Gen3SchemaDev 2.1.0__tar.gz → 2.2.0__tar.gz

{gen3schemadev-2.1.0 → gen3schemadev-2.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: Gen3SchemaDev
-Version: 2.1.0
+Version: 2.2.0
 Summary: Tool for data modelling in Gen3
 License: Apache 2.0
 License-File: LICENSE

{gen3schemadev-2.1.0 → gen3schemadev-2.2.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "Gen3SchemaDev"
-version = "2.1.0"
+version = "2.2.0"
 description = "Tool for data modelling in Gen3"
 authors = [
     {name = "JoshuaHarris391",email = "harjo391@gmail.com"}

{gen3schemadev-2.1.0 → gen3schemadev-2.2.0}/src/gen3schemadev/cli.py

@@ -10,7 +10,8 @@ from gen3schemadev.schema.gen3_template import (
     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.")
 

{gen3schemadev-2.1.0 → gen3schemadev-2.2.0}/src/gen3schemadev/converter.py

@@ -173,7 +173,7 @@ def get_node_links(node: str, data: DataSourceProtocol) -> list[dict]:
     return node_links
 
 
-def create_core_metadata_link(child_name: str) -> dict:
+def create_core_metadata_link(child_name: str, required: bool = False) -> dict:
     """
     Create a link dictionary for core metadata collections.
 
@@ -188,14 +188,33 @@ def create_core_metadata_link(child_name: str) -> dict:
     link_obj = LinkObj(
         name=link_suffix("core_metadata_collection"),
         backref=link_suffix(child_name),
-        label=None,
+        label="part_of",
         target_type="core_metadata_collection",
         multiplicity="one_to_one",
-        required=True
+        required=required
     )
     return link_obj.to_dict()
 
 
+def flip_multiplicity(multiplicity: str) -> str:
+    """
+    Flip the multiplicity of a link.
+
+    Args:
+        multiplicity: The current multiplicity of the link.
+
+    Returns:
+        The flipped multiplicity.
+    """
+    if multiplicity == "one_to_one" or multiplicity == "many_to_many":
+        return multiplicity
+    elif multiplicity == "one_to_many":
+        return "many_to_one"
+    elif multiplicity == "many_to_one":
+        return "one_to_many"
+    else:
+        raise ValueError(f"Invalid multiplicity: {multiplicity}")
+
 def convert_node_links(links: list[dict], required: bool = True) -> list[dict]:
     """
     Convert a list of link dictionaries into the Gen3 schema 'links' format.
@@ -212,9 +231,9 @@ def convert_node_links(links: list[dict], required: bool = True) -> list[dict]:
         link_obj = LinkObj(
             name=link_suffix(link['parent']),
             backref=link_suffix(link['child']),
-            label=None,
+            label="part_of",
             target_type=link['parent'],
-            multiplicity=link['multiplicity'],
+            multiplicity=flip_multiplicity(link['multiplicity']),
             required=required
         )
         link_list.append(link_obj.to_dict())
@@ -233,7 +252,7 @@ def add_core_metadata_link(links: list[dict], child_name: str) -> list[dict]:
     Returns:
         Updated list of link dictionaries including core metadata link.
     """
-    core_link = create_core_metadata_link(child_name)
+    core_link = create_core_metadata_link(child_name, required=False)
     return links + [core_link]
 
 
@@ -539,7 +558,7 @@ def construct_props(node_name: str, data: DataSourceProtocol) -> dict:
 
     # Add link properties
     for link in links:
-        link_prop = create_link_prop(link['parent'], link['multiplicity'])
+        link_prop = create_link_prop(link['parent'], flip_multiplicity(link['multiplicity']))
         props_dict.update(link_prop)
 
     # if it's an Enum, add the enum values

{gen3schemadev-2.1.0 → gen3schemadev-2.2.0}/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')

{gen3schemadev-2.1.0 → gen3schemadev-2.2.0}/src/gen3schemadev/schema/schema_templates/gen3_metaschema.yml

@@ -181,9 +181,8 @@ definitions:
       backref:
         $ref: "#/definitions/field"
       label:
-        anyOf:
-          - $ref: "#/definitions/field"
-          - type: 'null'
+        type: string
+        minLength: 1
       multiplicity:
         type: string
         enum:

gen3schemadev-2.2.0/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.

{gen3schemadev-2.1.0 → gen3schemadev-2.2.0}/src/gen3schemadev/validators/rule_validator.py

@@ -1,5 +1,6 @@
 # validates gen3 bundled jsonschema (.json) by testing gen3 specific business rules
 import logging
+from gen3schemadev.converter import link_suffix
 
 logger = logging.getLogger(__name__)
 
@@ -44,7 +45,7 @@ class RuleValidator:
                 links = self._get_links()
                 logger.debug(f"Got links for data_file: {links}")
                 for link in links:
-                    if link.get("name") == "core_metadata_collection":
+                    if link.get("name") == link_suffix("core_metadata_collection"):
                         logger.debug(
                             f"Found core_metadata_collection link for data_file node (id: {schema_id})."
                         )
@@ -54,7 +55,7 @@ class RuleValidator:
                 )
                 raise ValueError(
                     f"Schema '{schema_id}' with category 'data_file' must include a link with "
-                    f"'name': 'core_metadata_collection'. Please add this link to the 'links' section."
+                    f"'name': 'core_metadata_collections'. Please add this link to the 'links' section."
                 )
             return False
         except Exception as ex:
@@ -118,6 +119,7 @@ class RuleValidator:
             "updated_datetime",
             "file_state",
             "error_type",
+            "label"
         ]
         logger.debug(f"System properties: {system_props}")
         return system_props