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Add option to list run-compatible pathogen repos #503

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2 changes: 2 additions & 0 deletions CHANGES.md
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Expand Up @@ -15,6 +15,8 @@ development source code and as such may not be routinely kept up to date.

## Improvements

* `nextstrain setup --list` now lists the available pathogens for setup.
([#502](https://github.com/nextstrain/cli/issues/502)
* Added the following to the list of "well-known" environment variables that are
automatically passed thru to runtimes:

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2 changes: 2 additions & 0 deletions doc/changes.md
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Expand Up @@ -19,6 +19,8 @@ development source code and as such may not be routinely kept up to date.
(v-next-improvements)=
### Improvements

* `nextstrain setup --list` now lists the available pathogens for setup.
([#502](https://github.com/nextstrain/cli/issues/502)
* Added the following to the list of "well-known" environment variables that are
automatically passed thru to runtimes:

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5 changes: 5 additions & 0 deletions doc/commands/setup.rst
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Expand Up @@ -14,6 +14,7 @@ nextstrain setup

usage: nextstrain setup [--dry-run] [--force] [--set-default] <pathogen-name>[@<version>[=<url>]]
nextstrain setup [--dry-run] [--force] [--set-default] <runtime-name>
nextstrain setup --list
nextstrain setup --help


Expand Down Expand Up @@ -78,3 +79,7 @@ options

Use this pathogen version or runtime as the default if set up is successful.

.. option:: --list

List available pathogens.

44 changes: 42 additions & 2 deletions nextstrain/cli/command/setup.py
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Expand Up @@ -24,7 +24,7 @@
from ..errors import UserError
from ..util import colored, runner_module, runner_name, print_and_check_setup_tests
from ..types import Options, RunnerModule, SetupTestResults
from ..pathogens import PathogenVersion, pathogen_defaults
from ..pathogens import PathogenVersion, pathogen_defaults, fetch_nextstrain_run_pathogens
from ..runner import all_runners_by_name, runner_defaults


Expand All @@ -33,10 +33,35 @@
failure = partial(colored, "red")


def list_available_pathogens():
"""
Fetches and displays available pathogens with workflow compatibility details.
"""
print("Fetching available pathogens…")
print()

pathogens = fetch_nextstrain_run_pathogens()
pathogens = sorted(pathogens, key=lambda p: p["name"].lower())

for pathogen in pathogens:
print(pathogen["name"])

compatible_workflows = [
workflow
for workflow, workflow_info in pathogen.get("registration", {}).get("workflows", {}).items()
if isinstance(workflow_info, dict) and workflow_info.get("compatibility", {}).get("nextstrain run")
]
if compatible_workflows:
print(" Workflows compatible with nextstrain run:")
for workflow in compatible_workflows:
print(f" - {workflow}")


def register_parser(subparser):
"""
%(prog)s [--dry-run] [--force] [--set-default] <pathogen-name>[@<version>[=<url>]]
%(prog)s [--dry-run] [--force] [--set-default] <runtime-name>
%(prog)s --list
%(prog)s --help
"""
parser = subparser.add_parser("setup", help = "Set up a pathogen or runtime")
Expand All @@ -60,7 +85,9 @@ def register_parser(subparser):

A runtime is one of {{{', '.join(all_runners_by_name)}}}.
"""),
metavar = "<pathogen>|<runtime>")
metavar = "<pathogen>|<runtime>",
nargs = "?",
default = None)

parser.add_argument(
"--dry-run",
Expand All @@ -78,11 +105,24 @@ def register_parser(subparser):
help = "Use this pathogen version or runtime as the default if set up is successful.",
action = "store_true")

parser.add_argument(
"--list",
help = "List available pathogens.",
action = "store_true")

return parser


@console.auto_dry_run_indicator()
def run(opts: Options) -> int:
if opts.list:
list_available_pathogens()
return 0

if not opts.arg:
print("No pathogen or runtime specified. Run with --list to see available pathogens.")
return 1

try:
runner = runner_module(opts.arg)
except ValueError as e1:
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30 changes: 30 additions & 0 deletions nextstrain/cli/pathogens.py
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Expand Up @@ -1198,3 +1198,33 @@ def nextstrain_repo_zip_url(name: str, version: str) -> URL:
return URL(urlquote(revision), version_url)
else:
return version_url


def fetch_nextstrain_run_pathogens() -> List[Dict]:
"""
Fetches all pathogen repos from nextstrain.org, filtered to only those
with at least one `nextstrain run` compatible workflow.

Returns a list of dicts with "name" and optionally "registration" keys.
"""
url = URL("/pathogen-repos", NEXTSTRAIN_DOT_ORG)

with requests.Session() as http:
response = http.get(str(url), headers={"Accept": "application/json"})
response.raise_for_status()
return [repo for repo in response.json() if has_nextstrain_run_compatibility(repo)]


def has_nextstrain_run_compatibility(repo: Dict) -> bool:
"""
Returns True if the pathogen repo has at least one workflow with `nextstrain run` compatibility.
"""
workflows = repo.get("registration", {}).get("workflows", {})

for workflow in workflows.values():
if isinstance(workflow, dict):
compatibility = workflow.get("compatibility", {})
if compatibility.get("nextstrain run"):
return True

return False
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