updated config to be compatible with latest HOCON

ncats · Nov 8, 2024 · 2ebe70f · 2ebe70f
1 parent ff96939
commit 2ebe70f
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Showing 4 changed files with 78 additions and 22 deletions.
diff --git a/gsrs-module-substance-example/src/main/resources/application.conf b/gsrs-module-substance-example/src/main/resources/application.conf
@@ -25,29 +25,41 @@ ix.authentication.logheaders=false
 #logging.level.org.hibernate.type.descriptor.sql.BasicBinder=TRACE
 logging.level.gsrs.module.substance.scrubbers.basic=trace
 
-gsrs.matchableCalculators.substances =
-[
+gsrs.matchableCalculators.substances.list.CASNumberMatchableExtractor =
+
     {"matchableCalculationClass" : "gsrs.dataexchange.extractors.CASNumberMatchableExtractor",
         "config" :{
             "casCodeSystems": ["CAS", "CASNo", "CASNumber"]
         }
-    },
+    }
+
+gsrs.matchableCalculators.substances.list.AllNamesMatchableExtractor=
     {"matchableCalculationClass" : "gsrs.dataexchange.extractors.AllNamesMatchableExtractor","config" :{}},
+
+gsrs.matchableCalculators.substances.list.ApprovalIdMatchableExtractor=
     {"matchableCalculationClass" : "gsrs.dataexchange.extractors.ApprovalIdMatchableExtractor","config" :{}},
-    {"matchableCalculationClass" : "gsrs.dataexchange.extractors.DefinitionalHashMatchableExtractor","config" :{}},
+
+gsrs.matchableCalculators.substances.list.DefinitionalHashMatchableExtractor=
+    {"matchableCalculationClass" : "gsrs.dataexchange.extractors.DefinitionalHashMatchableExtractor","config" :{}}
+
+gsrs.matchableCalculators.substances.list.SelectedCodesMatchableExtractor=
     {"matchableCalculationClass" : "gsrs.dataexchange.extractors.SelectedCodesMatchableExtractor",
         "config" :
         {
             "codeSystems" :["CAS", "ChemBL", "NCI", "NSC", "EINECS"]
         }
-    },
-    {"matchableCalculationClass" : "gsrs.dataexchange.extractors.UUIDMatchableExtractor","config" :{}},
+    }
+
+gsrs.matchableCalculators.substances.list.UUIDMatchableExtractor=
+    {"matchableCalculationClass" : "gsrs.dataexchange.extractors.UUIDMatchableExtractor","config" :{}}
+
+gsrs.matchableCalculators.substances.list.CodeMatchableExtractor =
     {"matchableCalculationClass" : "gsrs.dataexchange.extractors.CodeMatchableExtractor",
         "config" :{
             "reqCodeSystems": ["FDA UNII"],
             "codeType": "PRIMARY",
             "codeKey": "CODE"
         }
     }
-]
+
 
diff --git a/gsrs-module-substance-example/src/main/resources/fda-extension.conf b/gsrs-module-substance-example/src/main/resources/fda-extension.conf
@@ -75,7 +75,7 @@ ix.ginas.export.factories.substances =[
 
 ix.ginas.approvalIdGenerator.generatorClass=ix.ginas.utils.UNIIGenerator
 
-gsrs.validators.substances.BdNumModificationValidator= {
+gsrs.validators.substances.list.BdNumModificationValidator= {
                 "validatorClass" = "fda.gsrs.substance.validators.BdNumModificationValidator",
                 "newObjClass" = "ix.ginas.models.v1.Substance",
                 "order"=4000

diff --git a/gsrs-module-substance-example/src/test/resources/application-test.conf b/gsrs-module-substance-example/src/test/resources/application-test.conf
@@ -61,7 +61,7 @@ gsrs.standardizers.substances = {
     }
 }
 
-gsrs.importAdapterFactories.substances.SDFImportAdapterFactory =
+gsrs.importAdapterFactories.substances.list.SDFImportAdapterFactory =
 		{
 			"adapterName": "SDF Adapter",
 			"order" : 10,
@@ -304,7 +304,7 @@ gsrs.importAdapterFactories.substances.SDFImportAdapterFactory =
 			}
 		}
 
-gsrs.importAdapterFactories.substances.DelimTextImportAdapterFactory ={
+gsrs.importAdapterFactories.substances.list.DelimTextImportAdapterFactory ={
 			"adapterName": "Delimited Text Adapter",
 			"order" : 40,
 			"importAdapterFactoryClass": "gsrs.module.substance.importers.DelimTextImportAdapterFactory",
@@ -439,7 +439,7 @@ gsrs.importAdapterFactories.substances.DelimTextImportAdapterFactory ={
 			}
 		}
 
-gsrs.importAdapterFactories.substances.ExcelFileImportAdapterFactory ={
+gsrs.importAdapterFactories.substances.list.ExcelFileImportAdapterFactory ={
 			"adapterName": "Excel File Adapter",
 			"order" : 41,
 			"importAdapterFactoryClass": "gsrs.module.substance.importers.ExcelFileImportAdapterFactory",
@@ -572,7 +572,7 @@ gsrs.importAdapterFactories.substances.ExcelFileImportAdapterFactory ={
 			}
 	}
 
-gsrs.importAdapterFactories.substances.GSRSJSONImportAdapterFactory={
+gsrs.importAdapterFactories.substances.list.GSRSJSONImportAdapterFactory={
 			"adapterName": "GSRS JSON Adapter",
 			"order" : 11,
 			"importAdapterFactoryClass"= "gsrs.module.substance.importers.GSRSJSONImportAdapterFactory",

diff --git a/gsrs-module-substances-core/src/main/resources/substances-core.conf b/gsrs-module-substances-core/src/main/resources/substances-core.conf
@@ -454,17 +454,61 @@ ix.gsrs.delimitedreports.inchikeysforambiguousstereo=true
 #if more than one Exporter supports the same file extension,
 #the class in the list that supports it fist wins.
 
-ix.ginas.export.factories.substances = [
-    #"gsrs.module.substance.ExtraColumnsSpreadsheetExporterFactory",
-	#"gsrs.module.substance.exporters.SdfExporterFactory",
-	"gsrs.module.substance.exporters.DefaultSubstanceSpreadsheetExporterFactory",
-	"gsrs.module.substance.exporters.JsonExporterFactory",
-	#"ix.ginas.exporters.FDANameExporterFactory",
-	#"ix.ginas.exporters.FDACodeExporterFactory",
-#	"ix.ginas.exporters.SPLValidatorXMLExporterFactory",
- # "ix.ginas.exporters.SRSLegacyDictionaryExporterFactory"
+ix.ginas.export.exporterfactories.substances.list.DefaultSubstanceSpreadsheetExporterFactory =
+  {
+    "exporterFactoryClass" = "gsrs.module.substance.exporters.DefaultSubstanceSpreadsheetExporterFactory",
+    "order" =  1000,
+    "parameters":{
+    }
+  }
+ix.ginas.export.exporterfactories.substances.list.JsonExporterFactory =
+  {
+    "exporterFactoryClass" = "gsrs.module.substance.exporters.JsonExporterFactory",
+    "order" =  1100,
+    "parameters":{
+    }
+  }
+ix.ginas.export.exporterfactories.substances.list.FDANameExporterFactory =
+  {
+    "exporterFactoryClass" = "fda.gsrs.substance.exporters.FDANameExporterFactory",
+    "order" =  1200,
+    "disabled" = true,
+    "parameters":{
+    }
+  }
+ix.ginas.export.exporterfactories.substances.list.FDACodeExporterFactory =
+  {
+    "exporterFactoryClass" = "fda.gsrs.substance.exporters.FDACodeExporterFactory",
+    "order" =  1300,
+    "disabled" = true,
+    "parameters":{
+    }
+  }
+ix.ginas.export.exporterfactories.substances.list.SPLValidatorXMLExporterFactory =
+  {
+    "exporterFactoryClass" = "fda.gsrs.substance.exporters.SPLValidatorXMLExporterFactory",
+    "order" =  1400,
+    "disabled" = true,
+    "parameters":{
+    }
+  }
+ix.ginas.export.exporterfactories.substances.list.SRSLegacyDictionaryExporterFactory =
+  {
+    "exporterFactoryClass" = "fda.gsrs.substance.exporters.SRSLegacyDictionaryExporterFactory",
+    "order" =  1500,
+    "disabled" = true,
+    "parameters":{
+    }
+  }
 
-]
+ix.ginas.export.exporterfactories.substances.list.SdfExporterFactory =
+  {
+    "exporterFactoryClass" = "gsrs.module.substance.exporters.SdfExporterFactory",
+    "order" =  1600,
+    "parameters":{
+      "approvalIDName": "UNII"
+    }
+  }
 
 ix.ginas.export.exporterfactories.substances = [
     {