diff --git a/gsrs-module-substance-example/src/main/resources/application.conf b/gsrs-module-substance-example/src/main/resources/application.conf index b8e306a3..61ac0bf6 100644 --- a/gsrs-module-substance-example/src/main/resources/application.conf +++ b/gsrs-module-substance-example/src/main/resources/application.conf @@ -25,23 +25,35 @@ 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"], @@ -49,5 +61,5 @@ gsrs.matchableCalculators.substances = "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 index 4e8b2951..b29a3368 100644 --- 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 index 936a5dd6..451c130e 100644 --- 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 index e7725722..b7db0e52 100644 --- 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 = [ {