Update synonyms handling

.github/workflows/tests.yml

@@ -16,7 +16,9 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
-        run: pip install tox
+        run: |
+          sudo apt-get install graphviz
+          pip install tox
       - name: Check manifest
         run: tox -e manifest
       - name: Check code quality with flake8
@@ -38,7 +40,9 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
-        run: pip install tox
+        run: |
+          sudo apt-get install graphviz
+          pip install tox
       - name: Check RST conformity with doc8
         run: tox -e doc8
       - name: Check README.rst
@@ -66,7 +70,9 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
-        run: pip install tox
+        run: |
+          sudo apt-get install graphviz
+          pip install tox
       - name: Test with pytest
         run:
           tox -e py

setup.cfg

@@ -69,6 +69,7 @@ install_requires =
     drugbank_downloader
     chembl_downloader
     umls_downloader
+    typing_extensions
 
 # Random options
 zip_safe = false

src/pyobo/reader.py

@@ -19,6 +19,8 @@
     Obo,
     Reference,
     Synonym,
+    SynonymSpecificities,
+    SynonymSpecificity,
     SynonymTypeDef,
     Term,
     TypeDef,
@@ -415,14 +417,14 @@ def _extract_synonym(
         logger.warning("[%s:%s] invalid synonym: %s", prefix, identifier, s)
         return None
 
-    specificity = None
-    for skos in "RELATED", "EXACT", "BROAD", "NARROW":
-        if rest.startswith(skos):
-            specificity = skos
-            rest = rest[len(skos) :].strip()
+    specificity: Optional[SynonymSpecificity] = None
+    for _specificity in SynonymSpecificities:
+        if rest.startswith(_specificity):
+            specificity = _specificity
+            rest = rest[len(_specificity) :].strip()
             break
 
-    stype = None
+    stype: Optional[SynonymTypeDef] = None
     if specificity is not None:  # go fishing for a synonym type definition
         for std in synonym_typedefs:
             if rest.startswith(std):

src/pyobo/ssg/index.html

@@ -35,17 +35,35 @@ <h5 class="card-header">
                     {% endfor %}
                 {% endif %}
             </dl>
-
-            {% if obo.synonym_typedefs %}
-                <h3>Synonym Definitions</h3>
-                <ul>
-                    {% for typedef in obo.synonym_typedefs %}
-                        <li>{{ typedef }}</li>
-                    {% endfor %}
-                </ul>
-            {% endif %}
         </div>
     </div>
+
+    {% if obo.synonym_typedefs %}
+    <div class="card" style="margin-top: 1em;">
+            <h5 class="card-header">
+                Synonym Type Definitions
+            </h5>
+            <table class="table table-striped">
+                <thead>
+                <tr>
+                    <th>ID</th>
+                    <th>Name</th>
+                    <th>Specificity</th>
+                </tr>
+                </thead>
+                <tbody>
+                {% for typedef in obo.synonym_typedefs %}
+                    <tr>
+                        <td>{{ typedef.id }}</td>
+                        <td>{{ typedef.name }}</td>
+                        <td>{{ typedef.specificity }}</td>
+                    </tr>
+                {% endfor %}
+                </tbody>
+            </table>
+        </div>
+    {% endif %}
+
     {% if manifest %}
         <div class="card" style="margin-top: 1em;">
             <h5 class="card-header">
@@ -57,6 +75,7 @@ <h5 class="card-header">
                     <th>Type</th>
                     <th>Local Identifier</th>
                     <th>Name</th>
+                    <th>Definition</th>
                 </tr>
                 </thead>
                 <tbody>
@@ -71,6 +90,7 @@ <h5 class="card-header">
                         </td>
                         <td align="right"><a href="{{ term.identifier }}">{{ term.identifier }}</a></td>
                         <td>{{ term.name }}</td>
+                        <td>{{ term.definition }}</td>
                     </tr>
                 {% endfor %}
                 </tbody>

src/pyobo/ssg/term.html

@@ -27,20 +27,13 @@ <h5 class="card-header">
 
                 {{ list_references(term.alt_ids, "Alt. IDs") }}
                 {% if term.synonyms %}
+                    {% for synonym in term.synonyms %}
                     <dt>
                         <span class="badge badge-primary">Synonym</span>
+                        {{ synonym.specificity.title() }}{% if synonym.type %}({{ synonym.type.name }}){% endif %}
                     </dt>
-                    <dd>
-                        {% if term.synonyms|length == 1 %}
-                            {{ term.synonyms[0].name }} (<span class="muted">{{ term.synonyms[0].specificity }}</span>)
-                        {% else %}
-                            <ul>
-                                {% for synonym in term.synonyms %}
-                                    <li>{{ synonym.name }} (<span class="muted">{{ synonym.specificity }}</span>)</li>
-                                {% endfor %}
-                            </ul>
-                        {% endif %}
-                    </dd>
+                    <dd>{{ synonym.name }}</dd>
+                    {% endfor %}
                 {% endif %}
                 {{ list_references(term.parents, "Parents") }}
                 {{ list_references(children, "Children") }}

src/pyobo/struct/__init__.py

@@ -6,6 +6,8 @@
 from .struct import (  # noqa: F401
     Obo,
     Synonym,
+    SynonymSpecificities,
+    SynonymSpecificity,
     SynonymTypeDef,
     Term,
     make_ad_hoc_ontology,

src/pyobo/struct/struct.py

@@ -35,6 +35,7 @@
 from more_click import force_option, verbose_option
 from networkx.utils import open_file
 from tqdm import tqdm
+from typing_extensions import Literal
 
 from .reference import Reference, Referenced
 from .typedef import (
@@ -65,13 +66,18 @@
 __all__ = [
     "Synonym",
     "SynonymTypeDef",
+    "SynonymSpecificity",
+    "SynonymSpecificities",
     "Term",
     "Obo",
     "make_ad_hoc_ontology",
 ]
 
 logger = logging.getLogger(__name__)
 
+SynonymSpecificity = Literal["EXACT", "NARROW", "BROAD", "RELATED"]
+SynonymSpecificities: Sequence[SynonymSpecificity] = ("EXACT", "NARROW", "BROAD", "RELATED")
+
 
 @dataclass
 class Synonym:
@@ -81,7 +87,7 @@ class Synonym:
     name: str
 
     #: The specificity of the synonym
-    specificity: str = "EXACT"
+    specificity: SynonymSpecificity = "EXACT"
 
     #: The type of synonym. Must be defined in OBO document!
     type: Optional["SynonymTypeDef"] = None
@@ -110,13 +116,19 @@ class SynonymTypeDef:
 
     id: str
     name: str
+    specificity: Optional[SynonymSpecificity] = None
 
     def to_obo(self) -> str:
         """Serialize to OBO."""
-        return f'synonymtypedef: {self.id} "{self.name}"'
+        if self.specificity:
+            return f'synonymtypedef: {self.id} "{self.name}" {self.specificity}'
+        else:
+            return f'synonymtypedef: {self.id} "{self.name}"'
 
     @classmethod
-    def from_text(cls, text) -> "SynonymTypeDef":
+    def from_text(
+        cls, text: str, specificity: Optional[SynonymSpecificity] = None
+    ) -> "SynonymTypeDef":
         """Get a type definition from text that's normalized."""
         return cls(
             id=text.lower()
@@ -126,6 +138,7 @@ def from_text(cls, text) -> "SynonymTypeDef":
             .replace(")", "")
             .replace("(", ""),
             name=text.replace('"', ""),
+            specificity=specificity,
         )