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Merge pull request #311 from thehyve/cdm-v5.4
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Add support for OMOP CDM v5.4
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Maxim Moinat authored Sep 28, 2021
2 parents 81cd8b8 + 0dbafba commit db893a7
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Showing 22 changed files with 503 additions and 1,164 deletions.
13 changes: 5 additions & 8 deletions rabbit-core/src/main/java/org/ohdsi/rabbitInAHat/dataModel/Database.java
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Expand Up @@ -34,15 +34,12 @@ public class Database implements Serializable {

public enum CDMVersion {
CDMV4("CDMV4.csv")
, CDMV5("CDMV5.csv")
, CDMV501("CDMV5.0.1.csv")
, CDMV510("CDMV5.1.0.csv")
, CDMV520("CDMV5.2.0.csv")
, CDMV530("CDMV5.3.0.csv")
, CDMV531("CDMV5.3.1.csv")
, CDMV531_O("CDMV5.3.1_Oncology.csv")
, CDMV50("CDMV5.0.csv")
, CDMV51("CDMV5.1.csv")
, CDMV52("CDMV5.2.csv")
, CDMV53("CDMV5.3.csv")
, CDMV54("CDMV5.4.csv")
, CDMV60("CDMV6.0.csv")
, CDMV60_O("CDMV6.0_Oncology.csv")
;

private final String fileName;
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41 changes: 21 additions & 20 deletions rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/RabbitInAHatMain.java
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Expand Up @@ -74,15 +74,13 @@ public class RabbitInAHatMain implements ResizeListener {
public final static String ACTION_FILTER = "Filter";
public final static String ACTION_MAKE_MAPPING = "Make Mappings";
public final static String ACTION_REMOVE_MAPPING = "Remove Mappings";
public final static String ACTION_SET_TARGET_V4 = "CDM v4";
public final static String ACTION_SET_TARGET_V5 = "CDM v5.0.0";
public final static String ACTION_SET_TARGET_V501 = "CDM v5.0.1";
public final static String ACTION_SET_TARGET_V510 = "CDM v5.1.0";
public final static String ACTION_SET_TARGET_V520 = "CDM v5.2.0";
public final static String ACTION_SET_TARGET_V530 = "CDM v5.3.0";
public final static String ACTION_SET_TARGET_V531 = "CDM v5.3.1";
public final static String ACTION_SET_TARGET_V60 = "CDM v6.0";
public final static String ACTION_SET_TARGET_V60_O = "CDM v6.0 + Oncology";
public final static String ACTION_SET_TARGET_V4 = "CDM v4";
public final static String ACTION_SET_TARGET_V50 = "CDM v5.0";
public final static String ACTION_SET_TARGET_V51 = "CDM v5.1";
public final static String ACTION_SET_TARGET_V52 = "CDM v5.2";
public final static String ACTION_SET_TARGET_V53 = "CDM v5.3";
public final static String ACTION_SET_TARGET_V54 = "CDM v5.4";
public final static String ACTION_SET_TARGET_V60 = "CDM v6.0-beta";
public final static String ACTION_ADD_STEM_TABLE = "Add stem table";
public final static String ACTION_REMOVE_STEM_TABLE = "Remove stem table";
public final static String ACTION_SET_TARGET_CUSTOM = "Load Custom...";
Expand Down Expand Up @@ -144,7 +142,7 @@ public void windowClosing(WindowEvent e) {
frame.setJMenuBar(createMenuBar());

ETL etl = new ETL();
etl.setTargetDatabase(Database.generateCDMModel(CDMVersion.CDMV60));
etl.setTargetDatabase(Database.generateCDMModel(CDMVersion.CDMV54));

ObjectExchange.etl = etl;

Expand Down Expand Up @@ -248,20 +246,18 @@ private JMenuBar createMenuBar() {

Map<String, CDMVersion> cdmOptions = new LinkedHashMap<>();
cdmOptions.put(ACTION_SET_TARGET_V4, CDMVersion.CDMV4);
cdmOptions.put(ACTION_SET_TARGET_V5, CDMVersion.CDMV5);
cdmOptions.put(ACTION_SET_TARGET_V501, CDMVersion.CDMV501);
cdmOptions.put(ACTION_SET_TARGET_V510, CDMVersion.CDMV510);
cdmOptions.put(ACTION_SET_TARGET_V520, CDMVersion.CDMV520);
cdmOptions.put(ACTION_SET_TARGET_V530, CDMVersion.CDMV530);
cdmOptions.put(ACTION_SET_TARGET_V531, CDMVersion.CDMV531);
cdmOptions.put(ACTION_SET_TARGET_V50, CDMVersion.CDMV50);
cdmOptions.put(ACTION_SET_TARGET_V51, CDMVersion.CDMV51);
cdmOptions.put(ACTION_SET_TARGET_V52, CDMVersion.CDMV52);
cdmOptions.put(ACTION_SET_TARGET_V53, CDMVersion.CDMV53);
cdmOptions.put(ACTION_SET_TARGET_V54, CDMVersion.CDMV54);
cdmOptions.put(ACTION_SET_TARGET_V60, CDMVersion.CDMV60);
cdmOptions.put(ACTION_SET_TARGET_V60_O, CDMVersion.CDMV60_O);

JRadioButtonMenuItem targetCDM;
ButtonGroup targetGroup = new ButtonGroup();
for (String optionName : cdmOptions.keySet()) {
targetCDM = new JRadioButtonMenuItem(optionName);
if (optionName.equals(ACTION_SET_TARGET_V60)) {
if (optionName.equals(ACTION_SET_TARGET_V54)) {
targetCDM.setSelected(true);
}
targetGroup.add(targetCDM);
Expand Down Expand Up @@ -472,8 +468,13 @@ private void doSetTargetCustom(String filename) {
etl.copyETLMappings(ObjectExchange.etl);
tableMappingPanel.setMapping(etl.getTableToTableMapping());
ObjectExchange.etl = etl;
} catch (IOException e) {
// Do nothing if error
} catch (Exception e) {
e.printStackTrace();
JOptionPane.showMessageDialog(
null, e.getMessage(),
"Error loading custom target database",
JOptionPane.ERROR_MESSAGE
);
}
}

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38 changes: 16 additions & 22 deletions rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/dataModel/StemTableFactory.java
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Expand Up @@ -23,28 +23,22 @@ public static void addStemTable(ETL etl) {
Database targetDatabase = etl.getTargetDatabase();
InputStream tableStream;
InputStream mappingStream;
if (targetDatabase.getDbName().toLowerCase().equals("cdmv5.0.1")) {
tableStream = StemTableFactory.class.getResourceAsStream("StemTableV5.0.1.csv");
mappingStream = StemTableFactory.class.getResourceAsStream("StemTableDefaultMappingV5.0.1.csv");
} else if (targetDatabase.getDbName().toLowerCase().equals("cdmv5.1.0")) {
tableStream = StemTableFactory.class.getResourceAsStream("StemTableV5.1.0.csv");
mappingStream = StemTableFactory.class.getResourceAsStream("StemTableDefaultMappingV5.1.0.csv");
} else if (targetDatabase.getDbName().toLowerCase().equals("cdmv5.2.0")) {
tableStream = StemTableFactory.class.getResourceAsStream("StemTableV5.2.0.csv");
mappingStream = StemTableFactory.class.getResourceAsStream("StemTableDefaultMappingV5.2.0.csv");
} else if (targetDatabase.getDbName().toLowerCase().equals("cdmv5.3.0")) {
tableStream = StemTableFactory.class.getResourceAsStream("StemTableV5.3.0.csv");
mappingStream = StemTableFactory.class.getResourceAsStream("StemTableDefaultMappingV5.3.0.csv");
} else if (targetDatabase.getDbName().toLowerCase().equals("cdmv5.3.1")) {
tableStream = StemTableFactory.class.getResourceAsStream("StemTableV5.3.1.csv");
mappingStream = StemTableFactory.class.getResourceAsStream("StemTableDefaultMappingV5.3.1.csv");
} else if (targetDatabase.getDbName().toLowerCase().equals("cdmv5.3.1_oncology")) {
tableStream = StemTableFactory.class.getResourceAsStream("StemTableV5.3.1.csv");
mappingStream = StemTableFactory.class.getResourceAsStream("StemTableDefaultMappingV5.3.1.csv");
} else if (targetDatabase.getDbName().toLowerCase().equals("cdmv6.0")) {
tableStream = StemTableFactory.class.getResourceAsStream("StemTableV6.0.csv");
mappingStream = StemTableFactory.class.getResourceAsStream("StemTableDefaultMappingV6.0.csv");
} else if (targetDatabase.getDbName().toLowerCase().equals("cdmv6.0_oncology")) {
if (targetDatabase.getDbName().equalsIgnoreCase("cdmv5.0")) {
tableStream = StemTableFactory.class.getResourceAsStream("StemTableV5.0.csv");
mappingStream = StemTableFactory.class.getResourceAsStream("StemTableDefaultMappingV5.0.csv");
} else if (targetDatabase.getDbName().equalsIgnoreCase("cdmv5.1")) {
tableStream = StemTableFactory.class.getResourceAsStream("StemTableV5.1.csv");
mappingStream = StemTableFactory.class.getResourceAsStream("StemTableDefaultMappingV5.1.csv");
} else if (targetDatabase.getDbName().equalsIgnoreCase("cdmv5.2")) {
tableStream = StemTableFactory.class.getResourceAsStream("StemTableV5.2.csv");
mappingStream = StemTableFactory.class.getResourceAsStream("StemTableDefaultMappingV5.2.csv");
} else if (targetDatabase.getDbName().equalsIgnoreCase("cdmv5.3")) {
tableStream = StemTableFactory.class.getResourceAsStream("StemTableV5.3.csv");
mappingStream = StemTableFactory.class.getResourceAsStream("StemTableDefaultMappingV5.3.csv");
} else if (targetDatabase.getDbName().equalsIgnoreCase("cdmv5.4")) {
tableStream = StemTableFactory.class.getResourceAsStream("StemTableV5.4.csv");
mappingStream = StemTableFactory.class.getResourceAsStream("StemTableDefaultMappingV5.4.csv");
} else if (targetDatabase.getDbName().equalsIgnoreCase("cdmv6.0")) {
tableStream = StemTableFactory.class.getResourceAsStream("StemTableV6.0.csv");
mappingStream = StemTableFactory.class.getResourceAsStream("StemTableDefaultMappingV6.0.csv");
} else {
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0 ...hdsi/rabbitInAHat/dataModel/CDMV5.0.1.csv → .../ohdsi/rabbitInAHat/dataModel/CDMV5.0.csv
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0 ...hdsi/rabbitInAHat/dataModel/CDMV5.1.0.csv → .../ohdsi/rabbitInAHat/dataModel/CDMV5.1.csv
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0 ...hdsi/rabbitInAHat/dataModel/CDMV5.2.0.csv → .../ohdsi/rabbitInAHat/dataModel/CDMV5.2.csv
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