Merge pull request #48 from AustralianBioCommons/feature-add-program-template

Add program template generation and update CLI logic

Author: JoshuaHarris391

src/gen3schemadev/cli.py

@@ -10,7 +10,8 @@
     generate_setting_template,
     generate_terms_template,
     generate_core_metadata_template,
-    generate_project_template
+    generate_project_template,
+    generate_program_template
 )
 from gen3schemadev.utils import write_yaml, load_yaml, bundle_yamls, write_json, resolve_schema, read_json
 from gen3schemadev.schema.input_schema import DataModel
@@ -184,7 +185,10 @@ def main():
         write_yaml(setting_dict, f"{args.output}/_settings.yaml")
         write_yaml(generate_terms_template(), f"{args.output}/_terms.yaml")
         write_yaml(generate_core_metadata_template(), f"{args.output}/core_metadata_collection.yaml")
-        write_yaml(generate_project_template(), f"{args.output}/project.yaml")
+        if 'project' not in node_names:
+            write_yaml(generate_project_template(), f"{args.output}/project.yaml")
+        if 'program' not in node_names:
+            write_yaml(generate_program_template(), f"{args.output}/program.yaml")
 
         print("Schema generation process complete.")
 

src/gen3schemadev/schema/gen3_template.py

@@ -74,4 +74,7 @@ def generate_core_metadata_template():
     return read_template_yaml('core_metadata_collection.yaml')
 
 def get_metaschema():
-    return read_template_yaml('gen3_metaschema.yml')
+    return read_template_yaml('gen3_metaschema.yml')
+
+def generate_program_template():
+    return read_template_yaml('program.yaml')

src/gen3schemadev/schema/schema_templates/program.yaml

@@ -0,0 +1,34 @@
+$schema: http://json-schema.org/draft-04/schema#
+id: program
+title: Program
+type: object
+category: administrative
+program: '*'
+project: '*'
+description: 'A broad framework of goals to be achieved. (NCIt C52647)
+
+  '
+additionalProperties: false
+submittable: false
+validators: null
+systemProperties:
+- id
+required:
+- name
+- dbgap_accession_number
+uniqueKeys:
+- - id
+- - name
+links: []
+properties:
+  type:
+    type: string
+  id:
+    $ref: _definitions.yaml#/UUID
+    systemAlias: node_id
+  name:
+    type: string
+    description: Full name/title of the program.
+  dbgap_accession_number:
+    type: string
+    description: The dbgap accession number provided for the program.

tests/input_example.yml

@@ -61,6 +61,11 @@ nodes:
 
 
 links:
+
+- parent: program # program is the root and is auto generated when you use the `gen3schemadev generate` command
+  multiplicity: one_to_many
+  child: project
+
 - parent: project
   multiplicity: one_to_many
   child: sample

tests/test_converter.py

@@ -467,7 +467,8 @@ def test_construct_prop_project(fixture_input_yaml_pass):
         "description": {
             "type": "string",
             "description": "Project containing synthetic data"
-        }
+        },
+        "programs": {'$ref': '_definitions.yaml#/to_one'},
     }
     assert result == expected
 

tests/test_gen3_template.py

@@ -109,4 +109,10 @@ def test_generate_project_template_reads_project_yaml():
     result = generate_project_template()
     assert isinstance(result, dict)
     assert "id" in result
-    assert result.get("id") == "project"
+    assert result.get("id") == "project"
+
+def test_generate_program_template_reads_program_yaml():
+    result = generate_program_template()
+    assert isinstance(result, dict)
+    assert "id" in result
+    assert result.get("id") == "program"