import os
from contextlib import redirect_stdout
from io import StringIO
from typing import Union, TextIO, Optional, Set, List, Any, Callable, Dict
import click
from jsonasobj2 import JsonObj, values
from linkml.generators.yumlgen import YumlGenerator
from linkml_runtime.linkml_model.meta import SchemaDefinition, ClassDefinition, SlotDefinition, Element, ClassDefinitionName, \
TypeDefinition, EnumDefinition, SubsetDefinition
from linkml_runtime.utils.formatutils import camelcase, be, underscore
from linkml.utils.generator import Generator, shared_arguments
from linkml.utils.typereferences import References
[docs]class MarkdownGenerator(Generator):
generatorname = os.path.basename(__file__)
generatorversion = "0.1.1"
directory_output = True
valid_formats = ["md"]
visit_all_class_slots = False
def __init__(self, schema: Union[str, TextIO, SchemaDefinition], no_types_dir: bool = False,
noyuml: bool = False, warn_on_exist:bool = False, **kwargs) -> None:
super().__init__(schema, **kwargs)
self.directory: Optional[str] = None
self.image_directory: Optional[str] = None
self.noimages: bool = False
self.noyuml = noyuml
self.no_types_dir = no_types_dir
self.warn_on_exist = warn_on_exist
self.gen_classes: Optional[Set[ClassDefinitionName]] = None
self.gen_classes_neighborhood: Optional[References] = None
self.BASE = None
[docs] def visit_schema(self, directory: str = None, classes: Set[ClassDefinitionName] = None, image_dir: bool = False,
index_file: str = 'index.md',
noimages: bool = False, **_) -> None:
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(f"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') as ixfile:
with redirect_stdout(ixfile):
self.frontmatter(f"{self.schema.name} schema")
self.para(be(self.schema.description))
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):
self.class_hier(cls)
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):
self.class_hier(cls)
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):
self.pred_hier(slot)
self.header(3, 'Enums')
for enu in sorted(self.schema.enums.values(), key=lambda e: e.name):
self.enum_hier(enu)
self.header(3, 'Subsets')
for subset in sorted(self.schema.subsets.values(), key=lambda s: s.name):
self.bullet(self.subset_link(subset, use_desc=True), 0)
self.header(3, 'Types')
self.header(4, 'Built in')
for builtin_name in sorted(self.synopsis.typebases.keys()):
self.bullet(f'**{builtin_name}**')
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}**'
self.bullet(self.type_link(typ, after_link=f' ({typ_typ})', use_desc=True))
[docs] def visit_class(self, cls: ClassDefinition) -> bool:
if self.gen_classes and cls.name not in self.gen_classes:
return False
with open(self.exist_warning(self.dir_path(cls)), 'w') as clsfile:
with redirect_stdout(clsfile):
class_curi = self.namespaces.uri_or_curie_for(self.namespaces._base, camelcase(cls.name))
class_uri = self.namespaces.uri_for(class_curi)
self.element_header(cls, cls.name, class_curi, class_uri)
print()
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('|', '|')
print(f'[]({img_url})')
self.mappings(cls)
if cls.id_prefixes:
self.header(2, 'Identifier prefixes')
for p in cls.id_prefixes:
self.bullet(f'{p}')
if cls.is_a is not None:
self.header(2, 'Parents')
self.bullet(f' is_a: {self.class_link(cls.is_a, use_desc=True)}')
if cls.mixins:
self.header(2, 'Uses Mixins')
for mixin in cls.mixins:
self.bullet(f' mixin: {self.class_link(mixin, use_desc=True)}')
if cls.name in self.synopsis.isarefs:
self.header(2, 'Children')
for child in sorted(self.synopsis.isarefs[cls.name].classrefs):
self.bullet(f'{self.class_link(child, use_desc=True)}')
if cls.name in self.synopsis.mixinrefs:
self.header(2, 'Mixin for')
for mixin in sorted(self.synopsis.mixinrefs[cls.name].classrefs):
self.bullet(f'{self.class_link(mixin, use_desc=True, after_link="(mixin)")}')
if cls.name in self.synopsis.classrefs:
self.header(2, 'Referenced by class')
for sn in sorted(self.synopsis.classrefs[cls.name].slotrefs):
slot = self.schema.slots[sn]
if slot.range == cls.name:
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)}**')
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:
self.header(3, 'Own')
for slot in own_slots:
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:
self.header(3, "Inherited from " + cls.is_a + ':')
for inherited_slot in inherited_slots:
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:
self.header(3, "Mixed in from " + mixer + ':')
self.slot_field(cls, slot)
self.element_properties(cls)
return False
[docs] def visit_type(self, typ: TypeDefinition) -> None:
with open(self.exist_warning(self.dir_path(typ)), 'w') as typefile:
with redirect_stdout(typefile):
type_uri = typ.definition_uri
type_curie = self.namespaces.curie_for(type_uri)
self.element_header(typ, typ.name, type_curie, type_uri)
print("| | | |")
print("| --- | --- | --- |")
if typ.typeof:
print(f"| Parent type | | {self.class_type_link(typ.typeof)} |")
print(f"| Root (builtin) type | | **{typ.base}** |")
if typ.repr:
print(f"| Representation | | {typ.repr} |")
self.element_properties(typ)
[docs] def visit_slot(self, aliased_slot_name: str, slot: SlotDefinition) -> None:
with open(self.exist_warning(self.dir_path(slot)), 'w') as slotfile:
with redirect_stdout(slotfile):
slot_curie = self.namespaces.uri_or_curie_for(self.namespaces._base, underscore(slot.name))
slot_uri = self.namespaces.uri_for(slot_curie)
self.element_header(slot,aliased_slot_name, slot_curie, slot_uri)
self.mappings(slot)
self.header(2, 'Domain and Range')
print(f'{self.class_link(slot.domain)} →{self.predicate_cardinality(slot)} '
f'{self.class_type_link(slot.range)}')
self.header(2, 'Parents')
if slot.is_a:
self.bullet(f' is_a: {self.slot_link(slot.is_a)}')
self.header(2, 'Children')
if slot.name in sorted(self.synopsis.isarefs):
for child in sorted(self.synopsis.isarefs[slot.name].slotrefs):
self.bullet(f' {self.slot_link(child)}')
self.header(2, 'Used by')
if slot.name in sorted(self.synopsis.slotrefs):
for rc in sorted(self.synopsis.slotrefs[slot.name].classrefs):
self.bullet(f'{self.class_link(rc)}')
if aliased_slot_name == 'relation':
if slot.subproperty_of:
self.bullet(f' reifies: {self.slot_link(slot.subproperty_of) if slot.subproperty_of in self.schema.slots else slot.subproperty_of}')
self.element_properties(slot)
[docs] def visit_enum(self, enum: EnumDefinition) -> None:
with open(self.exist_warning(self.dir_path(enum)), 'w') as enumfile:
with redirect_stdout(enumfile):
enum_curie = self.namespaces.uri_or_curie_for(self.namespaces._base, underscore(enum.name))
enum_uri = self.namespaces.uri_for(enum_curie)
self.element_header(obj=enum, name=enum.name, curie=enum_curie, uri=enum_uri)
self.element_properties(enum)
[docs] def visit_subset(self, subset: SubsetDefinition) -> None:
with open(self.exist_warning(self.dir_path(subset)), 'w') as subsetfile:
with redirect_stdout(subsetfile):
curie = self.namespaces.uri_or_curie_for(self.namespaces._base, underscore(subset.name))
uri = self.namespaces.uri_for(curie)
self.element_header(obj=subset, name=subset.name, curie=curie, uri=uri)
# TODO: consider showing hierarchy within a subset
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:
self.bullet(self.class_link(cls, use_desc=True), 0)
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:
self.bullet(self.class_link(cls, use_desc=True), 0)
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:
self.bullet(self.slot_link(slot, use_desc=True), 0)
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:
self.bullet(self.type_link(type, use_desc=True), 0)
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:
self.bullet(self.enum_link(type, use_desc=True), 0)
self.element_properties(subset)
[docs] def element_properties(self, obj: Element) -> None:
def identity(e: Any) -> Any:
return e
def prop_list(title: str, entries: Union[List, Dict], formatter: Optional[Callable[[Element], str]] = None) \
-> None:
if formatter is None:
formatter = identity
if isinstance(entries, (dict, JsonObj)):
entries = list(values(entries))
if entries:
print(f"| **{title}:** | | {formatter(entries[0])} |")
for entry in entries[1:]:
print(f"| | | {formatter(entry)} |")
def enum_list(title: str,obj:EnumDefinition) -> None:
# This data is from the enum provided in the YAML
self.header(2, title)
print(f"| Text | Description | Meaning | Other Information |")
print("| :--- | :---: | :---: | ---: |")
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 = ''
print(f'| {text} | {desc} | {meaning} | {other} |')
attributes = StringIO()
with redirect_stdout(attributes):
prop_list('Aliases', obj.aliases)
prop_list('Local names', obj.local_names, lambda e: f"{e.local_name_value} ({e.local_name_source})")
prop_list('Mappings', obj.mappings)
prop_list('Alt Descriptions', obj.alt_descriptions, lambda e: f"{e.description} ({e.source})")
# todos
# notes
prop_list('Comments', obj.comments)
prop_list('Examples', obj.examples)
prop_list('In Subsets', obj.in_subset)
# from_schema
# imported_from
prop_list('See also', obj.see_also)
prop_list('Exact Mappings', obj.exact_mappings)
prop_list('Close Mappings', obj.close_mappings)
prop_list('Narrow Mappings', obj.narrow_mappings)
prop_list('Broad Mappings', obj.broad_mappings)
prop_list('Related Mappings', obj.related_mappings)
# - exact mappings
# - close mappings
# - related mappings
# - deprecated element has exact replacement
# - deprecated element has possible replacement
if type(obj) == EnumDefinition:
enum_list('Permissible Values', obj)
if attributes.getvalue():
self.header(2, 'Other properties')
print("| | | |")
print("| --- | --- | --- |")
print(attributes.getvalue())
[docs] def class_hier(self, cls: ClassDefinition, level=0) -> None:
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):
self.class_hier(self.schema.classes[child], level+1)
[docs] def pred_hier(self, slot: SlotDefinition, level=0) -> None:
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):
self.pred_hier(self.schema.slots[child], level+1)
[docs] def enum_hier(self, enum: EnumDefinition, level=0) -> None:
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):
self.enum_hier(self.schema.enums[child], level+1)
[docs] 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'
[docs] def mappings(self, obj: [SlotDefinition, ClassDefinition]) -> None:
# TODO: get rid of this?
# self.header(2, 'Mappings')
# for mapping in obj.mappings:
# self.bullet(f"{self.xlink(mapping)} {self.to_uri(mapping)}")
# if obj.subclass_of:
# self.bullet(self.xlink(obj.subclass_of))
pass
[docs] 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
[docs] def slot_field(self, cls: ClassDefinition, slot: SlotDefinition) -> None:
self.bullet(f'{self.slot_link(slot)}{self.predicate_cardinality(slot)}')
if slot.description:
self.bullet(f'Description: {slot.description}', level=1)
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:
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)
self.bullet(f'in subsets: ({ssl})', level=1)
[docs] 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
# --
[docs] @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>"
[docs] @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>"
[docs] @staticmethod
def anchor(id_: str) -> None:
print(f'<a name="{id_}">', end='')
[docs] @staticmethod
def anchorend() -> None:
print('</a>')
[docs] @staticmethod
def para(txt: str) -> None:
print(f'\n{txt}\n')
[docs] @staticmethod
def bullet(txt: str, level=0) -> None:
print(f'{" " * level} * {txt}')
[docs] def frontmatter(self, thingtype: str, layout='default') -> None:
self.header(1, thingtype)
# print(f'---\nlayout: {layout}\n---\n')
[docs] 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
[docs] 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 '')
[docs] 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)
[docs] 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)
[docs] 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)
[docs] 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)
[docs] 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)
[docs] 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)
[docs] def xlink(self, id_: str) -> str:
return f'[{id_}]({self.id_to_url(id_)})'
[docs] 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
[docs] @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
@shared_arguments(MarkdownGenerator)
@click.command()
@click.option("--dir", "-d", help="Output directory")
@click.option("--classes", "-c", default=None, multiple=True, help="Class(es) to emit")
@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")
def cli(yamlfile, dir, img, index_file, notypesdir, warnonexist, **kwargs):
""" Generate markdown documentation of a LinkML model """
MarkdownGenerator(yamlfile, no_types_dir=notypesdir, warn_on_exist=warnonexist, **kwargs)\
.serialize(directory=dir, image_dir=img, **kwargs)
if __name__ == '__main__':
cli()