import os
import re
from dataclasses import dataclass
from typing import Any, Callable, Optional, Union
import click
from jsonasobj2 import JsonObj, values
from linkml_runtime.linkml_model.meta import (
ClassDefinition,
ClassDefinitionName,
Element,
EnumDefinition,
SlotDefinition,
SubsetDefinition,
TypeDefinition,
)
from linkml_runtime.utils.formatutils import be, camelcase, underscore
from linkml._version import __version__
from linkml.generators.yumlgen import YumlGenerator
from linkml.utils.deprecation import deprecation_warning
from linkml.utils.generator import Generator, shared_arguments
from linkml.utils.typereferences import References
[docs]@dataclass
class MarkdownGenerator(Generator):
"""
Generates markdown documentation for a LinkML schema
Each schema element (class, slot, type, enum) is translated into its own markdown file;
additionally, an index.md is generated that links everything together.
The markdown is suitable for deployment as a MkDocs or Sphinx site
.. admonition:: Deprecated
:class: warning
The MarkdownGenerator class is being deprecated in favor of DocGenerator which can
be found at the following path – `linkml/generators/docgen.py`. Going forward, DocGenerator
which can be invoked using the `gen-doc` command will be the preferred way to generate
Markdown documentation files for LinkML schemas.
.. deprecated:: v1.9.1
Recommendation: Update to use `gen-doc`
"""
def __post_init__(self) -> None:
deprecation_warning("gen-markdown")
super().__post_init__()
# ClassVars
generatorname = os.path.basename(__file__)
generatorversion = "0.2.1"
directory_output = True
valid_formats = ["md"]
visit_all_class_slots = False
uses_schemaloader = True
# ObjectVars
directory: Optional[str] = None
image_directory: Optional[str] = None
classes: set[ClassDefinitionName] = None
image_dir: bool = False
index_file: str = "index.md"
noimages: bool = False
noyuml: bool = False
no_types_dir: bool = False
warn_on_exist: bool = False
gen_classes: Optional[set[ClassDefinitionName]] = None
gen_classes_neighborhood: Optional[References] = None
def visit_schema(
self,
directory: str = None,
classes: set[ClassDefinitionName] = None,
image_dir: bool = False,
index_file: str = "index.md",
noimages: bool = False,
**_,
) -> str:
self.gen_classes = classes if classes else []
for cls in self.gen_classes:
if cls not in self.schema.classes:
raise ValueError("Unknown class name: {cls}")
if self.gen_classes:
self.gen_classes_neighborhood = self.neighborhood(list(self.gen_classes))
self.directory = directory
if directory:
os.makedirs(directory, exist_ok=True)
elif image_dir:
raise ValueError("Image directory can only be used with '-d' option")
if image_dir:
self.image_directory = os.path.join(directory, "images")
if not noimages:
os.makedirs(self.image_directory, exist_ok=True)
self.noimages = noimages
if not self.no_types_dir:
os.makedirs(os.path.join(directory, "types"), exist_ok=True)
with open(self.exist_warning(directory, index_file), "w", encoding="UTF-8") as ixfile:
items = []
items.append(self.frontmatter(f"{self.schema.name}"))
items.append(
self.para(
f"**metamodel version:** {self.schema.metamodel_version}\n\n**version:** {self.schema.version}"
)
)
items.append(self.para(be(self.schema.description)))
items.append(self.header(3, "Classes"))
for cls in sorted(self.schema.classes.values(), key=lambda c: c.name):
if not cls.is_a and not cls.mixin and self.is_secondary_ref(cls.name):
items.append(self.class_hier(cls))
items.append(self.header(3, "Mixins"))
for cls in sorted(self.schema.classes.values(), key=lambda c: c.name):
if cls.mixin and self.is_secondary_ref(cls.name):
items.append(self.class_hier(cls))
items.append(self.header(3, "Slots"))
for slot in sorted(self.schema.slots.values(), key=lambda s: s.name):
if not slot.is_a and self.is_secondary_ref(slot.name):
items.append(self.pred_hier(slot))
items.append(self.header(3, "Enums"))
for enu in sorted(self.schema.enums.values(), key=lambda e: e.name):
items.append(self.enum_hier(enu))
items.append(self.header(3, "Subsets"))
for subset in sorted(self.schema.subsets.values(), key=lambda s: s.name):
items.append(self.bullet(self.subset_link(subset, use_desc=True), 0))
items.append(self.header(3, "Types"))
items.append(self.header(4, "Built in"))
for builtin_name in sorted(self.synopsis.typebases.keys()):
items.append(self.bullet(f"**{builtin_name}**"))
items.append(self.header(4, "Defined"))
for typ in sorted(self.schema.types.values(), key=lambda t: t.name):
if self.is_secondary_ref(typ.name):
if typ.typeof:
typ_typ = self.type_link(typ.typeof)
else:
typ_typ = f"**{typ.base}**"
items.append(self.bullet(self.type_link(typ, after_link=f" ({typ_typ})", use_desc=True)))
items = [i for i in items if i is not None]
out = "\n".join(items) + "\n"
out = pad_heading(out)
ixfile.write(out)
return out
def visit_class(self, cls: ClassDefinition) -> str:
# allow client to relabel metamodel
mixin_local_name = self.get_metamodel_slot_name("Mixin")
class_local_name = self.get_metamodel_slot_name("Class")
if self.gen_classes and cls.name not in self.gen_classes:
return ""
with open(self.exist_warning(self.dir_path(cls)), "w", encoding="UTF-8") as clsfile:
items = []
class_curi = self.namespaces.uri_or_curie_for(str(self.namespaces._base), camelcase(cls.name))
class_uri = self.namespaces.uri_for(class_curi)
items.append(self.element_header(cls, cls.name, class_curi, class_uri))
items.append("")
if not self.noyuml:
if self.image_directory:
yg = YumlGenerator(self)
yg.serialize(
classes=[cls.name],
directory=self.image_directory,
load_image=not self.noimages,
)
img_url = os.path.join("images", os.path.basename(yg.output_file_name))
else:
yg = YumlGenerator(self)
img_url = (
yg.serialize(classes=[cls.name]).replace("?", "%3F").replace(" ", "%20").replace("|", "|")
)
items.append(f"[]({img_url})")
if cls.id_prefixes:
items.append(self.header(2, "Identifier prefixes"))
for p in cls.id_prefixes:
items.append(self.bullet(f"{p}"))
if cls.is_a is not None:
items.append(self.header(2, "Parents"))
items.append(self.bullet(f" is_a: {self.class_link(cls.is_a, use_desc=True)}"))
if cls.mixins:
items.append(self.header(2, f"Uses {mixin_local_name}"))
for mixin in cls.mixins:
items.append(self.bullet(f" mixin: {self.class_link(mixin, use_desc=True)}"))
if cls.name in self.synopsis.isarefs:
items.append(self.header(2, "Children"))
for child in sorted(self.synopsis.isarefs[cls.name].classrefs):
items.append(self.bullet(f"{self.class_link(child, use_desc=True)}"))
if cls.name in self.synopsis.mixinrefs:
items.append(self.header(2, f"{mixin_local_name} for"))
for mixin in sorted(self.synopsis.mixinrefs[cls.name].classrefs):
items.append(self.bullet(f'{self.class_link(mixin, use_desc=True, after_link="(mixin)")}'))
if cls.name in self.synopsis.classrefs:
items.append(self.header(2, f"Referenced by {class_local_name}"))
for sn in sorted(self.synopsis.classrefs[cls.name].slotrefs):
slot = self.schema.slots[sn]
if slot.range == cls.name:
items.append(
self.bullet(
f" **{self.class_link(slot.domain)}** "
f"*{self.slot_link(slot, add_subset=False)}*{self.predicate_cardinality(slot)} "
f"**{self.class_type_link(slot.range)}**"
)
)
items.append(self.header(2, "Attributes"))
# List all of the slots that directly belong to the class
slot_list = [slot for slot in [self.schema.slots[sn] for sn in cls.slots]]
own_slots = [slot for slot in slot_list if cls.name in slot.domain_of]
if own_slots:
items.append(self.header(3, "Own"))
for slot in own_slots:
items.append(self.slot_field(cls, slot))
slot_list.remove(slot)
# List all of the inherited slots
ancestors = set(self.ancestors(cls))
inherited_slots = [slot for slot in slot_list if set(slot.domain_of).intersection(ancestors)]
if inherited_slots:
items.append(self.header(3, "Inherited from " + cls.is_a + ":"))
for inherited_slot in inherited_slots:
items.append(self.slot_field(cls, inherited_slot))
slot_list.remove(inherited_slot)
# List all of the slots acquired through mixing
mixed_in_classes = set()
for mixin in cls.mixins:
mixed_in_classes.add(mixin)
mixed_in_classes.update(set(self.ancestors(self.schema.classes[mixin])))
for slot in slot_list:
mixers = set(slot.domain_of).intersection(mixed_in_classes)
for mixer in mixers:
items.append(self.header(3, "Mixed in from " + mixer + ":"))
items.append(self.slot_field(cls, slot))
items.append(self.element_properties(cls))
out = "\n".join(items)
out = pad_heading(out)
clsfile.write(out)
return out
def visit_type(self, typ: TypeDefinition) -> str:
with open(self.exist_warning(self.dir_path(typ)), "w", encoding="UTF-8") as typefile:
type_uri = typ.definition_uri
type_curie = self.namespaces.curie_for(type_uri)
out = self.element_header(typ, typ.name, type_curie, type_uri)
out = "\n".join([out, "| | | |"])
out = "\n".join([out, "| --- | --- | --- |"])
if typ.typeof:
out = "\n".join([out, f"| Parent type | | {self.class_type_link(typ.typeof)} |"])
out = "\n".join([out, f"| Root (builtin) type | | **{typ.base}** |"])
if typ.repr:
out = "\n".join([out, f"| Representation | | {typ.repr} |"])
out += self.element_properties(typ)
out += "\n"
out = pad_heading(out)
typefile.write(out)
return out
def visit_slot(self, aliased_slot_name: str, slot: SlotDefinition) -> str:
with open(self.exist_warning(self.dir_path(slot)), "w", encoding="UTF-8") as slotfile:
items = []
slot_curie = self.namespaces.uri_or_curie_for(str(self.namespaces._base), underscore(slot.name))
slot_uri = self.namespaces.uri_for(slot_curie)
items.append(self.element_header(slot, aliased_slot_name, slot_curie, slot_uri))
items.append(self.header(2, "Domain and Range"))
items.append(
f"{self.class_link(slot.domain)} →{self.predicate_cardinality(slot)} "
f"{self.class_type_link(slot.range)}"
)
items.append(self.header(2, "Parents"))
if slot.is_a:
items.append(self.bullet(f" is_a: {self.slot_link(slot.is_a)}"))
items.append(self.header(2, "Children"))
if slot.name in sorted(self.synopsis.isarefs):
for child in sorted(self.synopsis.isarefs[slot.name].slotrefs):
items.append(self.bullet(f" {self.slot_link(child)}"))
items.append(self.header(2, "Used by"))
if slot.name in sorted(self.synopsis.slotrefs):
for rc in sorted(self.synopsis.slotrefs[slot.name].classrefs):
items.append(self.bullet(f"{self.class_link(rc)}"))
if aliased_slot_name == "relation":
if slot.subproperty_of:
reifies = (
self.slot_link(slot.subproperty_of)
if slot.subproperty_of in self.schema.slots
else slot.subproperty_of
)
items.append(self.bullet(f" reifies: {reifies}"))
items.append(self.element_properties(slot))
out = "\n".join(items)
out = pad_heading(out)
slotfile.write(out)
return out
def visit_enum(self, enum: EnumDefinition) -> str:
with open(self.exist_warning(self.dir_path(enum)), "w", encoding="UTF-8") as enumfile:
items = []
enum_curie = self.namespaces.uri_or_curie_for(str(self.namespaces._base), underscore(enum.name))
enum_uri = self.namespaces.uri_for(enum_curie)
items.append(self.element_header(obj=enum, name=enum.name, curie=enum_curie, uri=enum_uri))
items.append(self.element_properties(enum))
out = "\n".join(items)
out = pad_heading(out)
enumfile.write(out)
return out
def visit_subset(self, subset: SubsetDefinition) -> str:
with open(self.exist_warning(self.dir_path(subset)), "w", encoding="UTF-8") as subsetfile:
items = []
curie = self.namespaces.uri_or_curie_for(str(self.namespaces._base), underscore(subset.name))
uri = self.namespaces.uri_for(curie)
items.append(self.element_header(obj=subset, name=subset.name, curie=curie, uri=uri))
# TODO: consider showing hierarchy within a subset
items.append(self.header(3, "Classes"))
for cls in sorted(self.schema.classes.values(), key=lambda c: c.name):
if not cls.mixin:
if cls.in_subset and subset.name in cls.in_subset:
items.append(self.bullet(self.class_link(cls, use_desc=True), 0))
items.append(self.header(3, "Mixins"))
for cls in sorted(self.schema.classes.values(), key=lambda c: c.name):
if cls.mixin:
if cls.in_subset and subset.name in cls.in_subset:
items.append(self.bullet(self.class_link(cls, use_desc=True), 0))
items.append(self.header(3, "Slots"))
for slot in sorted(self.schema.slots.values(), key=lambda s: s.name):
if slot.in_subset and subset.name in slot.in_subset:
items.append(self.bullet(self.slot_link(slot, use_desc=True), 0))
items.append(self.header(3, "Types"))
for type in sorted(self.schema.types.values(), key=lambda s: s.name):
if type.in_subset and subset.name in type.in_subset:
items.append(self.bullet(self.type_link(type, use_desc=True), 0))
items.append(self.header(3, "Enums"))
for enum in sorted(self.schema.enums.values(), key=lambda s: s.name):
if enum.in_subset and subset.name in enum.in_subset:
items.append(self.bullet(self.enum_link(enum, use_desc=True), 0))
items.append(self.element_properties(subset))
out = "\n".join(items)
out = pad_heading(out)
subsetfile.write(out)
return out
def element_header(self, obj: Element, name: str, curie: str, uri: str) -> str:
if isinstance(obj, TypeDefinition):
obj_type = "Type"
elif isinstance(obj, ClassDefinition):
obj_type = "Class"
elif isinstance(obj, SlotDefinition):
obj_type = "Slot"
elif isinstance(obj, EnumDefinition):
obj_type = "Enum"
elif isinstance(obj, SubsetDefinition):
obj_type = "Subset"
else:
obj_type = "Class"
header_label = f"{obj_type}: ~~{name}~~ _(deprecated)_" if obj.deprecated else f"{obj_type}: {name}"
out = self.header(1, header_label)
out += self.para(be(obj.description))
out = "\n".join([out, f"URI: [{curie}]({uri})", ""])
return out
def element_properties(self, obj: Element) -> str:
def identity(e: Any) -> Any:
return e
def prop_list(
title: str,
entries: Union[list, dict],
formatter: Optional[Callable[[Element], str]] = None,
) -> Optional[str]:
if formatter is None:
formatter = identity
if isinstance(entries, (dict, JsonObj)):
entries = list(values(entries))
if entries:
items = []
items.append(f"| **{title}:** | | {formatter(entries[0])} |")
for entry in entries[1:]:
items.append(f"| | | {formatter(entry)} |")
return "\n".join(items)
def enum_list(title: str, obj: EnumDefinition) -> str:
# This data is from the enum provided in the YAML
items = []
items.append(self.header(2, title))
items.append("| Text | Description | Meaning | Other Information |")
items.append("| :--- | :---: | :---: | ---: |")
for item, item_info in obj.permissible_values.items():
text = ""
desc = ""
meaning = ""
other = {}
for k in item_info:
if item_info[k] is not None and len(item_info[k]) > 0:
if k == "text":
text = item_info[k]
elif k == "description":
desc = item_info[k]
elif k == "meaning":
meaning = item_info[k]
else:
other[k] = item_info[k]
if not other:
other = ""
items.append(f"| {text} | {desc} | {meaning} | {other} |")
return "\n".join(items)
items = []
items.append(prop_list("Aliases", obj.aliases))
items.append(
prop_list(
"Local names",
obj.local_names,
lambda e: f"{e.local_name_value} ({e.local_name_source})",
)
)
items.append(prop_list("Mappings", obj.mappings))
items.append(
prop_list(
"Alt Descriptions",
obj.alt_descriptions,
lambda e: f"{e.description} ({e.source})",
)
)
# todos
# notes
items.append(prop_list("Comments", obj.comments))
items.append(prop_list("Examples", obj.examples))
items.append(prop_list("In Subsets", obj.in_subset))
# from_schema
# imported_from
items.append(prop_list("See also", [f"[{v}]({v})" for v in obj.see_also]))
items.append(prop_list("Exact Mappings", obj.exact_mappings))
items.append(prop_list("Close Mappings", obj.close_mappings))
items.append(prop_list("Narrow Mappings", obj.narrow_mappings))
items.append(prop_list("Broad Mappings", obj.broad_mappings))
items.append(prop_list("Related Mappings", obj.related_mappings))
items = [i for i in items if i is not None]
if len(items) > 0:
header = "\n".join([self.header(2, "Other properties"), "| | | |", "| --- | --- | --- |"])
items.insert(0, header)
# - exact mappings
# - close mappings
# - related mappings
# - deprecated element has exact replacement
# - deprecated element has possible replacement
if type(obj) is EnumDefinition:
items.insert(0, enum_list("Permissible Values", obj))
items.insert(1, "\n")
out = "\n".join(items)
return out
def class_hier(self, cls: ClassDefinition, level=0) -> str:
items = []
items.append(self.bullet(self.class_link(cls, use_desc=True), level))
if cls.name in sorted(self.synopsis.isarefs):
for child in sorted(self.synopsis.isarefs[cls.name].classrefs):
items.append(self.class_hier(self.schema.classes[child], level + 1))
return "\n".join(items) if items else None
def pred_hier(self, slot: SlotDefinition, level=0) -> str:
items = []
items.append(self.bullet(self.slot_link(slot, use_desc=True), level))
if slot.name in sorted(self.synopsis.isarefs):
for child in sorted(self.synopsis.isarefs[slot.name].slotrefs):
items.append(self.pred_hier(self.schema.slots[child], level + 1))
return "\n".join(items) if items else None
def enum_hier(self, enum: EnumDefinition, level=0) -> str:
items = []
items.append(self.bullet(self.enum_link(enum, use_desc=True), level))
if enum.name in sorted(self.synopsis.isarefs):
for child in sorted(self.synopsis.isarefs[enum.name].classrefs):
items.append(self.enum_hier(self.schema.enums[child], level + 1))
return "\n".join(items) if items else None
def dir_path(
self,
obj: Union[ClassDefinition, SlotDefinition, TypeDefinition, EnumDefinition],
) -> str:
filename = (
self.formatted_element_name(obj)
if isinstance(obj, ClassDefinition)
else (
underscore(obj.name)
if isinstance(obj, SlotDefinition)
else underscore(obj.name) if isinstance(obj, EnumDefinition) else camelcase(obj.name)
)
)
subdir = "/types" if isinstance(obj, TypeDefinition) and not self.no_types_dir else ""
return f"{self.directory}{subdir}/{filename}.md"
def is_secondary_ref(self, en: str) -> bool:
"""Determine whether 'en' is the name of something in the neighborhood of the requested classes
@param en: element name
@return: True if 'en' is the name of a slot, class or type in the immediate neighborhood of of what we are
building
"""
if not self.gen_classes:
return True
elif en in self.schema.classes:
return en in self.gen_classes_neighborhood.classrefs
elif en in self.schema.slots:
return en in self.gen_classes_neighborhood.slotrefs
elif en in self.schema.types:
return en in self.gen_classes_neighborhood.typerefs
else:
return True
def slot_field(self, cls: ClassDefinition, slot: SlotDefinition) -> str:
items = []
items.append(self.bullet(f"{self.slot_link(slot)}{self.predicate_cardinality(slot)}"))
if slot.description:
items.append(self.bullet(f"Description: {slot.description}", level=1))
items.append(self.bullet(f"Range: {self.class_type_link(slot.range)}", level=1))
# if slot.subproperty_of:
# self.bullet(f'edge label: {self.slot_link(slot.subproperty_of)}', level=1)
for example in slot.examples:
items.append(
self.bullet(
f'Example: {getattr(example, "value", " ")} {getattr(example, "description", " ")}',
level=1,
)
)
# if slot.name not in self.own_slot_names(cls):
# self.bullet(f'inherited from: {self.class_link(slot.domain)}', level=1)
if slot.in_subset:
ssl = ",".join(slot.in_subset)
items.append(self.bullet(f"in subsets: ({ssl})", level=1))
return "\n".join(items)
def to_uri(self, uri_or_curie: str) -> str:
"""Return the URI for the slot if known"""
if ":/" in uri_or_curie:
return uri_or_curie
elif self.namespaces.prefix_for(uri_or_curie) in self.namespaces:
return self.namespaces.uri_for(uri_or_curie)
else:
return "*(Unknown namespace)*"
# --
# FORMATTING
# --
@staticmethod
def predicate_cardinality(slot: SlotDefinition) -> str:
"""Emit cardinality for a suffix on a predicate"""
if slot.multivalued:
card_str = "1..\\*" if slot.required else "0..\\*"
else:
card_str = "1..1" if slot.required else "0..1"
return f" <sub>{card_str}</sub>"
@staticmethod
def range_cardinality(slot: SlotDefinition) -> str:
"""Emits cardinality decorator at end of type"""
if slot.multivalued:
card_str = "1..\\*" if slot.required else "0..\\*"
else:
card_str = "1..1" if slot.required else "0..1"
return f" <sub><b>{card_str}</b></sub>"
@staticmethod
def anchor(id_: str) -> str:
return f'<a name="{id_}">'
@staticmethod
def anchorend() -> str:
return "</a>"
def header(self, level: int, txt: str) -> str:
txt = self.get_metamodel_slot_name(txt)
out = f'\n{"#" * level} {txt}\n'
return out
@staticmethod
def para(txt: str) -> str:
return f"\n{txt}\n"
@staticmethod
def bullet(txt: str, level=0) -> str:
return f'{" " * level} * {txt}'
def frontmatter(self, thingtype: str, layout="default") -> str:
return self.header(1, thingtype)
# print(f'---\nlayout: {layout}\n---\n')
def bbin(self, obj: Element) -> str:
"""Boldify built in types
@param obj: object name or id
@return:
"""
return obj.name if isinstance(obj, Element) else f"**{obj}**" if obj in self.synopsis.typebases else obj
def desc_for(self, obj: Element, doing_descs: bool) -> str:
"""Return a description for object if it is unique (different than its parent)
@param obj: object to be described
@param doing_descs: If false, always return an empty string
@return: text or empty string
"""
if obj.description and doing_descs:
if isinstance(obj, SlotDefinition) and obj.is_a:
parent = self.schema.slots[obj.is_a]
elif isinstance(obj, ClassDefinition) and obj.is_a:
parent = self.schema.classes[obj.is_a]
else:
parent = None
return "" if parent and obj.description == parent.description else obj.description
return ""
def _link(
self,
obj: Optional[Element],
*,
after_link: str = None,
use_desc: bool = False,
add_subset: bool = True,
) -> str:
"""Create a link to ref if appropriate.
@param ref: the name or value of a class, slot, type or the name of a built in type.
@param after_link: Text to put between link and description
@param use_desc: True means append a description after the link if available
@param add_subset: True means add any subset information that is available
@return:
"""
nl = "\n"
if obj is None or not self.is_secondary_ref(obj.name):
return self.bbin(obj)
if isinstance(obj, SlotDefinition):
link_name = ((be(obj.domain) + "➞") if obj.alias else "") + self.aliased_slot_name(obj)
link_ref = underscore(obj.name)
elif isinstance(obj, TypeDefinition):
link_name = camelcase(obj.name)
link_ref = f"types/{link_name}" if not self.no_types_dir else f"{link_name}"
elif isinstance(obj, ClassDefinition):
link_name = camelcase(obj.name)
link_ref = camelcase(link_name)
elif isinstance(obj, SubsetDefinition):
link_name = camelcase(obj.name)
link_ref = camelcase(link_name)
else:
link_name = obj.name
link_ref = link_name
desc = self.desc_for(obj, use_desc)
return f"[{link_name}]" f"({link_ref}.{self.format})" + (f" {after_link} " if after_link else "") + (
f" - {desc.split(nl)[0]}" if desc else ""
)
def type_link(
self,
ref: Optional[Union[str, TypeDefinition]],
*,
after_link: str = None,
use_desc: bool = False,
add_subset: bool = True,
) -> str:
return self._link(
self.schema.types[ref] if isinstance(ref, str) else ref,
after_link=after_link,
use_desc=use_desc,
add_subset=add_subset,
)
def slot_link(
self,
ref: Optional[Union[str, SlotDefinition]],
*,
after_link: str = None,
use_desc: bool = False,
add_subset: bool = True,
) -> str:
return self._link(
self.schema.slots[ref] if isinstance(ref, str) else ref,
after_link=after_link,
use_desc=use_desc,
add_subset=add_subset,
)
def class_link(
self,
ref: Optional[Union[str, ClassDefinition]],
*,
after_link: str = None,
use_desc: bool = False,
add_subset: bool = True,
) -> str:
return self._link(
self.schema.classes[ref] if isinstance(ref, str) else ref,
after_link=after_link,
use_desc=use_desc,
add_subset=add_subset,
)
def class_type_link(
self,
ref: Optional[Union[str, ClassDefinition, TypeDefinition, EnumDefinition]],
*,
after_link: str = None,
use_desc: bool = False,
add_subset: bool = True,
) -> str:
if isinstance(ref, ClassDefinition):
return self.class_link(ref, after_link=after_link, use_desc=use_desc, add_subset=add_subset)
elif isinstance(ref, TypeDefinition):
return self.type_link(ref, after_link=after_link, use_desc=use_desc, add_subset=add_subset)
elif isinstance(ref, EnumDefinition):
return self.type_link(ref, after_link=after_link, use_desc=use_desc, add_subset=add_subset)
elif ref in self.schema.classes:
return self.class_link(ref, after_link=after_link, use_desc=use_desc, add_subset=add_subset)
elif ref in self.schema.enums:
return self.enum_link(ref, after_link=after_link, use_desc=use_desc, add_subset=add_subset)
else:
return self.type_link(ref, after_link=after_link, use_desc=use_desc, add_subset=add_subset)
def enum_link(
self,
ref: Optional[Union[str, EnumDefinition]],
*,
after_link: str = None,
use_desc: bool = False,
add_subset: bool = True,
) -> str:
return self._link(
self.schema.enums[ref] if isinstance(ref, str) else ref,
after_link=after_link,
use_desc=use_desc,
add_subset=add_subset,
)
def subset_link(
self,
ref: Optional[Union[str, SubsetDefinition]],
*,
after_link: str = None,
use_desc: bool = False,
) -> str:
return self._link(
self.schema.subsets[ref] if isinstance(ref, str) else ref,
after_link=after_link,
use_desc=use_desc,
)
def xlink(self, id_: str) -> str:
return f"[{id_}]({self.id_to_url(id_)})"
def exist_warning(self, *fpath: str) -> str:
"""Create a file name out of fpath and check whether it already exists"""
fname = os.path.join(*fpath)
if self.warn_on_exist and os.path.exists(fname):
self.logger.warning(f"File {fname} already exists")
return fname
@staticmethod
def id_to_url(id_: str) -> str:
uri = id_
if ":" in id_:
# TODO! use PC
if id_.startswith("SIO:"):
uri = id_.replace("SIO:", "http://semanticscience.org/resource/SIO_")
elif id_.startswith("HGNC:"):
uri = "https://monarchinitiative.org/gene/" + id_
else:
frag = id_.replace(":", "_")
base = "http://purl.obolibrary.org/obo/"
uri = base + frag
return uri
def pad_heading(text: str) -> str:
"""Add an extra newline to a non-top-level header that doesn't have one preceding it"""
return re.sub(r"(?<!\n)\n##", "\n\n##", text)
@shared_arguments(MarkdownGenerator)
@click.command(name="markdown")
@click.option("--dir", "-d", required=True, help="Output directory")
@click.option("--classes", "-c", multiple=True, help="Class(es) to emit")
@click.option("--map-fields", "-M", multiple=True, help="Map metamodel fields, e.g. slot=field")
@click.option("--img", "-i", is_flag=True, help="Download YUML images to 'image' directory")
@click.option("--index-file", "-I", help="Name of markdown file that holds index")
@click.option("--noimages", is_flag=True, help="Do not (re-)generate images")
@click.option("--noyuml", is_flag=True, help="Do not add yUML figures to pages")
@click.option("--notypesdir", is_flag=True, help="Do not create a separate types directory")
@click.option("--warnonexist", is_flag=True, help="Warn if output file already exists")
@click.version_option(__version__, "-V", "--version")
def cli(yamlfile, map_fields, dir, img, index_file, notypesdir, warnonexist, **kwargs):
"""Generate markdown documentation of a LinkML model.
.. warning::
`gen-markdown` is deprecated. Please use `gen-doc` instead.
"""
deprecation_warning("gen-markdown")
gen = MarkdownGenerator(yamlfile, no_types_dir=notypesdir, warn_on_exist=warnonexist, **kwargs)
if map_fields is not None:
gen.metamodel_name_map = {}
for mf in map_fields:
[k, v] = mf.split("=")
gen.metamodel_name_map[k] = v
gen.serialize(directory=dir, image_dir=img, **kwargs)
if __name__ == "__main__":
cli()