Merge pull request #14 from phac-nml/update/for-release

Added additional logging for validation of JSON schema
phac-nml · Jan 22, 2024 · f983e21 · f983e21
2 parents fd24a76 + 18527a0
commit f983e21
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Showing 2 changed files with 4 additions and 1 deletion.
diff --git a/plugins/nf-iridanext/src/main/nextflow/iridanext/IridaNextJSONOutput.groovy b/plugins/nf-iridanext/src/main/nextflow/iridanext/IridaNextJSONOutput.groovy
@@ -189,7 +189,8 @@ class IridaNextJSONOutput {
                 outputStream.close()
             }
         } catch (ValidationException e) {
-            log.error "Failed to write IRIDA Next JSON output to ${path}. JSON did not match schema ${jsonSchema}"
+            log.error "Failed to write IRIDA Next JSON output to ${path}. JSON did not match schema ${jsonSchema.getUri()}. " +
+                      "Message: ${e.getMessage()}"
             throw e
         }
     }

diff --git a/plugins/nf-iridanext/src/main/nextflow/iridanext/IridaNextObserver.groovy b/plugins/nf-iridanext/src/main/nextflow/iridanext/IridaNextObserver.groovy
@@ -139,6 +139,8 @@ class IridaNextObserver implements TraceObserver {
             SchemaStore schemaStore = new SchemaStore()
             Path jsonSchemaPathAsPath = Nextflow.file(jsonSchemaPath) as Path
             jsonSchema = schemaStore.loadSchema(jsonSchemaPathAsPath.toFile().toURI())
+            log.debug "Loaded custom schema ${jsonSchema.getUri()} for validating IRIDA Next output " +
+                      "from iridanext.output.schema=${jsonSchemaPath}"
         }
 
         // Used for overriding the "meta.id" key used to define identifiers for a scope