Adding ability to specify obographviz config inside a crawl config (#829

)

* Adding ability to specify obographviz config inside a crawl config

* format

docs/packages/implementations/index.rst

@@ -24,4 +24,5 @@ Implementations (also known as *adapters*) implement one or more :ref:`interface
    aggregator
    pantherdb
    robot-template
+   translator
    llm

docs/packages/implementations/translator.rst

@@ -0,0 +1,25 @@
+.. _translator_implementation:
+
+Translator Adapter
+=================
+
+About
+-----
+
+
+Command Line
+^^^^^^^^^^^^
+
+.. code::
+
+   runoak -i translator: mappings UniProtKB:P0DPQ9
+
+Code
+----
+
+.. currentmodule:: oaklib.implementations.translator.translator_implementation
+
+.. autoclass:: TranslatorImplementation
+
+
+

src/oaklib/cli.py

@@ -401,7 +401,7 @@ def clear_cli_settings():
     default="",
     help="A comma-separated list of display options. Use 'all' for all",
 )
-stylemap_otion = click.option(
+stylemap_option = click.option(
     "-S",
     "--stylemap",
     help="a json file to configure visualization. See https://berkeleybop.github.io/kgviz-model/",
@@ -1440,7 +1440,7 @@ def annotate(
     show_default=True,
     help="If set then extend input seed list to include all pairwise MRCAs",
 )
-@stylemap_otion
+@stylemap_option
 @stylemap_configure_option
 @click.option(
     "--max-hops",
@@ -1884,7 +1884,7 @@ def ancestors(
     "--predicate-weights",
     help="key-value pairs specified in YAML where keys are predicates or shorthands and values are weights",
 )
-@stylemap_otion
+@stylemap_option
 @stylemap_configure_option
 @click.option("-o", "--output", help="Path to output file")
 def paths(
@@ -3808,6 +3808,8 @@ def singletons(output: str, predicates: str, filter_obsoletes: bool):
     show_default=True,
     help="If true then draw a graph",
 )
+@stylemap_option
+@stylemap_configure_option
 @click.option("-d", "--directory", help="Directory to write output files")
 @click.option(
     "--whole-ontology/--no-whole-ontology",
@@ -3827,6 +3829,8 @@ def crawl(
     allowed_prefixes,
     mapping_predicates,
     viz,
+    stylemap,
+    configure,
     config_yaml,
     whole_ontology,
     directory,
@@ -3844,6 +3848,8 @@ def crawl(
 
     Documentation for this command will be provided in a separate notebook.
     """
+    # TODO: normalize this option; avoid confusing with 'config'
+    stylemap_configure = configure
     impl = settings.impl
     if viz:
         writer = None
@@ -3887,15 +3893,19 @@ def crawl(
         if output_type and output_type not in ["png", "svg", "dot", "jpeg"]:
             write_graph(graph, format=output_type, output=output)
         else:
-            stylemap = None
             if stylemap is None:
                 stylemap = default_stylemap_path()
+            if config.stylemap_overrides:
+                stylemap_configure = config.stylemap_overrides
+            if stylemap_configure:
+                # TODO: this is a bit backwards
+                stylemap_configure = yaml.dump(stylemap_configure)
             graph_to_image(
                 graph,
                 seeds=terms,
                 imgfile=output,
                 stylemap=stylemap,
-                # configure=configure,
+                configure=stylemap_configure,
                 format=output_type,
                 view=True,
             )
@@ -4755,7 +4765,7 @@ def associations(
     show_default=True,
     help="if view is set then open the image after rendering",
 )
-@stylemap_otion
+@stylemap_option
 @stylemap_configure_option
 @click.argument("terms", nargs=-1)
 def associations_graph(

src/oaklib/implementations/monarch/monarch_implementation.py

@@ -48,6 +48,7 @@ def associations(
         predicate_closure_predicates: Optional[List[PRED_CURIE]] = None,
         object_closure_predicates: Optional[List[PRED_CURIE]] = None,
         include_modified: bool = False,
+        **kwargs,
     ) -> Iterator[Association]:
         if subjects and not isinstance(subjects, list):
             subjects = list(subjects)
@@ -140,6 +141,7 @@ def relationships(
         include_abox: bool = True,
         include_entailed: bool = False,
         exclude_blank: bool = True,
+        **kwargs,
     ) -> Iterator[RELATIONSHIP]:
         for a in self.associations(subjects=subjects, predicates=predicates, objects=objects):
             yield a.subject, a.predicate, a.object

src/oaklib/utilities/mapping/mapping_crawler.py

@@ -38,6 +38,7 @@ class Config:
     max_visits: Optional[int] = 10000
     gap_fill: bool = True
     clique_directory: Optional[str] = None
+    stylemap_overrides: Optional[Dict[str, Any]] = None
 
 
 class MappingClique(BaseModel):

src/oaklib/utilities/mapping/mapping_validation.py

@@ -276,6 +276,12 @@ def validate_mappings(
                 m.predicate_id == HAS_DBXREF and xref_is_bijective
             ):
                 comments.append(f"cardinality is {m.mapping_cardinality}")
+        if object_adapter:
+            object_label = object_adapter.label(m.object_id)
+            if not object_label:
+                comments.append("no label for object")
+            elif m.object_label and m.object_label != object_label:
+                comments.append("object label mismatch")
         if comments:
             if autolabel:
                 if not m.subject_label and subject_adapter: