added support for qc_ruleset

smaht-dac · Jan 2, 2024 · d1d6e4f · d1d6e4f
1 parent baa661b
commit d1d6e4f
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Showing 2 changed files with 6 additions and 1 deletion.
diff --git a/pipeline_utils/lib/yaml_parser.py b/pipeline_utils/lib/yaml_parser.py
@@ -339,6 +339,8 @@ class YAMLMetaWorkflow(YAMLTemplate):
     RULE_SCHEMA = 'rule'
     FLAG_SCHEMA = 'flag'
     QC_RULE_SCHEMA = 'qc_rule'
+    QC_RULESET_SCHEMA = 'qc_ruleset'
+    QC_RULESET_PORTAL_SCHEMA = 'QC ruleset'
 
     def __init__(self, data):
         """Constructor method.
@@ -362,6 +364,9 @@ def _arguments(self, input, consortia):
                 self.ARGUMENT_NAME_SCHEMA: name,
                 self.ARGUMENT_TYPE_SCHEMA: type
             }
+            if type == self.QC_RULESET_SCHEMA: # replacing qc_ruleset
+                                               # with portal correspoding key
+                argument_[self.ARGUMENT_TYPE_SCHEMA] = self.QC_RULESET_PORTAL_SCHEMA
             if type == self.PARAMETER_SCHEMA:
                 argument_[self.VALUE_TYPE_SCHEMA] = format
             for k, v in values.items():

diff --git a/pipeline_utils/schemas/yaml_metaworkflow.py b/pipeline_utils/schemas/yaml_metaworkflow.py
@@ -94,7 +94,7 @@
             schema.PROPERTIES: {
                 'argument_type': {
                     schema.TYPE: schema.STRING,
-                    schema.PATTERN: '^file\\..+|^parameter\\..+'
+                    schema.PATTERN: '^file\\..+|^parameter\\..+|^qc_ruleset\\..+'
                 },
                 'dimensionality': {
                     schema.TYPE: schema.NUMBER