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Register subparsers recursively #1640

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ecf0be3
curate: Set shared parser separately
victorlin Sep 25, 2024
6babb82
curate: Validate records with a wrapper
victorlin Oct 31, 2024
11a3e15
curate: Pass command name to validate wrapper
victorlin Oct 31, 2024
2457a6d
Register subparsers recursively
victorlin Sep 25, 2024
b365f9d
Get subparser formatter class from top-level parser
victorlin Sep 24, 2024
6581f10
🚧 figure out why this breaks tests
victorlin Oct 31, 2024
f5e9472
Revert "🚧 figure out why this breaks tests"
victorlin Oct 31, 2024
a4ee061
fixup! curate: Validate records with a wrapper
victorlin Nov 1, 2024
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11 changes: 6 additions & 5 deletions augur/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@
from .debug import DEBUGGING
from .errors import AugurError
from .io.print import print_err
from .argparse_ import add_command_subparsers, add_default_command
from .argparse_ import register_commands, add_default_command

DEFAULT_AUGUR_RECURSION_LIMIT = 10000
sys.setrecursionlimit(int(os.environ.get("AUGUR_RECURSION_LIMIT") or DEFAULT_AUGUR_RECURSION_LIMIT))
Expand Down Expand Up @@ -52,14 +52,15 @@

def make_parser():
parser = argparse.ArgumentParser(
prog = "augur",
description = "Augur: A bioinformatics toolkit for phylogenetic analysis.")
prog = "augur",
description = "Augur: A bioinformatics toolkit for phylogenetic analysis.",
formatter_class = argparse.ArgumentDefaultsHelpFormatter,
)

add_default_command(parser)
add_version_alias(parser)

subparsers = parser.add_subparsers()
add_command_subparsers(subparsers, COMMANDS)
register_commands(parser, COMMANDS)

return parser

Expand Down
22 changes: 13 additions & 9 deletions augur/argparse_.py
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Original file line number Diff line number Diff line change
@@ -1,7 +1,8 @@
"""
Custom helpers for the argparse standard library.
"""
from argparse import Action, ArgumentDefaultsHelpFormatter, ArgumentParser, _ArgumentGroup
import argparse
from argparse import Action, ArgumentParser, _ArgumentGroup
from typing import Union
from .types import ValidationMode

Expand Down Expand Up @@ -32,16 +33,14 @@ def run(args):
parser.set_defaults(__command__ = default_command)


def add_command_subparsers(subparsers, commands, command_attribute='__command__'):
def register_commands(parser: argparse.ArgumentParser, commands, command_attribute='__command__'):
"""
Add subparsers for each command module.

Parameters
----------
subparsers: argparse._SubParsersAction
The special subparsers action object created by the parent parser
via `parser.add_subparsers()`.

parser
ArgumentParser object.
commands: list[types.ModuleType]
A list of modules that are commands that require their own subparser.
Each module is required to have a `register_parser` function to add its own
Expand All @@ -51,6 +50,8 @@ def add_command_subparsers(subparsers, commands, command_attribute='__command__'
Optional attribute name for the commands. The default is `__command__`,
which allows top level augur to run commands directly via `args.__command__.run()`.
"""
subparsers = parser.add_subparsers()

for command in commands:
# Allow each command to register its own subparser
subparser = command.register_parser(subparsers)
Expand All @@ -59,9 +60,8 @@ def add_command_subparsers(subparsers, commands, command_attribute='__command__'
if command_attribute:
subparser.set_defaults(**{command_attribute: command})

# Use the same formatting class for every command for consistency.
# Set here to avoid repeating it in every command's register_parser().
subparser.formatter_class = ArgumentDefaultsHelpFormatter
# Ensure all subparsers format like the top-level parser
subparser.formatter_class = parser.formatter_class

if not subparser.description and command.__doc__:
subparser.description = command.__doc__
Expand All @@ -70,6 +70,10 @@ def add_command_subparsers(subparsers, commands, command_attribute='__command__'
if not getattr(command, "run", None):
add_default_command(subparser)

# Recursively register any subcommands
if getattr(subparser, "subcommands", None):
register_commands(subparser, subparser.subcommands)
Comment on lines +73 to +75
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This breaks augur curate subcommands

$ cat records.ndjson | augur curate passthru
Traceback (most recent call last):
  File "…/augur/__init__.py", line 72, in run
    return args.__command__.run(args)
TypeError: run() missing 1 required positional argument: 'records'

because each subcommand's run function is expected to be called through augur curate's own run function, but it is now called directly at the top level.

Maybe recursively registering subcommands is not the right thing to do in this codebase.

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I remember having to work around the top level run when initially adding the augur curate subcommand.

augur/augur/curate/__init__.py

Lines 117 to 120 in 129fd7e

# Using a subcommand attribute so subcommands are not directly
# run by top level Augur. Process I/O in `curate`` so individual
# subcommands do not have to worry about it.
add_command_subparsers(subparsers, SUBCOMMANDS, SUBCOMMAND_ATTRIBUTE)

Would it be weird to keep augur curate as a special case?

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Two options:

  1. Further adapt how augur curate commands share functionality so calling their run() from the top-level works. This could be done relatively straightforwardly.
  2. Don't recursively register subcommands; leave the pattern of commands with subcommands invoking register_commands(…) themselves.

I don't think either gets the way of the functional improvements we want to make? So it's a matter of preference.

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Thanks for the input – I'll try option 1 above to align with Nextstrain CLI code.



class HideAsFalseAction(Action):
"""
Expand Down
225 changes: 1 addition & 224 deletions augur/curate/__init__.py
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Original file line number Diff line number Diff line change
@@ -1,18 +1,6 @@
"""
A suite of commands to help with data curation.
"""
import argparse
import sys
from collections import deque
from textwrap import dedent
from typing import Iterable, Set

from augur.argparse_ import ExtendOverwriteDefault, add_command_subparsers
from augur.errors import AugurError
from augur.io.json import dump_ndjson, load_ndjson
from augur.io.metadata import DEFAULT_DELIMITERS, InvalidDelimiter, read_table_to_dict, read_metadata_with_sequences, write_records_to_tsv
from augur.io.sequences import write_records_to_fasta
from augur.types import DataErrorMethod
from . import format_dates, normalize_strings, passthru, titlecase, apply_geolocation_rules, apply_record_annotations, abbreviate_authors, parse_genbank_location, transform_strain_name, rename


Expand All @@ -31,220 +19,9 @@
]


def create_shared_parser():
"""
Creates an argparse.ArgumentParser that is intended to be used as a parent
parser¹ for all `augur curate` subcommands. This should include all options
that are intended to be shared across the subcommands.

Note that any options strings used here cannot be used in individual subcommand
subparsers unless the subparser specifically sets `conflict_handler='resolve'` ²,
then the subparser option will override the option defined here.

Based on https://stackoverflow.com/questions/23296695/permit-argparse-global-flags-after-subcommand/23296874#23296874

¹ https://docs.python.org/3/library/argparse.html#parents
² https://docs.python.org/3/library/argparse.html#conflict-handler
"""
shared_parser = argparse.ArgumentParser(add_help=False)

shared_inputs = shared_parser.add_argument_group(
title="INPUTS",
description="""
Input options shared by all `augur curate` commands.
If no input options are provided, commands will try to read NDJSON records from stdin.
""")
shared_inputs.add_argument("--metadata",
help="Input metadata file. May be plain text (TSV, CSV) or an Excel or OpenOffice spreadsheet workbook file. When an Excel or OpenOffice workbook, only the first visible worksheet will be read and initial empty rows/columns will be ignored. Accepts '-' to read plain text from stdin.")
shared_inputs.add_argument("--id-column",
help="Name of the metadata column that contains the record identifier for reporting duplicate records. "
"Uses the first column of the metadata file if not provided. "
"Ignored if also providing a FASTA file input.")
shared_inputs.add_argument("--metadata-delimiters", default=DEFAULT_DELIMITERS, nargs="+", action=ExtendOverwriteDefault,
help="Delimiters to accept when reading a plain text metadata file. Only one delimiter will be inferred.")

shared_inputs.add_argument("--fasta",
help="Plain or gzipped FASTA file. Headers can only contain the sequence id used to match a metadata record. " +
"Note that an index file will be generated for the FASTA file as <filename>.fasta.fxi")
shared_inputs.add_argument("--seq-id-column",
help="Name of metadata column that contains the sequence id to match sequences in the FASTA file.")
shared_inputs.add_argument("--seq-field",
help="The name to use for the sequence field when joining sequences from a FASTA file.")

shared_inputs.add_argument("--unmatched-reporting",
type=DataErrorMethod.argtype,
choices=list(DataErrorMethod),
default=DataErrorMethod.ERROR_FIRST,
help="How unmatched records from combined metadata/FASTA input should be reported.")
shared_inputs.add_argument("--duplicate-reporting",
type=DataErrorMethod.argtype,
choices=list(DataErrorMethod),
default=DataErrorMethod.ERROR_FIRST,
help="How should duplicate records be reported.")

shared_outputs = shared_parser.add_argument_group(
title="OUTPUTS",
description="""
Output options shared by all `augur curate` commands.
If no output options are provided, commands will output NDJSON records to stdout.
""")
shared_outputs.add_argument("--output-metadata",
help="Output metadata TSV file. Accepts '-' to output TSV to stdout.")

shared_outputs.add_argument("--output-fasta",
help="Output FASTA file.")
shared_outputs.add_argument("--output-id-field",
help="The record field to use as the sequence identifier in the FASTA output.")
shared_outputs.add_argument("--output-seq-field",
help="The record field that contains the sequence for the FASTA output. "
"This field will be deleted from the metadata output.")

return shared_parser


def register_parser(parent_subparsers):
shared_parser = create_shared_parser()
parser = parent_subparsers.add_parser("curate", help=__doc__)

# Add print_help so we can run it when no subcommands are called
parser.set_defaults(print_help = parser.print_help)

# Add subparsers for subcommands
subparsers = parser.add_subparsers(dest="subcommand", required=False)
# Add the shared_parser to make it available for subcommands
# to include in their own parser
subparsers.shared_parser = shared_parser
# Using a subcommand attribute so subcommands are not directly
# run by top level Augur. Process I/O in `curate`` so individual
# subcommands do not have to worry about it.
add_command_subparsers(subparsers, SUBCOMMANDS, SUBCOMMAND_ATTRIBUTE)
parser.subcommands = SUBCOMMANDS

return parser


def validate_records(records: Iterable[dict], subcmd_name: str, is_input: bool) -> Iterable[dict]:
"""
Validate that the provided *records* all have the same fields.
Uses the keys of the first record to check against all other records.

Parameters
----------
records: iterable of dict

subcmd_name: str
The name of the subcommand whose output is being validated; used in
error messages displayed to the user.

is_input: bool
Whether the provided records come directly from user provided input
"""
error_message = "Records do not have the same fields! "
if is_input:
error_message += "Please check your input data has the same fields."
else:
# Hopefully users should not run into this error as it means we are
# not uniformly adding/removing fields from records
error_message += dedent(f"""\
Something unexpected happened during the augur curate {subcmd_name} command.
To report this, please open a new issue including the original command:
<https://github.com/nextstrain/augur/issues/new/choose>
""")

first_record_keys: Set[str] = set()
for idx, record in enumerate(records):
if idx == 0:
first_record_keys.update(record.keys())
else:
if set(record.keys()) != first_record_keys:
raise AugurError(error_message)
yield record


def run(args):
# Print help if no subcommands are used
if not getattr(args, SUBCOMMAND_ATTRIBUTE, None):
return args.print_help()

# Check provided args are valid and required combination of args are provided
if not args.fasta and (args.seq_id_column or args.seq_field):
raise AugurError("The --seq-id-column and --seq-field options should only be used when providing a FASTA file.")

if args.fasta and (not args.seq_id_column or not args.seq_field):
raise AugurError("The --seq-id-column and --seq-field options are required for a FASTA file input.")

if not args.output_fasta and (args.output_id_field or args.output_seq_field):
raise AugurError("The --output-id-field and --output-seq-field options should only be used when requesting a FASTA output.")

if args.output_fasta and (not args.output_id_field or not args.output_seq_field):
raise AugurError("The --output-id-field and --output-seq-field options are required for a FASTA output.")

# Read inputs
# Special case single hyphen as stdin
if args.metadata == '-':
args.metadata = sys.stdin.buffer

if args.metadata and args.fasta:
try:
records = read_metadata_with_sequences(
args.metadata,
args.metadata_delimiters,
args.fasta,
args.seq_id_column,
args.seq_field,
args.unmatched_reporting,
args.duplicate_reporting)
except InvalidDelimiter:
raise AugurError(
f"Could not determine the delimiter of {args.metadata!r}. "
f"Valid delimiters are: {args.metadata_delimiters!r}. "
"This can be changed with --metadata-delimiters."
)
elif args.metadata:
try:
records = read_table_to_dict(args.metadata, args.metadata_delimiters, args.duplicate_reporting, args.id_column)
except InvalidDelimiter:
raise AugurError(
f"Could not determine the delimiter of {args.metadata!r}. "
f"Valid delimiters are: {args.metadata_delimiters!r}. "
"This can be changed with --metadata-delimiters."
)
elif not sys.stdin.isatty():
records = load_ndjson(sys.stdin)
else:
raise AugurError(dedent("""\
No valid inputs were provided.
NDJSON records can be streamed from stdin or
input files can be provided via the command line options `--metadata` and `--fasta`.
See the command's help message for more details."""))

# Get the name of the subcmd being run
subcmd_name = args.subcommand

# Validate records have the same input fields
validated_input_records = validate_records(records, subcmd_name, True)

# Run subcommand to get modified records
modified_records = getattr(args, SUBCOMMAND_ATTRIBUTE).run(args, validated_input_records)

# Validate modified records have the same output fields
validated_output_records = validate_records(modified_records, subcmd_name, False)

# Output modified records
# First output FASTA, since the write fasta function yields the records again
# and removes the sequences from the records
if args.output_fasta:
validated_output_records = write_records_to_fasta(
validated_output_records,
args.output_fasta,
args.output_id_field,
args.output_seq_field)

if args.output_metadata:
write_records_to_tsv(validated_output_records, args.output_metadata)

if not (args.output_fasta or args.output_metadata):
dump_ndjson(validated_output_records)
else:
# Exhaust generator to ensure we run through all records
# when only a FASTA output is requested but not a metadata output
deque(validated_output_records, maxlen=0)
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