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Allowing users to save ETL specs as either .json.gz or plain .json, so
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ETL specs can work with version control.
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@schuemie
schuemie committed Jul 19, 2016
1 parent a2e07d3 commit 1f28066
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Showing 2 changed files with 54 additions and 39 deletions.
28 changes: 16 additions & 12 deletions src/org/ohdsi/rabbitInAHat/RabbitInAHatMain.java
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Original file line number Diff line number Diff line change
Expand Up @@ -73,6 +73,7 @@ public class RabbitInAHatMain implements ResizeListener, ActionListener {

public final static String WIKI_URL = "http://www.ohdsi.org/web/wiki/doku.php?id=documentation:software:whiterabbit#rabbit-in-a-hat";
private final static FileFilter FILE_FILTER_GZ = new FileNameExtensionFilter("GZIP Files (*.gz)", "gz");
private final static FileFilter FILE_FILTER_JSON = new FileNameExtensionFilter("JSON Files (*.json)", "json");
private final static FileFilter FILE_FILTER_DOCX = new FileNameExtensionFilter("Microsoft Word documents (*.docx)", "docx");
private final static FileFilter FILE_FILTER_CSV = new FileNameExtensionFilter("Text Files (*.csv)", "csv");
private final static FileFilter FILE_FILTER_R = new FileNameExtensionFilter("R script (*.r)", "r");
Expand Down Expand Up @@ -243,7 +244,7 @@ private JMenuBar createMenuBar() {
targetCDMV5.addActionListener(this);
targetCDMV5.setActionCommand(ACTION_CMD_SET_TARGET_V5);
setTarget.add(targetCDMV5);

JMenuItem targetCDMV501 = new JMenuItem(ACTION_CMD_SET_TARGET_V501);
targetCDMV501.addActionListener(this);
targetCDMV501.setActionCommand(ACTION_CMD_SET_TARGET_V501);
Expand Down Expand Up @@ -322,31 +323,32 @@ public void notifyResized(int height, boolean minimized, boolean maximized) {
* restrict files displayed
* @return if file selected, absolute path of selected file otherwise null
*/
private String choosePath(boolean saveMode, FileFilter filter) {
private String choosePath(boolean saveMode, FileFilter... filter) {
String result = null;

if (chooser == null) {
chooser = new JFileChooser();
}
chooser.setFileFilter(filter);
chooser.setFileFilter(filter[0]);
for (int i = 1; i < filter.length; i++)
chooser.addChoosableFileFilter(filter[i]);

int dialogResult = saveMode ? chooser.showSaveDialog(frame) : chooser.showOpenDialog(frame);
if (dialogResult == JFileChooser.APPROVE_OPTION)
result = chooser.getSelectedFile().getAbsolutePath();
return result;
}

private String chooseSavePath(FileFilter fileFilter) {
private String chooseSavePath(FileFilter... fileFilter) {
String path = choosePath(true, fileFilter);
if (path != null && fileFilter == FILE_FILTER_GZ && !path.toLowerCase().endsWith(".json.gz"))
if (path != null && fileFilter[0] == FILE_FILTER_GZ && !path.toLowerCase().endsWith(".json.gz") && !path.toLowerCase().endsWith(".json"))
path += ".json.gz";
if (path != null && fileFilter == FILE_FILTER_DOCX && !path.toLowerCase().endsWith(".docx"))
if (path != null && fileFilter[0] == FILE_FILTER_DOCX && !path.toLowerCase().endsWith(".docx"))
path += ".docx";

return path;
}

private String chooseOpenPath(FileFilter fileFilter) {
private String chooseOpenPath(FileFilter... fileFilter) {
return choosePath(false, fileFilter);
}

Expand All @@ -362,10 +364,10 @@ public void actionPerformed(ActionEvent event) {
doSave((filename == null || !filename.toLowerCase().endsWith(".json.gz")) ? chooseSavePath(FILE_FILTER_GZ) : filename);
break;
case ACTION_CMD_SAVE_AS:
doSave(chooseSavePath(FILE_FILTER_GZ));
doSave(chooseSavePath(FILE_FILTER_GZ, FILE_FILTER_JSON));
break;
case ACTION_CMD_OPEN_ETL_SPECS:
doOpenSpecs(chooseOpenPath(FILE_FILTER_GZ));
doOpenSpecs(chooseOpenPath(FILE_FILTER_GZ, FILE_FILTER_JSON));
break;
case ACTION_CMD_OPEN_SCAN_REPORT:
doOpenScanReport(chooseOpenPath());
Expand Down Expand Up @@ -494,7 +496,8 @@ private void doDiscardCounts() {
private void doSave(String filename) {
if (filename != null) {
frame.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
ETL.FileFormat fileFormat = filename.endsWith("json.gz") ? ETL.FileFormat.Json : ETL.FileFormat.Binary;
ETL.FileFormat fileFormat = filename.endsWith("json.gz") ? ETL.FileFormat.GzipJson : filename.endsWith("json") ? ETL.FileFormat.Json
: ETL.FileFormat.Binary;
ObjectExchange.etl.save(filename, fileFormat);
frame.setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
}
Expand All @@ -503,7 +506,8 @@ private void doSave(String filename) {
private void doOpenSpecs(String filename) {
if (filename != null) {
frame.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
ETL.FileFormat fileFormat = filename.endsWith(".json.gz") ? ETL.FileFormat.Json : ETL.FileFormat.Binary;
ETL.FileFormat fileFormat = filename.endsWith(".json.gz") ? ETL.FileFormat.GzipJson : filename.endsWith(".json") ? ETL.FileFormat.Json
: ETL.FileFormat.Binary;
try {
ObjectExchange.etl = ETL.fromFile(filename, fileFormat);
tableMappingPanel.setMapping(ObjectExchange.etl.getTableToTableMapping());
Expand Down
65 changes: 38 additions & 27 deletions src/org/ohdsi/rabbitInAHat/dataModel/ETL.java
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Original file line number Diff line number Diff line change
Expand Up @@ -36,59 +36,59 @@

public class ETL implements Serializable {
public enum FileFormat {
Binary, Json
Binary, Json, GzipJson
}

private Database sourceDb = new Database();
private Database cdmDb = new Database();
private Database cdmDb = new Database();
private List<ItemToItemMap> tableToTableMaps = new ArrayList<ItemToItemMap>();
private Map<ItemToItemMap, List<ItemToItemMap>> tableMapToFieldToFieldMaps = new HashMap<ItemToItemMap, List<ItemToItemMap>>();
private transient String filename = null;
private static final long serialVersionUID = 8987388381751618498L;

public ETL(){
public ETL() {
}
public ETL(Database sourceDB, Database targetDb){

public ETL(Database sourceDB, Database targetDb) {
this.setSourceDatabase(sourceDB);
this.setTargetDatabase(targetDb);
}
public void copyETLMappings(ETL etl){

public void copyETLMappings(ETL etl) {
Mapping<Table> oldTableMapping = etl.getTableToTableMapping();
Mapping<Table> newTableMapping = this.getTableToTableMapping();
for(Table sourceTable : sourceDb.getTables()){
for(Table targetTable : cdmDb.getTables()){
Mapping<Table> newTableMapping = this.getTableToTableMapping();

for (Table sourceTable : sourceDb.getTables()) {
for (Table targetTable : cdmDb.getTables()) {

ItemToItemMap copyMapping = oldTableMapping.getSourceToTargetMapByName(sourceTable, targetTable);
if( copyMapping != null ){

if (copyMapping != null) {
copyMapping.setSourceItem(sourceTable);
copyMapping.setTargetItem(targetTable);

newTableMapping.addSourceToTargetMap(copyMapping);

Mapping<Field> oldFieldMapping = etl.getFieldToFieldMapping(sourceTable, targetTable);
Mapping<Field> newFieldMapping = this.getFieldToFieldMapping(sourceTable, targetTable);
for(Field sourceField : sourceTable.getFields()){
for(Field targetField : targetTable.getFields()){

for (Field sourceField : sourceTable.getFields()) {
for (Field targetField : targetTable.getFields()) {
copyMapping = oldFieldMapping.getSourceToTargetMapByName(sourceField, targetField);
if(copyMapping != null){

if (copyMapping != null) {
copyMapping.setSourceItem(sourceField);
copyMapping.setTargetItem(targetField);

newFieldMapping.addSourceToTargetMap(copyMapping);
}
}
}
}
}
}
}
}

public void saveCurrentState() {

}
Expand Down Expand Up @@ -125,7 +125,6 @@ public void setTargetDatabase(Database targetDb) {
public void setSourceDatabase(Database sourceDb) {
this.sourceDb = sourceDb;
}


public Database getTargetDatabase() {
return cdmDb;
Expand All @@ -149,14 +148,21 @@ public void save(String filename, FileFormat format) {
out.writeObject(this);
}
break;
case Json:
case GzipJson:
String json = toJson();
try (FileOutputStream fileOutputStream = new FileOutputStream(filename);
GZIPOutputStream gzipOutputStream = new GZIPOutputStream(fileOutputStream);
OutputStreamWriter out = new OutputStreamWriter(gzipOutputStream, "UTF-8")) {
out.write(json);
}
break;
case Json:
String json2 = toJson();
try (FileOutputStream fileOutputStream = new FileOutputStream(filename);
OutputStreamWriter out = new OutputStreamWriter(fileOutputStream, "UTF-8")) {
out.write(json2);
}
break;
}
this.filename = filename;
} catch (IOException e) {
Expand Down Expand Up @@ -184,13 +190,18 @@ public static ETL fromFile(String filename, FileFormat format) {
result = (ETL) objectInputStream.readObject();
}
break;
case Json:
case GzipJson:
try (FileInputStream fileInputStream = new FileInputStream(filename);
GZIPInputStream gzipInputStream = new GZIPInputStream(fileInputStream);
JsonReader jr = new JsonReader(gzipInputStream)) {
result = (ETL) jr.readObject();
}
break;
case Json:
try (FileInputStream fileInputStream = new FileInputStream(filename); JsonReader jr = new JsonReader(fileInputStream)) {
result = (ETL) jr.readObject();
}
break;
}
result.filename = filename;
} catch (Exception exception) {
Expand Down

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