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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.ksb;
/*
* #%L
* AIW i2b2 ETL
* %%
* Copyright (C) 2012 - 2015 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 au.com.bytecode.opencsv.CSVReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.Reader;
import java.io.StringReader;
import java.sql.Clob;
import java.sql.Connection;
import org.apache.commons.lang3.ArrayUtils;
import org.arp.javautil.sql.DatabaseAPI;
import org.protempa.AbstractionDefinition;
import org.protempa.ContextDefinition;
import org.protempa.EventDefinition;
import org.protempa.KnowledgeSourceReadException;
import org.protempa.PropositionDefinition;
import org.protempa.TemporalPropositionDefinition;
import org.protempa.backend.AbstractCommonsKnowledgeSourceBackend;
import org.protempa.backend.annotations.BackendInfo;
import org.protempa.backend.annotations.BackendProperty;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Statement;
import java.util.ArrayList;
import java.util.Calendar;
import java.util.Collection;
import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Properties;
import java.util.Set;
import java.util.logging.Level;
import java.util.logging.Logger;
import org.arp.javautil.arrays.Arrays;
import org.arp.javautil.collections.Collections;
import org.arp.javautil.io.IOUtil;
import org.arp.javautil.sql.DatabaseProduct;
import org.arp.javautil.sql.InvalidConnectionSpecArguments;
import org.protempa.AbstractPropositionDefinition;
import org.protempa.Attribute;
import org.protempa.ConstantDefinition;
import org.protempa.PrimitiveParameterDefinition;
import org.protempa.PropertyDefinition;
import org.protempa.ReferenceDefinition;
import org.protempa.valueset.ValueSet;
import org.protempa.valueset.ValueSetElement;
import org.protempa.backend.BackendInitializationException;
import org.protempa.backend.BackendInstanceSpec;
import org.protempa.backend.BackendSourceIdFactory;
import org.protempa.dest.deid.DeidAttributes;
import org.protempa.proposition.value.BooleanValue;
import org.protempa.proposition.value.NominalValue;
import org.protempa.proposition.value.ValueType;
import org.xml.sax.SAXParseException;
import org.xml.sax.XMLReader;
/**
* Implements using an i2b2 metadata schema to
* store proposition definitions.
*/
@BackendInfo(displayName = "I2b2 Knowledge Source Backend")
public class I2b2KnowledgeSourceBackend extends AbstractCommonsKnowledgeSourceBackend {
private static final Logger LOGGER = Logger.getLogger(I2b2KnowledgeSourceBackend.class.getName());
private static final char DEFAULT_DELIMITER = '\t';
private static final Properties visitPropositionProperties;
private static final Properties patientAliasPropositionProperties;
private static final Properties patientPropositionProperties;
private static final Properties patientDetailsPropositionProperties;
private static final Properties providerPropositionProperties;
private final static String[] VALUE_TYPE_CDS = {"LAB", "DOC"};
private static final String defaultPatientPropositionId;
private static final String defaultPatientAliasPropositionId;
private static final String defaultPatientDetailsPropositionId;
private static final ValueSet defaultLanguagePropertyValueSet;
private static final ValueSet defaultMaritalStatusPropertyValueSet;
private static final ValueSet defaultReligionPropertyValueSet;
private static final ValueSet defaultGenderPropertyValueSet;
private static final ValueSet defaultRacePropertyValueSet;
private static final ValueSet defaultInoutPropertyValueSet;
private static final String defaultVisitPropositionId;
private static final Date DIMENSION_PROP_DEFS_CREATED_DATE;
static {
Calendar cal = Calendar.getInstance();
cal.clear();
cal.set(2015, Calendar.FEBRUARY, 8, 22, 13, 0);
DIMENSION_PROP_DEFS_CREATED_DATE = cal.getTime();
}
static {
try {
patientPropositionProperties = IOUtil.loadPropertiesFromResource(I2b2KnowledgeSourceBackend.class, "/patientProposition.properties");
visitPropositionProperties = IOUtil.loadPropertiesFromResource(I2b2KnowledgeSourceBackend.class, "/visitProposition.properties");
patientAliasPropositionProperties = IOUtil.loadPropertiesFromResource(I2b2KnowledgeSourceBackend.class, "/patientAliasProposition.properties");
patientDetailsPropositionProperties = IOUtil.loadPropertiesFromResource(I2b2KnowledgeSourceBackend.class, "/patientDetailsProposition.properties");
providerPropositionProperties = IOUtil.loadPropertiesFromResource(I2b2KnowledgeSourceBackend.class, "/providerProposition.properties");
} catch (IOException ex) {
throw new AssertionError("Can't find dimension proposition properties file: " + ex.getMessage());
}
defaultPatientPropositionId = patientPropositionProperties.getProperty("propositionId");
defaultPatientDetailsPropositionId = patientDetailsPropositionProperties.getProperty("propositionId");
defaultLanguagePropertyValueSet = parseValueSetResource(
patientDetailsPropositionProperties.getProperty("language.valueSet.id"),
patientDetailsPropositionProperties.getProperty("language.valueSet.resource.name"),
patientDetailsPropositionProperties.getProperty("language.valueSet.resource.hasHeader"),
patientDetailsPropositionProperties.getProperty("language.valueSet.resource.delimiter"),
patientDetailsPropositionProperties.getProperty("language.valueSet.resource.column.id"),
patientDetailsPropositionProperties.getProperty("language.valueSet.resource.column.displayName"),
patientDetailsPropositionProperties.getProperty("language.valueSet.resource.column.description"));
defaultMaritalStatusPropertyValueSet = parseValueSetResource(
patientDetailsPropositionProperties.getProperty("maritalStatus.valueSet.id"),
patientDetailsPropositionProperties.getProperty("maritalStatus.valueSet.resource.name"),
patientDetailsPropositionProperties.getProperty("maritalStatus.valueSet.resource.hasHeader"),
patientDetailsPropositionProperties.getProperty("maritalStatus.valueSet.resource.delimiter"),
patientDetailsPropositionProperties.getProperty("maritalStatus.valueSet.resource.column.id"),
patientDetailsPropositionProperties.getProperty("maritalStatus.valueSet.resource.column.displayName"),
patientDetailsPropositionProperties.getProperty("maritalStatus.valueSet.resource.column.description"));
defaultReligionPropertyValueSet = parseValueSetResource(
patientDetailsPropositionProperties.getProperty("religion.valueSet.id"),
patientDetailsPropositionProperties.getProperty("religion.valueSet.resource.name"),
patientDetailsPropositionProperties.getProperty("religion.valueSet.resource.hasHeader"),
patientDetailsPropositionProperties.getProperty("religion.valueSet.resource.delimiter"),
patientDetailsPropositionProperties.getProperty("religion.valueSet.resource.column.id"),
patientDetailsPropositionProperties.getProperty("religion.valueSet.resource.column.displayName"),
patientDetailsPropositionProperties.getProperty("religion.valueSet.resource.column.description"));
defaultGenderPropertyValueSet = parseValueSet(patientDetailsPropositionProperties.getProperty("gender.valueSet.id"), patientDetailsPropositionProperties.getProperty("gender.valueSet.values"));
defaultRacePropertyValueSet = parseValueSet(patientDetailsPropositionProperties.getProperty("race.valueSet.id"), patientDetailsPropositionProperties.getProperty("race.valueSet.values"));
defaultPatientAliasPropositionId = patientAliasPropositionProperties.getProperty("propositionId");
defaultVisitPropositionId = visitPropositionProperties.getProperty("propositionId");
defaultInoutPropertyValueSet = parseValueSet(visitPropositionProperties.getProperty("inout.valueSet.id"), visitPropositionProperties.getProperty("inout.valueSet.values"));
}
private ValueMetadataSupport valueMetadataSupport;
private final QuerySupport querySupport;
private final LevelReader levelReader;
private String patientPropositionId;
private String patientAliasPropositionId;
private String patientDetailsPropositionId;
private String visitPropositionId;
private String providerPropositionId;
private String providerNamePropertyName;
private String inoutPropertyName;
private String inoutPropertySource;
private ValueSet inoutPropertyValueSet;
private String inoutPropertyValueSetFile;
private boolean inoutPropertyValueSetHasHeader;
private char inoutPropertyValueSetDelimiter;
private int inoutPropertyValueSetIdColumn;
private Integer inoutPropertyValueSetDisplayNameColumn;
private Integer inoutPropertyValueSetDescriptionColumn;
private String visitAgePropertyName;
private String genderPropertyName;
private ValueSet genderPropertyValueSet;
private String genderPropertySource;
private String genderPropertyValueSetFile;
private boolean genderPropertyValueSetHasHeader;
private char genderPropertyValueSetDelimiter;
private int genderPropertyValueSetIdColumn;
private Integer genderPropertyValueSetDisplayNameColumn;
private Integer genderPropertyValueSetDescriptionColumn;
private String racePropertyName;
private ValueSet racePropertyValueSet;
private String racePropertySource;
private String racePropertyValueSetFile;
private boolean racePropertyValueSetHasHeader;
private char racePropertyValueSetDelimiter;
private int racePropertyValueSetIdColumn;
private Integer racePropertyValueSetDisplayNameColumn;
private Integer racePropertyValueSetDescriptionColumn;
private String languagePropertyName;
private ValueSet languagePropertyValueSet;
private String languagePropertySource;
private String languagePropertyValueSetFile;
private boolean languagePropertyValueSetHasHeader;
private char languagePropertyValueSetDelimiter;
private int languagePropertyValueSetIdColumn;
private Integer languagePropertyValueSetDisplayNameColumn;
private Integer languagePropertyValueSetDescriptionColumn;
private ValueSet maritalStatusPropertyValueSet;
private String maritalStatusPropertySource;
private String maritalStatusPropertyName;
private String maritalStatusPropertyValueSetFile;
private boolean maritalStatusPropertyValueSetHasHeader;
private char maritalStatusPropertyValueSetDelimiter;
private int maritalStatusPropertyValueSetIdColumn;
private Integer maritalStatusPropertyValueSetDisplayNameColumn;
private Integer maritalStatusPropertyValueSetDescriptionColumn;
private String religionPropertyName;
private ValueSet religionPropertyValueSet;
private String religionPropertySource;
private String religionPropertyValueSetFile;
private boolean religionPropertyValueSetHasHeader;
private char religionPropertyValueSetDelimiter;
private int religionPropertyValueSetIdColumn;
private Integer religionPropertyValueSetDisplayNameColumn;
private Integer religionPropertyValueSetDescriptionColumn;
private String dateOfBirthPropertyName;
private String ageInYearsPropertyName;
private String dateOfDeathPropertyName;
private String vitalStatusPropertyName;
private final String patientDisplayName;
private final String patientAliasDisplayName;
private String patientDetailsDisplayName;
private String visitDisplayName;
private String visitIdPropertyName;
private String providerDisplayName;
private final Map valueSets;
private final BackendSourceIdFactory sourceIdFactory;
private String patientPatientIdPropertyName;
private final String patientAliasPatientIdPropertyName;
private final String patientAliasFieldNamePropertyName;
private String patientDetailsPatientIdPropertyName;
private Map> modInterpCached;
private final String modInterpCachedSyncVariable = "MOD_INTERP_CACHED_SYNC";
public I2b2KnowledgeSourceBackend() {
this.querySupport = new QuerySupport();
this.levelReader = new LevelReader(this.querySupport);
this.valueSets = new HashMap<>();
/**
* Patient
*/
this.patientPropositionId = defaultPatientPropositionId;
this.patientDisplayName = patientPropositionProperties.getProperty("displayName");
this.patientPatientIdPropertyName = patientPropositionProperties.getProperty("patientId.propertyName");
this.patientAliasPropositionId = defaultPatientAliasPropositionId;
this.patientAliasDisplayName = patientAliasPropositionProperties.getProperty("displayName");
this.patientAliasPatientIdPropertyName = patientAliasPropositionProperties.getProperty("patientId.propertyName");
this.patientAliasFieldNamePropertyName = patientAliasPropositionProperties.getProperty("fieldName.propertyName");
this.patientDetailsPropositionId = defaultPatientDetailsPropositionId;
this.patientDetailsDisplayName = patientDetailsPropositionProperties.getProperty("displayName");
this.patientDetailsPatientIdPropertyName = patientDetailsPropositionProperties.getProperty("patientId.propertyName");
this.genderPropertyName = patientDetailsPropositionProperties.getProperty("gender.propertyName");
this.genderPropertyValueSet = defaultGenderPropertyValueSet;
if (this.genderPropertyValueSet != null) {
this.valueSets.put(this.genderPropertyValueSet.getId(), this.genderPropertyValueSet);
}
this.genderPropertySource = patientDetailsPropositionProperties.getProperty("gender.valueSet.source");
this.racePropertyName = patientDetailsPropositionProperties.getProperty("race.propertyName");
this.racePropertyValueSet = defaultRacePropertyValueSet;
if (this.racePropertyValueSet != null) {
this.valueSets.put(this.racePropertyValueSet.getId(), this.racePropertyValueSet);
}
this.racePropertySource = patientDetailsPropositionProperties.getProperty("race.valueSet.source");
this.languagePropertyName = patientDetailsPropositionProperties.getProperty("language.propertyName");
this.languagePropertyValueSet = defaultLanguagePropertyValueSet;
if (this.languagePropertyValueSet != null) {
this.valueSets.put(this.languagePropertyValueSet.getId(), this.languagePropertyValueSet);
}
this.languagePropertySource = patientDetailsPropositionProperties.getProperty("language.valueSet.source");
this.maritalStatusPropertyName = patientDetailsPropositionProperties.getProperty("maritalStatus.propertyName");
this.maritalStatusPropertyValueSet = defaultMaritalStatusPropertyValueSet;
if (this.maritalStatusPropertyValueSet != null) {
this.valueSets.put(this.maritalStatusPropertyValueSet.getId(), this.maritalStatusPropertyValueSet);
}
this.maritalStatusPropertySource = patientDetailsPropositionProperties.getProperty("maritalStatus.valueSet.source");
this.religionPropertyName = patientDetailsPropositionProperties.getProperty("religion.propertyName");
this.religionPropertyValueSet = defaultReligionPropertyValueSet;
if (this.religionPropertyValueSet != null) {
this.valueSets.put(this.religionPropertyValueSet.getId(), this.religionPropertyValueSet);
}
this.religionPropertySource = patientDetailsPropositionProperties.getProperty("religion.valueSet.source");
this.dateOfBirthPropertyName = patientDetailsPropositionProperties.getProperty("dateOfBirth.propertyName");
this.ageInYearsPropertyName = patientDetailsPropositionProperties.getProperty("ageInYears.propertyName");
this.dateOfDeathPropertyName = patientDetailsPropositionProperties.getProperty("dateOfDeath.propertyName");
this.vitalStatusPropertyName = patientDetailsPropositionProperties.getProperty("vitalStatus.propertyName");
/**
* Visit
*/
this.visitPropositionId = defaultVisitPropositionId;
this.visitDisplayName = visitPropositionProperties.getProperty("displayName");
this.inoutPropertyName = visitPropositionProperties.getProperty("inout.propertyName");
this.inoutPropertyValueSet = defaultInoutPropertyValueSet;
if (this.inoutPropertyValueSet != null) {
this.valueSets.put(this.inoutPropertyValueSet.getId(), this.inoutPropertyValueSet);
}
this.inoutPropertySource = visitPropositionProperties.getProperty("inout.valueSet.source");
this.visitAgePropertyName = visitPropositionProperties.getProperty("age.propertyName");
this.visitIdPropertyName = visitPropositionProperties.getProperty("id.propertyName");
/**
* Provider
*/
this.providerPropositionId = providerPropositionProperties.getProperty("propositionId");
this.providerDisplayName = visitPropositionProperties.getProperty("displayName");
this.providerNamePropertyName = providerPropositionProperties.getProperty("name.propertyName");
this.genderPropertyValueSetDelimiter = DEFAULT_DELIMITER;
this.racePropertyValueSetDelimiter = DEFAULT_DELIMITER;
this.languagePropertyValueSetDelimiter = DEFAULT_DELIMITER;
this.maritalStatusPropertyValueSetDelimiter = DEFAULT_DELIMITER;
this.religionPropertyValueSetDelimiter = DEFAULT_DELIMITER;
this.sourceIdFactory = new BackendSourceIdFactory(this);
}
/**
* Returns which Java database API this backend is configured to use.
*
* @return a {@link DatabaseAPI}. The default value is
* {@link org.arp.javautil.sql.DatabaseAPI}.DRIVERMANAGER
*/
public DatabaseAPI getDatabaseApi() {
return this.querySupport.getDatabaseApi();
}
/**
* Configures which Java database API to use ({@link java.sql.DriverManager}
* or {@link javax.sql.DataSource}. If null, the default is
* assigned
* ({@link org.arp.javautil.sql.DatabaseAPI}.DRIVERMANAGER).
*
* @param databaseApi a {@link DatabaseAPI}.
*/
public void setDatabaseApi(DatabaseAPI databaseApi) {
this.querySupport.setDatabaseApi(databaseApi);
}
public String getTargetTable() {
return this.querySupport.getExcludeTableName();
}
@BackendProperty
public void setTargetTable(String tableName) {
this.querySupport.setExcludeTableName(tableName);
}
/**
* Configures which Java database API to use ({@link java.sql.DriverManager}
* or {@link javax.sql.DataSource} by parsing a {@link DatabaseAPI}'s name.
* Cannot be null.
*
* @param databaseApiString a {@link DatabaseAPI}'s name.
*/
@BackendProperty(propertyName = "databaseAPI")
public void parseDatabaseApi(String databaseApiString) {
setDatabaseApi(DatabaseAPI.valueOf(databaseApiString));
}
public String getDatabaseId() {
return this.querySupport.getDatabaseId();
}
@BackendProperty
public void setDatabaseId(String databaseId) {
this.querySupport.setDatabaseId(databaseId);
}
public String getUsername() {
return this.querySupport.getUsername();
}
@BackendProperty
public void setUsername(String username) {
this.querySupport.setUsername(username);
}
public String getPassword() {
return this.querySupport.getPassword();
}
@BackendProperty
public void setPassword(String password) {
this.querySupport.setPassword(password);
}
public String getPatientPatientIdPropertyName() {
return patientPatientIdPropertyName;
}
@BackendProperty
public void setPatientPatientIdPropertyName(String patientPatientIdPropertyName) {
this.patientPatientIdPropertyName = patientPatientIdPropertyName;
}
public String getPatientDetailsPatientIdPropertyName() {
return patientDetailsPatientIdPropertyName;
}
@BackendProperty
public void setPatientDetailsPatientIdPropertyName(String patientDetailsPatientIdPropertyName) {
this.patientDetailsPatientIdPropertyName = patientDetailsPatientIdPropertyName;
}
public String getPatientPropositionId() {
return patientPropositionId;
}
@BackendProperty
public void setPatientPropositionId(String patientPropositionId) {
if (patientPropositionId != null) {
this.patientPropositionId = patientPropositionId;
} else {
this.patientPropositionId = defaultPatientPropositionId;
}
}
public String getPatientDetailsPropositionId() {
return patientDetailsPropositionId;
}
@BackendProperty
public void setPatientDetailsPropositionId(String patientDetailsPropositionId) {
if (patientDetailsPropositionId != null) {
this.patientDetailsPropositionId = patientDetailsPropositionId;
} else {
this.patientDetailsPropositionId = defaultPatientDetailsPropositionId;
}
}
public String getPatientDetailsDisplayName() {
return patientDetailsDisplayName;
}
@BackendProperty
public void setPatientDetailsDisplayName(String patientDetailsDisplayName) {
this.patientDetailsDisplayName = patientDetailsDisplayName;
}
public String getVisitPropositionId() {
return visitPropositionId;
}
@BackendProperty
public void setVisitPropositionId(String visitPropositionId) {
if (visitPropositionId != null) {
this.visitPropositionId = visitPropositionId;
} else {
this.visitPropositionId = defaultVisitPropositionId;
}
}
public String getVisitDisplayName() {
return visitDisplayName;
}
@BackendProperty
public void setVisitDisplayName(String visitDisplayName) {
this.visitDisplayName = visitDisplayName;
}
public String getProviderPropositionId() {
return providerPropositionId;
}
@BackendProperty
public void setProviderPropositionId(String providerPropositionId) {
if (providerPropositionId != null) {
this.providerPropositionId = providerPropositionId;
} else {
this.providerPropositionId = this.providerPropositionProperties.getProperty("propositionId");
}
}
public String getProviderDisplayName() {
return providerDisplayName;
}
@BackendProperty
public void setProviderDisplayName(String providerDisplayName) {
this.providerDisplayName = providerDisplayName;
}
public String getProviderNamePropertyName() {
return providerNamePropertyName;
}
@BackendProperty
public void setProviderNamePropertyName(String providerNamePropertyName) {
this.providerNamePropertyName = providerNamePropertyName;
}
public String getInoutPropertyName() {
return inoutPropertyName;
}
@BackendProperty
public void setInoutPropertyName(String inoutPropertyName) {
this.inoutPropertyName = inoutPropertyName;
}
public String getInoutPropertySource() {
return inoutPropertySource;
}
@BackendProperty
public void setInoutPropertySource(String inoutPropertySource) {
this.inoutPropertySource = inoutPropertySource;
}
public ValueSet getInoutPropertyValueSet() {
return inoutPropertyValueSet;
}
public void setInoutPropertyValueSet(ValueSet inoutPropertyValueSet) {
this.inoutPropertyValueSet = inoutPropertyValueSet;
}
@BackendProperty(propertyName = "inoutPropertyValueSet")
public void parseInoutPropertyValueSet(String valueSetStr) {
this.inoutPropertyValueSet = parseValueSet(this.visitPropositionId, valueSetStr);
}
public String getInoutPropertyValueSetFile() {
return inoutPropertyValueSetFile;
}
@BackendProperty
public void setInoutPropertyValueSetFile(String inoutPropertyValueSetFile) {
this.inoutPropertyValueSetFile = inoutPropertyValueSetFile;
}
public Boolean getInoutPropertyValueSetHasHeader() {
return inoutPropertyValueSetHasHeader;
}
@BackendProperty
public void setInoutPropertyValueSetHasHeader(Boolean inoutPropertyValueSetHasHeader) {
if (inoutPropertyValueSetHasHeader != null) {
this.inoutPropertyValueSetHasHeader = inoutPropertyValueSetHasHeader;
} else {
this.inoutPropertyValueSetHasHeader = false;
}
}
public String getInoutPropertyValueSetDelimiter() {
return Character.toString(inoutPropertyValueSetDelimiter);
}
@BackendProperty
public void setInoutPropertyValueSetDelimiter(String inoutPropertyValueSetDelimiter) {
if (inoutPropertyValueSetDelimiter != null) {
if (inoutPropertyValueSetDelimiter.length() > 1) {
throw new IllegalArgumentException("delimiter can only be one character");
}
if (inoutPropertyValueSetDelimiter.length() < 1) {
throw new IllegalArgumentException("delimiter must be at least one character");
}
}
if (inoutPropertyValueSetDelimiter != null) {
this.inoutPropertyValueSetDelimiter = inoutPropertyValueSetDelimiter.charAt(0);
} else {
this.inoutPropertyValueSetDelimiter = DEFAULT_DELIMITER;
}
}
public Integer getInoutPropertyValueSetIdColumn() {
return inoutPropertyValueSetIdColumn;
}
@BackendProperty
public void setInoutPropertyValueSetIdColumn(Integer inoutPropertyValueSetIdColumn) {
if (inoutPropertyValueSetIdColumn == null) {
throw new IllegalArgumentException("inoutPropertyValueSetIdColumn cannot be null");
}
this.inoutPropertyValueSetIdColumn = inoutPropertyValueSetIdColumn;
}
public Integer getInoutPropertyValueSetDisplayNameColumn() {
return inoutPropertyValueSetDisplayNameColumn;
}
@BackendProperty
public void setInoutPropertyValueSetDisplayNameColumn(Integer inoutPropertyValueSetDisplayNameColumn) {
this.inoutPropertyValueSetDisplayNameColumn = inoutPropertyValueSetDisplayNameColumn;
}
public Integer getInoutPropertyValueSetDescriptionColumn() {
return inoutPropertyValueSetDescriptionColumn;
}
@BackendProperty
public void setInoutPropertyValueSetDescriptionColumn(Integer inoutPropertyValueSetDescriptionColumn) {
this.inoutPropertyValueSetDescriptionColumn = inoutPropertyValueSetDescriptionColumn;
}
public String getVisitAgePropertyName() {
return visitAgePropertyName;
}
@BackendProperty
public void setVisitAgePropertyName(String visitAgePropertyName) {
this.visitAgePropertyName = visitAgePropertyName;
}
public String getGenderPropertyName() {
return genderPropertyName;
}
@BackendProperty
public void setGenderPropertyName(String genderPropertyName) {
this.genderPropertyName = genderPropertyName;
}
public ValueSet getGenderPropertyValueSet() {
return genderPropertyValueSet;
}
public void setGenderPropertyValueSet(ValueSet genderPropertyValueSet) {
this.genderPropertyValueSet = genderPropertyValueSet;
}
@BackendProperty(propertyName = "genderPropertyValueSet")
public void parseGenderPropertyValueSet(String valueSetStr) {
this.genderPropertyValueSet = parseValueSet(this.patientDetailsPropositionId, valueSetStr);
}
public String getGenderPropertySource() {
return genderPropertySource;
}
@BackendProperty
public void setGenderPropertySource(String genderPropertySource) {
this.genderPropertySource = genderPropertySource;
}
public String getGenderPropertyValueSetFile() {
return genderPropertyValueSetFile;
}
@BackendProperty
public void setGenderPropertyValueSetFile(String genderPropertyValueSetFile) {
this.genderPropertyValueSetFile = genderPropertyValueSetFile;
}
public Boolean getGenderPropertyValueSetHasHeader() {
return genderPropertyValueSetHasHeader;
}
@BackendProperty
public void setGenderPropertyValueSetHasHeader(Boolean genderPropertyValueSetHasHeader) {
if (genderPropertyValueSetHasHeader != null) {
this.genderPropertyValueSetHasHeader = genderPropertyValueSetHasHeader;
} else {
this.genderPropertyValueSetHasHeader = false;
}
}
public String getGenderPropertyValueSetDelimiter() {
return Character.toString(genderPropertyValueSetDelimiter);
}
@BackendProperty
public void setGenderPropertyValueSetDelimiter(String genderPropertyValueSetDelimiter) {
if (genderPropertyValueSetDelimiter != null) {
if (genderPropertyValueSetDelimiter.length() > 1) {
throw new IllegalArgumentException("delimiter can only be one character");
}
if (genderPropertyValueSetDelimiter.length() < 1) {
throw new IllegalArgumentException("delimiter must be at least one character");
}
}
if (genderPropertyValueSetDelimiter != null) {
this.genderPropertyValueSetDelimiter = genderPropertyValueSetDelimiter.charAt(0);
} else {
this.genderPropertyValueSetDelimiter = DEFAULT_DELIMITER;
}
}
public Integer getGenderPropertyValueSetIdColumn() {
return genderPropertyValueSetIdColumn;
}
@BackendProperty
public void setGenderPropertyValueSetIdColumn(Integer genderPropertyValueSetIdColumn) {
if (genderPropertyValueSetIdColumn == null) {
throw new IllegalArgumentException("genderPropertyValueSetIdColumn cannot be null");
}
this.genderPropertyValueSetIdColumn = genderPropertyValueSetIdColumn;
}
public Integer getGenderPropertyValueSetDisplayNameColumn() {
return genderPropertyValueSetDisplayNameColumn;
}
@BackendProperty
public void setGenderPropertyValueSetDisplayNameColumn(Integer genderPropertyValueSetDisplayNameColumn) {
this.genderPropertyValueSetDisplayNameColumn = genderPropertyValueSetDisplayNameColumn;
}
public Integer getGenderPropertyValueSetDescriptionColumn() {
return genderPropertyValueSetDescriptionColumn;
}
@BackendProperty
public void setGenderPropertyValueSetDescriptionColumn(Integer genderPropertyValueSetDescriptionColumn) {
this.genderPropertyValueSetDescriptionColumn = genderPropertyValueSetDescriptionColumn;
}
public String getRacePropertyName() {
return racePropertyName;
}
@BackendProperty
public void setRacePropertyName(String racePropertyName) {
this.racePropertyName = racePropertyName;
}
public ValueSet getRacePropertyValueSet() {
return racePropertyValueSet;
}
public void setRacePropertyValueSet(ValueSet racePropertyValueSet) {
this.racePropertyValueSet = racePropertyValueSet;
}
@BackendProperty(propertyName = "racePropertyValueSet")
public void parseRacePropertyValueSet(String valueSetStr) {
this.racePropertyValueSet = parseValueSet(this.patientDetailsPropositionId, valueSetStr);
}
public String getRacePropertyValueSetFile() {
return racePropertyValueSetFile;
}
@BackendProperty
public void setRacePropertyValueSetFile(String racePropertyValueSetFile) {
this.racePropertyValueSetFile = racePropertyValueSetFile;
}
public Boolean getRacePropertyValueSetHasHeader() {
return racePropertyValueSetHasHeader;
}
@BackendProperty
public void setRacePropertyValueSetHasHeader(Boolean racePropertyValueSetHasHeader) {
if (racePropertyValueSetHasHeader != null) {
this.racePropertyValueSetHasHeader = racePropertyValueSetHasHeader;
} else {
this.racePropertyValueSetHasHeader = false;
}
}
public String getRacePropertyValueSetDelimiter() {
return Character.toString(racePropertyValueSetDelimiter);
}
@BackendProperty
public void setRacePropertyValueSetDelimiter(String racePropertyValueSetDelimiter) {
if (racePropertyValueSetDelimiter != null) {
if (racePropertyValueSetDelimiter.length() > 1) {
throw new IllegalArgumentException("delimiter can only be one character");
}
if (racePropertyValueSetDelimiter.length() < 1) {
throw new IllegalArgumentException("delimiter must be at least one character");
}
}
if (racePropertyValueSetDelimiter != null) {
this.racePropertyValueSetDelimiter = racePropertyValueSetDelimiter.charAt(0);
} else {
this.racePropertyValueSetDelimiter = DEFAULT_DELIMITER;
}
}
public Integer getRacePropertyValueSetIdColumn() {
return racePropertyValueSetIdColumn;
}
@BackendProperty
public void setRacePropertyValueSetIdColumn(Integer racePropertyValueSetIdColumn) {
if (racePropertyValueSetIdColumn == null) {
throw new IllegalArgumentException("racePropertyValueSetIdColumn cannot be null");
}
this.racePropertyValueSetIdColumn = racePropertyValueSetIdColumn;
}
public Integer getRacePropertyValueSetDisplayNameColumn() {
return racePropertyValueSetDisplayNameColumn;
}
@BackendProperty
public void setRacePropertyValueSetDisplayNameColumn(Integer racePropertyValueSetDisplayNameColumn) {
this.racePropertyValueSetDisplayNameColumn = racePropertyValueSetDisplayNameColumn;
}
public Integer getRacePropertyValueSetDescriptionColumn() {
return racePropertyValueSetDescriptionColumn;
}
@BackendProperty
public void setRacePropertyValueSetDescriptionColumn(Integer racePropertyValueSetDescriptionColumn) {
this.racePropertyValueSetDescriptionColumn = racePropertyValueSetDescriptionColumn;
}
public String getRacePropertySource() {
return racePropertySource;
}
@BackendProperty
public void setRacePropertySource(String racePropertySource) {
this.racePropertySource = racePropertySource;
}
public String getLanguagePropertyName() {
return languagePropertyName;
}
@BackendProperty
public void setLanguagePropertyName(String languagePropertyName) {
this.languagePropertyName = languagePropertyName;
}
public ValueSet getLanguagePropertyValueSet() {
return languagePropertyValueSet;
}
public void setLanguagePropertyValueSet(ValueSet languagePropertyValueSet) {
this.languagePropertyValueSet = languagePropertyValueSet;
}
@BackendProperty(propertyName = "languagePropertyValueSet")
public void parseLanguagePropertyValueSet(String valueSetStr) {
this.languagePropertyValueSet = parseValueSet(this.patientDetailsPropositionId, valueSetStr);
}
public String getLanguagePropertyValueSetFile() {
return languagePropertyValueSetFile;
}
@BackendProperty
public void setLanguagePropertyValueSetFile(String languagePropertyValueSetFile) {
this.languagePropertyValueSetFile = languagePropertyValueSetFile;
}
public Boolean getLanguagePropertyValueSetHasHeader() {
return languagePropertyValueSetHasHeader;
}
@BackendProperty
public void setLanguagePropertyValueSetHasHeader(Boolean languagePropertyValueSetHasHeader) {
if (languagePropertyValueSetHasHeader != null) {
this.languagePropertyValueSetHasHeader = languagePropertyValueSetHasHeader;
} else {
this.languagePropertyValueSetHasHeader = false;
}
}
public String getLanguagePropertyValueSetDelimiter() {
return Character.toString(languagePropertyValueSetDelimiter);
}
@BackendProperty
public void setLanguagePropertyValueSetDelimiter(String languagePropertyValueSetDelimiter) {
if (languagePropertyValueSetDelimiter != null) {
if (languagePropertyValueSetDelimiter.length() > 1) {
throw new IllegalArgumentException("delimiter can only be one character");
}
if (languagePropertyValueSetDelimiter.length() < 1) {
throw new IllegalArgumentException("delimiter must be at least one character");
}
}
if (languagePropertyValueSetDelimiter != null) {
this.languagePropertyValueSetDelimiter = languagePropertyValueSetDelimiter.charAt(0);
} else {
this.languagePropertyValueSetDelimiter = DEFAULT_DELIMITER;
}
}
public Integer getLanguagePropertyValueSetIdColumn() {
return languagePropertyValueSetIdColumn;
}
@BackendProperty
public void setLanguagePropertyValueSetIdColumn(Integer languagePropertyValueSetIdColumn) {
if (languagePropertyValueSetIdColumn == null) {
throw new IllegalArgumentException("languagePropertyValueSetIdColumn cannot be null");
}
this.languagePropertyValueSetIdColumn = languagePropertyValueSetIdColumn;
}
public Integer getLanguagePropertyValueSetDisplayNameColumn() {
return languagePropertyValueSetDisplayNameColumn;
}
@BackendProperty
public void setLanguagePropertyValueSetDisplayNameColumn(Integer languagePropertyValueSetDisplayNameColumn) {
this.languagePropertyValueSetDisplayNameColumn = languagePropertyValueSetDisplayNameColumn;
}
public Integer getLanguagePropertyValueSetDescriptionColumn() {
return languagePropertyValueSetDescriptionColumn;
}
@BackendProperty
public void setLanguagePropertyValueSetDescriptionColumn(Integer languagePropertyValueSetDescriptionColumn) {
this.languagePropertyValueSetDescriptionColumn = languagePropertyValueSetDescriptionColumn;
}
public String getLanguagePropertySource() {
return languagePropertySource;
}
@BackendProperty
public void setLanguagePropertySource(String languagePropertySource) {
this.languagePropertySource = languagePropertySource;
}
public ValueSet getMaritalStatusPropertyValueSet() {
return maritalStatusPropertyValueSet;
}
public void setMaritalStatusPropertyValueSet(ValueSet maritalStatusPropertyValueSet) {
this.maritalStatusPropertyValueSet = maritalStatusPropertyValueSet;
}
@BackendProperty(propertyName = "maritalStatusPropertyValueSet")
public void parseMaritalStatusPropertyValueSet(String valueSetStr) {
this.maritalStatusPropertyValueSet = parseValueSet(this.patientDetailsPropositionId, valueSetStr);
}
public String getMaritalStatusPropertyValueSetFile() {
return maritalStatusPropertyValueSetFile;
}
@BackendProperty
public void setMaritalStatusPropertyValueSetFile(String maritalStatusPropertyValueSetFile) {
this.maritalStatusPropertyValueSetFile = maritalStatusPropertyValueSetFile;
}
public Boolean getMaritalStatusPropertyValueSetHasHeader() {
return maritalStatusPropertyValueSetHasHeader;
}
@BackendProperty
public void setMaritalStatusPropertyValueSetHasHeader(Boolean maritalStatusPropertyValueSetHasHeader) {
if (maritalStatusPropertyValueSetHasHeader != null) {
this.maritalStatusPropertyValueSetHasHeader = maritalStatusPropertyValueSetHasHeader;
} else {
this.maritalStatusPropertyValueSetHasHeader = false;
}
}
public String getMaritalStatusPropertyValueSetDelimiter() {
return Character.toString(maritalStatusPropertyValueSetDelimiter);
}
@BackendProperty
public void setMaritalStatusPropertyValueSetDelimiter(String maritalStatusPropertyValueSetDelimiter) {
if (maritalStatusPropertyValueSetDelimiter != null) {
if (maritalStatusPropertyValueSetDelimiter.length() > 1) {
throw new IllegalArgumentException("delimiter can only be one character");
}
if (maritalStatusPropertyValueSetDelimiter.length() < 1) {
throw new IllegalArgumentException("delimiter must be at least one character");
}
}
if (maritalStatusPropertyValueSetDelimiter != null) {
this.maritalStatusPropertyValueSetDelimiter = maritalStatusPropertyValueSetDelimiter.charAt(0);
} else {
this.maritalStatusPropertyValueSetDelimiter = DEFAULT_DELIMITER;
}
}
public Integer getMaritalStatusPropertyValueSetIdColumn() {
return maritalStatusPropertyValueSetIdColumn;
}
@BackendProperty
public void setMaritalStatusPropertyValueSetIdColumn(Integer maritalStatusPropertyValueSetIdColumn) {
if (maritalStatusPropertyValueSetIdColumn == null) {
throw new IllegalArgumentException("maritalStatusPropertyValueSetIdColumn cannot be null");
}
this.maritalStatusPropertyValueSetIdColumn = maritalStatusPropertyValueSetIdColumn;
}
public Integer getMaritalStatusPropertyValueSetDisplayNameColumn() {
return maritalStatusPropertyValueSetDisplayNameColumn;
}
@BackendProperty
public void setMaritalStatusPropertyValueSetDisplayNameColumn(Integer maritalStatusPropertyValueSetDisplayNameColumn) {
this.maritalStatusPropertyValueSetDisplayNameColumn = maritalStatusPropertyValueSetDisplayNameColumn;
}
public Integer getMaritalStatusPropertyValueSetDescriptionColumn() {
return maritalStatusPropertyValueSetDescriptionColumn;
}
@BackendProperty
public void setMaritalStatusPropertyValueSetDescriptionColumn(Integer maritalStatusPropertyValueSetDescriptionColumn) {
this.maritalStatusPropertyValueSetDescriptionColumn = maritalStatusPropertyValueSetDescriptionColumn;
}
public String getMaritalStatusPropertySource() {
return maritalStatusPropertySource;
}
@BackendProperty
public void setMaritalStatusPropertySource(String maritalStatusPropertySource) {
this.maritalStatusPropertySource = maritalStatusPropertySource;
}
public String getMaritalStatusPropertyName() {
return maritalStatusPropertyName;
}
@BackendProperty
public void setMaritalStatusPropertyName(String maritalStatusPropertyName) {
this.maritalStatusPropertyName = maritalStatusPropertyName;
}
public String getReligionPropertyName() {
return religionPropertyName;
}
@BackendProperty
public void setReligionPropertyName(String religionPropertyName) {
this.religionPropertyName = religionPropertyName;
}
public ValueSet getReligionPropertyValueSet() {
return religionPropertyValueSet;
}
public void setReligionPropertyValueSet(ValueSet religionPropertyValueSet) {
this.religionPropertyValueSet = religionPropertyValueSet;
}
@BackendProperty(propertyName = "religionPropertyValueSet")
public void parseReligionPropertyValueSet(String valueSetStr) {
this.religionPropertyValueSet = parseValueSet(this.patientDetailsPropositionId, valueSetStr);
}
public String getReligionPropertyValueSetFile() {
return religionPropertyValueSetFile;
}
@BackendProperty
public void setReligionPropertyValueSetFile(String religionPropertyValueSetFile) {
this.religionPropertyValueSetFile = religionPropertyValueSetFile;
}
public Boolean getReligionPropertyValueSetHasHeader() {
return religionPropertyValueSetHasHeader;
}
@BackendProperty
public void setReligionPropertyValueSetHasHeader(Boolean religionPropertyValueSetHasHeader) {
if (religionPropertyValueSetHasHeader != null) {
this.religionPropertyValueSetHasHeader = religionPropertyValueSetHasHeader;
} else {
this.religionPropertyValueSetHasHeader = false;
}
}
public String getReligionPropertyValueSetDelimiter() {
return Character.toString(religionPropertyValueSetDelimiter);
}
@BackendProperty
public void setReligionPropertyValueSetDelimiter(String religionPropertyValueSetDelimiter) {
if (religionPropertyValueSetDelimiter != null) {
if (religionPropertyValueSetDelimiter.length() > 1) {
throw new IllegalArgumentException("delimiter can only be one character");
}
if (religionPropertyValueSetDelimiter.length() < 1) {
throw new IllegalArgumentException("delimiter must be at least one character");
}
}
if (religionPropertyValueSetDelimiter != null) {
this.religionPropertyValueSetDelimiter = religionPropertyValueSetDelimiter.charAt(0);
} else {
this.religionPropertyValueSetDelimiter = DEFAULT_DELIMITER;
}
}
public Integer getReligionPropertyValueSetIdColumn() {
return religionPropertyValueSetIdColumn;
}
@BackendProperty
public void setReligionPropertyValueSetIdColumn(Integer religionPropertyValueSetIdColumn) {
if (religionPropertyValueSetIdColumn == null) {
throw new IllegalArgumentException("religionPropertyValueSetIdColumn cannot be null");
}
this.religionPropertyValueSetIdColumn = religionPropertyValueSetIdColumn;
}
public Integer getReligionPropertyValueSetDisplayNameColumn() {
return religionPropertyValueSetDisplayNameColumn;
}
@BackendProperty
public void setReligionPropertyValueSetDisplayNameColumn(Integer religionPropertyValueSetDisplayNameColumn) {
this.religionPropertyValueSetDisplayNameColumn = religionPropertyValueSetDisplayNameColumn;
}
public Integer getReligionPropertyValueSetDescriptionColumn() {
return religionPropertyValueSetDescriptionColumn;
}
@BackendProperty
public void setReligionPropertyValueSetDescriptionColumn(Integer religionPropertyValueSetDescriptionColumn) {
this.religionPropertyValueSetDescriptionColumn = religionPropertyValueSetDescriptionColumn;
}
public String getReligionPropertySource() {
return religionPropertySource;
}
@BackendProperty
public void setReligionPropertySource(String religionPropertySource) {
this.religionPropertySource = religionPropertySource;
}
public String getDateOfBirthPropertyName() {
return dateOfBirthPropertyName;
}
@BackendProperty
public void setDateOfBirthPropertyName(String dateOfBirthPropertyName) {
this.dateOfBirthPropertyName = dateOfBirthPropertyName;
}
public String getAgeInYearsPropertyName() {
return ageInYearsPropertyName;
}
@BackendProperty
public void setAgeInYearsPropertyName(String ageInYearsPropertyName) {
this.ageInYearsPropertyName = ageInYearsPropertyName;
}
public String getDateOfDeathPropertyName() {
return dateOfDeathPropertyName;
}
@BackendProperty
public void setDateOfDeathPropertyName(String dateOfDeathPropertyName) {
this.dateOfDeathPropertyName = dateOfDeathPropertyName;
}
public String getVitalStatusPropertyName() {
return vitalStatusPropertyName;
}
@BackendProperty
public void setVitalStatusPropertyName(String vitalStatusPropertyName) {
this.vitalStatusPropertyName = vitalStatusPropertyName;
}
@Override
public PropositionDefinition readPropositionDefinition(String id) throws KnowledgeSourceReadException {
if (LOGGER.isLoggable(Level.FINEST)) {
LOGGER.log(Level.FINEST, "Looking for proposition {0}", id);
}
if (id != null) {
PropositionDefinition result;
if (id.equals(this.patientDetailsPropositionId)) {
result = newPatientDetailsPropositionDefinition();
} else if (id.equals(this.patientPropositionId)) {
result = newPatientPropositionDefinition();
} else if (id.equals(this.visitPropositionId)) {
result = newVisitPropositionDefinition();
} else if (id.equals(this.providerPropositionId)) {
result = newProviderPropositionDefinition();
} else if (id.equals(this.patientAliasPropositionId)) {
result = newPatientAliasPropositionDefinition();
} else {
result = readPropDef(id);
}
if (result != null) {
LOGGER.log(Level.FINEST, "Found proposition id: {0}", id);
return result;
}
LOGGER.log(Level.FINER, "Failed to find proposition id: {0}", id);
}
return null;
}
@Override
public List readPropositionDefinitions(String[] ids) throws KnowledgeSourceReadException {
List results = new ArrayList<>();
if (ids != null) {
List propIdsToFind = readHardCodedPropDefs(ids, results);
results.addAll(readPropDefs(propIdsToFind));
}
return results;
}
private List readHardCodedPropDefs(String[] ids, List results) throws KnowledgeSourceReadException {
List propIdsToFind = new ArrayList<>();
for (String id : ids) {
if (id.equals(this.patientDetailsPropositionId)) {
results.add(newPatientDetailsPropositionDefinition());
} else if (id.equals(this.patientPropositionId)) {
results.add(newPatientPropositionDefinition());
} else if (id.equals(this.visitPropositionId)) {
results.add(newVisitPropositionDefinition());
} else if (id.equals(this.providerPropositionId)) {
results.add(newProviderPropositionDefinition());
} else if (id.equals(this.patientAliasPropositionId)) {
results.add(newPatientAliasPropositionDefinition());
} else {
propIdsToFind.add(id);
}
}
return propIdsToFind;
}
@Override
public String[] readIsA(String propId) throws KnowledgeSourceReadException {
Set parents = this.levelReader.readParentsFromDatabase(propId);
return parents.toArray(new String[parents.size()]);
}
private final QueryConstructor SEARCH_QUERY_CONSTRUCTOR = new QueryConstructor() {
@Override
public void appendStatement(StringBuilder sql, String table) {
sql.append("SELECT ").append(querySupport.getEurekaIdColumn()).append(" FROM ");
sql.append(table);
sql.append(" WHERE UPPER(C_NAME) LIKE UPPER(?) AND C_BASECODE IS NOT NULL");
}
};
private static final ResultSetReader> SEARCH_RESULT_SET_READER = new ResultSetReader>() {
@Override
public Set read(ResultSet rs) throws KnowledgeSourceReadException {
try {
Set result = new HashSet<>();
if (rs != null) {
while (rs.next()) {
result.add(rs.getString(1));
}
}
return result;
} catch (SQLException ex) {
throw new KnowledgeSourceReadException(ex);
}
}
};
@Override
public Set getKnowledgeSourceSearchResults(String searchKey) throws KnowledgeSourceReadException {
try (ConnectionSpecQueryExecutor queryExecutor = this.querySupport.getQueryExecutorInstance(SEARCH_QUERY_CONSTRUCTOR)) {
return queryExecutor.execute(
"%" + I2B2Util.escapeLike(searchKey) + "%",
SEARCH_RESULT_SET_READER
);
}
}
@Override
public void initialize(BackendInstanceSpec config) throws BackendInitializationException {
super.initialize(config);
this.valueMetadataSupport = new ValueMetadataSupport();
}
private ConstantDefinition newProviderPropositionDefinition() {
Date now = new Date();
ConstantDefinition providerDim = new ConstantDefinition(this.providerPropositionId);
providerDim.setDisplayName(this.providerPropositionId);
providerDim.setAccessed(now);
providerDim.setCreated(DIMENSION_PROP_DEFS_CREATED_DATE);
providerDim.setSourceId(this.sourceIdFactory.getInstance());
providerDim.setInDataSource(true);
providerDim.setPropertyDefinitions(
new PropertyDefinition(this.providerPropositionId, this.providerNamePropertyName, null, ValueType.NOMINALVALUE, null, this.providerPropositionId));
return providerDim;
}
private static class Root {
private final String tableCode;
private final String symbol;
private final String displayName;
Root(String tableCode, String displayName, String symbol) {
assert tableCode != null : "fullName cannot be null";
assert displayName != null : "displayName cannot be null";
assert symbol != null : "symbol cannot be null";
this.tableCode = tableCode;
this.displayName = displayName;
this.symbol = symbol;
}
public String getTableCode() {
return tableCode;
}
public String getDisplayName() {
return displayName;
}
public String getSymbol() {
return symbol;
}
}
private final QueryConstructor ROOT_QUERY_CONSTRUCTOR = new QueryConstructor() {
@Override
public void appendStatement(StringBuilder sql, String table) {
sql.append("SELECT A2.C_TABLE_CD, A1.C_NAME, A1.").append(querySupport.getEurekaIdColumn()).append(" FROM ");
sql.append(table);
sql.append(" A1 JOIN TABLE_ACCESS A2 ON (A1.C_FULLNAME=A2.C_FULLNAME) WHERE A2.C_TABLE_NAME='");
sql.append(table);
sql.append("'");
}
};
private static final ResultSetReader> ROOT_RESULT_SET_READER = new ResultSetReader>() {
@Override
public List read(ResultSet rs) throws KnowledgeSourceReadException {
List result = new ArrayList<>();
if (rs != null) {
try {
while (rs.next()) {
result.add(new Root(rs.getString(1), rs.getString(2), rs.getString(3)));
}
} catch (SQLException ex) {
throw new KnowledgeSourceReadException(ex);
}
}
return result;
}
};
private EventDefinition newVisitPropositionDefinition() throws KnowledgeSourceReadException {
Date now = new Date();
EventDefinition visitDim = new EventDefinition(this.visitPropositionId);
visitDim.setDisplayName(this.visitPropositionId);
visitDim.setAccessed(now);
visitDim.setCreated(DIMENSION_PROP_DEFS_CREATED_DATE);
visitDim.setSourceId(this.sourceIdFactory.getInstance());
visitDim.setInDataSource(true);
List visitDimPropertyDefs = new ArrayList<>();
visitDimPropertyDefs.add(new PropertyDefinition(this.visitPropositionId, this.visitAgePropertyName, null, ValueType.NUMERICALVALUE, null, this.visitPropositionId,
new Attribute[]{
new Attribute(DeidAttributes.IS_HIPAA_IDENTIFIER, BooleanValue.TRUE),
new Attribute(DeidAttributes.HIPAA_IDENTIFIER_TYPE, DeidAttributes.AGE)
}));
visitDimPropertyDefs.add(new PropertyDefinition(this.visitPropositionId, this.inoutPropertyName, null, ValueType.NOMINALVALUE, this.inoutPropertyValueSet.getId(), this.visitPropositionId));
visitDimPropertyDefs.add(new PropertyDefinition(this.visitPropositionId, this.visitIdPropertyName, null, ValueType.NOMINALVALUE, null, this.visitPropositionId,
new Attribute[]{
new Attribute(DeidAttributes.IS_HIPAA_IDENTIFIER, BooleanValue.TRUE),
new Attribute(DeidAttributes.HIPAA_IDENTIFIER_TYPE, DeidAttributes.OTHER)
}));
visitDim.setPropertyDefinitions(visitDimPropertyDefs.toArray(new PropertyDefinition[visitDimPropertyDefs.size()]));
List refDefs = new ArrayList<>();
refDefs.add(new ReferenceDefinition("provider", "Provider", new String[]{this.providerPropositionId}));
refDefs.add(new ReferenceDefinition("patientDetails", "Patient Details", new String[]{this.patientDetailsPropositionId}));
try (ConnectionSpecQueryExecutor queryExecutor = this.querySupport.getQueryExecutorInstance(ROOT_QUERY_CONSTRUCTOR)) {
for (Root root : queryExecutor.execute(ROOT_RESULT_SET_READER)) {
refDefs.add(new ReferenceDefinition(root.getTableCode(), root.getDisplayName(), new String[]{root.getSymbol()}));
}
}
visitDim.setReferenceDefinitions(refDefs.toArray(new ReferenceDefinition[refDefs.size()]));
return visitDim;
}
private ConstantDefinition newPatientPropositionDefinition() {
Date now = new Date();
ConstantDefinition patientDim = new ConstantDefinition(this.patientPropositionId);
patientDim.setAccessed(now);
patientDim.setSourceId(this.sourceIdFactory.getInstance());
patientDim.setCreated(DIMENSION_PROP_DEFS_CREATED_DATE);
patientDim.setDisplayName(this.patientDisplayName);
patientDim.setInDataSource(true);
patientDim.setPropertyDefinitions(
new PropertyDefinition(this.patientPropositionId, this.patientPatientIdPropertyName, null, ValueType.NOMINALVALUE, null, this.patientPropositionId)
);
patientDim.setReferenceDefinitions(
new ReferenceDefinition("patientDetails", "Patient Details", new String[]{this.patientDetailsPropositionId}),
new ReferenceDefinition("patientAliases", "Patient Aliases", new String[]{this.patientAliasPropositionId})
);
return patientDim;
}
private ConstantDefinition newPatientAliasPropositionDefinition() {
Date now = new Date();
ConstantDefinition patientDim = new ConstantDefinition(this.patientAliasPropositionId);
patientDim.setAccessed(now);
patientDim.setSourceId(this.sourceIdFactory.getInstance());
patientDim.setCreated(DIMENSION_PROP_DEFS_CREATED_DATE);
patientDim.setDisplayName(this.patientAliasDisplayName);
patientDim.setInDataSource(true);
patientDim.setPropertyDefinitions(
new PropertyDefinition(this.patientAliasPropositionId, this.patientAliasPatientIdPropertyName, null, ValueType.NOMINALVALUE, null, this.patientAliasPropositionId,
new Attribute[]{
new Attribute(DeidAttributes.IS_HIPAA_IDENTIFIER, BooleanValue.TRUE),
new Attribute(DeidAttributes.HIPAA_IDENTIFIER_TYPE, DeidAttributes.MRN)
}),
new PropertyDefinition(this.patientAliasPropositionId, this.patientAliasFieldNamePropertyName, null, ValueType.NOMINALVALUE, null, this.patientAliasPropositionId)
);
return patientDim;
}
private ConstantDefinition newPatientDetailsPropositionDefinition() {
Date now = new Date();
ConstantDefinition patientDim = new ConstantDefinition(this.patientDetailsPropositionId);
patientDim.setAccessed(now);
patientDim.setSourceId(this.sourceIdFactory.getInstance());
patientDim.setCreated(DIMENSION_PROP_DEFS_CREATED_DATE);
patientDim.setDisplayName(this.patientDetailsDisplayName);
patientDim.setInDataSource(true);
patientDim.setPropertyDefinitions(
new PropertyDefinition(this.patientDetailsPropositionId, this.ageInYearsPropertyName, null, ValueType.NUMERICALVALUE, null, this.patientDetailsPropositionId,
new Attribute[]{
new Attribute(DeidAttributes.IS_HIPAA_IDENTIFIER, BooleanValue.TRUE),
new Attribute(DeidAttributes.HIPAA_IDENTIFIER_TYPE, DeidAttributes.AGE)
}),
new PropertyDefinition(this.patientDetailsPropositionId, this.dateOfBirthPropertyName, null, ValueType.DATEVALUE, null, this.patientDetailsPropositionId,
new Attribute[]{
new Attribute(DeidAttributes.IS_HIPAA_IDENTIFIER, BooleanValue.TRUE),
new Attribute(DeidAttributes.HIPAA_IDENTIFIER_TYPE, DeidAttributes.BIRTHDATE)
}),
new PropertyDefinition(this.patientDetailsPropositionId, this.dateOfDeathPropertyName, null, ValueType.DATEVALUE, null, this.patientDetailsPropositionId,
new Attribute[]{
new Attribute(DeidAttributes.IS_HIPAA_IDENTIFIER, BooleanValue.TRUE),
new Attribute(DeidAttributes.HIPAA_IDENTIFIER_TYPE, DeidAttributes.BIRTHDATE)
}),
new PropertyDefinition(this.patientDetailsPropositionId, this.genderPropertyName, null, ValueType.NOMINALVALUE, this.genderPropertyValueSet.getId(), this.patientDetailsPropositionId),
new PropertyDefinition(this.patientDetailsPropositionId, this.languagePropertyName, null, ValueType.NOMINALVALUE, this.languagePropertyValueSet.getId(), this.patientDetailsPropositionId),
new PropertyDefinition(this.patientDetailsPropositionId, this.maritalStatusPropertyName, null, ValueType.NOMINALVALUE, this.maritalStatusPropertyValueSet.getId(), this.patientDetailsPropositionId),
new PropertyDefinition(this.patientDetailsPropositionId, this.racePropertyName, null, ValueType.NOMINALVALUE, this.racePropertyValueSet.getId(), this.patientDetailsPropositionId),
new PropertyDefinition(this.patientDetailsPropositionId, this.vitalStatusPropertyName, null, ValueType.BOOLEANVALUE, null, this.patientDetailsPropositionId),
new PropertyDefinition(this.patientDetailsPropositionId, this.patientDetailsPatientIdPropertyName, null, ValueType.NOMINALVALUE, null, this.patientDetailsPropositionId,
new Attribute[]{
new Attribute(DeidAttributes.IS_HIPAA_IDENTIFIER, BooleanValue.TRUE),
new Attribute(DeidAttributes.HIPAA_IDENTIFIER_TYPE, DeidAttributes.MRN)
}
)
);
patientDim.setReferenceDefinitions(
new ReferenceDefinition("encounters", "Encounters", new String[]{this.visitPropositionId})
);
return patientDim;
}
@Override
public AbstractionDefinition readAbstractionDefinition(String id) throws KnowledgeSourceReadException {
return null;
}
@Override
public List readAbstractionDefinitions(String[] ids) throws KnowledgeSourceReadException {
return java.util.Collections.emptyList();
}
@Override
public ContextDefinition readContextDefinition(String id) throws KnowledgeSourceReadException {
return null;
}
@Override
public List readContextDefinitions(String[] toArray) throws KnowledgeSourceReadException {
return java.util.Collections.emptyList();
}
@Override
public TemporalPropositionDefinition readTemporalPropositionDefinition(String id) throws KnowledgeSourceReadException {
if (LOGGER.isLoggable(Level.FINEST)) {
LOGGER.log(Level.FINEST, "Looking for proposition {0}", id);
}
if (id != null) {
TemporalPropositionDefinition result;
if (id.equals(this.visitPropositionId)) {
result = newVisitPropositionDefinition();
} else {
result = readPropDef(id);
}
if (result != null) {
LOGGER.log(Level.FINEST, "Found proposition id: {0}", id);
return result;
}
LOGGER.log(Level.FINER, "Failed to find proposition id: {0}", id);
}
return null;
}
@Override
public List readTemporalPropositionDefinitions(String[] ids) throws KnowledgeSourceReadException {
List results = new ArrayList<>();
if (ids != null) {
List propIdsToFind = readHardCodedTempPropDefs(ids, results);
results.addAll(readPropDefs(propIdsToFind));
}
return results;
}
private List readHardCodedTempPropDefs(String[] ids, List results) throws KnowledgeSourceReadException {
List propIdsToFind = new ArrayList<>();
for (String id : ids) {
if (id.equals(this.visitPropositionId)) {
results.add(newVisitPropositionDefinition());
} else {
propIdsToFind.add(id);
}
}
return propIdsToFind;
}
@Override
public String[] readAbstractedInto(String propId) throws KnowledgeSourceReadException {
return ArrayUtils.EMPTY_STRING_ARRAY;
}
@Override
public String[] readInduces(String propId) throws KnowledgeSourceReadException {
return ArrayUtils.EMPTY_STRING_ARRAY;
}
@Override
public String[] readSubContextOfs(String propId) throws KnowledgeSourceReadException {
return ArrayUtils.EMPTY_STRING_ARRAY;
}
@Override
public void close() {
super.close();
synchronized (this.modInterpCachedSyncVariable) {
this.modInterpCached = null;
}
}
private final QueryConstructor READ_ONE_PROPERTY_DEF_QUERY_CONSTRUCTOR = new QueryConstructor() {
@Override
public void appendStatement(StringBuilder sql, String table) {
sql.append("SELECT ").append(querySupport.getEurekaIdColumn()).append(", C_METADATAXML FROM ");
sql.append(table);
sql.append(" WHERE ").append(querySupport.getEurekaIdColumn()).append(" = ? AND C_SYNONYM_CD='N' AND M_APPLIED_PATH<>'@' AND C_BASECODE IS NOT NULL");
}
};
@Override
public ValueSet readValueSet(final String id) throws KnowledgeSourceReadException {
ValueSet result = this.valueSets.get(id);
if (result != null) {
return result;
}
try (Connection connection = this.querySupport.getConnection()) {
final ValueSetSupport vsSupport = new ValueSetSupport();
vsSupport.parseId(id);
if (!vsSupport.isValid()) {
return null;
}
try (QueryExecutor queryExecutor = this.querySupport.getQueryExecutorInstance(connection, READ_ONE_PROPERTY_DEF_QUERY_CONSTRUCTOR)) {
return queryExecutor.execute(vsSupport.getPropertyName(),
new ResultSetReader() {
@Override
public ValueSet read(ResultSet rs) throws KnowledgeSourceReadException {
try {
if (rs != null && rs.next()) {
Clob clob = rs.getClob(2);
if (clob != null) {
CMetadataXmlParser valueMetadataParser = new CMetadataXmlParser();
valueMetadataParser.setDeclaringPropId(vsSupport.getDeclaringPropId());
valueMetadataParser.setConceptBaseCode(vsSupport.getPropertyName());
XMLReader xmlReader = valueMetadataSupport.init(valueMetadataParser);
valueMetadataSupport.parseAndFreeClob(xmlReader, clob);
SAXParseException exception = valueMetadataParser.getException();
if (exception != null) {
throw exception;
}
return valueMetadataParser.getValueSet();
}
}
Map> modInterp = readModInterp(connection);
Map get = modInterp.get(vsSupport.getDeclaringPropId());
if (get != null && !get.isEmpty()) {
ValueSetElement[] elts = new ValueSetElement[get.size()];
int i = 0;
for (Map.Entry me : get.entrySet()) {
elts[i++] = new ValueSetElement(NominalValue.getInstance(me.getKey()), me.getKey());
}
return new ValueSet(id, null, elts, null);
}
return null;
} catch (SQLException | SAXParseException ex) {
throw new KnowledgeSourceReadException(ex);
}
}
}
);
}
} catch (InvalidConnectionSpecArguments | SQLException ex) {
throw new KnowledgeSourceReadException(ex);
}
}
private static final ResultSetReader> IN_DS_RESULT_SET_READER = new ResultSetReader>() {
@Override
public Collection read(ResultSet rs) throws KnowledgeSourceReadException {
List result = new ArrayList<>();
try {
if (rs != null) {
while (rs.next()) {
result.add(rs.getString(1));
}
}
} catch (SQLException ex) {
throw new KnowledgeSourceReadException(ex);
}
return result;
}
};
private final QueryConstructor IDS_PROPID_QC = new QueryConstructor() {
@Override
public void appendStatement(StringBuilder sql, String table) {
sql.append("SELECT DISTINCT A2.").append(querySupport.getEurekaIdColumn()).append(" FROM ");
sql.append(table);
sql.append(" A1 JOIN ");
sql.append(table);
sql.append(" A2 ON (A2.C_FULLNAME LIKE A1.C_FULLNAME || '%') WHERE A1.").append(querySupport.getEurekaIdColumn()).append(" = ? AND A1.C_SYNONYM_CD='N' AND A2.C_BASECODE IS NOT NULL");
}
};
private final QueryConstructor N_PROPID_QC = new QueryConstructor() {
@Override
public void appendStatement(StringBuilder sql, String table) {
sql.append("SELECT DISTINCT A2.").append(querySupport.getEurekaIdColumn()).append(" FROM ");
sql.append(table);
sql.append(" A1 JOIN ");
sql.append(table);
sql.append(" A2 ON (A2.C_FULLNAME LIKE A1.C_FULLNAME || '%') WHERE A1.").append(querySupport.getEurekaIdColumn()).append(" = ? AND A1.C_SYNONYM_CD='N'");
}
};
@Override
public Collection collectPropIdDescendantsUsingAllNarrower(boolean inDataSourceOnly, final String[] propIds) throws KnowledgeSourceReadException {
final Set result = new HashSet<>();
if (propIds != null && propIds.length > 0) {
try (ConnectionSpecQueryExecutor queryExecutor = this.querySupport.getQueryExecutorInstance(inDataSourceOnly ? IDS_PROPID_QC : N_PROPID_QC)) {
queryExecutor.prepare();
for (String propId : filterPropId(propIds, result)) {
result.addAll(queryExecutor.execute(
propId,
IN_DS_RESULT_SET_READER));
}
}
}
return result;
}
private Set filterPropId(String[] propIds, final Collection result) {
Set propIdsAsSet = Arrays.asSet(propIds);
for (Iterator itr = propIdsAsSet.iterator(); itr.hasNext();) {
String propId = itr.next();
if (patientPropositionId.equals(propId)) {
result.add(propId);
itr.remove();
} else if (patientDetailsPropositionId.equals(propId)) {
result.add(propId);
itr.remove();
} else if (visitPropositionId.equals(propId)) {
result.add(propId);
itr.remove();
} else if (providerPropositionId.equals(propId)) {
result.add(propId);
itr.remove();
}
}
return propIdsAsSet;
}
private Set filterPropDef(String[] propIds, final List result) throws KnowledgeSourceReadException {
Set propIdsAsSet = Arrays.asSet(propIds);
for (Iterator itr = propIdsAsSet.iterator(); itr.hasNext();) {
String propId = itr.next();
if (patientDetailsPropositionId.equals(propId)) {
result.add(newPatientDetailsPropositionDefinition());
itr.remove();
} else if (patientPropositionId.equals(propId)) {
result.add(newPatientPropositionDefinition());
itr.remove();
} else if (visitPropositionId.equals(propId)) {
result.add(newVisitPropositionDefinition());
itr.remove();
} else if (providerPropositionId.equals(propId)) {
result.add(newProviderPropositionDefinition());
itr.remove();
} else if (patientAliasPropositionId.equals(propId)) {
result.add(newPatientAliasPropositionDefinition());
}
}
return propIdsAsSet;
}
private final QueryConstructor COLLECT_SUBTREE_PROPID_QC = new QueryConstructor() {
@Override
public void appendStatement(StringBuilder sql, String table) {
sql.append("SELECT DISTINCT A1.").append(querySupport.getEurekaIdColumn()).append(" FROM ");
sql.append(table);
sql.append(" A1 WHERE A1.C_FULLNAME LIKE (SELECT A2.C_FULLNAME || '%' FROM ");
sql.append(table);
sql.append(" A2 WHERE A2.").append(querySupport.getEurekaIdColumn()).append(" = ? AND A2.C_SYNONYM_CD='N' AND ROWNUM=1)");
}
};
@Override
public Collection collectPropIdDescendantsUsingInverseIsA(final String[] propIds) throws KnowledgeSourceReadException {
final Set result = new HashSet<>();
if (propIds != null && propIds.length > 0) {
try (ConnectionSpecQueryExecutor queryExecutor = this.querySupport.getQueryExecutorInstance(COLLECT_SUBTREE_PROPID_QC)) {
queryExecutor.prepare();
for (String propId : filterPropId(propIds, result)) {
result.addAll(queryExecutor.execute(
propId,
IN_DS_RESULT_SET_READER));
}
}
}
return result;
}
private final QueryConstructor IDS_PROPDEF_QC_ROWNUM = new QueryConstructor() {
@Override
public void appendStatement(StringBuilder sql, String table) {
sql.append("SELECT C_NAME, C_FULLNAME, VALUETYPE_CD, C_COMMENT, C_METADATAXML, CASE WHEN C_BASECODE IS NOT NULL THEN 1 ELSE 0 END, ").append(querySupport.getEurekaIdColumn()).append(", IMPORT_DATE, UPDATE_DATE, DOWNLOAD_DATE FROM ");
sql.append(table);
sql.append(" WHERE C_FULLNAME LIKE (SELECT C_FULLNAME || '%' FROM ");
sql.append(table);
sql.append(" WHERE ").append(querySupport.getEurekaIdColumn()).append(" = ? AND C_SYNONYM_CD='N' AND C_BASECODE IS NOT NULL AND ROWNUM=1)");
}
};
private final QueryConstructor IDS_PROPDEF_QC_POSTGRESQL = new QueryConstructor() {
@Override
public void appendStatement(StringBuilder sql, String table) {
sql.append("SELECT C_NAME, C_FULLNAME, VALUETYPE_CD, C_COMMENT, C_METADATAXML, CASE WHEN C_BASECODE IS NOT NULL THEN 1 ELSE 0 END, ").append(querySupport.getEurekaIdColumn()).append(", IMPORT_DATE, UPDATE_DATE, DOWNLOAD_DATE FROM ");
sql.append(table);
sql.append(" WHERE C_FULLNAME LIKE (SELECT C_FULLNAME || '%' FROM ");
sql.append(table);
sql.append(" WHERE ").append(querySupport.getEurekaIdColumn()).append(" = ? AND C_SYNONYM_CD='N' AND C_BASECODE IS NOT NULL LIMIT 1) ESCAPE ''");
}
};
private final QueryConstructor N_PROPDEF_QC_ROWNUM = new QueryConstructor() {
@Override
public void appendStatement(StringBuilder sql, String table) {
sql.append("SELECT C_NAME, C_FULLNAME, VALUETYPE_CD, C_COMMENT, C_METADATAXML, CASE WHEN C_BASECODE IS NOT NULL THEN 1 ELSE 0 END, ").append(querySupport.getEurekaIdColumn()).append(", IMPORT_DATE, UPDATE_DATE, DOWNLOAD_DATE FROM ");
sql.append(table);
sql.append(" WHERE C_FULLNAME LIKE (SELECT C_FULLNAME || '%' FROM ");
sql.append(table);
sql.append(" WHERE ").append(querySupport.getEurekaIdColumn()).append(" = ? AND C_SYNONYM_CD='N' AND ROWNUM=1)");
}
};
private final QueryConstructor N_PROPDEF_QC_POSTGRESQL = new QueryConstructor() {
@Override
public void appendStatement(StringBuilder sql, String table) {
sql.append("SELECT C_NAME, C_FULLNAME, VALUETYPE_CD, C_COMMENT, C_METADATAXML, CASE WHEN C_BASECODE IS NOT NULL THEN 1 ELSE 0 END, ").append(querySupport.getEurekaIdColumn()).append(", IMPORT_DATE, UPDATE_DATE, DOWNLOAD_DATE FROM ");
sql.append(table);
sql.append(" WHERE C_FULLNAME LIKE (SELECT C_FULLNAME || '%' FROM ");
sql.append(table);
sql.append(" WHERE ").append(querySupport.getEurekaIdColumn()).append(" = ? AND C_SYNONYM_CD='N' LIMIT 1) ESCAPE ''");
}
};
@Override
public Collection collectPropDefDescendantsUsingAllNarrower(boolean inDataSourceOnly, final String[] propIds) throws KnowledgeSourceReadException {
DatabaseProduct databaseProduct = this.querySupport.getDatabaseProduct();
switch (databaseProduct) {
case POSTGRESQL:
return collectPropDefDescendantsCommon(propIds, inDataSourceOnly ? IDS_PROPDEF_QC_POSTGRESQL : N_PROPDEF_QC_POSTGRESQL);
default:
return collectPropDefDescendantsCommon(propIds, inDataSourceOnly ? IDS_PROPDEF_QC_ROWNUM : N_PROPDEF_QC_ROWNUM);
}
}
private final QueryConstructor COLLECT_SUBTREE_PROPDEF_QC_ROWNUM = new QueryConstructor() {
@Override
public void appendStatement(StringBuilder sql, String table) {
sql.append("SELECT A1.C_NAME, A1.C_FULLNAME, A1.VALUETYPE_CD, A1.C_COMMENT, A1.C_METADATAXML, CASE WHEN A1.C_BASECODE IS NOT NULL THEN 1 ELSE 0 END, A1.").append(querySupport.getEurekaIdColumn()).append(", A1.IMPORT_DATE, A1.UPDATE_DATE, A1.DOWNLOAD_DATE FROM ");
sql.append(table);
sql.append(" A1 WHERE A1.C_FULLNAME LIKE (SELECT A2.C_FULLNAME || '%' FROM ");
sql.append(table);
sql.append(" A2 WHERE A2.").append(querySupport.getEurekaIdColumn()).append(" = ? AND A2.C_SYNONYM_CD='N' AND ROWNUM=1)");
}
};
private final QueryConstructor COLLECT_SUBTREE_PROPDEF_QC_POSTGRESQL = new QueryConstructor() {
@Override
public void appendStatement(StringBuilder sql, String table) {
sql.append("SELECT A1.C_NAME, A1.C_FULLNAME, A1.VALUETYPE_CD, A1.C_COMMENT, A1.C_METADATAXML, CASE WHEN A1.C_BASECODE IS NOT NULL THEN 1 ELSE 0 END, A1.").append(querySupport.getEurekaIdColumn()).append(", A1.IMPORT_DATE, A1.UPDATE_DATE, A1.DOWNLOAD_DATE FROM ");
sql.append(table);
sql.append(" A1 WHERE A1.C_FULLNAME LIKE (SELECT A2.C_FULLNAME || '%' FROM ");
sql.append(table);
sql.append(" A2 WHERE A2.").append(querySupport.getEurekaIdColumn()).append(" = ? AND A2.C_SYNONYM_CD='N' LIMIT 1) ESCAPE ''");
}
};
@Override
public Collection collectPropDefDescendantsUsingInverseIsA(final String[] propIds) throws KnowledgeSourceReadException {
DatabaseProduct databaseProduct = this.querySupport.getDatabaseProduct();
switch (databaseProduct) {
case POSTGRESQL:
return collectPropDefDescendantsCommon(propIds, COLLECT_SUBTREE_PROPDEF_QC_POSTGRESQL);
default:
return collectPropDefDescendantsCommon(propIds, COLLECT_SUBTREE_PROPDEF_QC_ROWNUM);
}
}
private List collectPropDefDescendantsCommon(final String[] propIds, QueryConstructor queryConstructor) throws KnowledgeSourceReadException {
List result = new ArrayList<>();
if (propIds != null && propIds.length > 0) {
try (ConnectionSpecQueryExecutor queryExecutor = this.querySupport.getQueryExecutorInstance(queryConstructor)) {
queryExecutor.prepare();
ListResultSetReader reader = new ListResultSetReader();
for (String propId : filterPropDef(propIds, result)) {
result.addAll(queryExecutor.execute(propId, reader));
}
}
}
final Map resultMap = new HashMap<>();
for (PropositionDefinition propDef : result) {
resultMap.put(propDef.getId(), propDef);
}
Map> children = this.levelReader.readChildrenFromDatabase(resultMap.keySet());
for (Map.Entry> me : children.entrySet()) {
PropositionDefinition pd = resultMap.get(me.getKey());
Set value = me.getValue();
if (value != null && pd != null) {
((AbstractPropositionDefinition) pd).setInverseIsA(value.toArray(new String[value.size()]));
}
}
Map> partials;
try (Connection connection = this.querySupport.getConnection()) {
try {
try (UniqueIdTempTableHandler childTempTableHandler = new UniqueIdTempTableHandler(this.querySupport.getDatabaseProduct(), connection, false)) {
for (String child : resultMap.keySet()) {
childTempTableHandler.insert(child);
}
}
partials = new HashMap<>();
/*
* Getting temp space full errors with one query, so split it into one query per metadata table.
*/
for (String table : this.querySupport.getTableAccessReader().read(connection)) {
DatabaseProduct databaseProduct = this.querySupport.getDatabaseProduct();
try (QueryExecutor queryExecutor = this.querySupport.getQueryExecutorInstance(connection, databaseProduct == DatabaseProduct.ORACLE ? READ_ALL_PROPERTIES_CONSTRUCTOR_ORCL : READ_ALL_PROPERTIES_CONSTRUCTOR, table)) {
partials.putAll(queryExecutor.execute(ALL_PROPERTIES_RSR));
}
}
connection.commit();
} catch (SQLException ex) {
connection.rollback();
throw ex;
}
} catch (InvalidConnectionSpecArguments | SQLException ex) {
throw new KnowledgeSourceReadException(ex);
}
for (Map.Entry> me : partials.entrySet()) {
PropositionDefinition pd = resultMap.get(me.getKey());
if (pd != null) {
List value = me.getValue();
if (value != null) {
((AbstractPropositionDefinition) pd).setPropertyDefinitions(value.toArray(new PropertyDefinition[value.size()]));
}
}
}
return result;
}
private final QueryConstructor READ_ALL_PROPERTIES_CONSTRUCTOR = new QueryConstructor() {
@Override
public void appendStatement(StringBuilder sql, String table) {
sql.append("SELECT A1.C_NAME, A1.VALUETYPE_CD, A1.").append(querySupport.getEurekaIdColumn()).append(", A3.").append(querySupport.getEurekaIdColumn()).append(", A2.").append(querySupport.getEurekaIdColumn()).append(", A1.C_METADATAXML FROM ");
sql.append(table);
sql.append(" A3 JOIN EK_TEMP_UNIQUE_IDS A4 ON (A3.").append(querySupport.getEurekaIdColumn()).append("=A4.UNIQUE_ID) AND A3.C_SYNONYM_CD ='N' AND A3.M_APPLIED_PATH='@' JOIN ");
sql.append(table);
sql.append(" A1 ON (A3.C_FULLNAME LIKE A1.M_APPLIED_PATH AND A1.C_SYNONYM_CD ='N' AND A1.M_APPLIED_PATH<>'@' AND A1.C_BASECODE IS NOT NULL) JOIN ");
sql.append(table);
sql.append(" A2 ON (A2.C_FULLNAME = CASE WHEN SUBSTR(A1.M_APPLIED_PATH, LENGTH(A1.M_APPLIED_PATH), 1) = '%' THEN SUBSTR(A1.M_APPLIED_PATH, 1, LENGTH(A1.M_APPLIED_PATH) - 1) ELSE A1.M_APPLIED_PATH END AND A2.C_SYNONYM_CD ='N' AND A2.M_APPLIED_PATH ='@')");
}
};
private final QueryConstructor READ_ALL_PROPERTIES_CONSTRUCTOR_ORCL = new QueryConstructor() {
@Override
public void appendStatement(StringBuilder sql, String table) {
sql.append("SELECT A1.C_NAME, A1.VALUETYPE_CD, A1.").append(querySupport.getEurekaIdColumn()).append(", A3.").append(querySupport.getEurekaIdColumn()).append(", (SELECT ").append(querySupport.getEurekaIdColumn()).append(" FROM ");
sql.append(table);
sql.append(" WHERE C_FULLNAME = CASE WHEN SUBSTR(A1.M_APPLIED_PATH, LENGTH(A1.M_APPLIED_PATH), 1) = '%' THEN SUBSTR(A1.M_APPLIED_PATH, 1, LENGTH(A1.M_APPLIED_PATH) - 1) ELSE A1.M_APPLIED_PATH END AND C_SYNONYM_CD ='N' AND M_APPLIED_PATH ='@'), A1.C_METADATAXML FROM ");
sql.append(table);
sql.append(" A3 JOIN EK_TEMP_UNIQUE_IDS A4 ON (A3.").append(querySupport.getEurekaIdColumn()).append("=A4.UNIQUE_ID) AND A3.C_SYNONYM_CD ='N' AND A3.M_APPLIED_PATH='@' JOIN ");
sql.append(table);
sql.append(" A1 ON (A3.C_FULLNAME LIKE A1.M_APPLIED_PATH AND A1.C_SYNONYM_CD ='N' AND A1.M_APPLIED_PATH<>'@' AND A1.C_BASECODE IS NOT NULL)");
}
};
private final ResultSetReader>> ALL_PROPERTIES_RSR = new ResultSetReader>>() {
@Override
public Map> read(ResultSet rs) throws KnowledgeSourceReadException {
Map> result = new HashMap<>();
if (rs != null) {
try {
CMetadataXmlParser valueMetadataParser = new CMetadataXmlParser();
XMLReader xmlReader = valueMetadataSupport.init(valueMetadataParser);
Map> modInterp;
try (Connection connection = querySupport.getConnection()) {
modInterp = readModInterp(connection);
} catch (InvalidConnectionSpecArguments ex) {
throw new KnowledgeSourceReadException(ex);
}
Set> propertyDefUids = new HashSet<>();
while (rs.next()) {
String declaringConceptSymbol = rs.getString(5);
String conceptSymbol = rs.getString(4);
String symbol = rs.getString(3);
String name = rs.getString(1); // the display name
if (name == null) {
throw new KnowledgeSourceReadException("Null property symbol for concept " + symbol);
}
Clob clob = rs.getClob(6);
valueMetadataParser.setDeclaringPropId(declaringConceptSymbol);
valueMetadataParser.setConceptBaseCode(symbol);
valueMetadataSupport.parseAndFreeClob(xmlReader, clob);
ValueType valueType = valueMetadataParser.getValueType();
Map get = modInterp.get(declaringConceptSymbol);
if (get != null) {
ModInterp get1 = get.get(symbol);
if (get1 != null && get1.getPropertyName() != null) {
symbol = get1.getPropertyName();
}
if (get1 != null && get1.getDisplayName() != null) {
name = get1.getDisplayName();
}
if (get1 != null) {
valueType = ValueType.NOMINALVALUE;
}
}
if (get != null || clob != null) {
List l = new ArrayList<>(2);
l.add(conceptSymbol);
l.add(symbol);
if (propertyDefUids.add(l)) {
ValueSetSupport vsSupport = new ValueSetSupport();
vsSupport.setPropertyName(symbol);
vsSupport.setDeclaringPropId(declaringConceptSymbol);
Collections.putList(result, conceptSymbol, new PropertyDefinition(conceptSymbol, symbol, name, valueType, vsSupport.getId(), declaringConceptSymbol));
}
}
}
} catch (SQLException ex) {
throw new KnowledgeSourceReadException(ex);
}
}
return result;
}
};
private TemporalPropositionDefinition newTemporalPropositionDefinition(ResultSet rs, Date accessed) throws SAXParseException, KnowledgeSourceReadException, SQLException {
if (Arrays.contains(VALUE_TYPE_CDS, rs.getString(3))) {
CMetadataXmlParser valueMetadataParser = new CMetadataXmlParser();
XMLReader xmlReader = valueMetadataSupport.init(valueMetadataParser);
valueMetadataSupport.parseAndFreeClob(xmlReader, rs.getClob(4));
SAXParseException exception = valueMetadataParser.getException();
if (exception != null) {
throw exception;
}
ValueType valueType = valueMetadataParser.getValueType();
PrimitiveParameterDefinition result = new PrimitiveParameterDefinition(rs.getString(7));
result.setDisplayName(rs.getString(1));
result.setDescription(rs.getString(4));
result.setInDataSource(rs.getBoolean(6));
result.setValueType(valueType);
result.setAccessed(accessed);
result.setCreated(rs.getTimestamp(8));
result.setUpdated(rs.getTimestamp(9));
result.setDownloaded(rs.getTimestamp(10));
result.setSourceId(this.sourceIdFactory.getInstance());
return result;
} else {
EventDefinition result = new EventDefinition(rs.getString(7));
result.setDisplayName(rs.getString(1));
result.setDescription(rs.getString(4));
result.setInDataSource(rs.getBoolean(6));
result.setAccessed(accessed);
result.setCreated(rs.getTimestamp(8));
result.setUpdated(rs.getTimestamp(9));
result.setDownloaded(rs.getTimestamp(10));
result.setSourceId(this.sourceIdFactory.getInstance());
return result;
}
}
private class ListResultSetReader implements ResultSetReader> {
private Set propIds;
ListResultSetReader() {
this.propIds = new HashSet<>();
}
@Override
public List read(ResultSet rs) throws KnowledgeSourceReadException {
try {
List r = new ArrayList<>();
if (rs != null) {
Date now = new Date();
while (rs.next()) {
if (this.propIds.add(rs.getString(7))) {
r.add(newTemporalPropositionDefinition(rs, now));
}
}
}
return r;
} catch (SQLException | SAXParseException ex) {
throw new KnowledgeSourceReadException(ex);
}
}
}
private final ResultSetReader resultSetReader = new ResultSetReader() {
@Override
public TemporalPropositionDefinition read(ResultSet rs) throws KnowledgeSourceReadException {
try {
if (rs != null && rs.next()) {
AbstractPropositionDefinition abd = (AbstractPropositionDefinition) newTemporalPropositionDefinition(rs, new Date());
Set children = levelReader.readChildrenFromDatabase(rs.getString(2));
abd.setInverseIsA(children.toArray(new String[children.size()]));
List propDefs = readPropertyDefinitions(rs.getString(7), rs.getString(2));
abd.setPropertyDefinitions(propDefs.toArray(new PropertyDefinition[propDefs.size()]));
return (TemporalPropositionDefinition) abd;
} else {
return null;
}
} catch (SQLException | SAXParseException ex) {
throw new KnowledgeSourceReadException(ex);
}
}
};
private final QueryConstructor READ_FACT_QUERY_CONSTRUCTOR = new QueryConstructor() {
@Override
public void appendStatement(StringBuilder sql, String table) {
sql.append("SELECT C_NAME, C_FULLNAME, VALUETYPE_CD, C_COMMENT, C_METADATAXML, CASE WHEN C_BASECODE IS NOT NULL THEN 1 ELSE 0 END, ").append(querySupport.getEurekaIdColumn()).append(", IMPORT_DATE, UPDATE_DATE, DOWNLOAD_DATE FROM ");
sql.append(table);
sql.append(" WHERE C_SYNONYM_CD='N' AND ").append(querySupport.getEurekaIdColumn()).append(" = ?");
}
};
private TemporalPropositionDefinition readPropDef(final String id) throws KnowledgeSourceReadException {
try (ConnectionSpecQueryExecutor queryExecutor = this.querySupport.getQueryExecutorInstance(READ_FACT_QUERY_CONSTRUCTOR)) {
return queryExecutor.execute(
id,
resultSetReader);
}
}
private final ResultSetReader> resultSetReaderAll = new ResultSetReader>() {
@Override
public List read(ResultSet rs) throws KnowledgeSourceReadException {
try {
List r = new ArrayList<>();
if (rs != null) {
Set propIds = new HashSet<>();
while (rs.next()) {
AbstractPropositionDefinition abd = (AbstractPropositionDefinition) newTemporalPropositionDefinition(rs, new Date());
if (propIds.add(abd.getId())) {
Set children = levelReader.readChildrenFromDatabase(rs.getString(2));
abd.setInverseIsA(children.toArray(new String[children.size()]));
List propDefs = readPropertyDefinitions(rs.getString(7), rs.getString(2));
abd.setPropertyDefinitions(propDefs.toArray(new PropertyDefinition[propDefs.size()]));
r.add((TemporalPropositionDefinition) abd);
}
}
}
return r;
} catch (SQLException | SAXParseException ex) {
throw new KnowledgeSourceReadException(ex);
}
}
};
private final QueryConstructor READ_PROPDEFS_QUERY_CONSTRUCTOR = new QueryConstructor() {
@Override
public void appendStatement(StringBuilder sql, String table) {
sql.append("SELECT C_NAME, C_FULLNAME, VALUETYPE_CD, C_COMMENT, C_METADATAXML, CASE WHEN C_BASECODE IS NOT NULL THEN 1 ELSE 0 END, ").append(querySupport.getEurekaIdColumn()).append(", IMPORT_DATE, UPDATE_DATE, DOWNLOAD_DATE FROM ");
sql.append(table);
sql.append(" JOIN EK_TEMP_UNIQUE_IDS ON UNIQUE_ID=").append(querySupport.getEurekaIdColumn()).append(" WHERE C_SYNONYM_CD='N'");
}
};
private List readPropDefs(final List ids) throws KnowledgeSourceReadException {
List result = new ArrayList<>();
try (Connection connection = this.querySupport.getConnection()) {
try {
try (UniqueIdTempTableHandler uniqIdTempTableHandler = new UniqueIdTempTableHandler(this.querySupport.getDatabaseProduct(), connection, false)) {
for (String id : ids) {
uniqIdTempTableHandler.insert(id);
}
}
try (QueryExecutor queryExecutor = this.querySupport.getQueryExecutorInstance(connection, READ_PROPDEFS_QUERY_CONSTRUCTOR)) {
result.addAll(queryExecutor.execute(
resultSetReaderAll));
}
connection.commit();
} catch (SQLException ex) {
try {
connection.rollback();
} catch (SQLException ignore) {
}
throw ex;
}
} catch (SQLException | InvalidConnectionSpecArguments ex) {
throw new KnowledgeSourceReadException(ex);
}
return result;
}
private final QueryConstructor READ_PROP_DEF_QUERY_CONSTRUCTOR = new QueryConstructor() {
@Override
public void appendStatement(StringBuilder sql, String table) {
sql.append("SELECT A1.").append(querySupport.getEurekaIdColumn()).append(", A1.C_NAME, A1.C_METADATAXML, (SELECT A2.").append(querySupport.getEurekaIdColumn()).append(" FROM ");
sql.append(table);
sql.append(" A2 WHERE A2.C_FULLNAME LIKE (CASE WHEN SUBSTR(A1.M_APPLIED_PATH, LENGTH(A1.M_APPLIED_PATH), 1) = '%' THEN SUBSTR(A1.M_APPLIED_PATH, 1, LENGTH(A1.M_APPLIED_PATH) - 1) ELSE A1.M_APPLIED_PATH END)) FROM ");
sql.append(table);
sql.append(" A1 WHERE ? LIKE A1.M_APPLIED_PATH");
}
};
private List readPropertyDefinitions(final String symbol, String fullName) throws KnowledgeSourceReadException {
final Map> modInterp = readModInterp(null);
try (ConnectionSpecQueryExecutor queryExecutor = this.querySupport.getQueryExecutorInstance(READ_PROP_DEF_QUERY_CONSTRUCTOR)) {
return queryExecutor.execute(fullName,
new ResultSetReader>() {
@Override
public List read(ResultSet rs) throws KnowledgeSourceReadException {
try {
List result = new ArrayList<>();
if (rs != null && rs.isBeforeFirst()) {
CMetadataXmlParser valueMetadataParser = new CMetadataXmlParser();
XMLReader xmlReader = valueMetadataSupport.init(valueMetadataParser);
Set> propertyDefUids = new HashSet<>();
while (rs.next()) {
String propertySymbol = rs.getString(1);
String propertyDisplayName = rs.getString(2);
if (propertySymbol == null) {
throw new KnowledgeSourceReadException("Null property symbol for concept " + symbol);
}
String declaringSymbol = rs.getString(4);
valueMetadataParser.setDeclaringPropId(declaringSymbol);
valueMetadataParser.setConceptBaseCode(propertySymbol);
Clob clob = rs.getClob(3);
valueMetadataSupport.parseAndFreeClob(xmlReader, clob);
SAXParseException exception = valueMetadataParser.getException();
if (exception != null) {
throw exception;
}
ValueType valueType = valueMetadataParser.getValueType();
ValueSet valueSet = valueMetadataParser.getValueSet();
String valueSetId = valueSet != null ? valueSet.getId() : null;
Map modInterpVal = modInterp.get(declaringSymbol);
ModInterp modInterpValPropertySym;
if (modInterpVal != null) {
modInterpValPropertySym = modInterpVal.get(propertySymbol);
if (modInterpValPropertySym != null) {
propertySymbol = modInterpValPropertySym.getPropertyName();
valueType = ValueType.NOMINALVALUE;
propertyDisplayName = modInterpValPropertySym.getDisplayName();
ValueSetSupport vsSupport = new ValueSetSupport();
vsSupport.setPropertyName(propertySymbol);
vsSupport.setDeclaringPropId(declaringSymbol);
valueSetId = vsSupport.getId();
}
} else {
modInterpValPropertySym = null;
}
if (clob != null || modInterpValPropertySym != null) {
List l = new ArrayList<>(2);
l.add(symbol);
l.add(propertySymbol);
if (propertyDefUids.add(l)) {
result.add(
new PropertyDefinition(
symbol,
propertySymbol,
propertyDisplayName,
valueType,
valueSetId,
declaringSymbol));
}
}
}
}
return result;
} catch (SQLException | SAXParseException ex) {
throw new KnowledgeSourceReadException(ex);
}
}
});
}
}
private Map> readModInterp(Connection connection) throws KnowledgeSourceReadException {
synchronized (this.modInterpCachedSyncVariable) {
if (this.modInterpCached == null) {
Map> modInterp = new HashMap<>();
LOGGER.fine("Getting modifier information from EK_MODIFIER_INTERP");
try (Connection conn = connection != null ? connection : this.querySupport.getConnection();
Statement stmt = conn.createStatement();
ResultSet rs = stmt.executeQuery("SELECT DECLARING_CONCEPT, C_BASECODE, PROPERTYNAME, DISPLAYNAME FROM EK_MODIFIER_INTERP")) {
while (rs.next()) {
String declaringSymbol = rs.getString(1);
String propertySymbol = rs.getString(2);
String propertyName = rs.getString(3);
String displayName = rs.getString(4);
Map modInterpVal = modInterp.get(declaringSymbol);
if (modInterpVal == null) {
modInterpVal = new HashMap<>();
modInterp.put(declaringSymbol, modInterpVal);
}
modInterpVal.put(propertySymbol, new ModInterp(propertyName, displayName));
}
} catch (InvalidConnectionSpecArguments | SQLException ex) {
throw new KnowledgeSourceReadException(ex);
}
LOGGER.fine("Done!");
this.modInterpCached = modInterp;
}
}
return this.modInterpCached;
}
private static ValueSet parseValueSet(String valueSetId, String vses) {
try (Reader reader = new StringReader(vses);
CSVReader r = new CSVReader(reader, ',')) {
String[] readNext = r.readNext();
ValueSetElement[] vsesArr = new ValueSetElement[readNext.length];
for (int i = 0; i < readNext.length; i++) {
try (Reader reader2 = new StringReader(readNext[i]);
CSVReader r2 = new CSVReader(reader2, '|')) {
String[] segments = r2.readNext();
vsesArr[i] = new ValueSetElement(NominalValue.getInstance(segments[0]), segments[1], null);
}
}
return new ValueSet(valueSetId, null, vsesArr, null);
} catch (IOException ignore) {
throw new AssertionError("Should never happen");
}
}
private static ValueSet parseValueSetResource(String valueSetId, String name, String hasHeader, String delimiter, String idCol, String displayNameCol, String descriptionCol) {
boolean header = Boolean.parseBoolean(hasHeader);
int id = Integer.parseInt(idCol) - 1;
int displayName;
if (displayNameCol != null) {
displayName = Integer.parseInt(displayNameCol) - 1;
} else {
displayName = -1;
}
int description;
if (descriptionCol != null) {
description = Integer.parseInt(descriptionCol) - 1;
} else {
description = -1;
}
int maxIndex = Math.max(id, displayName);
maxIndex = Math.max(maxIndex, description);
try (Reader reader = new InputStreamReader(I2b2KnowledgeSourceBackend.class.getResourceAsStream(name));
CSVReader r = new CSVReader(reader, delimiter.charAt(0))) {
String[] cols;
List vsel = new ArrayList<>();
boolean first = header;
while ((cols = r.readNext()) != null) {
if (first) {
first = false;
} else if (cols.length - 1 >= maxIndex) {
vsel.add(new ValueSetElement(NominalValue.getInstance(cols[id]), displayName > -1 ? cols[displayName] : null, null));
}
}
return new ValueSet(valueSetId, null, vsel.toArray(new ValueSetElement[vsel.size()]), null);
} catch (IOException ex) {
throw new AssertionError("Should never happen");
}
}
}
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