TES_PATH)
+
+ assert response.status_code == 502
+
+
+class TestProxyUpstreamFailures:
+ """How upstream problems are reported to the client."""
+
+ @pytest.mark.parametrize("status", [400, 401, 403, 500])
+ def test_upstream_error_reaches_the_client_intact(self, proxy, status):
+ """
+ An error the upstream raised is forwarded with its status and body.
+
+ A 400 or 401 is read in full before it can be told apart from a nonce
+ challenge, so those two take the buffered path and the others are streamed;
+ either way the client has to end up with the same status and explanation.
+ """
+ proxy.upstream.error_status = status
+ proxy.upstream.error_body = b'{"error": "invalid_token"}'
+
+ response = proxy.get(TES_PATH)
+
+ assert response.status_code == status
+ assert response.json() == {"error": "invalid_token"}
+
+ def test_compressed_upstream_error_is_reframed_before_forwarding(self, proxy):
+ """
+ A compressed error body is forwarded decoded, without its stale headers.
+
+ Classifying a 400 decodes the body, so leaving `content-encoding` in place
+ would tell the client to gunzip plain text.
+ """
+ body = b'{"error": "invalid_request"}'
+ proxy.upstream.error_status = 400
+ proxy.upstream.error_body = gzip.compress(body)
+ proxy.upstream.error_content_encoding = b"gzip"
+
+ response = proxy.get(TES_PATH)
+
+ assert response.status_code == 400
+ assert response.content == body
+ assert "content-encoding" not in response.headers
+
+ def test_unreachable_upstream_becomes_a_502(self, proxy):
+ """A connection failure is reported as a bad gateway, not a crash."""
+ proxy.config["S3_ENDPOINT"] = f"http://127.0.0.1:{_unused_port()}/s3"
+
+ response = proxy.get(S3_PATH)
+
+ assert response.status_code == 502
+ assert "Upstream request failed" in response.text
+
+
+class TestProxyUpstreamTimeouts:
+ """How long the proxy waits on an upstream before giving up."""
+
+ def test_upstream_that_never_answers_becomes_a_504(self, proxy):
+ """An upstream that stops responding times out instead of hanging forever."""
+ proxy.upstream.slow_response_seconds = 0.4
+ proxy.app._client.timeout = httpx2.Timeout(0.1)
+
+ response = proxy.get(TES_PATH)
+
+ assert response.status_code == 504
+
+ @pytest.mark.parametrize("action", ["read", "write"])
+ def test_upstream_transfers_outlive_the_httpx_default_timeout(self, ec_key, action):
+ """
+ The proxy waits longer than httpx2's default before giving up on a transfer.
+
+ A workflow moves objects that take far longer than httpx2's 5s default, so
+ inheriting that default would truncate them.
+ """
+ default = getattr(httpx2.AsyncClient().timeout, action)
+ configured = getattr(AsyncDPoPProxy({"KEY": ec_key})._client.timeout, action)
+
+ assert configured is not None, f"no {action} timeout leaves a transfer hanging"
+ assert configured > default
+
+
+class TestProxyAsgiScopes:
+ """Which ASGI protocols the proxy app serves."""
+
+ def test_non_http_scope_is_rejected(self, proxy):
+ """Only HTTP scopes are served; anything else gets a 404."""
+ sent = _run_asgi(proxy.app, {"type": "websocket"})
+
+ assert sent[0]["status"] == 404
+
+
+class TestProxyStartCommand:
+ """`gen3 dpop proxy start` option wiring and error reporting."""
+
+ @staticmethod
+ def _invoke(
+ args: list[str], auth_factory: Any = None, wait: Any = None
+ ) -> tuple[Result, Any, MagicMock]:
+ """
+ Run the command with the proxy stubbed out and the block short-circuited.
+
+ Args:
+ args (list[str]): Arguments after `proxy start`.
+ auth_factory (Any): Factory to put in the context, or None for a mock.
+ wait (Any): Side effect for the wait the command blocks on, so a test
+ can interrupt it instead of returning from it.
+
+ Returns:
+ tuple[Result, Any, MagicMock]: The CLI result, the auth factory, and
+ the patched dpop_proxy_context.
+ """
+ auth_factory = auth_factory or MagicMock()
+ with patch("gen3.cli.dpop.dpop_proxy_context") as proxy_context, patch(
+ "threading.Event.wait", side_effect=wait, return_value=None
+ ):
+ proxy_context.return_value.__enter__.return_value = (TASK_TOKEN, 8000)
+ result = CliRunner().invoke(
+ dpop,
+ ["proxy", "start"] + args,
+ obj={"auth_factory": auth_factory},
+ )
+ return result, auth_factory, proxy_context
+
+ @staticmethod
+ def _invoke_with_failure(error: BaseException) -> Result:
+ """Run the command with the proxy raising `error` on startup."""
+ with patch("gen3.cli.dpop.dpop_proxy_context", side_effect=error):
+ return CliRunner().invoke(
+ dpop, ["proxy", "start"], obj={"auth_factory": MagicMock()}
+ )
+
+ @pytest.mark.parametrize(
+ "args,expected",
+ [
+ # Defaults: no --port means "let the OS pick", hence None not 0.
+ ([], {"port": None, "task_token_type": "WORKFLOW"}),
+ (["--port", "8123"], {"port": 8123}),
+ (["--task-token-type", "TASK"], {"task_token_type": "TASK"}),
+ (["--task-token-expiration", "1800"], {"task_token_expiration": 1800}),
+ (
+ ["--tes-endpoint", "https://gen3.example.com/ga4gh/tes"],
+ {"tes_endpoint": "https://gen3.example.com/ga4gh/tes"},
+ ),
+ (
+ ["--s3-endpoint", "https://gen3.example.com/s3"],
+ {"s3_endpoint": "https://gen3.example.com/s3"},
+ ),
+ ],
+ )
+ def test_options_reach_the_proxy_context(self, args, expected):
+ """Each option is forwarded to dpop_proxy_context unchanged."""
+ result, _, proxy_context = self._invoke(args)
+
+ assert result.exit_code == 0
+ assert expected.items() <= proxy_context.call_args.kwargs.items()
+
+ @pytest.mark.parametrize(
+ "env,args,expected_port",
+ [
+ pytest.param({}, [], None, id="unset_lets_the_os_pick"),
+ pytest.param({"GEN3_DPOP_PROXY_PORT": "8000"}, [], 8000, id="env_pins_it"),
+ pytest.param(
+ {"GEN3_DPOP_PROXY_PORT": "8000"},
+ ["--port", "9111"],
+ 9111,
+ id="flag_beats_env",
+ ),
+ # `export GEN3_DPOP_PROXY_PORT=` is how people unset it, so it must
+ # not become a usage error.
+ pytest.param({"GEN3_DPOP_PROXY_PORT": ""}, [], None, id="empty_is_unset"),
+ ],
+ )
+ def test_port_can_be_pinned_with_an_environment_variable(
+ self, env, args, expected_port, monkeypatch
+ ):
+ """GEN3_DPOP_PROXY_PORT saves retyping --port on every run."""
+ for name, value in env.items():
+ monkeypatch.setenv(name, value)
+
+ result, _, proxy_context = self._invoke(args)
+
+ assert result.exit_code == 0
+ assert proxy_context.call_args.kwargs["port"] == expected_port
+
+ def test_the_bound_port_is_reported_to_the_user(self, caplog):
+ """
+ The port the proxy came up on is announced once it is serving.
+
+ With no port requested the OS picks one, so this line is the only place a
+ client can learn where to send its requests.
+ """
+ with caplog.at_level(stdlib_logging.WARNING, logger="gen3.cli.dpop"):
+ result, _, _ = self._invoke([])
+
+ assert result.exit_code == 0
+ assert "127.0.0.1:8000" in caplog.text
+
+ def test_credentials_come_from_the_root_group(self):
+ """Auth is resolved through the lazy factory the root group installs."""
+ result, auth_factory, proxy_context = self._invoke([])
+
+ assert result.exit_code == 0
+ auth_factory.get.assert_called_once_with()
+ assert proxy_context.call_args.kwargs["auth"] is auth_factory.get.return_value
+
+ def test_ctrl_c_stops_the_proxy_without_an_error(self):
+ """Ctrl+C is the documented way to stop the proxy, so it is not a failure."""
+ result, _, _ = self._invoke([], wait=KeyboardInterrupt)
+
+ assert result.exit_code == 0
+
+ @pytest.mark.parametrize(
+ "error",
+ [
+ Gen3AuthError("Requested a task token lifetime of 345600 seconds"),
+ ProxyStartupError("Something is already listening on 127.0.0.1:8000"),
+ MissingDPoPNonceError("Server did not provide a nonce"),
+ requests.ConnectionError("Failed to establish a new connection"),
+ ImportError("The DPoP proxy needs uvicorn"),
+ ],
+ )
+ def test_expected_failures_are_reported_without_a_traceback(self, error):
+ """Actionable failures exit 1 with just their message."""
+ result = self._invoke_with_failure(error)
+
+ assert result.exit_code == 1
+ assert "Traceback" not in result.output
+ assert str(error) in result.output
+
+ def test_unexpected_failures_keep_their_traceback(self):
+ """A bug in the SDK is not disguised as user error."""
+ result = self._invoke_with_failure(ZeroDivisionError("bug"))
+
+ assert isinstance(result.exception, ZeroDivisionError)
+
+
+def _jwt_segment(token: str, index: int) -> dict:
+ """Decode one segment of a JWT without verifying the signature."""
+ segment = token.split(".")[index]
+ padded = segment + "=" * (-len(segment) % 4)
+ return json.loads(base64.urlsafe_b64decode(padded).decode("utf-8"))
+
+
+def _expected_ath(token: str) -> str:
+ """Compute the ath claim value for an access token per RFC 9449 4.2."""
+ digest = hashlib.sha256(token.encode("ascii")).digest()
+ return base64.urlsafe_b64encode(digest).rstrip(b"=").decode("ascii")
+
+
+def _run_asgi(app: Any, scope: dict) -> list[dict]:
+ """Call an ASGI app once with an empty receive queue and collect what it sends."""
+ sent: list[dict] = []
+
+ async def send(message):
+ sent.append(message)
+
+ async def receive():
+ return {"type": "http.request", "body": b"", "more_body": False}
+
+ loop = asyncio.new_event_loop()
+ try:
+ loop.run_until_complete(app(scope, receive, send))
+ finally:
+ loop.close()
+ return sent
+
+
+def _unused_port() -> int:
+ """Ask the OS for a free port and release it, so a caller can try to bind it."""
+ with socket.socket() as probe:
+ probe.bind(("127.0.0.1", 0))
+ return probe.getsockname()[1]
+
+
+@contextmanager
+def _running(app: Any, **kwargs) -> Generator[int, None, None]:
+ """Serve an ASGI app for the duration of the block, yielding its bound port."""
+ server, thread, port = start_proxy_server(app, log_level="error", **kwargs)
+ try:
+ yield port
+ finally:
+ server.should_exit = True
+ thread.join(timeout=10)
+
+
+class _Upstream:
+ """
+ Echo server standing in for the TES and S3 endpoints.
+
+ Every response is driven by an attribute rather than the request itself, so a
+ test can ask for a nonce challenge, an error, a slow reply, or a large body on
+ any path.
+ """
+
+ def __init__(self) -> None:
+ self.requests: list[dict] = []
+ self.nonce_challenges_sent = 0
+ self.nonce_challenges_to_send = 0
+ self.nonce_header = b"server-nonce-1"
+ self.slow_response_seconds = 0.0
+ self.response_megabytes = 0
+ self.error_status = 0
+ self.error_body = b""
+ self.error_content_encoding = b""
+
+ @property
+ def last_request(self) -> dict:
+ """The most recent request the upstream received."""
+ return self.requests[-1]
+
+ async def __call__(self, scope, receive, send) -> None:
+ body = b""
+ more_body = True
+ while more_body:
+ message = await receive()
+ body += message.get("body", b"")
+ more_body = message.get("more_body", False)
+
+ self.requests.append(
+ {
+ "method": scope["method"],
+ "path": scope["path"],
+ "query": scope["query_string"].decode(),
+ "headers": {k.decode(): v.decode() for k, v in scope["headers"]},
+ # Kept alongside the dict, which collapses a header sent twice with different case.
+ "header_names": [k.decode().lower() for k, _ in scope["headers"]],
+ "body_length": len(body),
+ }
+ )
+
+ if self.nonce_challenges_to_send > 0:
+ self.nonce_challenges_to_send -= 1
+ self.nonce_challenges_sent += 1
+ await self._send_nonce_challenge(send)
+ return
+
+ if self.error_status:
+ await self._send_error(send)
+ return
+
+ if self.slow_response_seconds:
+ await asyncio.sleep(self.slow_response_seconds)
+
+ if self.response_megabytes:
+ await self._send_megabytes(send, self.response_megabytes)
+ return
+
+ await self._send_json(send, {"path": scope["path"], "body_length": len(body)})
+
+ async def _send_json(self, send, payload: dict) -> None:
+ """Send a small JSON body."""
+ encoded = json.dumps(payload).encode()
+ await send(
+ {
+ "type": "http.response.start",
+ "status": 200,
+ "headers": [
+ (b"content-type", b"application/json"),
+ (b"content-length", str(len(encoded)).encode()),
+ ],
+ }
+ )
+ await send({"type": "http.response.body", "body": encoded})
+
+ async def _send_megabytes(self, send, count: int) -> None:
+ """Stream `count` megabytes back in 1 MiB chunks."""
+ chunk = b"z" * (1024 * 1024)
+ await send(
+ {
+ "type": "http.response.start",
+ "status": 200,
+ "headers": [
+ (b"content-type", b"application/octet-stream"),
+ (b"content-length", str(count * len(chunk)).encode()),
+ ],
+ }
+ )
+ for _ in range(count):
+ await send({"type": "http.response.body", "body": chunk, "more_body": True})
+ await send({"type": "http.response.body", "body": b""})
+
+ async def _send_error(self, send) -> None:
+ """Refuse the request the way an upstream reports a problem of its own."""
+ headers = [
+ (b"content-type", b"application/json"),
+ (b"content-length", str(len(self.error_body)).encode()),
+ ]
+ if self.error_content_encoding:
+ headers.append((b"content-encoding", self.error_content_encoding))
+
+ await send(
+ {
+ "type": "http.response.start",
+ "status": self.error_status,
+ "headers": headers,
+ }
+ )
+ await send({"type": "http.response.body", "body": self.error_body})
+
+ async def _send_nonce_challenge(self, send) -> None:
+ """Reply the way a resource server demands a fresh DPoP nonce."""
+ body = b'{"error": "use_dpop_nonce"}'
+ await send(
+ {
+ "type": "http.response.start",
+ "status": 401,
+ "headers": [
+ (b"content-type", b"application/json"),
+ (b"content-length", str(len(body)).encode()),
+ (b"www-authenticate", b'DPoP error="use_dpop_nonce"'),
+ (b"dpop-nonce", self.nonce_header),
+ ],
+ }
+ )
+ await send({"type": "http.response.body", "body": body})
+
+
+@dataclass
+class _Proxy:
+ """A running AsyncDPoPProxy in front of a running echo upstream."""
+
+ upstream: _Upstream
+ upstream_port: int
+ config: dict
+ app: AsyncDPoPProxy
+ url: str
+
+ def request(self, method: str, path: str, **kwargs) -> requests.Response:
+ """
+ Send a request through the proxy.
+
+ Presents the task token the way Nextflow does, unless the caller set its own
+ Authorization header, since the proxy refuses a caller that does not hold it.
+ """
+ kwargs.setdefault("timeout", 60)
+ headers = dict(kwargs.pop("headers", None) or {})
+ if not any(name.lower() == "authorization" for name in headers):
+ headers["Authorization"] = f"Bearer {TASK_TOKEN}"
+ return requests.request(method, f"{self.url}{path}", headers=headers, **kwargs)
+
+ def get(self, path: str, **kwargs) -> requests.Response:
+ """GET through the proxy."""
+ return self.request("GET", path, **kwargs)
+
+ def put(self, path: str, **kwargs) -> requests.Response:
+ """PUT through the proxy."""
+ return self.request("PUT", path, **kwargs)
+
+ def raw_get_status(self, target: str) -> int:
+ """
+ GET an un-normalized request target and return the status code.
+
+ `requests` resolves `..` in a URL before sending, so a traversal attempt
+ has to be written onto the wire directly to reach the proxy intact.
+ """
+ port = int(self.url.rsplit(":", 1)[1])
+ request = (
+ f"GET {target} HTTP/1.1\r\n"
+ f"Host: 127.0.0.1:{port}\r\n"
+ f"Authorization: Bearer {TASK_TOKEN}\r\n\r\n"
+ )
+ with socket.create_connection(("127.0.0.1", port), timeout=60) as client:
+ client.sendall(request.encode())
+ status_line = client.recv(64).split(b"\r\n")[0]
+ return int(status_line.split()[1])
+
+ def proof(self, index: int = 1) -> dict:
+ """Decode the DPoP proof the upstream saw last (payload, or header if 0)."""
+ return _jwt_segment(self.upstream.last_request["headers"]["dpop"], index)
+
+
+def _warnings(records: list[stdlib_logging.LogRecord]) -> list[str]:
+ """The messages logged at WARNING or above."""
+ return [r.getMessage() for r in records if r.levelno >= stdlib_logging.WARNING]
+
+
+def _exchange(ec_key: jwk.Key, **overrides: Any) -> tuple[str, str | None]:
+ """Exchange an API key for a task token, overriding any default argument."""
+ kwargs: dict[str, Any] = {
+ "key": ec_key,
+ "token_endpoint": TOKEN_ENDPOINT,
+ "api_key": "some-api-key", # pragma: allowlist secret
+ "task_token_type": "WORKFLOW",
+ }
+ return exchange_api_key_for_task_token(**{**kwargs, **overrides})
+
+
+def _refusal(ec_key: jwk.Key, **overrides: Any) -> Gen3AuthError:
+ """Attempt an exchange expected to fail and return the error it raised."""
+ with pytest.raises(Gen3AuthError) as raised:
+ _exchange(ec_key, **overrides)
+ return raised.value
diff --git a/tests/dpop/test_dpop_nextflow.py b/tests/dpop/test_dpop_nextflow.py
new file mode 100644
index 000000000..a5f31e3a2
--- /dev/null
+++ b/tests/dpop/test_dpop_nextflow.py
@@ -0,0 +1,368 @@
+"""
+Test `gen3 nextflow run` (gen3.cli.nextflow, gen3.dpop_nextflow).
+
+Every test drives the real command through CliRunner with two things stubbed: the
+DPoP proxy, so nothing is exchanged for a task token or listens on a socket, and
+subprocess.run, so the argv and environment Nextflow would have been given can be
+read back without Nextflow being installed.
+"""
+
+from pathlib import Path
+from typing import Any, Callable, Iterator
+from unittest.mock import MagicMock, patch
+
+import pytest
+from click.testing import CliRunner, Result
+
+from gen3.auth import Gen3AuthError
+from gen3.cli.nextflow import nextflow
+from tests.dpop.conftest import COMMONS, TASK_TOKEN
+
+PROXY_PORT = 61234
+
+
+class _CompletedProcess:
+ """Stand-in for subprocess.CompletedProcess carrying an exit code."""
+
+ def __init__(self, returncode: int) -> None:
+ self.returncode = returncode
+
+
+@pytest.fixture
+def fake_proxy() -> Iterator[MagicMock]:
+ """Patch dpop_proxy_context so no token exchange or proxy startup happens."""
+ with patch("gen3.dpop_nextflow.dpop_proxy_context") as proxy_context:
+ proxy_context.return_value.__enter__.return_value = (TASK_TOKEN, PROXY_PORT)
+ yield proxy_context
+
+
+@pytest.fixture
+def nextflow_process() -> Iterator[MagicMock]:
+ """
+ Patch the subprocess.run that starts Nextflow.
+
+ A test that needs a failed run sets `return_value` or `side_effect` on the mock
+ before invoking the command.
+ """
+ with patch("subprocess.run", return_value=_CompletedProcess(0)) as run:
+ yield run
+
+
+@pytest.fixture
+def generated_config(nextflow_process) -> dict[str, Any]:
+ """
+ Capture the config `nextflow run` was given.
+
+ The file is deleted when the run ends, so it has to be read while the child
+ process is notionally running.
+ """
+ captured: dict[str, Any] = {}
+
+ def capture(*args: Any, **kwargs: Any) -> _CompletedProcess:
+ argv = args[0]
+ captured["path"] = Path(argv[argv.index("-c") + 1])
+ captured["contents"] = captured["path"].read_text()
+ return _CompletedProcess(0)
+
+ nextflow_process.side_effect = capture
+ return captured
+
+
+@pytest.fixture
+def auth_factory() -> MagicMock:
+ """
+ The lazy auth factory the root group installs, naming the fake commons.
+
+ Built per test: a factory shared between them would carry call history from
+ one into the next, so nothing could be asserted about who asked for auth.
+ """
+ factory = MagicMock()
+ factory.get.return_value.endpoint = COMMONS
+ return factory
+
+
+@pytest.fixture
+def run_cli(
+ auth_factory, fake_proxy, nextflow_process
+) -> Callable[[list[str]], Result]:
+ """
+ Run `gen3 nextflow run` with the arguments a user would type.
+
+ Depends on both stubs so that no test can reach a real commons or a real
+ `nextflow`, whether or not it asserts on them.
+ """
+
+ def invoke(args: list[str]) -> Result:
+ return CliRunner().invoke(
+ nextflow, ["run"] + args, obj={"auth_factory": auth_factory}
+ )
+
+ return invoke
+
+
+class TestNextflowInvocation:
+ """What the Nextflow child process is given, and what its exit means."""
+
+ def test_nextflow_args_are_forwarded(self, run_cli, nextflow_process):
+ """Nextflow's own flags are appended to `nextflow run`, not rejected by Click."""
+ run_cli(["main.nf", "-profile", "gen3", "-resume"])
+
+ argv = nextflow_process.call_args.args[0]
+ assert argv[:6] == [
+ "nextflow",
+ "run",
+ "main.nf",
+ "-profile",
+ "gen3",
+ "-resume",
+ ]
+ assert argv[-2] == "-c"
+
+ def test_a_double_dash_hands_colliding_params_to_nextflow(
+ self, run_cli, nextflow_process, fake_proxy
+ ):
+ """`--port` is a plausible pipeline param, so it has to be passable through."""
+ run_cli(["main.nf", "--", "--port", "8080"])
+
+ assert fake_proxy.call_args.kwargs["port"] is None
+ assert _pipeline_args(nextflow_process) == ["main.nf", "--port", "8080"]
+
+ def test_token_and_port_are_exported_to_nextflow(self, run_cli, nextflow_process):
+ """The child environment carries the task token and the proxy port."""
+ run_cli(["main.nf"])
+
+ env = nextflow_process.call_args.kwargs["env"]
+ assert env["GEN3_DPOP_BOUND_TASK_TOKEN"] == TASK_TOKEN
+ assert env["GEN3_DPOP_PROXY_PORT"] == str(PROXY_PORT)
+
+ def test_parent_environment_is_preserved(
+ self, run_cli, nextflow_process, monkeypatch
+ ):
+ """Existing environment variables still reach Nextflow."""
+ monkeypatch.setenv("NXF_HOME", "/tmp/nxf-home")
+
+ run_cli(["main.nf"])
+
+ assert nextflow_process.call_args.kwargs["env"]["NXF_HOME"] == "/tmp/nxf-home"
+
+ @pytest.mark.parametrize("return_code", [0, 1, 3, 137])
+ def test_the_pipeline_exit_code_becomes_the_cli_exit_code(
+ self, run_cli, nextflow_process, return_code
+ ):
+ """Click discards return values, so a failed pipeline has to be exited on."""
+ nextflow_process.return_value = _CompletedProcess(return_code)
+
+ assert run_cli(["main.nf"]).exit_code == return_code
+
+ def test_a_child_that_cannot_run_still_stops_the_proxy(
+ self, run_cli, nextflow_process, fake_proxy
+ ):
+ """The proxy holds a task token, so it must not outlive a failed run."""
+ nextflow_process.side_effect = OSError("boom")
+
+ result = run_cli(["main.nf"])
+
+ assert isinstance(result.exception, OSError)
+ fake_proxy.return_value.__exit__.assert_called_once()
+
+
+class TestGeneratedConfig:
+ """The override that redirects a commons-facing config to the proxy."""
+
+ def test_it_is_the_last_config_so_it_wins(self, run_cli, nextflow_process):
+ """Nextflow lets the last -c win, so ours has to come after the user's."""
+ run_cli(["main.nf", "-c", "mine.config"])
+
+ argv = nextflow_process.call_args.args[0]
+ assert argv[:5] == ["nextflow", "run", "main.nf", "-c", "mine.config"]
+ assert argv[-2] == "-c"
+ assert argv[-1].endswith("gen3-dpop.config")
+
+ def test_it_redirects_both_endpoints_to_the_proxy(self, run_cli, generated_config):
+ """The whole point: traffic aimed at the commons goes to the proxy instead."""
+ run_cli(["main.nf"])
+
+ contents = generated_config["contents"]
+ proxy = f"http://127.0.0.1:{PROXY_PORT}"
+ assert f"endpoint = '{proxy}/ga4gh/tes'" in contents
+ assert f"endpoint = '{proxy}/s3'" in contents
+ assert "s3PathStyleAccess = true" in contents
+
+ @pytest.mark.parametrize(
+ "owned_by_the_user", ["workDir", "region", "executor", "plugins"]
+ )
+ def test_it_overrides_nothing_else(
+ self, run_cli, generated_config, owned_by_the_user
+ ):
+ """A setting the proxy does not force must be left to the user's config."""
+ run_cli(["main.nf"])
+
+ # The header comment names these to explain what is left alone, so only the
+ # config statements themselves can be checked for them.
+ statements = "\n".join(
+ line
+ for line in generated_config["contents"].splitlines()
+ if not line.strip().startswith("//")
+ )
+ assert owned_by_the_user not in statements
+
+ def test_the_upstreams_are_named_so_users_can_see_where_traffic_goes(
+ self, run_cli, generated_config
+ ):
+ """127.0.0.1 endpoints are alarming without saying what is behind them."""
+ run_cli(["main.nf"])
+
+ assert f"{COMMONS}/ga4gh/tes" in generated_config["contents"]
+ assert f"{COMMONS}/workflows/s3" in generated_config["contents"]
+
+ def test_the_token_is_not_written_to_the_file(self, run_cli, generated_config):
+ """A temp file holding a bearer-equivalent credential is world-readable."""
+ run_cli(["main.nf"])
+
+ assert TASK_TOKEN not in generated_config["contents"]
+ assert "env('GEN3_DPOP_BOUND_TASK_TOKEN')" in generated_config["contents"]
+
+ def test_the_file_is_cleaned_up_after_the_run(self, run_cli, generated_config):
+ """The token lives in the environment, but the config still goes away."""
+ run_cli(["main.nf"])
+
+ assert not generated_config["path"].exists()
+
+ def test_no_config_is_passed_when_it_is_turned_off(self, run_cli, nextflow_process):
+ """--no-generated-config means the user's config is the only one."""
+ run_cli(["main.nf", "--no-generated-config"])
+
+ assert "-c" not in nextflow_process.call_args.args[0]
+
+
+class TestProxyOptions:
+ """The options the command owns rather than forwarding to Nextflow."""
+
+ @pytest.mark.parametrize(
+ "args,expected",
+ [
+ # No --port means "let the OS pick", so it arrives as None not 0.
+ pytest.param(
+ [],
+ {
+ "port": None,
+ "task_token_type": "WORKFLOW",
+ "task_token_expiration": None,
+ "tes_endpoint": None,
+ "s3_endpoint": None,
+ },
+ id="defaults",
+ ),
+ pytest.param(["--port", "8123"], {"port": 8123}, id="port"),
+ pytest.param(
+ ["--task-token-type", "TASK"], {"task_token_type": "TASK"}, id="type"
+ ),
+ pytest.param(
+ ["--task-token-expiration", "1800"],
+ {"task_token_expiration": 1800},
+ id="expiration",
+ ),
+ pytest.param(
+ ["--tes-endpoint", f"{COMMONS}/ga4gh/tes"],
+ {"tes_endpoint": f"{COMMONS}/ga4gh/tes"},
+ id="tes_endpoint",
+ ),
+ pytest.param(
+ ["--s3-endpoint", f"{COMMONS}/workflows/s3"],
+ {"s3_endpoint": f"{COMMONS}/workflows/s3"},
+ id="s3_endpoint",
+ ),
+ ],
+ )
+ def test_proxy_options_are_forwarded(
+ self, run_cli, fake_proxy, nextflow_process, args, expected
+ ):
+ """Every proxy option reaches the proxy, and none of them reach Nextflow."""
+ result = run_cli(["main.nf"] + args)
+
+ assert result.exit_code == 0
+ assert expected.items() <= fake_proxy.call_args.kwargs.items()
+ assert _pipeline_args(nextflow_process) == ["main.nf"]
+
+ def test_port_can_be_pinned_with_an_environment_variable(
+ self, run_cli, fake_proxy, monkeypatch
+ ):
+ """The same variable the proxy exports also pins the port on the way in."""
+ monkeypatch.setenv("GEN3_DPOP_PROXY_PORT", "8000")
+
+ result = run_cli(["main.nf"])
+
+ assert result.exit_code == 0
+ assert fake_proxy.call_args.kwargs["port"] == 8000
+
+ def test_credentials_come_from_the_root_group(
+ self, run_cli, auth_factory, fake_proxy
+ ):
+ """Auth is resolved through the lazy factory the root group installs."""
+ result = run_cli(["main.nf"])
+
+ assert result.exit_code == 0
+ auth_factory.get.assert_called_once_with()
+ assert fake_proxy.call_args.kwargs["auth"] is auth_factory.get.return_value
+
+ def test_an_endpoint_off_the_commons_fails_before_the_token_exchange(
+ self, run_cli, fake_proxy, nextflow_process
+ ):
+ """Endpoints are resolved first, so a bad one costs no credentials."""
+ result = run_cli(
+ ["main.nf", "--tes-endpoint", "https://other.example.com/ga4gh/tes"]
+ )
+
+ assert result.exit_code == 1
+ assert not fake_proxy.called
+ assert not nextflow_process.called
+
+
+class TestErrorReporting:
+ """How a failed run is reported to whoever typed the command."""
+
+ @pytest.mark.parametrize(
+ "failing_fixture,error",
+ [
+ pytest.param(
+ "fake_proxy",
+ Gen3AuthError("the commons explained why"),
+ id="token_exchange",
+ ),
+ pytest.param(
+ "nextflow_process",
+ FileNotFoundError("nextflow is not installed"),
+ id="missing_executable",
+ ),
+ ],
+ )
+ def test_expected_failures_are_reported_without_a_traceback(
+ self, request, run_cli, failing_fixture, error
+ ):
+ """An actionable failure exits 1 with its own message and no traceback."""
+ request.getfixturevalue(failing_fixture).side_effect = error
+
+ result = run_cli(["main.nf"])
+
+ assert result.exit_code == 1
+ assert "Traceback" not in result.output
+ assert str(error) in result.output
+
+ def test_unexpected_failures_keep_their_traceback(self, run_cli, nextflow_process):
+ """A bug in the SDK is not disguised as user error."""
+ nextflow_process.side_effect = ZeroDivisionError("bug")
+
+ assert isinstance(run_cli(["main.nf"]).exception, ZeroDivisionError)
+
+ def test_help_does_not_require_credentials(self):
+ """`--help` works without any Gen3 credentials configured."""
+ result = CliRunner().invoke(nextflow, ["run", "--help"])
+
+ assert result.exit_code == 0
+ assert "Usage:" in result.output
+
+
+def _pipeline_args(nextflow_process: MagicMock) -> list[str]:
+ """The arguments Nextflow got, without `nextflow run` or the generated `-c`."""
+ argv = nextflow_process.call_args.args[0]
+ return argv[2:-2]
diff --git a/tests/fake_indexd.py b/tests/fake_indexd.py
new file mode 100644
index 000000000..930effd2c
--- /dev/null
+++ b/tests/fake_indexd.py
@@ -0,0 +1,410 @@
+"""
+An in-memory stand-in for the indexd HTTP API, for tests that need a live index.
+
+One store, served either by patching the SDK's HTTP clients - `requests` (Gen3Index and
+indexclient) and `httpx` (drsclient) - or over a real socket for code that leaves the
+process and so cannot see those patches.
+
+Only the endpoints and query parameters the tests exercise are implemented. Unknown
+query parameters are ignored rather than filtered on, so a test that needs a new filter
+has to add it here.
+"""
+
+import json
+import threading
+from collections.abc import Generator
+from contextlib import ExitStack, contextmanager
+from copy import deepcopy
+from datetime import datetime, timezone
+from http.server import BaseHTTPRequestHandler, ThreadingHTTPServer
+from types import MappingProxyType
+from typing import Any
+from unittest.mock import patch
+from urllib.parse import parse_qs, urlparse
+from uuid import uuid4
+
+import httpx
+import requests_mock
+from drsclient import client as drsclient_module
+
+# Gen3Index reads "http://localhost" as indexd deployed on its own rather than behind a
+# commons, and drops the `/index` service location. Tools under test build their own
+# Gen3Index from this URL, so it has to keep that property.
+BASE_URL = "http://localhost:8001"
+
+DEFAULT_PAGE_SIZE = 100
+
+# indexd's own test configuration mints GUIDs as "", and a caller
+# that lets indexd choose the GUID can assert on that prefix.
+DEFAULT_PREFIX = "testprefix/"
+
+# Read-only, and copied per record
+_RECORD_DEFAULTS = MappingProxyType(
+ {
+ "acl": [],
+ "authz": [],
+ "content_created_date": None,
+ "content_updated_date": None,
+ "description": None,
+ "file_name": None,
+ "form": "object",
+ "hashes": {},
+ "metadata": {},
+ "size": None,
+ "uploader": None,
+ "urls": [],
+ "urls_metadata": {},
+ "version": None,
+ }
+)
+
+
+class FakeIndexd:
+ """
+ The store, its request handler, and the patches that route clients to it.
+
+ Attributes:
+ baseurl (str): The URL clients should be pointed at.
+ records (dict): Index records by did, in creation order.
+ bundles (dict): Bundle records by bundle_id, in creation order.
+ """
+
+ def __init__(self, baseurl: str = BASE_URL) -> None:
+ self.baseurl = baseurl
+ self.records: dict[str, dict] = {}
+ self.bundles: dict[str, dict] = {}
+
+ @contextmanager
+ def serving_in_process(self) -> Generator["FakeIndexd", None, None]:
+ """
+ Route this process's requests and httpx calls to this store.
+
+ Yields:
+ FakeIndexd: This instance, once the patches are in place.
+ """
+ with ExitStack() as stack:
+ mocker = stack.enter_context(requests_mock.Mocker())
+ mocker.register_uri(
+ requests_mock.ANY, requests_mock.ANY, text=self._serve_requests
+ )
+ # drsclient builds its own httpx client per call, so the class it
+ # instantiates is the only place a transport can be injected.
+ stack.enter_context(
+ patch("drsclient.client.SyncClient", self._mocked_httpx_client())
+ )
+ yield self
+
+ @contextmanager
+ def serving_over_http(self) -> Generator["FakeIndexd", None, None]:
+ """
+ Serve this store over a real socket, and point `baseurl` at it.
+
+ For code that leaves the process: `download_object_manifest` fans out with
+ `asyncio.create_subprocess_shell`, and the children's HTTP traffic cannot be
+ intercepted by any in-process patch.
+
+ Yields:
+ FakeIndexd: This instance, once the server is accepting connections.
+ """
+ server = ThreadingHTTPServer(("127.0.0.1", 0), _handler_for(self))
+ thread = threading.Thread(target=server.serve_forever, daemon=True)
+ thread.start()
+
+ # Gen3Index only drops the `/index` service location for "http://localhost".
+ self.baseurl = f"http://localhost:{server.server_address[1]}"
+ try:
+ yield self
+ finally:
+ server.shutdown()
+ server.server_close()
+ thread.join()
+
+ def handle(
+ self, method: str, url: str, body: bytes | None
+ ) -> tuple[int, Any, bool]:
+ """
+ Serve one request.
+
+ Args:
+ method (str): HTTP method.
+ url (str): Full request URL.
+ body (bytes | None): Request body, if any.
+
+ Returns:
+ tuple[int, Any, bool]: Status code, payload, and whether the payload is
+ already text rather than something to serialize as JSON.
+ """
+ parsed = urlparse(url)
+ path = parsed.path.rstrip("/") or "/"
+ query = {key: values[-1] for key, values in parse_qs(parsed.query).items()}
+ payload = json.loads(body) if body else {}
+
+ if path == "/_status":
+ return 200, "Healthy", True
+ if path == "/_version":
+ return 200, {"version": "fake", "commit": "0" * 40}, False
+ if path == "/_stats":
+ return 200, self._stats(), False
+ if path == "/urls":
+ return 200, self._urls(query), False
+ if path == "/bulk/documents":
+ return (
+ 200,
+ [self.records[did] for did in payload if did in self.records],
+ False,
+ )
+ if path == "/index":
+ if method == "POST":
+ return self._create(payload)
+ return 200, self._list(query), False
+ if path == "/bundle":
+ if method == "POST":
+ return self._create_bundle(payload)
+ return 200, {"records": list(self.bundles.values())}, False
+ if path.startswith("/ga4gh/drs/v1/objects/"):
+ return self._fetch(path[len("/ga4gh/drs/v1/objects/") :])
+ if path.startswith("/index/"):
+ return self._index_route(method, path[len("/index/") :], query, payload)
+ if path.startswith("/bundle/"):
+ return self._fetch(path[len("/bundle/") :])
+
+ # Anything else is either a global (dist resolution) lookup or a route this
+ # stub does not implement; the two are told apart by whether it resolves.
+ return self._fetch(path.lstrip("/"))
+
+ def _index_route(
+ self, method: str, rest: str, query: dict, payload: Any
+ ) -> tuple[int, Any, bool]:
+ """Serve the `/index/...` routes, whose dids may themselves contain a `/`."""
+ if rest == "blank":
+ return self._create_blank(payload)
+ if rest.startswith("blank/"):
+ return self._update(rest[len("blank/") :], payload)
+ if rest.endswith("/versions"):
+ versions = self._versions(rest[: -len("/versions")])
+ return 200, {str(i): record for i, record in enumerate(versions)}, False
+ if rest.endswith("/latest"):
+ return self._latest(rest[: -len("/latest")], query)
+
+ if method == "POST":
+ return self._add_version(rest, payload)
+ if method == "PUT":
+ return self._update(rest, payload)
+ if method == "DELETE":
+ if rest not in self.records:
+ return 404, {"error": "no record found"}, False
+ del self.records[rest]
+ return 200, "", True
+ return self._fetch(rest)
+
+ def _fetch(self, guid: str) -> tuple[int, Any, bool]:
+ """Look a guid up as a record did, a bundle id, or a baseid."""
+ if guid in self.records:
+ return 200, self.records[guid], False
+ if guid in self.bundles:
+ return 200, self.bundles[guid], False
+
+ by_baseid = [r for r in self.records.values() if r["baseid"] == guid]
+ if by_baseid:
+ return 200, by_baseid[-1], False
+ return 404, {"error": "no record found"}, False
+
+ def _create(self, payload: dict) -> tuple[int, Any, bool]:
+ """Create a record, keeping any did or baseid the caller chose."""
+ did = payload.get("did") or f"{DEFAULT_PREFIX}{uuid4()}"
+ if did in self.records:
+ return 409, {"error": f"{did} already exists"}, False
+
+ record = {key: deepcopy(value) for key, value in _RECORD_DEFAULTS.items()}
+ record.update({k: v for k, v in payload.items() if v is not None})
+ now = datetime.now(timezone.utc).isoformat()
+ record.update(
+ {
+ "did": did,
+ "baseid": payload.get("baseid") or str(uuid4()),
+ "rev": uuid4().hex[:8],
+ "created_date": now,
+ "updated_date": now,
+ }
+ )
+ self.records[did] = record
+ return 200, self._identity(record), False
+
+ def _create_blank(self, payload: dict) -> tuple[int, Any, bool]:
+ """A blank record carries an uploader and nothing to download yet."""
+ return self._create(
+ {"uploader": payload.get("uploader"), "file_name": payload.get("file_name")}
+ )
+
+ def _add_version(self, did: str, payload: dict) -> tuple[int, Any, bool]:
+ """Add a version of an existing record, which shares its baseid."""
+ if did not in self.records:
+ return 404, {"error": "no record found"}, False
+
+ new_version = dict(payload)
+ new_version.pop("rev", None)
+ new_version["baseid"] = self.records[did]["baseid"]
+ if new_version.get("did") == did:
+ new_version.pop("did")
+ return self._create(new_version)
+
+ def _update(self, did: str, payload: dict) -> tuple[int, Any, bool]:
+ """Apply an update and bump the revision, as a write to indexd would."""
+ if did not in self.records:
+ return 404, {"error": "no record found"}, False
+
+ record = self.records[did]
+ record.update({k: v for k, v in payload.items() if k not in ("did", "rev")})
+ record["rev"] = uuid4().hex[:8]
+ record["updated_date"] = datetime.now(timezone.utc).isoformat()
+ return 200, self._identity(record), False
+
+ def _versions(self, did: str) -> list[dict]:
+ """Every record sharing a baseid with `did`, in creation order."""
+ if did not in self.records:
+ return []
+ baseid = self.records[did]["baseid"]
+ return [r for r in self.records.values() if r["baseid"] == baseid]
+
+ def _latest(self, did: str, query: dict) -> tuple[int, Any, bool]:
+ """The newest version of a record, optionally skipping unversioned ones."""
+ versions = self._versions(did)
+ if query.get("has_version") == "true":
+ versions = [r for r in versions if r["version"]]
+ if not versions:
+ return 404, {"error": "no record found"}, False
+ return 200, versions[-1], False
+
+ def _list(self, query: dict) -> dict:
+ """Serve `GET /index` with the filters and paging the tests use."""
+ limit = int(query.get("limit", DEFAULT_PAGE_SIZE))
+ records = self._filtered(query)
+
+ if "start" in query:
+ dids = [r["did"] for r in records]
+ after = dids.index(query["start"]) + 1 if query["start"] in dids else 0
+ records = records[after:]
+ elif "page" in query:
+ page = int(query["page"])
+ records = records[page * limit : (page + 1) * limit]
+
+ return {"records": records[:limit], "limit": limit, "start": query.get("start")}
+
+ def _urls(self, query: dict) -> dict:
+ """`GET /urls` answers with the urls of the matching records, keyed by did."""
+ return {r["did"]: r["urls"] for r in self._filtered(query)}
+
+ def _filtered(self, query: dict) -> list[dict]:
+ """The records matching `hash`, `size` and `ids`; other filters are ignored."""
+ records = list(self.records.values())
+
+ if "ids" in query:
+ wanted = query["ids"].split(",")
+ records = [r for r in records if r["did"] in wanted]
+ if "size" in query:
+ records = [r for r in records if str(r["size"]) == query["size"]]
+ if "hash" in query:
+ algorithm, _, value = query["hash"].partition(":")
+ records = [r for r in records if r["hashes"].get(algorithm) == value]
+ return records
+
+ def _stats(self) -> dict:
+ """`GET /_stats`, which paging callers read the record count from."""
+ return {
+ "fileCount": len(self.records),
+ "totalFileSize": sum(r["size"] or 0 for r in self.records.values()),
+ }
+
+ def _create_bundle(self, payload: dict) -> tuple[int, Any, bool]:
+ """Store a bundle, keeping the checksums the caller supplied."""
+ bundle_id = payload.get("bundle_id") or str(uuid4())
+ bundle = dict(payload)
+ bundle.update(
+ {
+ "id": bundle_id,
+ "bundle_id": bundle_id,
+ "name": payload.get("name") or bundle_id,
+ "checksums": payload.get("checksums", []),
+ "size": payload.get("size", 0),
+ "created_time": datetime.now(timezone.utc).isoformat(),
+ }
+ )
+ self.bundles[bundle_id] = bundle
+ return 200, {"bundle_id": bundle_id, "name": bundle["name"]}, False
+
+ @staticmethod
+ def _identity(record: dict) -> dict:
+ """What indexd echoes back from a write: enough to fetch the record again."""
+ return {key: record[key] for key in ("did", "rev", "baseid")}
+
+ def _serve_requests(self, request: Any, context: Any) -> str:
+ """requests_mock callback: serve `request` and return the body as text."""
+ status, payload, is_text = self.handle(
+ request.method, request.url, request.body
+ )
+ context.status_code = status
+ if is_text:
+ return payload
+ context.headers["Content-Type"] = "application/json"
+ return json.dumps(payload)
+
+ def _serve_httpx(self, request: httpx.Request) -> httpx.Response:
+ """httpx.MockTransport handler, for drsclient."""
+ status, payload, is_text = self.handle(
+ request.method, str(request.url), request.content
+ )
+ if is_text:
+ return httpx.Response(status, text=payload)
+ return httpx.Response(status, json=payload)
+
+ def _mocked_httpx_client(self) -> type[drsclient_module.SyncClient]:
+ """A drsclient SyncClient subclass that talks to this store."""
+ transport = httpx.MockTransport(self._serve_httpx)
+
+ class MockedSyncClient(drsclient_module.SyncClient):
+ def __init__(self, *args, **kwargs) -> None:
+ kwargs["transport"] = transport
+ super().__init__(*args, **kwargs)
+
+ return MockedSyncClient
+
+
+def _handler_for(fake: FakeIndexd) -> type[BaseHTTPRequestHandler]:
+ """
+ Build a BaseHTTPRequestHandler serving `fake`.
+
+ Args:
+ fake (FakeIndexd): The store to serve.
+
+ Returns:
+ type[BaseHTTPRequestHandler]: A handler class for ThreadingHTTPServer.
+ """
+
+ class Handler(BaseHTTPRequestHandler):
+ protocol_version = "HTTP/1.1"
+
+ def do_GET(self) -> None:
+ self._serve("GET")
+
+ def do_POST(self) -> None:
+ self._serve("POST")
+
+ def log_message(self, format: str, *args: Any) -> None:
+ """Keep the default per-request logging out of the test output."""
+ pass
+
+ def _serve(self, method: str) -> None:
+ length = int(self.headers.get("Content-Length") or 0)
+ body = self.rfile.read(length) if length else None
+ status, payload, is_text = fake.handle(method, self.path, body)
+
+ content = (payload if is_text else json.dumps(payload)).encode()
+ self.send_response(status)
+ self.send_header(
+ "Content-Type", "text/plain" if is_text else "application/json"
+ )
+ self.send_header("Content-Length", str(len(content)))
+ self.end_headers()
+ self.wfile.write(content)
+
+ return Handler
diff --git a/tests/test_import.py b/tests/test_import.py
index 07b5e6dfb..909062e34 100644
--- a/tests/test_import.py
+++ b/tests/test_import.py
@@ -6,11 +6,6 @@ def test_import():
import gen3
-def test_cdisutilstest():
-
- import cdisutilstest
-
-
def test_indexclient():
import indexclient
diff --git a/tests/test_manifests.py b/tests/test_manifests.py
index 2e29adb04..2f4aa94dd 100644
--- a/tests/test_manifests.py
+++ b/tests/test_manifests.py
@@ -17,6 +17,10 @@
CURRENT_DIR = os.path.dirname(os.path.realpath(__file__))
+# Two test files attach a FileHandler to this path and delete it on teardown, so a
+# name shared across xdist workers lets one truncate another's log mid-test.
+LOG_FILE = f"gen3tests-{os.environ.get('PYTEST_XDIST_WORKER', 'main')}.logs"
+
@pytest.fixture(autouse=True)
def set_log_level_to_error():
@@ -25,9 +29,9 @@ def set_log_level_to_error():
"""
logging.setLevel(default_logging.ERROR)
- if os.path.exists("gen3tests.logs"):
- os.remove("gen3tests.logs")
- logfile_handler = default_logging.FileHandler("gen3tests.logs")
+ if os.path.exists(LOG_FILE):
+ os.remove(LOG_FILE)
+ logfile_handler = default_logging.FileHandler(LOG_FILE)
logfile_handler.setFormatter(default_logging.Formatter(LOG_FORMAT))
logging.addHandler(logfile_handler)
yield
@@ -51,11 +55,11 @@ def read(self):
self.logs += line
return self.logs
- yield Logfile(filename="gen3tests.logs")
+ yield Logfile(filename=LOG_FILE)
# cleanup after each use
- if os.path.exists("gen3tests.logs"):
- os.remove("gen3tests.logs")
+ if os.path.exists(LOG_FILE):
+ os.remove(LOG_FILE)
@patch("gen3.tools.indexing.verify_manifest.Gen3Index")
@@ -124,11 +128,11 @@ def test_verify_manifest(mock_index):
assert "no_record" in logs["dg.TEST/9c205cd7-c399-4503-9f49-5647188bde66"]
-def test_download_manifest(monkeypatch, gen3_index):
+def test_download_manifest(monkeypatch, gen3_index_over_http):
"""
Test that dowload manifest generates a file with expected content.
"""
- rec1 = gen3_index.create_record(
+ rec1 = gen3_index_over_http.create_record(
did="dg.TEST/f2a39f98-6ae1-48a5-8d48-825a0c52a22b",
hashes={"md5": "a1234567891234567890123456789012"},
size=123,
@@ -136,7 +140,7 @@ def test_download_manifest(monkeypatch, gen3_index):
authz=["/programs/DEV/projects/test"],
urls=["s3://testaws/aws/test.txt", "gs://test/test.txt"],
)
- rec2 = gen3_index.create_record(
+ rec2 = gen3_index_over_http.create_record(
did="dg.TEST/1e9d3103-cbe2-4c39-917c-b3abad4750d2",
hashes={"md5": "b1234567891234567890123456789012"},
size=234,
@@ -145,7 +149,7 @@ def test_download_manifest(monkeypatch, gen3_index):
urls=["gs://test/test.txt"],
file_name="test.txt",
)
- rec3 = gen3_index.create_record(
+ rec3 = gen3_index_over_http.create_record(
did="dg.TEST/ed8f4658-6acd-4f96-9dd8-3709890c959e",
hashes={"md5": "e1234567891234567890123456789012"},
size=345,
@@ -154,7 +158,7 @@ def test_download_manifest(monkeypatch, gen3_index):
urls=["gs://test/test3.txt"],
)
# record with space
- rec4 = gen3_index.create_record(
+ rec4 = gen3_index_over_http.create_record(
did="dg.TEST/a802e27d-4a5b-42e3-92b0-ba19e81b9dce",
hashes={"md5": "f1234567891234567890123456789012"},
size=345,
@@ -169,7 +173,7 @@ def test_download_manifest(monkeypatch, gen3_index):
loop = get_or_create_event_loop_for_thread()
loop.run_until_complete(
async_download_object_manifest(
- "http://localhost:8001",
+ gen3_index_over_http.client.url,
output_filename="tests/outputs/object-manifest.csv",
num_processes=1,
)
@@ -241,7 +245,7 @@ def test_download_manifest(monkeypatch, gen3_index):
).get("file_name")
-def test_download_manifest_with_input_manifest(monkeypatch, gen3_index):
+def test_download_manifest_with_input_manifest(monkeypatch, gen3_index_over_http):
"""
Test that dowload manifest generates a file with expected content when
provided an initial input manifest.
@@ -257,7 +261,7 @@ def test_download_manifest_with_input_manifest(monkeypatch, gen3_index):
]
)
- rec1 = gen3_index.create_record(
+ rec1 = gen3_index_over_http.create_record(
did="dg.TEST/f2a39f98-6ae1-48a5-8d48-825a0c52a22b",
hashes={"md5": "a1234567891234567890123456789012"},
size=123,
@@ -265,7 +269,7 @@ def test_download_manifest_with_input_manifest(monkeypatch, gen3_index):
authz=["/programs/DEV/projects/test"],
urls=["s3://testaws/aws/test.txt", "gs://test/test.txt"],
)
- rec2 = gen3_index.create_record(
+ rec2 = gen3_index_over_http.create_record(
did="dg.TEST/1e9d3103-cbe2-4c39-917c-b3abad4750d2",
hashes={"md5": "b1234567891234567890123456789012"},
size=234,
@@ -274,7 +278,7 @@ def test_download_manifest_with_input_manifest(monkeypatch, gen3_index):
urls=["gs://test/test.txt"],
file_name="test.txt",
)
- rec3 = gen3_index.create_record(
+ rec3 = gen3_index_over_http.create_record(
did="dg.TEST/ed8f4658-6acd-4f96-9dd8-3709890c959e",
hashes={"md5": "e1234567891234567890123456789012"},
size=345,
@@ -283,7 +287,7 @@ def test_download_manifest_with_input_manifest(monkeypatch, gen3_index):
urls=["gs://test/test3.txt"],
)
# record with space
- rec4 = gen3_index.create_record(
+ rec4 = gen3_index_over_http.create_record(
did="dg.TEST/a802e27d-4a5b-42e3-92b0-ba19e81b9dce",
hashes={"md5": "f1234567891234567890123456789012"},
size=345,
@@ -297,7 +301,7 @@ def test_download_manifest_with_input_manifest(monkeypatch, gen3_index):
loop = get_or_create_event_loop_for_thread()
loop.run_until_complete(
async_download_object_manifest(
- "http://localhost:8001",
+ gen3_index_over_http.client.url,
output_filename="tests/outputs/object-manifest.csv",
num_processes=1,
input_manifest=file_path,
diff --git a/tests/validate_manifest_format/test_is_valid_manifest_format.py b/tests/validate_manifest_format/test_is_valid_manifest_format.py
index 99bb7fb36..acc8194cb 100644
--- a/tests/validate_manifest_format/test_is_valid_manifest_format.py
+++ b/tests/validate_manifest_format/test_is_valid_manifest_format.py
@@ -6,6 +6,10 @@
from gen3.tools.indexing import is_valid_manifest_format
from gen3.tools.utils import Columns
+# Two test files attach a FileHandler to this path and delete it on teardown, so a
+# name shared across xdist workers lets one truncate another's log mid-test.
+LOG_FILE = f"gen3tests-{os.environ.get('PYTEST_XDIST_WORKER', 'main')}.logs"
+
@pytest.fixture(autouse=True)
def set_log_level_to_warning():
@@ -14,9 +18,9 @@ def set_log_level_to_warning():
"""
logging.setLevel(default_logging.WARNING)
- if os.path.exists("gen3tests.logs"):
- os.remove("gen3tests.logs")
- logfile_handler = default_logging.FileHandler("gen3tests.logs")
+ if os.path.exists(LOG_FILE):
+ os.remove(LOG_FILE)
+ logfile_handler = default_logging.FileHandler(LOG_FILE)
logfile_handler.setFormatter(default_logging.Formatter(LOG_FORMAT))
logging.addHandler(logfile_handler)
yield
@@ -40,11 +44,11 @@ def read(self):
self.logs += line
return self.logs
- yield Logfile(filename="gen3tests.logs")
+ yield Logfile(filename=LOG_FILE)
# cleanup after each use
- if os.path.exists("gen3tests.logs"):
- os.remove("gen3tests.logs")
+ if os.path.exists(LOG_FILE):
+ os.remove(LOG_FILE)
def test_is_valid_manifest_format_with_no_errors(logfile):