tailor MIXS docs to make it less LinkML-savvy

GenomicsStandardsConsortium · Oct 18, 2023 · b96404b · b96404b
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diff --git a/src/doc-templates/class.md.jinja2 b/src/doc-templates/class.md.jinja2
@@ -1,12 +1,21 @@
-{% if element.is_a == "Checklist" -%}
-    # Checklist: {{ gen.name(element) }}
-{% elif element.is_a == "Extension" -%}
-    # Extension: {{ gen.name(element) }}
-{% elif element.mixins and element.is_a -%}
-    # Combination: {{ gen.name(element) }}
-{% else -%}
-    # Class: {{ gen.name(element) }}
-{% endif %}
+{%- if element.is_a == "Checklist" -%}
+    {%- set type = "Checklist" -%}
+{%- elif element.is_a == "Extension" -%}
+    {%- set type = "Extension" -%}
+{%- elif element.mixins and element.is_a -%}
+    {%- set type = "Combination" -%}
+{%- else -%}
+    {%- set type = "Class" -%}
+{%- endif -%}
+
+{%- if element.title -%}
+    {%- set title = element.title ~ ' (' ~ gen.name(element) ~ ')' -%}
+{%- else -%}
+    {%- set title = gen.name(element) -%}
+{%- endif -%}
+
+# {{ type }}: {{ title }}
+
 
 {%- if header -%}
 {{header}}
@@ -24,26 +33,23 @@ _{{ element_description_line }}_
 * __NOTE__: this is an abstract class and should not be instantiated directly
 {% endif %}
 
-{% if schemaview.class_parents(element.name) or schemaview.class_children(element.name, mixins=False) %}
-
-## Inheritance
-{{ gen.inheritance_tree(element, mixins=True) }}
-{% else %}
-<!-- no inheritance hierarchy -->
+{% if element.mixins and element.is_a -%}
+## Composition
+{{ gen.link(element.is_a) }} [Checklist] + {{ gen.link(element.mixins[0]) }} [Extension]
 {% endif %}
 
 ## Terms
 
-| Name | Cardinality and Range | Description | Inheritance |
+| MIXS ID | Name | Cardinality and Range | Description |
 | ---  | --- | --- | --- |
 {% if gen.get_direct_slots(element)|length > 0 %}
 {%- for slot in gen.get_direct_slots(element) -%}
-| {{ gen.link(slot) }} | {{ gen.cardinality(slot) }} <br/> {{ gen.link(slot.range) }} | {{ slot.description|enshorten }} | direct |
+| {{ gen.uri_link(slot) }} | {{ gen.link(slot) }} | {{ gen.cardinality(slot) }} <br/> {{ gen.link(slot.range) }} | {{ slot.description|enshorten }} |
 {% endfor -%}
 {% endif -%}
 {% if gen.get_indirect_slots(element)|length > 0 %}
 {%- for slot in gen.get_indirect_slots(element) -%}
-| {{ gen.link(slot) }} | {{ gen.cardinality(slot) }} <br/> {{ gen.link(slot.range) }} | {{ slot.description|enshorten }} | {{ gen.links(gen.get_slot_inherited_from(element.name, slot.name))|join(', ') }} |
+| {{ gen.uri_link(slot) }} | {{ gen.link(slot) }} | {{ gen.cardinality(slot) }} <br/> {{ gen.link(slot.range) }} | {{ slot.description|enshorten }} |
 {% endfor -%}
 {% endif %}
 

diff --git a/src/doc-templates/common_metadata.md.jinja2 b/src/doc-templates/common_metadata.md.jinja2
@@ -17,22 +17,6 @@
 {% endfor %}
 {% endif -%}
 
-{% if element.comments -%}
-## Comments
-
-{% for x in element.comments -%}
-* {{x}}
-{% endfor %}
-{% endif -%}
-
-{% if element.todos -%}
-## TODOs
-
-{% for x in element.todos -%}
-* {{x}}
-{% endfor %}
-{% endif -%}
-
 {% if element.see_also -%}
 ## See Also
 
@@ -41,38 +25,18 @@
 {% endfor %}
 {% endif -%}
 
-## Identifier and Mapping Information
 
-{% if element.id_prefixes %}
-### Valid ID Prefixes
-
-Instances of this class *should* have identifiers with one of the following prefixes:
-{% for p in element.id_prefixes %}
-* {{p}}
-{% endfor %}
-
-{% endif %}
+{% set annotations_data = [] %}
 
+{% for a in element.annotations -%}
+    {%- if a|string|first != '_' and element.annotations[a].value is not none and element.annotations[a].value != '' -%}
+        {%- set _ = annotations_data.append({'a': a, 'value': element.annotations[a].value}) -%}
+    {%- endif -%}
+{% endfor -%}
 
-{% if element.annotations %}
+{% if annotations_data %}
 ### Annotations
-
-| property | value |
-| --- | --- |
-{% for a in element.annotations -%}
-{%- if a|string|first != '_' -%}
-| {{ a }} | {{ element.annotations[a].value }} |
-{%- endif -%}
+{% for item in annotations_data -%}
+* {{ item['a'] }}: {{ item['value'] }}
 {% endfor %}
 {% endif %}
-
-{% if element.from_schema or element.imported_from %}
-### Schema Source
-
-{% if element.from_schema %}
-* from schema: {{ element.from_schema }}
-{% endif %}
-{% if element.imported_from %}
-* imported from: {{ element.imported_from }}
-{% endif %}
-{% endif %}
diff --git a/src/doc-templates/slot.md.jinja2 b/src/doc-templates/slot.md.jinja2
@@ -1,4 +1,10 @@
-# Term: {{ gen.name(element) }}
+{%- if element.title %}
+    {%- set title = element.title ~ ' (' ~ element.name ~ ')' -%}
+{%- else %}
+    {%- set title = gen.name(element) -%}
+{%- endif -%}
+
+# Term: {{ title }}
 
 {%- if header -%}
 {{header}}
@@ -26,14 +32,7 @@ URI: {{ gen.uri_link(element) }}
 ## Properties
 
 * Range: {{gen.link(element.range)}}
-{% if element.multivalued %}
-* Multivalued: {{ element.multivalued }}
-{% endif -%}
-{% if element.required %}
-* Required: {{ element.required }}
-{% elif element.recommended %}
-* Recommended: {{ element.recommended }}
-{% endif -%}
+* Cardinality: {{ gen.cardinality(element) }}
 {% if element.minimum_value is not none %}
 * Minimum Value: {{ element.minimum_value|int }}
 {% endif -%}