Source code for linkml.generators.yumlgen

"""Generate yuml

https://yuml.me/diagram/scruffy/class/samples

"""
import logging
import os
from typing import Union, TextIO, Set, List, Optional, Callable, cast

import click
import requests
from rdflib import Namespace

from linkml_runtime.linkml_model.meta import ClassDefinitionName, SchemaDefinition, SlotDefinition, \
    ClassDefinition
from linkml_runtime.utils.formatutils import camelcase, underscore
from linkml.utils.generator import Generator, shared_arguments

yuml_is_a = '^-'
yuml_uses = 'uses -.->'
yuml_injected = '< -.- inject'
yuml_slot_type = ':'
yuml_inline = '++- '
yuml_inline_rev = '-++'
yuml_ref = '- '

yuml_base = 'https://yuml.me/diagram/nofunky'
yuml_scale = ''                # ';scale:180' ';scale:80' for small
yuml_dir = ';dir:TB'           # '
yuml_class = '/class/'
YUML = Namespace(yuml_base + yuml_scale + yuml_dir + yuml_class)


[docs]class YumlGenerator(Generator): generatorname = os.path.basename(__file__) generatorversion = "0.1.1" valid_formats = ['yuml', 'png', 'pdf', 'jpg', 'json', 'svg'] visit_all_class_slots = False def __init__(self, schema: Union[str, TextIO, SchemaDefinition], **args) -> None: super().__init__(schema, **args) self.referenced:Optional[Set[ClassDefinitionName]] = None # List of classes that have to be emitted self.generated:Optional[Set[ClassDefinitionName]] = None # List of classes that have been emitted self.box_generated:Optional[Set[ClassDefinitionName]] = None # Class boxes that have been emitted self.associations_generated:Optional[Set[ClassDefinitionName]] = None # Classes with associations generated self.focus_classes: Optional[Set[ClassDefinitionName]] = None # Classes to be completely filled self.gen_classes:Optional[Set[ClassDefinitionName]] = None # Classes to be generated self.output_file_name: Optional[str] = None # Location of output file if directory used
[docs] def visit_schema(self, classes: Set[ClassDefinitionName]=None, directory: Optional[str] = None, load_image: bool=True, **_) -> None: if directory: os.makedirs(directory, exist_ok=True) if classes is not None: for cls in classes: if cls not in self.schema.classes: raise ValueError(f"Unknown class name: {cls}") self.box_generated = set() self.associations_generated = set() self.focus_classes = classes if classes: self.gen_classes = self.neighborhood(list(classes)).classrefs.union(classes) else: self.gen_classes = self.synopsis.roots.classrefs self.referenced = self.gen_classes self.generated = set() yumlclassdef: List[str] = [] while self.referenced.difference(self.generated): cn = sorted(list(self.referenced.difference(self.generated)), reverse=True)[0] self.generated.add(cn) assocs = self.class_associations(ClassDefinitionName(cn), cn in self.referenced) if assocs: yumlclassdef.append(assocs) else: yumlclassdef.append(self.class_box(ClassDefinitionName(cn))) yuml_url = str(YUML) + ','.join(yumlclassdef) + \ (('.' + self.format) if self.format not in ('yuml', 'svg') else '') file_suffix = '.svg' if self.format == 'yuml' else '.' + self.format if directory: self.output_file_name = os.path.join(directory, camelcase(sorted(classes)[0] if classes else self.schema.name) + file_suffix) if load_image: resp = requests.get(yuml_url, stream=True) if resp.ok: with open(self.output_file_name, 'wb') as f: for chunk in resp.iter_content(chunk_size=2048): f.write(chunk) else: self.logger.error(f"{resp.reason} accessing {yuml_url}") else: print(str(YUML)+','.join(yumlclassdef), end='')
[docs] def class_box(self, cn: ClassDefinitionName) -> str: """ Generate a box for the class. Populate its interior only if (a) it hasn't previously been generated and (b) it appears in the gen_classes list @param cn: @return: """ slot_defs: List[str] = [] if cn not in self.box_generated and (not self.focus_classes or cn in self.focus_classes): cls = self.schema.classes[cn] for slot in self.filtered_cls_slots(cn, all_slots=True, filtr=lambda s: s.range not in self.schema.classes): if True or cn in slot.domain_of: mod = self.prop_modifier(cls, slot) slot_defs.append(underscore(self.aliased_slot_name(slot)) + mod + ':' + underscore(slot.range) + self.cardinality(slot)) self.box_generated.add(cn) self.referenced.add(cn) return '[' + camelcase(cn) + ('|' + ';'.join(slot_defs) if slot_defs else '') + ']'
[docs] def class_associations(self, cn: ClassDefinitionName, must_render: bool=False) -> str: """ Emit all associations for a focus class. If none are specified, all classes are generated @param cn: Name of class to be emitted @param must_render: True means render even if this is a target (class is specifically requested) @return: YUML representation of the association """ # NOTE: YUML diagrams draw in the opposite order in which they are created, so we work from bottom to top and # from right to left assocs: List[str] = [] if cn not in self.associations_generated and (not self.focus_classes or cn in self.focus_classes): cls = self.schema.classes[cn] # Slots that reference other classes for slot in self.filtered_cls_slots(cn, False, lambda s: s.range in self.schema.classes)[::-1]: # Swap the two boxes because, in the case of self reference, the last definition wins if not slot.range in self.associations_generated and cn in slot.domain_of: rhs = self.class_box(cn) lhs = self.class_box(cast(ClassDefinitionName, slot.range)) assocs.append(lhs + '<' + self.aliased_slot_name(slot) + self.prop_modifier(cls, slot) + self.cardinality(slot, False) + (yuml_inline_rev if slot.inlined else yuml_ref) + rhs) # Slots in other classes that reference this for slotname in sorted(self.synopsis.rangerefs.get(cn, [])): slot = self.schema.slots[slotname] # Don't do self references twice # Also, slot must be owned by the class if cls.name not in slot.domain_of and cls.name not in self.associations_generated: for dom in [self.schema.classes[dof] for dof in slot.domain_of]: assocs.append(self.class_box(dom.name) + (yuml_inline if slot.inlined else yuml_ref) + self.aliased_slot_name(slot) + self.prop_modifier(dom, slot) + self.cardinality(slot, False) + '>' + self.class_box(cn)) # Mixins used in the class for mixin in cls.mixins: assocs.append(self.class_box(cn) + yuml_uses + self.class_box(mixin)) # Classes that use the class as a mixin if cls.name in self.synopsis.mixinrefs: for mixin in sorted(self.synopsis.mixinrefs[cls.name].classrefs, reverse=True): assocs.append(self.class_box(ClassDefinitionName(mixin)) + yuml_uses + self.class_box(cn)) # Classes that inject information if cn in self.synopsis.applytos.classrefs: for injector in sorted(self.synopsis.applytorefs[cn].classrefs, reverse=True): assocs.append(self.class_box(cn) + yuml_injected + self.class_box(ClassDefinitionName(injector))) self.associations_generated.add(cn) # Children if cn in self.synopsis.isarefs: for is_a_cls in sorted(self.synopsis.isarefs[cn].classrefs, reverse=True): assocs.append(self.class_box(cn) + yuml_is_a + self.class_box(ClassDefinitionName(is_a_cls))) # Parent if cls.is_a and cls.is_a not in self.associations_generated: assocs.append(self.class_box(cls.is_a) + yuml_is_a + self.class_box(cn)) return ','.join(assocs)
[docs] @staticmethod def cardinality(slot: SlotDefinition, is_attribute: bool = True) -> str: if is_attribute: if slot.multivalued: return ' %2B' if slot.required else ' *' else: return '' if slot.required else ' %3F' else: if slot.multivalued: return ' 1..*' if slot.required else ' 0..*' else: return ' 1..1' if slot.required else ' 0..1'
[docs] def filtered_cls_slots(self, cn: ClassDefinitionName, all_slots: bool=True, filtr: Callable[[SlotDefinition], bool] = None) -> List[SlotDefinition]: """ Return the set of slots associated with the class that meet the filter criteria. Slots will be returned in defining order, with class slots returned last @param cn: name of class to filter @param all_slots: True means include attributes @param filtr: Slot filter predicate @return: List of slot definitions """ if filtr is None: filtr = lambda x: True rval = [] cls = self.schema.classes[cn] cls_slots = self.all_slots(cls, cls_slots_first=True) for slot in cls_slots: if (all_slots or slot.range in self.schema.classes) and filtr(slot): rval.append(slot) return rval
[docs] def prop_modifier(self, cls: ClassDefinition, slot: SlotDefinition) -> str: """ Return the modifiers for the slot: (i) - inherited (m) - inherited through mixin (a) - injected (pk) - primary ckey @param cls: @param slot: @return: """ pk = '(pk)' if slot.key else '' inherited = slot.name not in self.own_slot_names(cls) mixin = inherited and slot.name in \ [mslot.name for mslot in [self.schema.classes[m] for m in cls.mixins]] injected = cls.name in self.synopsis.applytos.classrefs and \ slot.name in [aslot.name for aslot in [self.schema.classes[a] for a in sorted(self.synopsis.applytorefs[cls.name].classrefs)]] return pk + ('(a)' if injected else '(m)' if mixin else '(i)' if inherited else '')
@shared_arguments(YumlGenerator) @click.command() @click.option("--classes", "-c", default=None, multiple=True, help="Class(es) to emit") @click.option("--directory", "-d", help="Output directory - if supplied, YUML rendering will be saved in file") def cli(yamlfile, **args): """ Generate a UML representation of a LinkML model """ print(YumlGenerator(yamlfile, **args).serialize(**args), end="") if __name__ == '__main__': cli()