def prepare_workflow_page(workflow: Workflow, versions: List[str]):
if not workflow:
return None
metadata: WorkflowMetadata = workflow.bind_metadata() or workflow.metadata
if not workflow.friendly_name():
raise Exception(
f"Tool '{type(workflow).__name__}' ({workflow.id()}) did not provide the required 'friendly_name' for the docs"
)
fn = workflow.friendly_name() if workflow.friendly_name() else workflow.id(
)
en = f" ({workflow.id()})" if fn != workflow.id() else ""
tn = fn + en
onelinedescription = prepare_byline(metadata.short_documentation,
metadata.contributors, versions)
citation = "\n\n".join(
[el for el in [metadata.citation, metadata.doi] if el])
formatted_url = (format_rst_link(metadata.documentationUrl,
metadata.documentationUrl)
if metadata.documentationUrl else
"*No URL to the documentation was provided*")
toolmetadata = [
("ID", f"``{workflow.id()}``"),
("URL", formatted_url),
("Versions", ", ".join(str(s)
for s in versions[::-1]) if versions else ""),
("Authors", ", ".join(metadata.contributors)),
("Citations", citation),
("Created", str(metadata.dateCreated)),
("Updated", str(metadata.dateUpdated)),
]
embeddedtoolsraw = {
f"{s.tool.id()}/{s.tool.version()}": s.tool
for s in workflow.step_nodes.values()
}
embeddedtools = tabulate(
[[tool.friendly_name(), f"``{key}``"]
for key, tool in embeddedtoolsraw.items()],
tablefmt="rst",
)
input_headers = ["name", "type", "documentation"]
required_input_tuples = [[
i.id(), i.intype.id(), i.doc.doc if i.doc else ""
] for i in workflow.tool_inputs() if not i.intype.optional]
optional_input_tuples = [[
i.id(), i.intype.id(), i.doc.doc if i.doc else ""
] for i in workflow.tool_inputs() if i.intype.optional]
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(workflow.id(), v)
formatted_toolincludes_array.append(".. include:: " + link)
if v == workflow.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.doc]
for o in workflow.tool_outputs()]
formatted_outputs = tabulate(output_tuples, output_headers, tablefmt="rst")
tool_prov = ""
if workflow.tool_provider() is None:
print("Tool :" + workflow.id() + " has no company")
else:
tool_prov = "." + workflow.tool_provider().lower()
workflow_image = ("" if not SHOW_WORKFLOW_IMAGE else """
Workflow
--------
.. raw:: html
<script src="https://cdnjs.cloudflare.com/ajax/libs/vue/2.6.10/vue.min.js"></script>
<script src="https://unpkg.com/vue-cwl/dist/index.js"></script>
<div id="vue" style="width: 800px; height: 500px; border-radius: 5px; overflow: hidden;">
<cwl cwl-url="https://unpkg.com/[email protected]/cwl-samples/fastqc.json"></cwl>
</div>
<script>
new Vue({{
el: '#vue',
components: {{
cwl: vueCwl.default
}}
}});
</script>
""")
nl = "\n"
return f"""\
def prepare_workflow_page(workflow: Workflow, versions: List[str]):
if not workflow:
return None
metadata: WorkflowMetadata = workflow.bind_metadata() or workflow.metadata
if not workflow.friendly_name():
raise Exception(
f"Tool '{type(workflow).__name__}' ({workflow.id()}) did not provide the required 'friendly_name' for the docs"
)
fn = workflow.friendly_name() if workflow.friendly_name() else workflow.id(
)
en = f" ({workflow.id()})" if fn != workflow.id() else ""
tn = fn + en
onelinedescription = prepare_byline(workflow.id(),
metadata.short_documentation,
metadata.contributors, versions)
citation = "\n\n".join(
[el for el in [metadata.citation, metadata.doi] if el])
formatted_url = (format_rst_link(metadata.documentationUrl,
metadata.documentationUrl)
if metadata.documentationUrl else
"*No URL to the documentation was provided*")
toolmetadata = [
("ID", f"``{workflow.id()}``"),
("URL", formatted_url),
("Versions", ", ".join(str(s)
for s in versions[::-1]) if versions else ""),
("Authors", ", ".join(metadata.contributors)),
("Citations", citation),
("Created", str(metadata.dateCreated)),
("Updated", str(metadata.dateUpdated)),
]
embeddedtoolsraw = {
f"{s.tool.id()}/{s.tool.version()}": s.tool
for s in workflow.step_nodes.values()
}
embeddedtools = tabulate(
[[tool.friendly_name(), f"``{key}``"]
for key, tool in embeddedtoolsraw.items()],
tablefmt="rst",
)
input_headers = ["name", "type", "documentation"]
required_input_tuples = [[
i.id(), i.intype.id(), i.doc.doc if i.doc else ""
] for i in workflow.tool_inputs() if not i.intype.optional]
optional_input_tuples = [[
i.id(), i.intype.id(), i.doc.doc if i.doc else ""
] for i in workflow.tool_inputs() if i.intype.optional]
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(workflow.id(), v)
formatted_toolincludes_array.append(".. include:: " + link)
if v == workflow.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.doc]
for o in workflow.tool_outputs()]
formatted_outputs = tabulate(output_tuples, output_headers, tablefmt="rst")
cwl = workflow.translate("cwl",
to_console=False,
allow_empty_container=True)[0]
wdl = workflow.translate("wdl",
to_console=False,
allow_empty_container=True)[0]
tool_prov = ""
if workflow.tool_provider() is None:
print("Tool :" + workflow.id() + " has no company")
else:
tool_prov = "." + workflow.tool_provider().lower()
workflow_image = requote_uri(workflow.versioned_id()) + ".dot.png"
nl = "\n"
return f"""\