Regroup all ROBOT-related options in a dedicated robot section.

This is proof-of-concept reorganisation of the configuration schema to
test the whole idea that we can make relatively big changes to the
schema while preserving compatibility with existing files.

We create a new subsection in the top-level `project` dictionary, called
`robot`, intended to host all ROBOT-related options.

That is, the following options and group, that are currently directly
under the top-level object:

  obo_format_options: ...
  robot_relax_options: ...
  robot_reduce_options: ...
  robot_plugins:
    plugins:
      - name: my_plugin
  robot_report:
    release_reports: True
    fail_on: ERROR
    ...

are now renamed and regrouped into a single `robot` section:

  robot:
    obo_format_options: ...
    relax_options: ...
    reduce_options: ...
    plugins:
      - name: my_plugin
    report:
      release_reports: True
      fail_on: ERROR
      ...

Author: gouttegd

odk/odk.py

@@ -596,13 +596,29 @@ class RobotPlugin(JsonSchemaMixin):
 
 @dataclass_json
 @dataclass
-class PluginsGroup(JsonSchemaMixin):
+class RobotOptionsGroup(JsonSchemaMixin):
     """
-    A configuration section to list extra ROBOT plugins not provided by the ODK
+    A configuration section for additional options specific to ROBOT.
     """
 
+    reasoner : str = "ELK"
+    """Reasoner to use in robot commands that need one."""
+
+    obo_format_options : str = ""
+    """Additional options to pass to robot convert when exporting to OBO. Default is '--clean-obo "strict drop-untranslatable-axioms"'."""
+
+    relax_options : str = "--include-subclass-of true"
+    """Additional options to pass to robot relax command."""
+
+    reduce_options : str = "--include-subproperties true"
+    """Additional options to pass to robot reduce command."""
+
     plugins : Optional[List[RobotPlugin]] = None
-    """The list of plugins to use"""
+    """List of ROBOT plugins used by this project."""
+
+    report : Dict[str, Any] = field(default_factory=lambda: ReportConfig().to_dict())
+    """Settings for ROBOT report, ROBOT verify and additional reports that are generated."""
+
 
 
 @dataclass_json
@@ -664,9 +680,6 @@ class OntologyProject(JsonSchemaMixin):
     export_project_yaml: bool = False
     """Flag to set if you want a full project.yaml to be exported, including all the default options."""
 
-    reasoner : str = "ELK"
-    """Name of reasoner to use in ontology pipeline, see robot reason docs for allowed values"""
-    
     exclude_tautologies : str = "structural"
     """Remove tautologies such as A SubClassOf: owl:Thing or owl:Nothing SubclassOf: A. For more information see http://robot.obolibrary.org/reason#excluding-tautologies"""
 
@@ -771,15 +784,6 @@ class OntologyProject(JsonSchemaMixin):
     travis_emails : Optional[List[Email]] = None ## ['obo-ci-reports-all@groups.io']
     """Emails to use in travis configurations. """
 
-    obo_format_options : str = ""
-    """Additional args to pass to robot when saving to obo. The default is '--clean-obo "strict drop-untranslatable-axioms"'."""
-
-    robot_relax_options : str = "--include-subclass-of true"
-    """Additional options to pass to robot's relax command."""
-
-    robot_reduce_options : str = "--include-subproperties true"
-    """Additional options to pass to robot's reduce command."""
-
     catalog_file : str = "catalog-v001.xml"
     """Name of the catalog file to be used by the build."""
 
@@ -798,17 +802,14 @@ class OntologyProject(JsonSchemaMixin):
     contributors : Optional[List[Person]] = None
     """List of ontology contributors (currently setting this has no effect)"""
 
-    robot_report : Dict[str, Any] = field(default_factory=lambda: ReportConfig().to_dict())
-    """Block that includes settings for ROBOT report, ROBOT verify and additional reports that are generated"""
-
     ensure_valid_rdfxml : bool = True
     """When enabled, ensure that any RDF/XML product file is valid"""
 
     extra_rdfxml_checks : bool = False
     """When enabled, RDF/XML product files are checked against additional parsers"""
 
-    robot_plugins : Optional[PluginsGroup] = None
-    """Block that includes information on the extra ROBOT plugins used by this project"""
+    robot : RobotOptionsGroup = field(default_factory=lambda: RobotOptionsGroup())
+    """Block for ROBOT-related options"""
 
     # product groups
     import_group : Optional[ImportGroup] = None
@@ -855,10 +856,10 @@ 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"'
+        if not '--clean-obo' in self.robot.obo_format_options:
+            if len(self.robot.obo_format_options) > 0:
+                self.robot.obo_format_options += ' '
+            self.robot.obo_format_options += '--clean-obo "strict drop-untranslatable-axioms"'
 
 @dataclass
 class ExecutionContext(JsonSchemaMixin):
@@ -938,7 +939,13 @@ def update_config_dict(obj):
     """
     changes = [
             # old key path               new key path
-            ('example.old.key',         'example.new.key')
+            ('reasoner',                'robot.reasoner'),
+            ('obo_format_options',      'robot.obo_format_options'),
+            ('relax_options',           'robot.relax_options'),
+            ('reduce_options',          'robot.reduce_options'),
+            ('robot_plugins.plugins',   'robot.plugins'),
+            ('robot_plugins',           None),
+            ('robot_report',            'robot.report'),
             ]
     for old, new in changes:
         v = pop_key(obj, old)
@@ -1435,7 +1442,7 @@ def update(templatedir):
                 policies.append(('.github/workflows/' + workflow + '.yml', ALWAYS))
         if project.documentation is not None and 'docs' in project.workflows:
             policies.append(('.github/workflows/docs.yml', ALWAYS))
-    if not project.robot_report.get('custom_profile', False):
+    if not project.robot.report.get('custom_profile', False):
         policies.append(('src/ontology/profile.txt', NEVER))
 
     # Proceed with template instantiation, using the policies
@@ -1523,7 +1530,7 @@ def seed(config, clean, outdir, templatedir, dependencies, title, user, source,
         logging.info("No templates folder in /tools/; assume not in docker context")
         templatedir = "./template"
     policies = []
-    if not project.robot_report.get('custom_profile', False):
+    if not project.robot.report.get('custom_profile', False):
         policies.append(('src/ontology/profile.txt', NEVER))
     tgts += install_template_files(mg, templatedir, outdir, policies)
 

template/_dynamic_documentation.jinja2

@@ -802,19 +802,20 @@ We can define custom checks using [SPARQL](https://www.w3.org/TR/rdf-sparql-quer
 
 1. Add the SPARQL query in `src/sparql`. The name of the file should end with `-violation.sparql`. Please give a name that helps to understand which violation the query wants to check.
 2. Add the name of the new file to odk configuration file `src/ontology/uberon-odk.yaml`:
-    1. Include the name of the file (without the `-violation.sparql` part) to the list inside the key `custom_sparql_checks` that is inside `robot_report` key.
-    1. If the `robot_report` or `custom_sparql_checks` keys are not available, please add this code block to the end of the file.
+    1. Include the name of the file (without the `-violation.sparql` part) to the list inside the key `custom_sparql_checks` that is inside `robot.report` key.
+    1. If the `robot.report` or `custom_sparql_checks` keys are not available, please add this code block to the end of the file.
 
         ``` yaml
-          robot_report:
-            release_reports: False
-            fail_on: ERROR
-            use_labels: False
-            custom_profile: True
-            report_on:
-              - edit
-            custom_sparql_checks:
-              - name-of-the-file-check
+          robot:
+            report:
+              release_reports: False
+              fail_on: ERROR
+              use_labels: False
+              custom_profile: True
+              report_on:
+                - edit
+              custom_sparql_checks:
+                - name-of-the-file-check
         ```
 3. Update the repository so your new SPARQL check will be included in the QC.
 

template/_dynamic_sparql.jinja2

@@ -17,7 +17,7 @@ WHERE {
 {#
     SPARQL QUERY QC checks
 -#}
-{% if project.robot_report.custom_sparql_checks is not defined or 'owldef-self-reference' in project.robot_report.custom_sparql_checks -%}
+{% if project.robot.report.custom_sparql_checks is not defined or 'owldef-self-reference' in project.robot.report.custom_sparql_checks -%}
 ^^^ src/sparql/owldef-self-reference-violation.sparql
 PREFIX rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 PREFIX oio: <http://www.geneontology.org/formats/oboInOwl#>
@@ -31,7 +31,7 @@ SELECT ?term WHERE {
   FILTER(isIRI(?term) && ({% if project.namespaces %}{% for ns in project.namespaces %}STRSTARTS(str(?term), "{{ ns }}"){% if not loop.last %} || {% endif %}{% endfor %}{% else %}STRSTARTS(str(?term), "{{ project.uribase }}/{{ project.id.upper() }}_"){% endif %}))
 }
 {% endif -%}
-{% if project.robot_report.custom_sparql_checks is not defined or 'redundant-subClassOf' in project.robot_report.custom_sparql_checks -%}
+{% if project.robot.report.custom_sparql_checks is not defined or 'redundant-subClassOf' in project.robot.report.custom_sparql_checks -%}
 ^^^ src/sparql/redundant-subClassOf-violation.sparql
 PREFIX oio: <http://www.geneontology.org/formats/oboInOwl#>
 PREFIX owl: <http://www.w3.org/2002/07/owl#>
@@ -48,7 +48,7 @@ SELECT ?term ?xl ?y ?yl ?z ?zl WHERE {
   FILTER(isIRI(?term) && ({% if project.namespaces %}{% for ns in project.namespaces %}STRSTARTS(str(?term), "{{ ns }}"){% if not loop.last %} || {% endif %}{% endfor %}{% else %}STRSTARTS(str(?term), "{{ project.uribase }}/{{ project.id.upper() }}_"){% endif %}))
 }
 {% endif -%}
-{% if project.robot_report.custom_sparql_checks is not defined or 'taxon-range' in project.robot_report.custom_sparql_checks -%}
+{% if project.robot.report.custom_sparql_checks is not defined or 'taxon-range' in project.robot.report.custom_sparql_checks -%}
 ^^^ src/sparql/taxon-range-violation.sparql
 PREFIX never_in_taxon: <http://purl.obolibrary.org/obo/RO_0002161>
 PREFIX present_in_taxon: <http://purl.obolibrary.org/obo/RO_0002175>
@@ -61,7 +61,7 @@ WHERE {
   FILTER(isIRI(?term) && ({% if project.namespaces %}{% for ns in project.namespaces %}STRSTARTS(str(?term), "{{ ns }}"){% if not loop.last %} || {% endif %}{% endfor %}{% else %}STRSTARTS(str(?term), "{{ project.uribase }}/{{ project.id.upper() }}_"){% endif %}))
 }
 {% endif -%}
-{% if project.robot_report.custom_sparql_checks is not defined or 'iri-range' in project.robot_report.custom_sparql_checks -%}
+{% if project.robot.report.custom_sparql_checks is not defined or 'iri-range' in project.robot.report.custom_sparql_checks -%}
 ^^^ src/sparql/iri-range-violation.sparql
 PREFIX never_in_taxon: <http://purl.obolibrary.org/obo/RO_0002161>
 PREFIX present_in_taxon: <http://purl.obolibrary.org/obo/RO_0002175>
@@ -82,7 +82,7 @@ WHERE {
   FILTER (!isIRI(?value))
 }
 {% endif -%}
-{% if project.robot_report.custom_sparql_checks is not defined or 'iri-range-advanced' in project.robot_report.custom_sparql_checks -%}
+{% if project.robot.report.custom_sparql_checks is not defined or 'iri-range-advanced' in project.robot.report.custom_sparql_checks -%}
 ^^^ src/sparql/iri-range-advanced-violation.sparql
 PREFIX never_in_taxon: <http://purl.obolibrary.org/obo/RO_0002161>
 PREFIX present_in_taxon: <http://purl.obolibrary.org/obo/RO_0002175>
@@ -105,7 +105,7 @@ WHERE {
   FILTER (!isIRI(?value))
 }
 {% endif -%}
-{% if project.robot_report.custom_sparql_checks is not defined or 'label-with-iri' in project.robot_report.custom_sparql_checks -%}
+{% if project.robot.report.custom_sparql_checks is not defined or 'label-with-iri' in project.robot.report.custom_sparql_checks -%}
 ^^^ src/sparql/label-with-iri-violation.sparql
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 
@@ -116,7 +116,7 @@ WHERE {
   FILTER(isIRI(?term) && ({% if project.namespaces %}{% for ns in project.namespaces %}STRSTARTS(str(?term), "{{ ns }}"){% if not loop.last %} || {% endif %}{% endfor %}{% else %}STRSTARTS(str(?term), "{{ project.uribase }}/{{ project.id.upper() }}_"){% endif %}))
 }
 {% endif -%}
-{% if project.robot_report.custom_sparql_checks is not defined or 'multiple-replaced_by' in project.robot_report.custom_sparql_checks -%}
+{% if project.robot.report.custom_sparql_checks is not defined or 'multiple-replaced_by' in project.robot.report.custom_sparql_checks -%}
 ^^^ src/sparql/multiple-replaced_by-violation.sparql
 PREFIX replaced_by: <http://purl.obolibrary.org/obo/IAO_0100001>
 
@@ -130,7 +130,7 @@ SELECT DISTINCT ?entity ?property ?value WHERE {
   BIND(CONCAT(str(?value1), CONCAT("|", str(?value2))) as ?value)
 }
 {% endif -%}
-{% if project.robot_report.custom_sparql_checks is not defined or 'term-tracker-uri' in project.robot_report.custom_sparql_checks -%}
+{% if project.robot.report.custom_sparql_checks is not defined or 'term-tracker-uri' in project.robot.report.custom_sparql_checks -%}
 ^^^ src/sparql/term-tracker-uri-violation.sparql
 PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
 PREFIX term_tracker_item: <http://purl.obolibrary.org/obo/IAO_0000233>
@@ -141,7 +141,7 @@ SELECT ?term ?term_tracker ?term_tracker_type WHERE {
   BIND(DATATYPE(?term_tracker) as ?term_tracker_type) 
 }
 {% endif -%}
-{% if project.robot_report.custom_sparql_checks is not defined or 'illegal-date' in project.robot_report.custom_sparql_checks -%}
+{% if project.robot.report.custom_sparql_checks is not defined or 'illegal-date' in project.robot.report.custom_sparql_checks -%}
 ^^^ src/sparql/illegal-date-violation.sparql
 PREFIX dct: <http://purl.org/dc/terms/>
 PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
@@ -155,7 +155,7 @@ SELECT DISTINCT ?term ?property ?value WHERE
   FILTER (datatype(?value) != xsd:dateTime || !regex(str(?value), '^\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}Z'))
 }
 {% endif -%}
-{% if project.robot_report.custom_sparql_checks is not defined or 'dc-properties' in project.robot_report.custom_sparql_checks -%}
+{% if project.robot.report.custom_sparql_checks is not defined or 'dc-properties' in project.robot.report.custom_sparql_checks -%}
 ^^^ src/sparql/dc-properties-violation.sparql
 # The purpose of this violation is to make sure people update
 # from using the deprecated DC Elements 1.1 namespace (http://purl.org/dc/elements/1.1/)