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AIW i2b2 ETL is a Protempa query results handler for loading data and
abstractions into i2b2.
package edu.emory.cci.aiw.i2b2etl.dsb;
/*
* #%L
* AIW i2b2 ETL
* %%
* Copyright (C) 2012 - 2014 Emory University
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import java.io.IOException;
import java.sql.Connection;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.logging.Logger;
import org.arp.javautil.sql.InvalidConnectionSpecArguments;
import org.protempa.DataSourceReadException;
import org.protempa.KeySetSpec;
import org.protempa.backend.BackendInitializationException;
import org.protempa.backend.BackendInstanceSpec;
import org.protempa.backend.annotations.BackendInfo;
import org.protempa.backend.annotations.BackendProperty;
import org.protempa.backend.dsb.relationaldb.ColumnSpec;
import org.protempa.backend.dsb.relationaldb.Operator;
import org.protempa.backend.dsb.relationaldb.EntitySpec;
import org.protempa.backend.dsb.relationaldb.JDBCDateTimeTimestampDateValueFormat;
import org.protempa.backend.dsb.relationaldb.JDBCDateTimeTimestampPositionParser;
import org.protempa.backend.dsb.relationaldb.JDBCPositionFormat;
import org.protempa.backend.dsb.relationaldb.JoinSpec;
import org.protempa.backend.dsb.relationaldb.PropertySpec;
import org.protempa.backend.dsb.relationaldb.ReferenceSpec;
import org.protempa.backend.dsb.relationaldb.RelationalDbDataSourceBackend;
import org.protempa.backend.dsb.relationaldb.mappings.DefaultMappings;
import org.protempa.backend.dsb.relationaldb.mappings.Mappings;
import org.protempa.proposition.value.AbsoluteTimeGranularity;
import org.protempa.proposition.value.AbsoluteTimeGranularityFactory;
import org.protempa.proposition.value.AbsoluteTimeUnit;
import org.protempa.proposition.value.AbsoluteTimeUnitFactory;
import org.protempa.proposition.value.GranularityFactory;
import org.protempa.proposition.value.UnitFactory;
import org.protempa.proposition.value.ValueType;
/**
*
* @author Andrew Post
*/
@BackendInfo(displayName = "I2B2 Data Source Backend")
public final class I2B2DataSourceBackend extends RelationalDbDataSourceBackend {
private final static AbsoluteTimeUnitFactory ABS_TIME_UNIT_FACTORY
= new AbsoluteTimeUnitFactory();
private final static AbsoluteTimeGranularityFactory ABS_TIME_GRANULARITY_FACTORY
= new AbsoluteTimeGranularityFactory();
private static final JDBCPositionFormat POSITION_PARSER
= new JDBCDateTimeTimestampPositionParser();
private final static String PATIENT_DIMENSION = "patient_dimension";
private final static String VISIT_DIMENSION = "visit_dimension";
private final static String OBSERVATION_FACT = "observation_fact";
private final static String PROVIDER_DIMENSION = "provider_dimension";
private final static Logger LOGGER
= Logger.getLogger(I2B2DataSourceBackend.class.getPackage().getName());
private Long resultInstanceId;
public I2B2DataSourceBackend() {
setDefaultKeyIdTable(PATIENT_DIMENSION);
/*
* Per the i2b2 1.7 CRC design docs and stored procedure
* implementation,
* to_char(patient_num) = patient_ide when patient_ide_source = 'HIVE'.
*/
setDefaultKeyIdColumn("patient_num");
setDefaultKeyIdJoinKey("patient_num");
}
@Override
public void initialize(BackendInstanceSpec config) throws BackendInitializationException {
super.initialize(config);
}
@Override
protected EntitySpec[] constantSpecs(String keyIdSchema, String keyIdTable, String keyIdColumn, String keyIdJoinKey) throws IOException {
Mappings riId = new DefaultMappings(new HashMap() {
{
put(resultInstanceId, "" + resultInstanceId);
}
});
Mappings hive = new DefaultMappings(new HashMap() {
{
put("HIVE", "HIVE");
}
});
String schemaName = getSchemaName();
return new EntitySpec[]{
new EntitySpec("Patients",
null,
new String[]{"Patient"},
true,
new ColumnSpec(keyIdSchema, keyIdTable, keyIdColumn),
new ColumnSpec[]{
new ColumnSpec(keyIdSchema, keyIdTable, keyIdColumn)
},
null,
null,
new PropertySpec[]{
/*
* This should be patient_ide where patient_ide_source = 'HIVE'.
*/
new PropertySpec("patientId", null, new ColumnSpec(keyIdSchema, keyIdTable, keyIdColumn), ValueType.NOMINALVALUE)
},
new ReferenceSpec[]{
new ReferenceSpec("encounters", "Encounters", new ColumnSpec[]{new ColumnSpec(keyIdSchema, keyIdTable, new JoinSpec(keyIdJoinKey, "patient_num", new ColumnSpec(schemaName, VISIT_DIMENSION, "encounter_num")))}, ReferenceSpec.Type.MANY),
new ReferenceSpec("patientDetails", "Patient Details", new ColumnSpec[]{new ColumnSpec(keyIdSchema, keyIdTable, keyIdColumn)}, ReferenceSpec.Type.MANY),
new ReferenceSpec("patientAliases", "Patient Aliases", new ColumnSpec[]{new ColumnSpec(keyIdSchema, keyIdTable, new JoinSpec(keyIdJoinKey, "patient_num", new ColumnSpec(schemaName, "PATIENT_MAPPING", "PATIENT_IDE")))}, ReferenceSpec.Type.MANY)
},
null, null,
isInKeySetMode()
? new ColumnSpec[]{
new ColumnSpec(keyIdSchema, keyIdTable, "RESULT_INSTANCE_ID", Operator.EQUAL_TO, riId)
}
: null,
null, null, null, null, null),
new EntitySpec("Patient Aliases",
null,
new String[]{"PatientAlias"},
true,
new ColumnSpec(keyIdSchema, keyIdTable, keyIdColumn, new JoinSpec(keyIdJoinKey, "patient_num", new ColumnSpec(schemaName, "PATIENT_MAPPING"))),
new ColumnSpec[]{
new ColumnSpec(schemaName, "PATIENT_MAPPING", "PATIENT_IDE"),
new ColumnSpec(schemaName, "PATIENT_MAPPING", "PATIENT_IDE_SOURCE")
},
null,
null,
new PropertySpec[]{
new PropertySpec("patientId", null, new ColumnSpec(schemaName, "PATIENT_MAPPING", "PATIENT_IDE"), ValueType.NOMINALVALUE),
new PropertySpec("fieldName", null, new ColumnSpec(schemaName, "PATIENT_MAPPING", "PATIENT_IDE_SOURCE"), ValueType.NOMINALVALUE)
},
null,
null, null,
isInKeySetMode()
? new ColumnSpec[]{
new ColumnSpec(schemaName, "PATIENT_MAPPING", new JoinSpec("patient_num", keyIdJoinKey, new ColumnSpec(keyIdSchema, keyIdTable, "RESULT_INSTANCE_ID", Operator.EQUAL_TO, riId))),
new ColumnSpec(schemaName, "PATIENT_MAPPING", "PATIENT_IDE_SOURCE", Operator.NOT_EQUAL_TO, hive)
}
: new ColumnSpec[]{new ColumnSpec(schemaName, "PATIENT_MAPPING", "PATIENT_IDE_SOURCE", Operator.NOT_EQUAL_TO, hive)},
null, null, null, null, null),
new EntitySpec("Patient Details",
null,
new String[]{"PatientDetails"},
true,
new ColumnSpec(keyIdSchema, keyIdTable, keyIdColumn, new JoinSpec(keyIdJoinKey, "patient_num", new ColumnSpec(schemaName, PATIENT_DIMENSION))),
new ColumnSpec[]{
new ColumnSpec(schemaName, PATIENT_DIMENSION, "patient_num")
},
null,
null,
new PropertySpec[]{
new PropertySpec("patientId", null, new ColumnSpec(schemaName, PATIENT_DIMENSION, "patient_num"), ValueType.NOMINALVALUE),
new PropertySpec("gender", null, new ColumnSpec(schemaName, PATIENT_DIMENSION, "SEX_CD", Operator.EQUAL_TO, getMappingsFactory().getInstance("gender.txt"), true), ValueType.NOMINALVALUE),
new PropertySpec("race", null, new ColumnSpec(schemaName, PATIENT_DIMENSION, "RACE_CD", Operator.EQUAL_TO, getMappingsFactory().getInstance("race.txt"), true), ValueType.NOMINALVALUE),
new PropertySpec("ethnicity", null, new ColumnSpec(schemaName, PATIENT_DIMENSION, "RACE_CD", Operator.EQUAL_TO, getMappingsFactory().getInstance("ethnicity.txt"), true), ValueType.NOMINALVALUE),
new PropertySpec("dateOfBirth", null, new ColumnSpec(schemaName, PATIENT_DIMENSION, "BIRTH_DATE"), ValueType.DATEVALUE, new JDBCDateTimeTimestampDateValueFormat()),
new PropertySpec("language", null, new ColumnSpec(schemaName, PATIENT_DIMENSION, "LANGUAGE_CD", Operator.EQUAL_TO, getMappingsFactory().getInstance("language.txt"), true), ValueType.NOMINALVALUE),
new PropertySpec("maritalStatus", null, new ColumnSpec(schemaName, PATIENT_DIMENSION, "MARITAL_STATUS_CD", Operator.EQUAL_TO, getMappingsFactory().getInstance("marital_status.txt"), true), ValueType.NOMINALVALUE),},
new ReferenceSpec[]{
new ReferenceSpec("encounters", "Encounters",
new ColumnSpec[]{
new ColumnSpec(schemaName, PATIENT_DIMENSION, new JoinSpec("patient_num", "patient_num", new ColumnSpec(schemaName, VISIT_DIMENSION, "encounter_num")))
}, ReferenceSpec.Type.MANY),
new ReferenceSpec("patient", "Patients",
new ColumnSpec[]{new ColumnSpec(schemaName, PATIENT_DIMENSION, "patient_num")
}, ReferenceSpec.Type.ONE)
},
null, null,
isInKeySetMode()
? new ColumnSpec[]{
new ColumnSpec(schemaName, PATIENT_DIMENSION, new JoinSpec("patient_num", keyIdJoinKey, new ColumnSpec(keyIdSchema, keyIdTable, "RESULT_INSTANCE_ID", Operator.EQUAL_TO, riId)))}
: null,
null, null, null, null, null),
new EntitySpec("Providers", null,
new String[]{"AttendingPhysician"},
false,
new ColumnSpec(keyIdSchema, keyIdTable, keyIdColumn, new JoinSpec(keyIdJoinKey, "patient_num", new ColumnSpec(schemaName, PATIENT_DIMENSION, new JoinSpec("patient_num", "patient_num", new ColumnSpec(schemaName, VISIT_DIMENSION, new JoinSpec("encounter_num", "encounter_num", new ColumnSpec(schemaName, OBSERVATION_FACT, new JoinSpec("provider_id", "provider_id", new ColumnSpec(schemaName, PROVIDER_DIMENSION))))))))),
new ColumnSpec[]{
new ColumnSpec(schemaName, PROVIDER_DIMENSION, "provider_id")
},
null,
null,
new PropertySpec[]{
new PropertySpec("fullName", null, new ColumnSpec(schemaName, PROVIDER_DIMENSION, "NAME_CHAR"), ValueType.NOMINALVALUE)
}, null, null, null, null, null, null, null, null, null),};
}
@Override
protected EntitySpec[] eventSpecs(String keyIdSchema, String keyIdTable, String keyIdColumn, String keyIdJoinKey) throws IOException {
Mappings riId = new DefaultMappings(new HashMap() {
{
put(resultInstanceId, "" + resultInstanceId);
}
});
String schemaName = getSchemaName();
Mappings icd9DxMappings = getMappingsFactory().getInstance("icd9_diagnosis.txt");
Mappings icd9PxMappings = getMappingsFactory().getInstance("icd9_procedure.txt");
EntitySpec[] eventSpecs = {
new EntitySpec("Encounters",
null,
new String[]{"Encounter"},
true,
new ColumnSpec(keyIdSchema, keyIdTable, keyIdColumn, new JoinSpec(keyIdJoinKey, "patient_num", new ColumnSpec(schemaName, PATIENT_DIMENSION, new JoinSpec("patient_num", "patient_num", new ColumnSpec(schemaName, VISIT_DIMENSION))))),
new ColumnSpec[]{
/*
* This should be encounter_ide where encounter_ide_source = 'HIVE'.
* Like with patient_num, encounter_num = encounter_ide
* when encounter_ide_source = 'HIVE'.
*/
new ColumnSpec(schemaName, VISIT_DIMENSION, "encounter_num")
},
new ColumnSpec(schemaName, VISIT_DIMENSION, "START_DATE"),
new ColumnSpec(schemaName, VISIT_DIMENSION, "END_DATE"),
new PropertySpec[]{
new PropertySpec("encounterId", null, new ColumnSpec(schemaName, VISIT_DIMENSION, "encounter_num"), ValueType.NOMINALVALUE), /*new PropertySpec("type", null, new ColumnSpec(schemaName, "ENCOUNTER", "PATIENTTYPE", ColumnSpec.Operator.EQUAL_TO, getMappingsFactory().propertyNameOrPropIdToSqlCodeArray("type_encounter_07182011.txt"), true), ValueType.NOMINALVALUE),
new PropertySpec("healthcareEntity", null, new ColumnSpec(schemaName, "ENCOUNTER", "UNIVCODE", ColumnSpec.Operator.EQUAL_TO, getMappingsFactory().propertyNameOrPropIdToSqlCodeArray("entity_healthcare_07182011.txt"), true), ValueType.NOMINALVALUE),
new PropertySpec("dischargeDisposition", null, new ColumnSpec(schemaName, "ENCOUNTER", "DISCHARGESTATUSCODE", ColumnSpec.Operator.EQUAL_TO, getMappingsFactory().propertyNameOrPropIdToSqlCodeArray("disposition_discharge_07182011.txt"), true), ValueType.NOMINALVALUE),
new PropertySpec("dischargeDispositionCat", null, new ColumnSpec(schemaName, "ENCOUNTER", "DISCHARGESTATUSCODE", ColumnSpec.Operator.EQUAL_TO, getMappingsFactory().propertyNameOrPropIdToSqlCodeArray("disposition_discharge_category_10072011.txt"), true), ValueType.NOMINALVALUE),
new PropertySpec("aprdrgRiskMortalityValue", null, new ColumnSpec(schemaName, "ENCOUNTER", "APRRISKOFMORTALITY"), ValueType.NUMERICALVALUE), new PropertySpec("aprdrgSeverityValue", null, new ColumnSpec(schemaName, "ENCOUNTER", "APRSEVERITYOFILLNESS"), ValueType.NOMINALVALUE),
new PropertySpec("insuranceType", null, new ColumnSpec(schemaName, "ENCOUNTER", "HOSPITALPRIMARYPAYER", ColumnSpec.Operator.EQUAL_TO, getMappingsFactory().propertyNameOrPropIdToSqlCodeArray("insurance_types_07182011.txt")), ValueType.NOMINALVALUE)*/},
new ReferenceSpec[]{
new ReferenceSpec("patient", "Patients",
new ColumnSpec[]{
new ColumnSpec(schemaName, VISIT_DIMENSION, "patient_num")
}, ReferenceSpec.Type.ONE),
new ReferenceSpec("patientDetails", "Patient Details",
new ColumnSpec[]{
new ColumnSpec(schemaName, VISIT_DIMENSION, "patient_num")
},
ReferenceSpec.Type.ONE),
new ReferenceSpec("diagnosisCodes", "Diagnosis Codes",
new ColumnSpec[]{
new ColumnSpec(schemaName, VISIT_DIMENSION, new JoinSpec("encounter_num", "encounter_num", new ColumnSpec(schemaName, OBSERVATION_FACT, "encounter_num"))),
new ColumnSpec(schemaName, VISIT_DIMENSION, new JoinSpec("encounter_num", "encounter_num", new ColumnSpec(schemaName, OBSERVATION_FACT, "concept_cd"))),
new ColumnSpec(schemaName, VISIT_DIMENSION, new JoinSpec("encounter_num", "encounter_num", new ColumnSpec(schemaName, OBSERVATION_FACT, "provider_id"))),
new ColumnSpec(schemaName, VISIT_DIMENSION, new JoinSpec("encounter_num", "encounter_num", new ColumnSpec(schemaName, OBSERVATION_FACT, "start_date")))
}, ReferenceSpec.Type.MANY),
new ReferenceSpec("procedures", "ICD9 Procedure Codes",
new ColumnSpec[]{
new ColumnSpec(schemaName, VISIT_DIMENSION, new JoinSpec("encounter_num", "encounter_num", new ColumnSpec(schemaName, OBSERVATION_FACT, "encounter_num"))),
new ColumnSpec(schemaName, VISIT_DIMENSION, new JoinSpec("encounter_num", "encounter_num", new ColumnSpec(schemaName, OBSERVATION_FACT, "concept_cd"))),
new ColumnSpec(schemaName, VISIT_DIMENSION, new JoinSpec("encounter_num", "encounter_num", new ColumnSpec(schemaName, OBSERVATION_FACT, "provider_id"))),
new ColumnSpec(schemaName, VISIT_DIMENSION, new JoinSpec("encounter_num", "encounter_num", new ColumnSpec(schemaName, OBSERVATION_FACT, "start_date")))
}, ReferenceSpec.Type.MANY),
new ReferenceSpec("msdrg", "MSDRG Codes",
new ColumnSpec[]{
new ColumnSpec(schemaName, VISIT_DIMENSION, new JoinSpec("encounter_num", "encounter_num", new ColumnSpec(schemaName, OBSERVATION_FACT, "encounter_num"))),
new ColumnSpec(schemaName, VISIT_DIMENSION, new JoinSpec("encounter_num", "encounter_num", new ColumnSpec(schemaName, OBSERVATION_FACT, "concept_cd"))),
new ColumnSpec(schemaName, VISIT_DIMENSION, new JoinSpec("encounter_num", "encounter_num", new ColumnSpec(schemaName, OBSERVATION_FACT, "provider_id"))),
new ColumnSpec(schemaName, VISIT_DIMENSION, new JoinSpec("encounter_num", "encounter_num", new ColumnSpec(schemaName, OBSERVATION_FACT, "start_date")))
}, ReferenceSpec.Type.ONE),
new ReferenceSpec("aprdrg", "APR DRG Codes",
new ColumnSpec[]{
new ColumnSpec(schemaName, VISIT_DIMENSION, new JoinSpec("encounter_num", "encounter_num", new ColumnSpec(schemaName, OBSERVATION_FACT, "encounter_num"))),
new ColumnSpec(schemaName, VISIT_DIMENSION, new JoinSpec("encounter_num", "encounter_num", new ColumnSpec(schemaName, OBSERVATION_FACT, "concept_cd"))),
new ColumnSpec(schemaName, VISIT_DIMENSION, new JoinSpec("encounter_num", "encounter_num", new ColumnSpec(schemaName, OBSERVATION_FACT, "provider_id"))),
new ColumnSpec(schemaName, VISIT_DIMENSION, new JoinSpec("encounter_num", "encounter_num", new ColumnSpec(schemaName, OBSERVATION_FACT, "start_date")))
}, ReferenceSpec.Type.ONE),
/*
* Assumes every fact for an encounter has the same provider. PCORI CDM requires this.
* This is not quite right. It will cause providers to get duplicated x the number of encounters in which each appears. With the i2b2 destination, this appears
* harmless because the aiw-i2b2-etl code ends up resolving the duplicates anyway.
*/
new ReferenceSpec("provider", "Providers",
new ColumnSpec[]{
new ColumnSpec(schemaName, VISIT_DIMENSION, new JoinSpec("encounter_num", "encounter_num", new ColumnSpec(schemaName, OBSERVATION_FACT, "provider_id")))
}, ReferenceSpec.Type.ONE)
/*new ReferenceSpec("chargeAmount", "Hospital Charge Amount", new ColumnSpec[]{new ColumnSpec(schemaName, "ENCOUNTER", "RECORD_ID")}, ReferenceSpec.Type.ONE)*/
},
null, null, isInKeySetMode()
? new ColumnSpec[]{
new ColumnSpec(schemaName, VISIT_DIMENSION, new JoinSpec("patient_num", keyIdJoinKey, new ColumnSpec(keyIdSchema, keyIdTable, "RESULT_INSTANCE_ID", Operator.EQUAL_TO, riId)))}
: null, null, null, AbsoluteTimeGranularity.DAY, POSITION_PARSER, null),
new EntitySpec("Diagnosis Codes",
null,
icd9DxMappings.readTargets(),
true,
new ColumnSpec(keyIdSchema, keyIdTable, keyIdColumn, new JoinSpec(keyIdJoinKey, "patient_num", new ColumnSpec(schemaName, PATIENT_DIMENSION, new JoinSpec("patient_num", "patient_num", new ColumnSpec(schemaName, VISIT_DIMENSION, new JoinSpec("encounter_num", "encounter_num", new ColumnSpec(schemaName, OBSERVATION_FACT))))))),
new ColumnSpec[]{
new ColumnSpec(schemaName, OBSERVATION_FACT, "encounter_num"),
new ColumnSpec(schemaName, OBSERVATION_FACT, "concept_cd"),
new ColumnSpec(schemaName, OBSERVATION_FACT, "provider_id"),
new ColumnSpec(schemaName, OBSERVATION_FACT, "start_date")
},
new ColumnSpec(schemaName, OBSERVATION_FACT, "START_DATE"),
null,
new PropertySpec[]{
new PropertySpec("code", null, new ColumnSpec(schemaName, OBSERVATION_FACT, "concept_cd"), ValueType.NOMINALVALUE), //new PropertySpec("position", null, new ColumnSpec(schemaName, "ENCOUNTER", new JoinSpec("RECORD_ID", "RECORD_ID", new ColumnSpec(schemaName, "DIAGNOSIS", "SEQ_NBR", ColumnSpec.Operator.EQUAL_TO, getMappingsFactory().propertyNameOrPropIdToSqlCodeArray("icd9_diagnosis_position_07182011.txt")))), ValueType.NOMINALVALUE)
},
null,
null,
new ColumnSpec(schemaName, OBSERVATION_FACT, "concept_cd", Operator.EQUAL_TO, icd9DxMappings, false),
isInKeySetMode()
? new ColumnSpec[]{
new ColumnSpec(schemaName, OBSERVATION_FACT, new JoinSpec("encounter_num", "encounter_num", new ColumnSpec(schemaName, VISIT_DIMENSION, new JoinSpec("patient_num", keyIdJoinKey, new ColumnSpec(keyIdSchema, keyIdTable, "RESULT_INSTANCE_ID", Operator.EQUAL_TO, riId)))))}
: null, null, null,
AbsoluteTimeGranularity.DAY,
POSITION_PARSER,
AbsoluteTimeUnit.YEAR),
new EntitySpec("ICD9 Procedure Codes",
null,
icd9PxMappings.readTargets(),
true,
new ColumnSpec(keyIdSchema, keyIdTable, keyIdColumn, new JoinSpec(keyIdJoinKey, "patient_num", new ColumnSpec(schemaName, PATIENT_DIMENSION, new JoinSpec("patient_num", "patient_num", new ColumnSpec(schemaName, VISIT_DIMENSION, new JoinSpec("encounter_num", "encounter_num", new ColumnSpec(schemaName, OBSERVATION_FACT))))))),
new ColumnSpec[]{
new ColumnSpec(schemaName, OBSERVATION_FACT, "encounter_num"),
new ColumnSpec(schemaName, OBSERVATION_FACT, "concept_cd"),
new ColumnSpec(schemaName, OBSERVATION_FACT, "provider_id"),
new ColumnSpec(schemaName, OBSERVATION_FACT, "start_date")
},
new ColumnSpec(schemaName, OBSERVATION_FACT, "START_DATE"),
null,
new PropertySpec[]{
new PropertySpec("code", null, new ColumnSpec(schemaName, OBSERVATION_FACT, "concept_cd"), ValueType.NOMINALVALUE),}, null, null,
new ColumnSpec(schemaName, OBSERVATION_FACT, "concept_cd", Operator.EQUAL_TO, icd9PxMappings, false),
isInKeySetMode()
? new ColumnSpec[]{
new ColumnSpec(schemaName, OBSERVATION_FACT, new JoinSpec("encounter_num", "encounter_num", new ColumnSpec(schemaName, VISIT_DIMENSION, new JoinSpec("patient_num", keyIdJoinKey, new ColumnSpec(keyIdSchema, keyIdTable, "RESULT_INSTANCE_ID", Operator.EQUAL_TO, riId)))))}
: null, null, null,
AbsoluteTimeGranularity.DAY,
POSITION_PARSER,
null),};
return eventSpecs;
}
@Override
protected EntitySpec[] primitiveParameterSpecs(String keyIdSchema, String keyIdTable, String keyIdColumn, String keyIdJoinKey) throws IOException {
return new EntitySpec[0];
}
@Override
public GranularityFactory getGranularityFactory() {
return ABS_TIME_GRANULARITY_FACTORY;
}
@Override
public UnitFactory getUnitFactory() {
return ABS_TIME_UNIT_FACTORY;
}
@BackendProperty(displayName = "Query Master ID")
public void setResultInstanceId(Long resultInstanceId) {
this.resultInstanceId = resultInstanceId;
setKeyLoaderKeyIdSchema(getSchemaName());
setKeyLoaderKeyIdTable("QT_PATIENT_SET_COLLECTION");
setKeyLoaderKeyIdColumn("PATIENT_NUM");
setKeyLoaderKeyIdJoinKey("PATIENT_NUM");
}
public Long getResultInstanceId() {
return this.resultInstanceId;
}
@Override
public KeySetSpec[] getSelectedKeySetSpecs() throws DataSourceReadException {
List result = new ArrayList<>();
if (this.resultInstanceId != null) {
try (Connection con = this.getConnectionSpecInstance().getOrCreate();
PreparedStatement stmt = con.prepareStatement("SELECT A1.NAME, A1.USER_ID, A3.DESCRIPTION FROM QT_QUERY_MASTER A1 JOIN QT_QUERY_INSTANCE A2 ON (A1.QUERY_MASTER_ID=A2.QUERY_MASTER_ID) JOIN QT_QUERY_RESULT_INSTANCE A3 ON (A2.QUERY_INSTANCE_ID=A3.QUERY_INSTANCE_ID) WHERE A3.RESULT_INSTANCE_ID = ? AND A1.DELETE_FLAG = 'N' AND A2.DELETE_FLAG = 'N' AND A3.RESULT_TYPE_ID = 1")) {
stmt.setLong(1, this.resultInstanceId);
try (ResultSet rs = stmt.executeQuery()) {
if (rs.next()) {
result.add(new KeySetSpec(getSourceSystem(), "" + this.resultInstanceId, rs.getString(1) + " (" + rs.getString(2) + ")", rs.getString(3)));
}
}
} catch (SQLException | InvalidConnectionSpecArguments ex) {
throw new DataSourceReadException(ex);
}
}
return result.toArray(new KeySetSpec[result.size()]);
}
@Override
public String getKeyType() {
return "Patient";
}
}