Merge pull request #71 from uclahs-cds/yashpatel-fix-choices

Fix choices

CHANGELOG.md

@@ -8,23 +8,28 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ---
 
 ## [Unreleased]
+
+---
+
+## [1.3.0] - 2024-09-04
 ### Added
 - `sanitize_uclahs_cds_id` function
 - Functional testing framework with concrete tests for `methods.set_env()`
-- Functional test for `bam_parser.parse_bam_header()`.
+- Functional test for `bam_parser.parse_bam_header()`
 - Dump parameters with `json_extractor.store_params_json()`
 - Option to allow empty fields in a CSV to be parsed without error
 - Function to save process logs, even after failure
 
 ### Fixed
-- Fixed retry for potentially undefined variable `proc_name_keys`. #57
+- Fix retry for potentially undefined variable `proc_name_keys` #57
 - Fix `schema.check_write_permission` when `null` is returned by `getParentFile` #59
+- Fix checking of `choices` to properly check choices when given
 
 ### Changed
 - Allow `set_resources_allocation` to use maximum allocation values defined in params
 - Add `def`s to multiple variables that should not be globally defined
 - Allow specific schema validation function to accept pre-loaded schema as input
-- Add try-catch to schema validation to log the parameter being failed to validate.
+- Add try-catch to schema validation to log the parameter being failed to validate
 - Rename `check_bam_list` function to more general `check_readable_file_list`
 - Allow Path schema type to be a GString
 

config/schema/schema.config

@@ -19,6 +19,12 @@ schema {
     path_types = ['Path']
     custom_types = [:]
 
+    single_choice_types = [
+        'String',
+        'Path',
+        'Number',
+        'Integer'
+    ]
 
     /**
     * Load the schema file.
@@ -208,7 +214,9 @@ schema {
                 schema.check_path(options[name], properties.mode)
             } else if (schema.custom_types.containsKey(properties.type)) {
                 schema.custom_types[properties.type](options, name, properties)
-            } else if (properties.containsKey('choices')) {
+            }
+
+            if (properties.type in schema.single_choice_types && properties.containsKey('choices')) {
                 schema.check_choices_singular(options, name, properties.choices)
             }
         } else {