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Sync markdown_parse with Galaxy #99

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Jul 23, 2024
Merged

Sync markdown_parse with Galaxy #99

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70 changes: 47 additions & 23 deletions gxformat2/markdown_parse.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
Galaxy Markdown. Keeping things isolated to allow re-use of these utilities in other
projects (e.g. gxformat2).
"""

import re
from typing import (
cast,
Expand All @@ -24,36 +25,56 @@ class DynamicArguments:


DYNAMIC_ARGUMENTS = DynamicArguments()
SHARED_ARGUMENTS: List[str] = ["collapse"]
VALID_ARGUMENTS: Dict[str, Union[List[str], DynamicArguments]] = {
"history_link": ["history_id"],
"history_dataset_display": ["input", "output", "history_dataset_id"],
"history_dataset_embedded": ["input", "output", "history_dataset_id"],
"history_dataset_as_image": ["input", "output", "history_dataset_id", "path"],
"history_dataset_as_table": [
"input",
"output",
"history_dataset_id",
"path",
"title",
"footer",
"show_column_headers",
"compact",
],
"history_dataset_peek": ["input", "output", "history_dataset_id"],
"history_dataset_info": ["input", "output", "history_dataset_id"],
"history_dataset_link": ["input", "output", "history_dataset_id", "path", "label"],
"history_dataset_index": ["input", "output", "history_dataset_id", "path"],
"history_dataset_name": ["input", "output", "history_dataset_id"],
"history_dataset_type": ["input", "output", "history_dataset_id"],
"history_dataset_collection_display": ["input", "output", "history_dataset_collection_id"],
"workflow_display": ["workflow_id"],
"job_metrics": ["step", "job_id"],
"job_parameters": ["step", "job_id"],
"tool_stderr": ["step", "job_id"],
"tool_stdout": ["step", "job_id"],
"workflow_display": ["workflow_id", "workflow_checkpoint"],
"workflow_license": ["workflow_id"],
"workflow_image": ["workflow_id", "size", "workflow_checkpoint"],
"job_metrics": ["step", "job_id", "implicit_collection_jobs_id"],
"job_parameters": ["step", "job_id", "implicit_collection_jobs_id"],
"tool_stderr": ["step", "job_id", "implicit_collection_jobs_id"],
"tool_stdout": ["step", "job_id", "implicit_collection_jobs_id"],
"generate_galaxy_version": [],
"generate_time": [],
"instance_access_link": [],
"instance_resources_link": [],
"instance_help_link": [],
"instance_support_link": [],
"instance_citation_link": [],
"instance_terms_link": [],
"instance_organization_link": [],
"visualization": DYNAMIC_ARGUMENTS,
# Invocation Flavored Markdown
"invocation_time": ["invocation_id"],
"invocation_outputs": [],
"invocation_inputs": [],
}
GALAXY_FLAVORED_MARKDOWN_CONTAINERS = list(VALID_ARGUMENTS.keys())
GALAXY_FLAVORED_MARKDOWN_CONTAINER_REGEX = r"(?P<container>%s)" % "|".join(GALAXY_FLAVORED_MARKDOWN_CONTAINERS)
GALAXY_FLAVORED_MARKDOWN_CONTAINER_REGEX = r"(?P<container>{})".format("|".join(GALAXY_FLAVORED_MARKDOWN_CONTAINERS))

ARG_VAL_REGEX = r"""[\w_\-]+|\"[^\"]+\"|\'[^\']+\'"""
FUNCTION_ARG = r"\s*[\w\|]+\s*=\s*(?:%s)\s*" % ARG_VAL_REGEX
FUNCTION_ARG = rf"\s*[\w\|]+\s*=\s*(?:{ARG_VAL_REGEX})\s*"
# embed commas between arguments
FUNCTION_MULTIPLE_ARGS = rf"(?P<firstargcall>{FUNCTION_ARG})(?P<restargcalls>(?:,{FUNCTION_ARG})*)"
FUNCTION_MULTIPLE_ARGS_PATTERN = re.compile(FUNCTION_MULTIPLE_ARGS)
Expand All @@ -64,21 +85,29 @@ class DynamicArguments:

def validate_galaxy_markdown(galaxy_markdown, internal=True):
"""Validate the supplied markdown and throw an ValueError with reason if invalid."""

def invalid_line(template, line_no, **kwd):
if "line" in kwd:
kwd["line"] = kwd["line"].rstrip("\r\n")
raise ValueError("Invalid line %d: %s" % (line_no + 1, template.format(**kwd)))

def _validate_arg(arg_str, valid_args, line_no):
if arg_str is not None:
arg_name = arg_str.split("=", 1)[0].strip()
if arg_name not in valid_args and arg_name not in SHARED_ARGUMENTS:
invalid_line("Invalid argument to Galaxy directive [{argument}]", line_no, argument=arg_name)

expecting_container_close_for = None
last_line_no = 0
function_calls = 0
for (line, fenced, open_fence, line_no) in _split_markdown_lines(galaxy_markdown):
for line, fenced, open_fence, line_no in _split_markdown_lines(galaxy_markdown):
last_line_no = line_no

def invalid_line(template, **kwd):
if "line" in kwd:
kwd["line"] = line.rstrip("\r\n")
raise ValueError("Invalid line %d: %s" % (line_no + 1, template.format(**kwd)))

expecting_container_close = expecting_container_close_for is not None
if not fenced and expecting_container_close:
invalid_line(
"[{line}] is not expected close line for [{expected_for}]",
line_no,
line=line,
expected_for=expecting_container_close_for,
)
Expand All @@ -94,6 +123,7 @@ def invalid_line(template, **kwd):
if not VALID_CONTAINER_END_PATTERN.match(line):
invalid_line(
"Invalid command close line [{line}] for [{expected_for}]",
line_no,
line=line,
expected_for=expecting_container_close_for,
)
Expand All @@ -109,7 +139,7 @@ def invalid_line(template, **kwd):
if func_call_match:
function_calls += 1
if function_calls > 1:
invalid_line("Only one Galaxy directive is allowed per fenced Galaxy block (```galaxy)")
invalid_line("Only one Galaxy directive is allowed per fenced Galaxy block (```galaxy)", line_no)
container = func_call_match.group("container")
valid_args_raw = VALID_ARGUMENTS[container]
if isinstance(valid_args_raw, DynamicArguments):
Expand All @@ -118,26 +148,20 @@ def invalid_line(template, **kwd):

first_arg_call = func_call_match.group("firstargcall")

def _validate_arg(arg_str):
if arg_str is not None:
arg_name = arg_str.split("=", 1)[0].strip()
if arg_name not in valid_args:
invalid_line("Invalid argument to Galaxy directive [{argument}]", argument=arg_name)

_validate_arg(first_arg_call)
_validate_arg(first_arg_call, valid_args, line_no)
rest = func_call_match.group("restargcalls")
while rest:
rest = rest.strip().split(",", 1)[1]
arg_match = FUNCTION_MULTIPLE_ARGS_PATTERN.match(rest)
if not arg_match:
break
first_arg_call = arg_match.group("firstargcall")
_validate_arg(first_arg_call)
_validate_arg(first_arg_call, valid_args, line_no)
rest = arg_match.group("restargcalls")

continue
else:
invalid_line("Invalid embedded Galaxy markup line [{line}]", line=line)
invalid_line("Invalid embedded Galaxy markup line [{line}]", line_no, line=line)

# Markdown unrelated to Galaxy object containers.
continue
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