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markdown embed
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@jmchilton
jmchilton committed Nov 4, 2024
1 parent 3ff3843 commit c7adf48
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Showing 7 changed files with 367 additions and 76 deletions.
4 changes: 3 additions & 1 deletion client/src/components/PageEditor/PageEditor.vue
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
:title="title"
:page-id="pageId"
:public-url="publicUrl"
:content="content"
:content="contentEditor"
:content-data="contentData" />
</template>

Expand Down Expand Up @@ -35,6 +35,7 @@ export default {
contentFormat: null,
contentData: null,
content: null,
contentEditor: null,
publicUrl: null,
loading: true,
};
Expand All @@ -44,6 +45,7 @@ export default {
.then((data) => {
this.publicUrl = `${getAppRoot()}u/${data.username}/p/${data.slug}`;
this.content = data.content;
this.contentEditor = data.content_editor;
this.contentFormat = data.content_format;
this.contentData = data;
this.title = data.title;
Expand Down
108 changes: 72 additions & 36 deletions lib/galaxy/managers/markdown_parse.py
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Original file line number Diff line number Diff line change
Expand Up @@ -70,8 +70,25 @@ class DynamicArguments:
"invocation_outputs": [],
"invocation_inputs": [],
}
EMBED_CAPABLE_DIRECTIVES = [
"history_dataset_name",
"history_dataset_type",
"workflow_license",
"invocation_time",
"generate_time",
"generate_galaxy_version",
"instance_access_link",
"instance_resources_link",
"instance_help_link",
"instance_support_link",
"instance_citation_link",
"instance_terms_link",
"instance_organization_link",
]

GALAXY_FLAVORED_MARKDOWN_CONTAINERS = list(VALID_ARGUMENTS.keys())
GALAXY_FLAVORED_MARKDOWN_CONTAINER_REGEX = r"(?P<container>{})".format("|".join(GALAXY_FLAVORED_MARKDOWN_CONTAINERS))
GALAXY_FLAVORED_MARKDOWN_EMBED_CONTAIN_REGEX = r"(?P<container>{})".format("|".join(EMBED_CAPABLE_DIRECTIVES))

ARG_VAL_REGEX = r"""[\w_\-]+|\"[^\"]+\"|\'[^\']+\'"""
FUNCTION_ARG = rf"\s*[\w\|]+\s*=\s*(?:{ARG_VAL_REGEX})\s*"
Expand All @@ -82,21 +99,15 @@ class DynamicArguments:
GALAXY_MARKDOWN_FUNCTION_CALL_LINE = re.compile(FUNCTION_CALL_LINE_TEMPLATE % GALAXY_FLAVORED_MARKDOWN_CONTAINER_REGEX)
WHITE_SPACE_ONLY_PATTERN = re.compile(r"^[\s]+$")

GALAXY_MARKDOWN_EMBED_FUNCTION_CALL_LINE = FUNCTION_CALL_LINE_TEMPLATE % GALAXY_FLAVORED_MARKDOWN_EMBED_CONTAIN_REGEX
GALAXY_MARKDOWN_EMBED_FUNCTION_CALL_LINE_PATT = re.compile(GALAXY_MARKDOWN_EMBED_FUNCTION_CALL_LINE)
EMBED_DIRECTIVE_REGEX = re.compile(r"\$\{galaxy\s+%s\}" % GALAXY_MARKDOWN_EMBED_FUNCTION_CALL_LINE) # noqa: UP031
EMBED_DIRECTIVE_REGEX_ANY = re.compile(r"\$\{galaxy\s+.*\}")


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
Expand All @@ -105,23 +116,33 @@ def _validate_arg(arg_str, valid_args, line_no):

expecting_container_close = expecting_container_close_for is not None
if not fenced and expecting_container_close:
invalid_line(
_invalid_line(
"[{line}] is not expected close line for [{expected_for}]",
line_no,
line=line,
expected_for=expecting_container_close_for,
)
continue
elif not fenced:
continue
first_match_any = EMBED_DIRECTIVE_REGEX_ANY.search(line)
first_match = EMBED_DIRECTIVE_REGEX.search(line)
if first_match_any:
if not first_match:
_invalid_line(
"[{line}] contains invalid template expansion",
line_no,
line=line,
)
else:
_check_func_call(first_match, line_no)
elif fenced and expecting_container_close and BLOCK_FENCE_END.match(line):
# reset
expecting_container_close_for = None
function_calls = 0
elif open_fence and GALAXY_FLAVORED_MARKDOWN_CONTAINER_LINE_PATTERN.match(line):
if expecting_container_close:
if not VALID_CONTAINER_END_PATTERN.match(line):
invalid_line(
_invalid_line(
"Invalid command close line [{line}] for [{expected_for}]",
line_no,
line=line,
Expand All @@ -139,29 +160,10 @@ def _validate_arg(arg_str, valid_args, line_no):
if func_call_match:
function_calls += 1
if function_calls > 1:
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):
continue
valid_args = cast(List[str], valid_args_raw)

first_arg_call = func_call_match.group("firstargcall")

_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, valid_args, line_no)
rest = arg_match.group("restargcalls")

continue
_invalid_line("Only one Galaxy directive is allowed per fenced Galaxy block (```galaxy)", line_no)
_check_func_call(func_call_match, line_no)
else:
invalid_line("Invalid embedded Galaxy markup line [{line}]", line_no, line=line)
_invalid_line("Invalid embedded Galaxy markup line [{line}]", line_no, line=line)

# Markdown unrelated to Galaxy object containers.
continue
Expand All @@ -172,6 +174,40 @@ def _validate_arg(arg_str, valid_args, line_no):
raise ValueError(msg)


def _invalid_line(template: str, line_no: int, **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: str, valid_args, line_no: int):
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)


def _check_func_call(func_call_match, line_no):
container = func_call_match.group("container")
valid_args_raw = VALID_ARGUMENTS[container]
if isinstance(valid_args_raw, DynamicArguments):
return
valid_args = cast(List[str], valid_args_raw)

first_arg_call = func_call_match.group("firstargcall")

_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, valid_args, line_no)
rest = arg_match.group("restargcalls")


def _split_markdown_lines(markdown):
"""Yield lines of a markdown document line-by-line keeping track of fencing.
Expand Down
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