Use the new --clean-obo option.

Use ROBOT's new `--clean-obo` option when producing the OBO artefacts.

Since there is already a `obo_format_options` in the ODK configuration,
we reuse it, and set the default value to

  --clean-obo 'strict drop-untranslatable-axioms'

We default to dropping the untranslatable axioms because this has always
been the standard behaviour of the ODK (before this option existed, this
was done by forcibly grepping out the `owl-axioms` tag from the OBO
files).

I would prefer to default to `--clean-obo simple`, which has the
additional effect of forcibly removing GCI axioms. However this is a
consequential change, one that we should probably not force upon our
users.

We set the default value using some custom code, instead of statically
when declaring the `obo_format_options` field. This way, if a user has
already set this option to something in her configuration file, she will
still get the default behaviour of dropping the untranslatable axioms.
But we do _not_ touch the value set by the user if it already contains a
`--clean-obo` flag.

Author: gouttegd

odk/odk.py

@@ -791,7 +791,7 @@ class OntologyProject(JsonSchemaMixin):
     """Emails to use in travis configurations. """
 
     obo_format_options : str = ""
-    """Additional args to pass to robot when saving to obo. TODO consider changing to a boolean for checks"""
+    """Additional args to pass to robot when saving to obo. The default is '--clean-obo "strict drop-untranslatable-axioms"'."""
 
     catalog_file : str = "catalog-v001.xml"
     """Name of the catalog file to be used by the build."""
@@ -854,7 +854,8 @@ def fill_missing(self):
         The config can be lazy and just specify an id list.
         These are used to create stub product objects.
 
-        (this adds complexity and may be removed)
+        This method is also intended to perform any checks
+        and initialisations on the entire configuration tree.
         """
         if self.import_group is not None:
             self.import_group.fill_missing(self)
@@ -867,6 +868,11 @@ def fill_missing(self):
         if self.components is not None:
             self.components.fill_missing(self)
 
+        if not '--clean-obo' in self.obo_format_options:
+            if len(self.obo_format_options) > 0:
+                self.obo_format_options += ' '
+            self.obo_format_options += '--clean-obo "strict drop-untranslatable-axioms"'
+
 @dataclass
 class ExecutionContext(JsonSchemaMixin):
     """

template/src/ontology/Makefile.jinja2

@@ -917,7 +917,7 @@ $(SUBSETDIR)/%.owl: $(ONT).owl | $(SUBSETDIR) all_robot_plugins
 
 {% if 'obo' in project.export_formats %}
 $(SUBSETDIR)/%.obo: $(SUBSETDIR)/%.owl
-	$(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo
+	$(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@
 {% endif -%}
 {% if 'ttl' in project.export_formats %}
 $(SUBSETDIR)/%.ttl: $(SUBSETDIR)/%.owl
@@ -1249,7 +1249,7 @@ $(TRANSLATIONSDIR)/%.babelon.json: $(TRANSLATIONSDIR)/%.babelon.tsv
 {% if r.startswith('custom-') %}{% set release = r | replace("custom-","") %}{% else %}{% set release = "$(ONT)-" ~ r %}{% endif -%}
 {% if 'obo' in project.export_formats -%}
 {{ release }}.obo: {{ release }}.owl
-	$(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo
+	$(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@
 {% endif -%}
 {% if 'ttl' in project.export_formats -%}
 {{ release }}.ttl: {{ release }}.owl
@@ -1287,7 +1287,7 @@ $(ONT).owl: $(ONT)-{{ project.primary_release }}.owl
 
 {% if 'obo' in project.export_formats -%}
 $(ONT).obo: $(ONT).owl
-	$(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo
+	$(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@
 {% endif -%}
 {% if 'ttl' in project.export_formats -%}
 $(ONT).ttl: $(ONT).owl