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DO NOT merge! Broken tests #381

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DO NOT merge! Broken tests #381

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2fa438e
got tests to compile
ChemMitch Nov 7, 2024
9f43921
updating config so tests can run. part-way there
ChemMitch Nov 7, 2024
ea62d5e
misc attempts
ChemMitch Nov 8, 2024
ff96939
some corrections; more remain
ChemMitch Nov 8, 2024
2ebe70f
updated config to be compatible with latest HOCON
ChemMitch Nov 8, 2024
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26 changes: 19 additions & 7 deletions gsrs-module-substance-example/src/main/resources/application.conf
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Original file line number Diff line number Diff line change
Expand Up @@ -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"
}
}
]


40 changes: 25 additions & 15 deletions gsrs-module-substance-example/src/main/resources/fda-extension.conf
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Expand Up @@ -24,9 +24,11 @@ gsrs.microservice.clinicaltrialseurope.api.headers= {
"auth-key"="myKey"
}

gsrs.entityProcessors +={
gsrs.entityProcessors.list.UniqueCodeGenerator =
{
"entityClassName" = "ix.ginas.models.v1.Substance",
"processor" = "gsrs.module.substance.processors.UniqueCodeGenerator",
"order" = 8010,
"with"= {
"useLegacy"=true,
"codesystem"="BDNUM",
Expand All @@ -39,16 +41,27 @@ gsrs.entityProcessors +={
}
}

gsrs.entityProcessors +=
{
"entityClassName" = "ix.ginas.models.v1.Substance",
"processor" = "gsrs.module.substance.processors.ApprovalIdProcessor",
"parameters" = {
"codeSystem" = "FDA UNII"
}
gsrs.entityProcessors.list.ApprovalIdProcessor =
{
"entityClassName" = "ix.ginas.models.v1.Substance",
"processor" = "gsrs.module.substance.processors.ApprovalIdProcessor",
"order" = 6010
}

ix.ginas.export.factories.substances = ${ix.ginas.export.factories.substances}[


#gsrs.entityProcessors.ApprovalIdProcessor=
# {
# "order":124,
# "entityClassName": "ix.ginas.models.v1.Substance",
# "processor" = "gsrs.module.substance.processors.ApprovalIdProcessor",
# "parameters" = {
# "codeSystem" = "FDA UNII"
# }
# }

#removed ${ix.ginas.export.factories.substances}
ix.ginas.export.factories.substances =[
#"gsrs.module.substance.ExtraColumnsSpreadsheetExporterFactory",

"fda.gsrs.substance.exporters.FDANameExporterFactory",
Expand All @@ -62,11 +75,8 @@ ix.ginas.export.factories.substances = ${ix.ginas.export.factories.substances}[

ix.ginas.approvalIdGenerator.generatorClass=ix.ginas.utils.UNIIGenerator


gsrs.validators.substances += {

gsrs.validators.substances.list.BdNumModificationValidator= {
"validatorClass" = "fda.gsrs.substance.validators.BdNumModificationValidator",
"newObjClass" = "ix.ginas.models.v1.Substance"
"newObjClass" = "ix.ginas.models.v1.Substance",
"order"=4000
}


10 changes: 6 additions & 4 deletions ...ubstance-example/src/test/java/example/imports/DefaultImportAdapterFactoryConfigTest.java
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Expand Up @@ -34,18 +34,20 @@ public void testSetup() throws IllegalAccessException, NoSuchFieldException, Jso
String substanceContext = "substances";
//build up a complete configuration
GsrsFactoryConfiguration config = new GsrsFactoryConfiguration();
Map<String, List<Map<String, Object>>> adapterConfig = new HashMap<>();
Map<String, Map<String, Map<String, Object>>> adapterConfig = new HashMap<>();
Map<String, Object> oneAdapter = new HashMap<>();
oneAdapter.put("importAdapterFactoryClass", "gsrs.module.substance.importers.SDFImportAdapterFactory");
oneAdapter.put("adapterName", "NSRS SDF Adapter");
oneAdapter.put("extensions", Arrays.asList("sdf", "sd"));
oneAdapter.put("parameters", buildConfigParameters());
oneAdapter.put("stagingAreaServiceClass", gsrs.stagingarea.service.DefaultStagingAreaService.class);
oneAdapter.put("entityServiceClass", "gsrs.dataexchange.SubstanceStagingAreaEntityService");
List<Map<String, Object>> adapters = new ArrayList<>();
adapters.add(oneAdapter);
Map<String,Map<String, Object>> adapters = new HashMap<>();
adapters.put("NSRS SDF Adapter", oneAdapter);
adapterConfig.put(substanceContext, adapters);
config.setImportAdapterFactories(adapterConfig);
Map<String, Map<String, Map<String, Map<String, Object>>>> higherLevelMap = new HashMap<>();
higherLevelMap.put("imports", adapterConfig);
config.setImportAdapterFactories(higherLevelMap);
ConfigBasedGsrsImportAdapterFactoryFactory factoryFactory = new ConfigBasedGsrsImportAdapterFactoryFactory();
Field configField = factoryFactory.getClass().getDeclaredField("gsrsFactoryConfiguration"); //gsrs.imports.ConfigBasedGsrsImportAdapterFactoryFactory.
configField.setAccessible(true);
Expand Down
18 changes: 10 additions & 8 deletions gsrs-module-substance-example/src/test/java/example/imports/StagingAreaServiceTest.java
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Expand Up @@ -33,41 +33,43 @@ public void setup() throws NoSuchFieldException, IllegalAccessException {
log.trace("setting up staging area service");
stagingAreaService = new DefaultStagingAreaService();
stagingAreaService = AutowireHelper.getInstance().autowireAndProxy(stagingAreaService);
Map<String, List<Map<String, Object>>> matchableCalculatorConfig = new HashMap<>();
List<Map<String, Object>> configs = new ArrayList<>();
Map<String, Map<String, Map<String, Object>>> matchableCalculatorConfig = new HashMap<>();
Map<String, Map<String, Object>> configs = new HashMap<>();
Map<String, Object> casExtractor = new HashMap<>();
casExtractor.put("matchableCalculationClass", CASNumberMatchableExtractor.class);
LinkedHashMap<String, Object> config= new LinkedHashMap<>();
config.put("casCodeSystems", Arrays.asList("CAS", "CASNo", "CASNumber"));
casExtractor.put("config", config);
configs.add(casExtractor);
configs.put("CASNumberMatchableExtractor", casExtractor);

Map<String, Object> namesExtractor = new HashMap<>();
namesExtractor.put("matchableCalculationClass", AllNamesMatchableExtractor.class);
configs.add(namesExtractor);
configs.put("AllNamesMatchableExtractor", namesExtractor);

Map<String, Object> defHashExtractor = new HashMap<>();
defHashExtractor.put("matchableCalculationClass", DefinitionalHashMatchableExtractor.class);
configs.add(defHashExtractor);
configs.put("DefinitionalHashMatchableExtractor", defHashExtractor);

Map<String, Object> selectedCodesExtractor = new HashMap<>();
selectedCodesExtractor.put("matchableCalculationClass", SelectedCodesMatchableExtractor.class);
LinkedHashMap<String, Object> config2= new LinkedHashMap<>();
config2.put("codeSystems", Arrays.asList("CAS", "ChemBL", "NCI", "NSC", "EINECS"));
selectedCodesExtractor.put("config", config2);
configs.add(selectedCodesExtractor);
configs.put("SelectedCodesMatchableExtractor", selectedCodesExtractor);

Map<String, Object> uuidExtractor = new HashMap<>();
uuidExtractor.put("matchableCalculationClass", UUIDMatchableExtractor.class);
configs.add(uuidExtractor);
configs.put("UUIDMatchableExtractor", uuidExtractor);
matchableCalculatorConfig.put("substances", configs);

SubstanceStagingAreaEntityService stagingAreaEntityService = new SubstanceStagingAreaEntityService();
stagingAreaEntityService = AutowireHelper.getInstance().autowireAndProxy(stagingAreaEntityService);
Field factoryConfigField= stagingAreaEntityService.getClass().getDeclaredField("gsrsFactoryConfiguration");
factoryConfigField.setAccessible(true);
GsrsFactoryConfiguration factoryConfiguration= (GsrsFactoryConfiguration) factoryConfigField.get(stagingAreaEntityService);
factoryConfiguration.setMatchableCalculators(matchableCalculatorConfig);
Map<String,Map<String, Map<String,Map<String, Object>>>> oneUp = new HashMap<>();
oneUp.put("matchableCalculatorConfig", matchableCalculatorConfig);
factoryConfiguration.setMatchableCalculators(oneUp);
stagingAreaService.registerEntityService(stagingAreaEntityService);
}
}
Expand Down
28 changes: 16 additions & 12 deletions gsrs-module-substance-example/src/test/resources/application-test.conf
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Expand Up @@ -61,11 +61,10 @@ gsrs.standardizers.substances = {
}
}

gsrs.importAdapterFactories.substances =
[
gsrs.importAdapterFactories.substances.list.SDFImportAdapterFactory =
{

"adapterName": "SDF Adapter",
"order" : 10,
"importAdapterFactoryClass": "gsrs.module.substance.importers.SDFImportAdapterFactory",
"stagingAreaServiceClass": "gsrs.stagingarea.service.DefaultStagingAreaService",
"entityServiceClass" :"gsrs.dataexchange.SubstanceStagingAreaEntityService",
Expand Down Expand Up @@ -303,9 +302,11 @@ gsrs.importAdapterFactories.substances =
}
]
}
},
{
}

gsrs.importAdapterFactories.substances.list.DelimTextImportAdapterFactory ={
"adapterName": "Delimited Text Adapter",
"order" : 40,
"importAdapterFactoryClass": "gsrs.module.substance.importers.DelimTextImportAdapterFactory",
"stagingAreaServiceClass": "gsrs.stagingarea.service.DefaultStagingAreaService",
"entityServiceClass" :"gsrs.dataexchange.SubstanceStagingAreaEntityService",
Expand Down Expand Up @@ -436,9 +437,11 @@ gsrs.importAdapterFactories.substances =
],
"lineValueDelimiter": ","
}
},
{
}

gsrs.importAdapterFactories.substances.list.ExcelFileImportAdapterFactory ={
"adapterName": "Excel File Adapter",
"order" : 41,
"importAdapterFactoryClass": "gsrs.module.substance.importers.ExcelFileImportAdapterFactory",
"stagingAreaServiceClass": "gsrs.stagingarea.service.DefaultStagingAreaService",
"entityServiceClass" :"gsrs.dataexchange.SubstanceStagingAreaEntityService",
Expand Down Expand Up @@ -567,10 +570,12 @@ gsrs.importAdapterFactories.substances =
],
"lineValueDelimiter": ","
}
},
{
}

gsrs.importAdapterFactories.substances.list.GSRSJSONImportAdapterFactory={
"adapterName": "GSRS JSON Adapter",
"importAdapterFactoryClass": "gsrs.module.substance.importers.GSRSJSONImportAdapterFactory",
"order" : 11,
"importAdapterFactoryClass"= "gsrs.module.substance.importers.GSRSJSONImportAdapterFactory",
"stagingAreaServiceClass": "gsrs.stagingarea.service.DefaultStagingAreaService",
"entityServiceClass" :"gsrs.dataexchange.SubstanceStagingAreaEntityService",
"description" : "GSRS legacy JSON file importer",
Expand All @@ -583,7 +588,6 @@ gsrs.importAdapterFactories.substances =
#the things used to instantiate the adapter

}
}
]
}

gsrs.substance.structures.saltFilePath=salt_data_public.tsv
73 changes: 60 additions & 13 deletions gsrs-module-substances-core/src/main/resources/substances-core.conf
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Expand Up @@ -431,14 +431,17 @@ server.servlet-path=/loop-service

server.use-forward-headers=true

ix.api.registeredfunctions =${ix.api.registeredfunctions}[
#${ix.api.registeredfunctions}
ix.api.registeredfunctions.InChIRegisteredFunction =
{
"class":"ix.core.util.pojopointer.extensions.InChIRegisteredFunction"
},
}

ix.api.registeredfunctions.InChIFullRegisteredFunction=
{
"class":"ix.core.util.pojopointer.extensions.InChIFullRegisteredFunction"
}
]

substance.renderer.style="CONF"
substance.renderer.configPath="substances-default-renderer.json"

Expand All @@ -451,17 +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 = [
{
Expand Down