Show provenance for annotations in web app (#1095)

This is a proof of concept showing that we can propagate information
about _where_ a field displayed on the Bioregistry came from. This is
important because the Bioregistry imports data from other registries, so
it's useful to know where an annotation (e.g., the name associated with
a prefix) came from, and under what license it's being reused.

setup.cfg

@@ -15,6 +15,7 @@ ignore =
     W503
     # no quotes in strings
     B028
+    E704
 exclude =
     .tox,
     .git,

src/bioregistry/app/templates/resource.html

@@ -1,7 +1,7 @@
 {% extends "base.html" %}
 {% import "macros.html" as utils %}
 
-{% block title %}{{ config.METAREGISTRY_TITLE }} - {{ name }}{% endblock %}
+{% block title %}{{ config.METAREGISTRY_TITLE }} - {{ name_pack.value }}{% endblock %}
 
 {% block styles %}
 {{ super() }}
@@ -57,7 +57,10 @@
             <div class="row align-items-center">
                 <div class="col-8">
                     <h5 style="margin: 0"><a href="{{ url_for("metaregistry_ui.resources") }}">Registry</a> <i
-                            class="fas fa-angle-right"></i> {{ name }}
+                            class="fas fa-angle-right"></i> {{ name_pack.value }}
+                        <a type="button" data-toggle="modal" data-target="#name-modal">
+                            <i class="far fa-question-circle"></i>
+                        </a>
                         {{ utils.render_resource_warnings(resource) }}
                     </h5>
                 </div>
@@ -79,7 +82,7 @@ <h5 style="margin: 0"><a href="{{ url_for("metaregistry_ui.resources") }}">Regis
                         </div>
                     </div>
                     <a class="btn btn-sm btn-outline-dark" style="margin-right: 0.5em"
-                       href="https://github.com/biopragmatics/bioregistry/issues/new?labels=Update&template=update-misc.yml&prefix={{ prefix }}&title=Update+{{ name }}">
+                       href="https://github.com/biopragmatics/bioregistry/issues/new?labels=Update&template=update-misc.yml&prefix={{ prefix }}&title=Update+{{ name_pack.value }}">
                         Suggest
                     </a>
                     </div>
@@ -90,7 +93,7 @@ <h5 style="margin: 0"><a href="{{ url_for("metaregistry_ui.resources") }}">Regis
             {% if description %}
                 <p>
                 {% if resource.get_logo() %}
-                <img style="max-height: 70px; float: right;" src="{{ resource.get_logo() }}" alt="Logo for {{ resource.get_name() }}"/>
+                <img style="max-height: 70px; float: right;" src="{{ resource.get_logo() }}" alt="Logo for {{ name_pack.value }}"/>
                 {% endif %}
                 {{ description }}
                 </p>
@@ -264,7 +267,7 @@ <h5 style="margin: 0"><a href="{{ url_for("metaregistry_ui.resources") }}">Regis
                 <dd>
                     {% if pattern %}
                         <p>
-                            Local identifiers in {{ name }} should match this
+                            Local identifiers in {{ name_pack.value }} should match this
                             regular expression:<br/><kbd>{{ pattern }}</kbd>
                         </p>
                     {% elif has_no_terms %}
@@ -299,7 +302,7 @@ <h5 style="margin: 0"><a href="{{ url_for("metaregistry_ui.resources") }}">Regis
                 <dt>Pattern for CURIES</dt>
                 <dd>
                     <p>
-                        Compact URIs (CURIEs) constructed from {{ name }} should match
+                        Compact URIs (CURIEs) constructed from {{ name_pack.value }} should match
                         this regular expression:<br/><kbd>{{ curie_pattern }}</kbd>
                     </p>
                 </dd>
@@ -502,7 +505,7 @@ <h5 class="card-header">Ontology</h5>
         <div class="card" style="margin-top: 20px">
             <a id="mappings"></a>
             <h5 class="card-header">
-                Metaregistry <i class="fas fa-angle-right"></i> {{ name }}
+                Metaregistry <i class="fas fa-angle-right"></i> {{ name_pack.value }}
             </h5>
             <div class="card-body">
                 <p>
@@ -547,7 +550,7 @@ <h5 class="card-header">
                         {# <td>{{ resource.get_prefix_key("name", mapping.metaprefix) or "" }}</td> #}
                         <td style="text-align: center;">
                             <a data-toggle="tooltip" data-html="true"
-                               title="Report misalignment between {{ name }} and <code>{{ mapping.metaprefix }}:{{ mapping.xref }}</code>"
+                               title="Report misalignment between {{ name_pack.value }} and <code>{{ mapping.metaprefix }}:{{ mapping.xref }}</code>"
                                href="https://github.com/biopragmatics/bioregistry/issues/new?labels=Update%2CPrefix&template=mismatch.yml&title=Remove+incorrect+mapping+from+{{ resource.prefix }}+to+%60{{ mapping.metaprefix }}%3A{{ mapping.xref }}%60&prefix={{ resource.prefix }}&metaprefix={{ mapping.metaprefix }}&external-prefix={{ mapping.xref }}">
                                 <i class="fas fa-pen"></i>
                             </a>
@@ -610,7 +613,7 @@ <h5 style="margin: 0">Providers</h5>
                 {% if providers %}
                 <p>
                     The local unique identifier <code>{{ example }}</code> is used to demonstrate the providers
-                    available for {{ name }}. A guide for curating additional providers can be found
+                    available for {{ name_pack.value }}. A guide for curating additional providers can be found
                     <a href="https://biopragmatics.github.io/bioregistry/curation/providers">here</a>.
                 </p>
                 {% else %}
@@ -703,6 +706,28 @@ <h5 class="modal-title" id="versionModalLabel">Programmatic Access to Version</h
     </div>
     {% endif %}
 
+    <div class="modal fade" id="name-modal" tabindex="-1" role="dialog" aria-labelledby="nameModalLabel" aria-hidden="true">
+        <div class="modal-dialog" role="document">
+            <div class="modal-content">
+                <div class="modal-header">
+                    <h5 class="modal-title" id="nameModalLabel">Programmatic Access to Name</h5>
+                    <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+                        <span aria-hidden="true">&times;</span>
+                    </button>
+                </div>
+                <div class="modal-body">
+                    <p>
+                    This name annotation was originally annotated in
+                        <a href="{{ url_for("metaregistry_ui.metaresource", metaprefix=name_pack.metaprefix) }}">{{ name_pack.name }}</a>
+                        and is redistributed under the {{ name_pack.license }} license.
+                    </p>
+                    <p>Get the name:</p>
+                    {{ utils.code_example(prefix, "get_name", name_pack.value) }}
+                </div>
+            </div>
+        </div>
+    </div>
+
     {% if resource_license %}
     <div class="modal fade" id="license-modal" tabindex="-1" role="dialog" aria-labelledby="licenseModalLabel" aria-hidden="true">
         <div class="modal-dialog" role="document">

src/bioregistry/app/ui.py

@@ -122,13 +122,14 @@ def resource(prefix: str) -> str | flask.Response:
     example_curie_extras = [
         _resource.get_curie(example_extra, use_preferred=True) for example_extra in example_extras
     ]
+    name_pack = manager._repack(_resource.get_name(provenance=True))
     return render_template(
         "resource.html",
         zip=zip,
         prefix=prefix,
         resource=_resource,
         bioschemas=json.dumps(_resource.get_bioschemas_jsonld(), ensure_ascii=False),
-        name=manager.get_name(prefix),
+        name_pack=name_pack,
         example=example,
         example_extras=example_extras,
         example_curie=example_curie,

src/bioregistry/resolve.py

@@ -6,12 +6,12 @@
 import typing
 from collections.abc import Mapping
 from functools import lru_cache
-from typing import Any
+from typing import Any, Literal, overload
 
 import curies
 
 from .constants import MaybeCURIE
-from .resource_manager import manager
+from .resource_manager import MetaresourceAnnotatedValue, manager
 from .schema import Attributable, Resource
 
 __all__ = [
@@ -82,9 +82,25 @@ def get_resource(prefix: str) -> Resource | None:
     return manager.get_resource(prefix)
 
 
-def get_name(prefix: str) -> str | None:
-    """Get the name for the given prefix, it it's available."""
-    return manager.get_name(prefix)
+# docstr-coverage:excused `overload`
+@overload
+def get_name(prefix: str, *, provenance: Literal[False] = False) -> None | str: ...
+
+
+# docstr-coverage:excused `overload`
+@overload
+def get_name(
+    prefix: str, *, provenance: Literal[True] = True
+) -> None | MetaresourceAnnotatedValue[str]: ...
+
+
+def get_name(
+    prefix: str, *, provenance: bool = False
+) -> str | MetaresourceAnnotatedValue[str] | None:
+    """Get the name for the given prefix, if it's available."""
+    if provenance:
+        return manager.get_name(prefix, provenance=True)
+    return manager.get_name(prefix, provenance=False)
 
 
 def get_description(prefix: str, *, use_markdown: bool = False) -> str | None:
@@ -160,12 +176,13 @@ def get_pattern(prefix: str) -> str | None:
     return manager.get_pattern(prefix)
 
 
-def get_namespace_in_lui(prefix: str) -> bool | None:
+def get_namespace_in_lui(
+    prefix: str, *, provenance: bool = False
+) -> bool | MetaresourceAnnotatedValue[bool] | None:
     """Check if the namespace should appear in the LUI."""
-    entry = get_resource(prefix)
-    if entry is None:
-        return None
-    return entry.get_namespace_in_lui()
+    if provenance:
+        return manager.get_namespace_in_lui(prefix, provenance=True)
+    return manager.get_namespace_in_lui(prefix, provenance=False)
 
 
 def get_appears_in(prefix: str) -> list[str] | None:

src/bioregistry/resource_manager.py

@@ -6,12 +6,18 @@
 import typing
 from collections import Counter, defaultdict
 from collections.abc import Iterable, Mapping, Sequence
+from dataclasses import dataclass
 from functools import cache
 from pathlib import Path
 from typing import (
     Any,
     Callable,
+    Generic,
+    Literal,
+    TypeVar,
+    Union,
     cast,
+    overload,
 )
 
 import curies
@@ -39,6 +45,7 @@
     Resource,
     sanitize_model,
 )
+from .schema.struct import MetaprefixAnnotatedValue
 from .schema_utils import (
     _collections_from_path,
     _contexts_from_path,
@@ -56,6 +63,31 @@
 
 logger = logging.getLogger(__name__)
 
+X = TypeVar("X", bound=Union[int, str])
+
+
+@dataclass
+class MetaresourceAnnotatedValue(Generic[X]):
+    """A pack for a value that has extra information."""
+
+    value: X
+    registry: Registry
+
+    @property
+    def metaprefix(self) -> str:
+        """Get prefix for the source registry for the annotation."""
+        return self.registry.prefix
+
+    @property
+    def name(self) -> str:
+        """Get the name of the source registry for the annotation."""
+        return self.registry.name
+
+    @property
+    def license(self) -> str:
+        """Get the license for the annotation."""
+        return self.registry.license or "unknown"
+
 
 def _synonym_to_canonical(registry: Mapping[str, Resource]) -> NormDict:
     """Return a mapping from several variants of each synonym to the canonical namespace."""
@@ -505,12 +537,75 @@ def get_uri_prefix(self, prefix: str, priority: Sequence[str] | None = None) ->
             return None
         return entry.get_uri_prefix(priority=priority)
 
-    def get_name(self, prefix: str) -> str | None:
-        """Get the name for the given prefix, it it's available."""
+    # docstr-coverage:excused `overload`
+    @overload
+    def _repack(self, obj: None) -> None: ...
+
+    # docstr-coverage:excused `overload`
+    @overload
+    def _repack(self, obj: X) -> X: ...
+
+    # docstr-coverage:excused `overload`
+    @overload
+    def _repack(self, obj: MetaprefixAnnotatedValue[X]) -> MetaresourceAnnotatedValue[X]: ...
+
+    def _repack(
+        self, obj: None | X | MetaprefixAnnotatedValue[X]
+    ) -> MetaresourceAnnotatedValue[X] | X | None:
+        if obj is None:
+            return None
+        elif isinstance(obj, MetaprefixAnnotatedValue):
+            mp = self.get_registry(obj.metaprefix)
+            if mp is None:
+                raise ValueError
+            return MetaresourceAnnotatedValue(obj.value, mp)
+        else:
+            return obj
+
+    # docstr-coverage:excused `overload`
+    @overload
+    def get_name(self, prefix: str, *, provenance: Literal[False] = False) -> str | None: ...
+
+    # docstr-coverage:excused `overload`
+    @overload
+    def get_name(
+        self, prefix: str, *, provenance: Literal[True] = True
+    ) -> MetaresourceAnnotatedValue[str] | None: ...
+
+    def get_name(
+        self, prefix: str, *, provenance: bool = False
+    ) -> str | MetaresourceAnnotatedValue[str] | None:
+        """Get the name for the given prefix, if it's available."""
+        entry = self.get_resource(prefix)
+        if entry is None:
+            return None
+        if provenance:
+            _tmp = entry.get_name(provenance=True)
+            return self._repack(_tmp)
+        return entry.get_name(provenance=False)
+
+    # docstr-coverage:excused `overload`
+    @overload
+    def get_namespace_in_lui(
+        self, prefix: str, *, provenance: Literal[False] = False
+    ) -> bool | None: ...
+
+    # docstr-coverage:excused `overload`
+    @overload
+    def get_namespace_in_lui(
+        self, prefix: str, *, provenance: Literal[True] = True
+    ) -> None | MetaresourceAnnotatedValue[bool]: ...
+
+    def get_namespace_in_lui(
+        self, prefix: str, *, provenance: bool = False
+    ) -> None | bool | MetaresourceAnnotatedValue[bool]:
+        """Get the name for the given prefix, if it's available."""
         entry = self.get_resource(prefix)
         if entry is None:
             return None
-        return entry.get_name()
+        if provenance:
+            return self._repack(entry.get_namespace_in_lui(provenance=True))
+        return entry.get_namespace_in_lui(provenance=False)
 
     def get_description(self, prefix: str, *, use_markdown: bool = False) -> str | None:
         """Get the description for the given prefix, it it's available."""