def prepare_container_warning_for_commandtool(tool: CommandTool):
if tool.container() is not None and len(tool.container()) > 0:
return ""
return f"""\
def prepare_commandtool_page(tool: CommandTool, versions: List[str]):
if not tool:
return None
# tool_modules = tool.__module__.split(".") # janis._bioinformatics_.tools.$toolproducer.$toolname.$version
metadata: ToolMetadata = tool.bind_metadata() or tool.metadata
if not tool.friendly_name():
raise Exception(
f"Tool '{type(tool).__name__}' ({tool.id()}) did not provide the required 'friendly_name' for the docs"
)
fn = tool.friendly_name() if tool.friendly_name() else tool.id()
en = f" ({tool.id()})" if fn != tool.id() else ""
tn = fn + en
onelinedescription = prepare_byline(metadata.short_documentation,
metadata.contributors, versions)
toolmetadata = [
t for t in [
("ID", f"``{tool.id()}``"),
("Python",
f"``{tool.__module__} import {tool.__class__.__name__}``"),
("Versions", ", ".join(versions)),
("Container", tool.container()),
("Authors", ", ".join(metadata.contributors)),
("Citations", metadata.citation),
("DOI", metadata.doi) if metadata.doi else None,
("Created", str(metadata.dateCreated)),
("Updated", str(metadata.dateUpdated)),
] if t and len(t) == 2
]
formatted_url = (format_rst_link(metadata.documentationUrl,
metadata.documentationUrl)
if metadata.documentationUrl else
"*No URL to the documentation was provided*")
input_headers = ["name", "type", "prefix", "position", "documentation"]
argument_headers = ["value", "prefix", "position", "documentation"]
required_input_tuples = [[
i.id(), i.input_type.id(), i.prefix, i.position, i.doc
] for i in tool.inputs() if not i.input_type.optional]
optional_input_tuples = [[
i.id(), i.input_type.id(), i.prefix, i.position, i.doc
] for i in tool.inputs() if i.input_type.optional]
formatted_args = None
args = tool.arguments()
if args:
argument_tuples = [[str(a.value), a.prefix, a.position, a.doc]
for a in tool.arguments()]
fargs = tabulate(argument_tuples,
headers=argument_headers,
tablefmt="rst")
formatted_args = "Arguments\n----------\n\n" + fargs
formatted_inputs = tabulate(required_input_tuples + optional_input_tuples,
input_headers,
tablefmt="rst")
formatted_toolversions_array = []
formatted_toolincludes_array = []
for v in versions:
link = get_tool_url(tool.id(), v)
formatted_toolincludes_array.append(".. include:: " + link)
if v == tool.version():
formatted_toolversions_array.append(
f"- {v} (current)"
) # + format_rst_link(v + " (current)", link))
else:
formatted_toolversions_array.append(
"- " + format_rst_link(v, link + ".html"))
output_headers = ["name", "type", "documentation"]
output_tuples = [[o.id(), o.outtype.id(), o.doc]
for o in tool.tool_outputs()]
tool_prov = ""
if tool.tool_provider() is None:
print("Tool :" + tool.id() + " has no company")
else:
tool_prov = "." + tool.tool_provider().lower()
nl = "\n"
return f"""\