Add permutations feature to DOSDP patterns schema

requirements.txt

@@ -3,7 +3,7 @@ jsonschema
 requests
 jsonpath_rw
 ruamel.yaml
-jsonschema2md
+jsonschema2md>=0.4,<0.5
 pandas
 tabulate
 

setup.py

@@ -41,7 +41,7 @@ def update_relative_links(readme_content):
     package_dir={'': 'src'},
     packages=["dosdp", "schema", "dosdp.document", "dosdp.document.pattern", "dosdp.document.schema"],
     include_package_data=True,
-    install_requires=["PyYAML", "jsonschema", "requests", "jsonpath_rw", "ruamel.yaml", "jsonschema2md", "pandas"],
+    install_requires=["PyYAML", "jsonschema", "requests", "jsonpath_rw", "ruamel.yaml", "jsonschema2md>=0.4,<0.5", "pandas", "tabulate"],
     entry_points={
         "console_scripts": [
             "dosdp=dosdp.__main__:main",

src/dosdp/document/pattern/patterns_create_docs.py

@@ -136,7 +136,7 @@ def generate_pattern_documentation(pattern_file, md_file_path, sample_data_dir=N
                 else:
                     print("No matches!")
             except Exception as e:
-                logging.error("Error processing the tsv file!", e)
+                logging.error("Error processing the tsv file! %s", e)
         else:
             logging.warning("Data dir: '" + os.path.join(str(sample_data_dir),
                                                          sample_file) + "' does not exist to provide sample data!")

src/schema/dosdp_schema.yaml

@@ -93,6 +93,15 @@ definitions:
          leaving this field out.
         items: {type: string}
         type: array
+      permutations:
+        description: >
+         Optional list of permutation specifications. For each variable specified,
+         generates additional annotations using the values of the specified annotation
+         properties from the filler term. The label-based annotation is always generated
+         in addition to the permutations. If multiple permutation entries exist for
+         different variables, the cartesian product of all values is generated.
+        type: array
+        items: { $ref: '#/definitions/permutation' }
       multi_clause:
         items: { $ref: '#/definitions/multi_clause_printf' }
 
@@ -219,6 +228,24 @@ definitions:
         type: string
         description: perl style regex sub.  May include backreferences.
 
+  permutation:
+    type: object
+    additionalProperties: False
+    required: [var, annotationProperties]
+    properties:
+      var:
+        description: >
+          The name of a single variable for which to generate permutations.
+          Must correspond to a variable specified in the 'vars' field of the pattern.
+        type: string
+      annotationProperties:
+        description: >
+          A list of annotation property names (as declared in the annotationProperties
+          dictionary) whose values from the filler term will be used to generate
+          additional annotations. Each value found generates a separate annotation.
+        type: array
+        items: { type: string }
+
   opa:
     type: object
     additionalProperties: False
@@ -272,6 +299,15 @@ definitions:
          used in the substitution.
         items: {type: string}
         type: array
+      permutations:
+        description: >
+         Optional list of permutation specifications. For each variable specified,
+         generates additional annotations using the values of the specified annotation
+         properties from the filler term. The label-based annotation is always generated
+         in addition to the permutations. If multiple permutation entries exist for
+         different variables, the cartesian product of all values is generated.
+        type: array
+        items: { $ref: '#/definitions/permutation' }
       multi_clause:
         items: { $ref: '#/definitions/multi_clause_printf' }
 

src/schema/test/positive_test_set/patterns/acute_with_permutations.yaml

@@ -0,0 +1,49 @@
+pattern_name: acute_with_permutations
+
+pattern_iri: http://purl.obolibrary.org/obo/mondo/patterns/acute_with_permutations.yaml
+
+description: 'Test pattern demonstrating the permutations feature for synonym generation.
+  This pattern generates additional synonyms by permuting over the exact_synonym
+  values of the disease filler term.'
+
+contributors:
+- https://orcid.org/0000-0002-6601-2165
+
+classes:
+  acute: PATO:0000389
+  disease: MONDO:0000001
+
+relations:
+  has modifier: RO:0002573
+
+annotationProperties:
+  exact_synonym: oio:hasExactSynonym
+  related_synonym: oio:hasRelatedSynonym
+
+vars:
+  disease: '''disease'''
+
+name:
+  text: acute %s
+  vars:
+  - disease
+
+annotations:
+- annotationProperty: exact_synonym
+  text: '%s, acute'
+  permutations:
+  - var: disease
+    annotationProperties:
+    - exact_synonym
+  vars:
+  - disease
+
+def:
+  text: Acute form of %s.
+  vars:
+  - disease
+
+equivalentTo:
+  text: '%s and ''has modifier'' some ''acute'''
+  vars:
+  - disease