diff --git a/src/main/java/fr/inra/po2vocabmanager/utils/DataTreeCell.java b/src/main/java/fr/inra/po2vocabmanager/utils/DataTreeCell.java
index e7deb82ecdea8c6faf94bec608065a74144a704c..325cd0277eb4ba244e3c7b8c95b2aa9e0b47199e 100644
--- a/src/main/java/fr/inra/po2vocabmanager/utils/DataTreeCell.java
+++ b/src/main/java/fr/inra/po2vocabmanager/utils/DataTreeCell.java
@@ -21,6 +21,7 @@ package fr.inra.po2vocabmanager.utils;
import fr.inra.po2vocabmanager.MainApp;
import fr.inra.po2vocabmanager.model.DataNode;
import fr.inrae.po2engine.externalTools.RDF4JTools;
+import fr.inrae.po2engine.model.Replicate;
import fr.inrae.po2engine.model.dataModel.*;
import fr.inrae.po2engine.utils.ImportReport;
import fr.inrae.po2engine.utils.Report;
@@ -182,7 +183,7 @@ public class DataTreeCell extends TextFieldTreeCell<DataNode> {
return s;
}
- private static void newStepImport(ItineraryFile iti, StepFile parent) {
+ private static void newStepImport(ItineraryFile iti, StepFile parent, int replicateID) {
File fileImport = getFile(MainApp.primaryStage);
if (fileImport == null) {
return;
@@ -190,7 +191,7 @@ public class DataTreeCell extends TextFieldTreeCell<DataNode> {
MainApp.logger.info("start importing file " + fileImport.getName());
ImportReport importReport = iti.checkImportStepFromXLSX(fileImport);
if(importReport.success()) {
- StepFile step = iti.importStepFromXLSX(fileImport);
+ StepFile step = iti.importStepFromXLSX(fileImport, replicateID);
if(parent != null && step != null) {
parent.addSubStep(step);
}
@@ -274,15 +275,15 @@ public class DataTreeCell extends TextFieldTreeCell<DataNode> {
}
- private static void newItineraryObsImport(ItineraryFile iti) {
+ private static void newItineraryObsImport(ItineraryFile iti, int replicateID) {
File fileImport = getFile(MainApp.primaryStage);
if (fileImport == null) {
return;
}
MainApp.logger.info("start importing/create file " + fileImport.getName());
- Report r = iti.checkCreateObservationFromXLSX(fileImport);
+ Report r = iti.checkCreateObservationFromXLSX(fileImport, replicateID);
if(r.success()) {
- ObservationFile obs = iti.createObservationFromXLSX(fileImport);
+ ObservationFile obs = iti.createObservationFromXLSX(fileImport, replicateID);
handleInterfaceUpdate(obs.getItineraryFile().getProcessFile(), r.success(), "File import completed");
MainApp.getDataControler().selectNode(obs);
MainApp.logger.info("import done with sucess");
@@ -328,15 +329,402 @@ public class DataTreeCell extends TextFieldTreeCell<DataNode> {
result.ifPresent(step -> addStepData(itineraryFile, parentStep, current, true, step));
}
- private void newStepObsImport(StepFile step) {
+ private static void stepImport(StepFile file, boolean isNewStep, int replicateID) {
+ File fileImport = getFile(MainApp.primaryStage);
+ if (fileImport != null) {
+ MainApp.logger.info("start importing file " + fileImport.getName());
+ ImportReport importReport = file.realPreConst(fileImport, isNewStep);
+ if(importReport.success()) {
+
+ // validation de l'import par l'utilisateur
+ Dialog<ButtonType> validateImport = new Dialog();
+ validateImport.setTitle("import validation");
+ validateImport.initOwner(MainApp.primaryStage);
+ validateImport.initModality(Modality.WINDOW_MODAL);
+ ButtonType importButtonType = new ButtonType("Import", ButtonBar.ButtonData.OK_DONE);
+ validateImport.getDialogPane().getButtonTypes().addAll(importButtonType, ButtonType.CANCEL);
+
+ GridPane paneImport = new GridPane();
+ paneImport.setHgap(20);
+ paneImport.setVgap(20);
+
+ Integer comptLine = 0;
+ Text stepText = new Text(file.getNameProperty().getValue());
+ Text sepa = new Text(" : ");
+ paneImport.add(new ImageView(UITools.getImage("resources/images/treeview/step.png")), 0, comptLine);
+ paneImport.add(stepText, 1, comptLine);
+ paneImport.add(sepa, 2, comptLine);
+ paneImport.add(new ImageView(UITools.getImage("resources/images/update_30.png")), 3, comptLine);
+
+ comptLine++;
+
+
+ for (ObservationFile obsF : file.getObservationFiles()) {
+ Text obsText = new Text(obsF.getCID().getValue().get());
+ Text sepa2 = new Text(" : ");
+ paneImport.add(new ImageView(UITools.getImage("resources/images/treeview/observation.png")), 0, comptLine);
+ paneImport.add(obsText, 1, comptLine);
+ paneImport.add(sepa2, 2, comptLine);
+ if (importReport.getObsMapping().containsValue(obsF)) {
+ paneImport.add(new ImageView(UITools.getImage("resources/images/update_30.png")), 3, comptLine);
+ } else {
+ paneImport.add(new ImageView(UITools.getImage("resources/images/del_30.png")), 3, comptLine);
+ }
+ comptLine++;
+ }
+
+ for(XSSFSheet oo : importReport.getObsMapping().keySet()) {
+ if(importReport.getObsMapping().get(oo) == null) { // new obs
+ Text obsText = new Text(oo.getSheetName());
+ Text sepa2 = new Text(" : ");
+ paneImport.add(new ImageView(UITools.getImage("resources/images/treeview/observation.png")), 0, comptLine);
+ paneImport.add(obsText, 1, comptLine);
+ paneImport.add(sepa2, 2, comptLine);
+ paneImport.add(new ImageView(UITools.getImage("resources/images/add_30.png")), 3, comptLine);
+ comptLine++;
+ }
+ }
+
+ for (CompositionFile compoF : file.getCompositionFile().keySet()) {
+ Text compoText = new Text(compoF.getCompositionID().getValue().get());
+ Text sepa2 = new Text(" : ");
+ paneImport.add(new ImageView(UITools.getImage("resources/images/treeview/composition.png")), 0, comptLine);
+ paneImport.add(compoText, 1, comptLine);
+ paneImport.add(sepa2, 2, comptLine);
+ if(importReport.getCompoMapping().values().stream().map(org.apache.commons.lang3.tuple.Pair::getLeft).noneMatch(c -> c.equals(compoF))) {
+ paneImport.add(new ImageView(UITools.getImage("resources/images/del_30.png")), 3, comptLine);
+ } else {
+ paneImport.add(new ImageView(UITools.getImage("resources/images/update_30.png")), 3, comptLine);
+ }
+ comptLine++;
+ }
+
+ for(XSSFSheet oo : importReport.getCompoMapping().keySet()) {
+ if(importReport.getCompoMapping().get(oo).getLeft() == null) { // new Compo
+ Text compoText = new Text(oo.getSheetName());
+ Text sepa2 = new Text(" : ");
+ paneImport.add(new ImageView(UITools.getImage("resources/images/treeview/composition.png")), 0, comptLine);
+ paneImport.add(compoText, 1, comptLine);
+ paneImport.add(sepa2, 2, comptLine);
+ paneImport.add(new ImageView(UITools.getImage("resources/images/add_30.png")), 3, comptLine);
+ comptLine++;
+ }
+ }
+
+ validateImport.getDialogPane().setContent(paneImport);
+ Optional<ButtonType> result = Optional.empty();
+ if(!isNewStep) {
+ result = validateImport.showAndWait();
+ }
+ if (isNewStep || result.isPresent() && result.get() == importButtonType) {
+ // l'utilisateur valide la la mise à jour
+ Report report = file.constructDataFromImport(fileImport, isNewStep, replicateID);
+ handleInterfaceUpdate(file.getGeneralFile(), report.success(), report.toString());
+ MainApp.getDataControler().selectNode(file);
+ }
+ } else {
+ showErrorImportAlert(importReport.toString());
+ }
+ } else {
+ }
+ }
+
+ private static void importObservation(ObservationFile obsFile, int replicateID) {
+ File fileImport = getFile(MainApp.primaryStage);
+ if (fileImport != null) {
+ MainApp.logger.info("start importing/update file " + fileImport.getName());
+ // temp obs file
+ ObservationFile tempF = null;
+ if(obsFile.getStepFile() != null) {
+ Report r = obsFile.getStepFile().checkUpdateObservationFromXLSX(fileImport, obsFile, replicateID);
+ if(r.success()) {
+ obsFile.getStepFile().updateObservationFromXLSX(fileImport, obsFile, replicateID);
+ MainApp.getDataControler().refreshTree();
+ MainApp.getDataControler().showNodeDetails(obsFile, obsFile);
+ MainApp.logger.info("import done with sucess");
+ } else {
+ showErrorImportAlert(r.prettyPrintError());
+ }
+ }
+ if(obsFile.getItineraryFile() != null) {
+ Report r = obsFile.getItineraryFile().checkUpdateObservationFromXLSX(fileImport, obsFile, replicateID);
+ if(r.success()) {
+ obsFile.getItineraryFile().updateObservationFromXLSX(fileImport, obsFile, replicateID);
+ MainApp.getDataControler().refreshTree();
+ MainApp.getDataControler().showNodeDetails(obsFile, obsFile);
+ MainApp.logger.info("import done with sucess");
+ } else {
+ showErrorImportAlert(r.prettyPrintError());
+ }
+ }
+ }
+ }
+
+ private static void exportObservation(ObservationFile obsFile, int replicateID) {
+ List<String> choices = new ArrayList<>();
+ choices.add("with ontology");
+ choices.add("without ontology");
+ ChoiceDialog<String> dialog = new ChoiceDialog<>("without ontology", choices);
+ dialog.setTitle("Export Observation");
+ dialog.setHeaderText(null);
+ dialog.setContentText("Export Observation data ");
+ dialog.initModality(Modality.WINDOW_MODAL);
+ dialog.initOwner(MainApp.primaryStage);
+ Boolean exportOnto = false;
+ Optional<String> result = dialog.showAndWait();
+
+ if (result.isPresent() ) {
+ exportOnto = result.get().equals("with ontology");
+ Boolean finalExportOnto = exportOnto;
+ if (exportOnto && MainApp.getOntologyControler().getCurrentOntology() == null) {
+ Alert noOntology = new Alert(Alert.AlertType.ERROR);
+ noOntology.setTitle("No ontology loaded");
+ noOntology.setHeaderText("Please load an ontology");
+ noOntology.setContentText("In order to create an export file, please load the corresponding ontology");
+ noOntology.initOwner(MainApp.primaryStage);
+ noOntology.initModality(Modality.APPLICATION_MODAL);
+ noOntology.showAndWait();
+ } else {
+ XSSFWorkbook book = new XSSFWorkbook();
+
+
+ Task<Boolean> taskExport = new Task<Boolean>() {
+ @Override
+ protected Boolean call() throws Exception {
+ XSSFSheet sheet = Tools.createSheet(book,"obs|"+Tools.removeNonAlphaNumChar(obsFile.getNameProperty().getValue()));
+
+ Integer compteur = 0;
+ Integer maxColumn = 0;
+ for (LinkedList<String> line : obsFile.getDataForExcel(replicateID)) {
+ XSSFRow r = sheet.createRow(compteur++);
+ Integer compteurCell = 0;
+ for (String val : line) {
+ r.createCell(compteurCell++).setCellValue(val);
+ maxColumn = Math.max(maxColumn, compteurCell);
+ }
+ }
+ Tools.autoResize(sheet, maxColumn);
+
+
+ if(finalExportOnto) {
+
+ JSONObject hierarchyVocab = MainApp.getOntologyControler().getHierarchyVocabJSON();
+ // Récupération de l'ontology au format JSON
+ XSSFSheet sheetOntoVocab = Tools.createSheet(book,"onto-vocab|" + Tools.removeNonAlphaNumChar(MainApp.getOntologyControler().getCurrentOntology().getName().getValue()));
+ JSONArray vocab = (JSONArray) hierarchyVocab.get("vocabulary");
+
+ compteur = 0;
+ maxColumn = 0;
+ for (
+ int i = 0; i < vocab.length(); i++) {
+ JSONArray array = (JSONArray) vocab.get(i);
+ XSSFRow r = sheetOntoVocab.createRow(compteur++);
+ for (int j = 0; j < array.length(); j++) {
+ r.createCell(j).setCellValue((String) array.get(j));
+ maxColumn = Math.max(maxColumn, j);
+ }
+ }
+ Tools.autoResize(sheetOntoVocab, maxColumn);
+
+
+ XSSFSheet sheetOntohierarchy = Tools.createSheet(book,"onto-hierarchy|" + Tools.removeNonAlphaNumChar(MainApp.getOntologyControler().getCurrentOntology().getName().getValue()));
+ JSONArray hierarchy = (JSONArray) hierarchyVocab.get("hierarchy");
+
+ compteur = 0;
+ maxColumn = 0;
+
+ for (
+ int x = 0; x < hierarchy.length(); x++) {
+ XSSFRow r = sheetOntohierarchy.createRow(compteur++);
+ JSONArray arrayDesc = (JSONArray) hierarchy.get(x);
+ for (int j = 0; j < arrayDesc.length(); j++) {
+ r.createCell(j).setCellValue((String) arrayDesc.get(j));
+ maxColumn = Math.max(maxColumn, j);
+ }
+ }
+ Tools.autoResize(sheetOntohierarchy, maxColumn);
+ }
+ return true;
+ }
+ };
+ taskExport.setOnSucceeded(workerStateEvent -> {
+ FileChooser fileChooser = new FileChooser();
+ fileChooser.setTitle("Export file");
+ String fileName = obsFile.getFileName();
+ if(replicateID != -1) {
+ fileName+="-"+replicateID;
+ }
+ fileChooser.setInitialFileName(fileName+".xlsx");
+ File fileExport = fileChooser.showSaveDialog(MainApp.primaryStage);
+ if (fileExport != null) {
+ try {
+ FileOutputStream fout = new FileOutputStream(fileExport, false);
+ book.write(fout);
+ fout.close();
+ } catch (IOException ex) {
+ MainApp.logger.error(ex.getMessage());
+ }
+ }
+ });
+ new Thread(taskExport).start();
+ }
+ }
+ }
+
+ private static void exportStepFile(StepFile stepFile, int replicateID) {
+
+ List<String> choices = new ArrayList<>();
+ choices.add("with ontology");
+ choices.add("without ontology");
+ ChoiceDialog<String> dialog = new ChoiceDialog<>("without ontology", choices);
+ dialog.setTitle("Export Step");
+ dialog.setHeaderText(null);
+ dialog.setContentText("Export step data ");
+ dialog.initModality(Modality.WINDOW_MODAL);
+ dialog.initOwner(MainApp.primaryStage);
+ Boolean exportOnto = false;
+ Optional<String> result = dialog.showAndWait();
+
+ if (result.isPresent() ) {
+ exportOnto = result.get().equals("with ontology");
+ if(exportOnto && MainApp.getOntologyControler().getCurrentOntology() == null) {
+ Alert noOntology = new Alert(Alert.AlertType.ERROR);
+ noOntology.setTitle("No ontology loaded");
+ noOntology.setHeaderText("Please load an ontology");
+ noOntology.setContentText("In order to create an export file, please load the corresponding ontology");
+ noOntology.initOwner(MainApp.primaryStage);
+ noOntology.initModality(Modality.APPLICATION_MODAL);
+ noOntology.showAndWait();
+ } else {
+ XSSFWorkbook book = new XSSFWorkbook();
+ Boolean finalExportOnto = exportOnto;
+ Task<Boolean> taskExport = new Task<Boolean>() {
+ @Override
+ protected Boolean call() throws Exception {
+ XSSFSheet sheet = Tools.createSheet(book,"step|"+ DigestUtils.md5Hex(stepFile.getNameProperty().getValue()));
+
+ Integer compteur = 0;
+ Integer maxColumn = 0;
+
+ for (LinkedList<String> line : stepFile.getDataForExcel(true, replicateID)) {
+ XSSFRow r = sheet.createRow(compteur++);
+ Integer compteurCell = 0;
+ for (String val : line) {
+ r.createCell(compteurCell++).setCellValue(val);
+ maxColumn = Math.max(maxColumn, compteurCell);
+ }
+ }
+
+
+ // composition
+ for (Map.Entry<CompositionFile, Boolean> entry : stepFile.getCompositionFile().entrySet()) {
+ XSSFSheet sheetCompo = Tools.createSheet(book,"compo-"+(entry.getValue() ? "input" : "output")+"|"+Tools.removeNonAlphaNumChar(entry.getKey().getCompositionID().getValue().get()));
+ Integer compteurCompo = 0;
+ Integer maxColumnCompo = 0;
+ for (LinkedList<String> line : entry.getKey().getDataForExcel()) {
+ XSSFRow r = sheetCompo.createRow(compteurCompo++);
+ Integer compteurCell = 0;
+ for (String val : line) {
+ r.createCell(compteurCell++).setCellValue(val);
+ maxColumnCompo = Math.max(maxColumnCompo, compteurCell);
+ }
+ }
+ Tools.autoResize(sheetCompo, maxColumnCompo);
+ }
+
+
+
+ Tools.autoResize(sheet, maxColumn);
+
+ for(ObservationFile obs : stepFile.getObservationFiles()) {
+ XSSFSheet sheetObs = Tools.createSheet(book,"obs|"+Tools.removeNonAlphaNumChar(obs.getCID().getValue().get()));
+
+ Integer compteurObs = 0;
+ Integer maxColumnObs = 0;
+ for (LinkedList<String> line : obs.getDataForExcel(replicateID)) {
+ XSSFRow r = sheetObs.createRow(compteurObs++);
+ Integer compteurCell = 0;
+ for (String val : line) {
+ r.createCell(compteurCell++).setCellValue(val);
+ maxColumnObs = Math.max(maxColumnObs, compteurCell);
+ }
+ }
+ Tools.autoResize(sheetObs, maxColumnObs);
+ }
+
+ if(finalExportOnto) {
+
+ JSONObject hierarchyVocab = MainApp.getOntologyControler().getHierarchyVocabJSON();
+ // Récupération de l'ontology au format JSON
+ XSSFSheet sheetOntoVocab = Tools.createSheet(book,"onto-vocab|" + Tools.removeNonAlphaNumChar(MainApp.getOntologyControler().getCurrentOntology().getName().getValue()));
+ JSONArray vocab = (JSONArray) hierarchyVocab.get("vocabulary");
+
+ compteur = 0;
+ maxColumn = 0;
+ for (int i = 0; i < vocab.length(); i++) {
+ JSONArray array = (JSONArray) vocab.get(i);
+ XSSFRow r = sheetOntoVocab.createRow(compteur++);
+ for (int j = 0; j < array.length(); j++) {
+ r.createCell(j).setCellValue((String) array.get(j));
+ maxColumn = Math.max(maxColumn, j);
+ }
+ }
+ Tools.autoResize(sheetOntoVocab, maxColumn);
+
+
+ XSSFSheet sheetOntohierarchy = Tools.createSheet(book,"onto-hierarchy|" + Tools.removeNonAlphaNumChar(MainApp.getOntologyControler().getCurrentOntology().getName().getValue()));
+ JSONArray hierarchy = (JSONArray) hierarchyVocab.get("hierarchy");
+
+ compteur = 0;
+ maxColumn = 0;
+
+ for (int x = 0; x < hierarchy.length(); x++) {
+ XSSFRow r = sheetOntohierarchy.createRow(compteur++);
+ JSONArray arrayDesc = (JSONArray) hierarchy.get(x);
+ for (int j = 0; j < arrayDesc.length(); j++) {
+ r.createCell(j).setCellValue((String) arrayDesc.get(j));
+ maxColumn = Math.max(maxColumn, j);
+ }
+ }
+ Tools.autoResize(sheetOntohierarchy, maxColumn);
+ }
+ return true;
+ }
+ };
+ taskExport.setOnSucceeded(workerStateEvent -> {
+ FileChooser fileChooser = new FileChooser();
+ fileChooser.setTitle("Export file");
+ String fileName = stepFile.getNameProperty().getValue();
+ if(replicateID != -1) {
+ fileName+="-"+replicateID;
+ }
+ fileChooser.setInitialFileName(fileName+".xlsx");
+ File fileExport = fileChooser.showSaveDialog(MainApp.primaryStage);
+ if (fileExport != null) {
+ try {
+ FileOutputStream fout = new FileOutputStream(fileExport, false);
+ book.write(fout);
+ fout.close();
+ } catch (IOException ex) {
+ MainApp.logger.error(ex.getMessage());
+ }
+ }
+ });
+ new Thread(taskExport).start();
+ }
+ }
+
+ }
+
+ private void newStepObsImport(StepFile step, int replicateID) {
File fileImport = getFile(MainApp.primaryStage);
if (fileImport == null) {
return;
}
MainApp.logger.info("start importing/create file " + fileImport.getName());
- Report r = step.checkCreateObservationFromXLSX(fileImport);
+ Report r = step.checkCreateObservationFromXLSX(fileImport, replicateID);
if(r.success()) {
- ObservationFile obs = step.createObservationFromXLSX(fileImport);
+ ObservationFile obs = step.createObservationFromXLSX(fileImport, replicateID);
handleInterfaceUpdate(obs.getStepFile().getGeneralFile(), r.success(), "File import completed");
MainApp.getDataControler().selectNode(obs);
MainApp.logger.info("import done with sucess");
@@ -345,10 +733,38 @@ public class DataTreeCell extends TextFieldTreeCell<DataNode> {
}
}
+ private static void handleInterfaceUpdate(GeneralFile file, boolean reportBoolean, String reportString) {
+ if(reportBoolean) {
+ MainApp.getDataControler().buildProcessTree(file);
+ showOkImportAlert();
+ } else {
+ showErrorImportAlert(reportString);
+ }
+ }
+
+ private static void showErrorImportAlert(String report) {
+ Alert errorImport = new Alert(Alert.AlertType.ERROR);
+ errorImport.setTitle("Import error");
+ errorImport.setContentText(report);
+ errorImport.initModality(Modality.APPLICATION_MODAL);
+ errorImport.initOwner(MainApp.primaryStage);
+ errorImport.showAndWait();
+ }
+
+ private static void showOkImportAlert() {
+ Alert okImport = new Alert(Alert.AlertType.INFORMATION);
+ okImport.setGraphic(new ImageView(UITools.getImage("resources/images/valid.png")));
+ okImport.setHeaderText(null);
+ okImport.setTitle("Successful import");
+ okImport.setContentText("Successful import");
+ okImport.initModality(Modality.APPLICATION_MODAL);
+ okImport.initOwner(MainApp.primaryStage);
+ okImport.showAndWait();
+ }
+
@Override
public void updateItem(DataNode item, boolean empty) {
super.updateItem(item, empty);
-
if (empty || item == null) {
setText(null);
setGraphic(null);
@@ -356,30 +772,41 @@ public class DataTreeCell extends TextFieldTreeCell<DataNode> {
setContextMenu(null);
} else {
setText(item.toString());
- if(/*!item.getType().equals(DataNodeType.ITINERARY) && */item.getFile() != null) {
+ if(item.getFile() != null) {
if(item.getFile().isSelectedInTree()) {
setBackground(new Background(new BackgroundFill(Color.DEEPSKYBLUE,CornerRadii.EMPTY,Insets.EMPTY)));
} else {
setBackground(null);
}
+ }
+ if (item.getType().equals(DataNodeType.PROCESS)) {
+ GeneralFile processFile = (GeneralFile)item.getFile();
+// setContentDisplay(ContentDisplay.RIGHT);
+ if(processFile.getListReplicate().size() > 1) {
+ Label l = new Label();
+ l.textProperty().bind(item.nameProperty());
+ ComboBox<Replicate> comboReplicate = new ComboBox<>();
+ comboReplicate.setItems(processFile.getListReplicate());
+ if(processFile.getCurrentReplicate() != null) {
+ comboReplicate.setValue(processFile.getCurrentReplicate());
+ }
+ comboReplicate.getSelectionModel().selectedItemProperty().addListener((observable, oldValue, newValue) -> {
+ if(newValue != null && newValue != oldValue) {
+ processFile.setCurrentReplicate(newValue);
+ if(MainApp.getDataControler().getTree().getSelectionModel().getSelectedItem() != null) {
+ DataNode currentSelectedNode = MainApp.getDataControler().getTree().getSelectionModel().getSelectedItem().getValue();
+ if(currentSelectedNode.getType().equals(DataNodeType.OBSERVATION) || currentSelectedNode.getType().equals(DataNodeType.STEP) || currentSelectedNode.getType().equals(DataNodeType.PROCESS) ) {
+ MainApp.getDataControler().showNodeDetails(currentSelectedNode, currentSelectedNode);
+ }
+ }
+ }
+ });
+ setText("");
+ setGraphic(new HBox(item.getGraphic(), l, comboReplicate));
+ }
}
-// if(item.getType().equals(DataNodeType.ITINERARY) ) {
-// if(item.getItineraryFile().getItiPart().isSelectedInTree()) {
-// setBackground(new Background(new BackgroundFill(Color.DEEPSKYBLUE,CornerRadii.EMPTY,Insets.EMPTY)));
-// } else {
-// setBackground(null);
-// }
-// }
-// if(item.getItineraryPart() != null) {
-// if(item.getItineraryPart().isSelectedInTree()) {
-// setBackground(new Background(new BackgroundFill(Color.LIGHTGRAY,CornerRadii.EMPTY,Insets.EMPTY)));
-// } else {
-// setBackground(null);
-// }
-//
-// }
setEditable(false);
ContextMenu menu = new ContextMenu();
switch (item.getType()) {
@@ -658,6 +1085,19 @@ public class DataTreeCell extends TextFieldTreeCell<DataNode> {
menu.getItems().add(downloadSHACLConstraints);
break;
case PROCESS:
+ MenuItem newRep = new MenuItem("New biological replicate");
+ newRep.setGraphic(new ImageView(UITools.getImage("resources/images/treeview/replicate_16.png")));
+ newRep.disableProperty().bind(Bindings.not(mainApp.getEditProperty()));
+ newRep.setOnAction(event -> {
+ GeneralFile current = (GeneralFile) item.getFile();
+ Replicate newReplicate = current.addReplicate("new replicate", "");
+ if(newReplicate != null) {
+ current.setCurrentReplicate(newReplicate);
+ MainApp.getDataControler().showNodeDetails(getItem(), getItem());
+ }
+ });
+ menu.getItems().add(newRep);
+
Menu newIti = new Menu("New Itinerary");
newIti.setGraphic(new ImageView(UITools.getImage("resources/images/treeview/itinerary.png")));
newIti.disableProperty().bind(Bindings.not(mainApp.getEditProperty()));
@@ -752,6 +1192,7 @@ public class DataTreeCell extends TextFieldTreeCell<DataNode> {
menu.getItems().add(deleteProcess);
break;
case OBSERVATION:
+ ObservationFile obsFile = (ObservationFile) item.getFile();
MenuItem addDataObs = new MenuItem("New Data Table");
addDataObs.setGraphic(new ImageView(UITools.getImage("resources/images/add_16.png")));
addDataObs.disableProperty().bind(Bindings.not(mainApp.getEditProperty()));
@@ -797,166 +1238,78 @@ public class DataTreeCell extends TextFieldTreeCell<DataNode> {
});
menu.getItems().add(addDataObs);
- MenuItem exportObs = new MenuItem("Export Observation");
- exportObs.setGraphic(new ImageView(UITools.getImage("resources/images/file-export-16.png")));
- exportObs.setOnAction(event -> {
-
- List<String> choices = new ArrayList<>();
- choices.add("with ontology");
- choices.add("without ontology");
- ChoiceDialog<String> dialog = new ChoiceDialog<>("without ontology", choices);
- dialog.setTitle("Export Observation");
- dialog.setHeaderText(null);
- dialog.setContentText("Export Observation data ");
- dialog.initModality(Modality.WINDOW_MODAL);
- dialog.initOwner(MainApp.primaryStage);
- Boolean exportOnto = false;
- Optional<String> result = dialog.showAndWait();
-
- if (result.isPresent() ) {
- exportOnto = result.get().equals("with ontology");
- Boolean finalExportOnto = exportOnto;
- if (exportOnto && mainApp.getOntologyControler().getCurrentOntology() == null) {
- Alert noOntology = new Alert(Alert.AlertType.ERROR);
- noOntology.setTitle("No ontology loaded");
- noOntology.setHeaderText("Please load an ontology");
- noOntology.setContentText("In order to create an export file, please load the corresponding ontology");
- noOntology.initOwner(MainApp.primaryStage);
- noOntology.initModality(Modality.APPLICATION_MODAL);
- noOntology.showAndWait();
- } else {
- ObservationFile file = (ObservationFile) item.getFile();
- XSSFWorkbook book = new XSSFWorkbook();
-
-
- Task<Boolean> taskExport = new Task<Boolean>() {
- @Override
- protected Boolean call() throws Exception {
- XSSFSheet sheet = Tools.createSheet(book,"obs|"+Tools.removeNonAlphaNumChar(file.getNameProperty().getValue()));
-
- Integer compteur = 0;
- Integer maxColumn = 0;
- for (LinkedList<String> line : file.getDataForExcel()) {
- XSSFRow r = sheet.createRow(compteur++);
- Integer compteurCell = 0;
- for (String val : line) {
- r.createCell(compteurCell++).setCellValue(val);
- maxColumn = Math.max(maxColumn, compteurCell);
- }
- }
- Tools.autoResize(sheet, maxColumn);
+ GeneralFile processFile = null;
+ if(obsFile.getStepFile() != null) {
+ processFile = obsFile.getStepFile().getGeneralFile();
+ } else {
+ processFile = obsFile.getItineraryFile().getProcessFile();
+ }
+ if(processFile.getListReplicate().size() > 1) {
+ Menu exportObs = new Menu("Export Observation");
+ exportObs.setGraphic(new ImageView(UITools.getImage("resources/images/file-export-16.png")));
- if(finalExportOnto) {
+ MenuItem exportCurRep = new MenuItem("for current replicate");
+ GeneralFile finalProcessFile = processFile;
+ exportCurRep.setOnAction(event -> {
+ exportObservation(obsFile, finalProcessFile.getCurrentReplicate().getId());
+ });
+ MenuItem exportAllRep = new MenuItem("for all replicates");
+ exportAllRep.setOnAction(event -> {
+ exportObservation(obsFile, -1);
+ });
- JSONObject hierarchyVocab = mainApp.getOntologyControler().getHierarchyVocabJSON();
- // Récupération de l'ontology au format JSON
- XSSFSheet sheetOntoVocab = Tools.createSheet(book,"onto-vocab|" + Tools.removeNonAlphaNumChar(mainApp.getOntologyControler().getCurrentOntology().getName().getValue()));
- JSONArray vocab = (JSONArray) hierarchyVocab.get("vocabulary");
+ exportObs.getItems().add(exportCurRep);
+ exportObs.getItems().add(exportAllRep);
+ menu.getItems().add(exportObs);
+ } else {
+ MenuItem exportObs = new MenuItem("Export Observation");
+ exportObs.setGraphic(new ImageView(UITools.getImage("resources/images/file-export-16.png")));
+ exportObs.setOnAction(event -> {
+ exportObservation(obsFile, 0);
+ });
+ menu.getItems().add(exportObs);
+ }
- compteur = 0;
- maxColumn = 0;
- for (
- int i = 0; i < vocab.length(); i++) {
- JSONArray array = (JSONArray) vocab.get(i);
- XSSFRow r = sheetOntoVocab.createRow(compteur++);
- for (int j = 0; j < array.length(); j++) {
- r.createCell(j).setCellValue((String) array.get(j));
- maxColumn = Math.max(maxColumn, j);
- }
- }
- Tools.autoResize(sheetOntoVocab, maxColumn);
- XSSFSheet sheetOntohierarchy = Tools.createSheet(book,"onto-hierarchy|" + Tools.removeNonAlphaNumChar(mainApp.getOntologyControler().getCurrentOntology().getName().getValue()));
- JSONArray hierarchy = (JSONArray) hierarchyVocab.get("hierarchy");
- compteur = 0;
- maxColumn = 0;
+ if(processFile.getListReplicate().size() > 1) {
+ Menu importObs = new Menu("Import Observation");
+ importObs.disableProperty().bind(Bindings.not(mainApp.getEditProperty()));
+ importObs.setGraphic(new ImageView(UITools.getImage("resources/images/file-import-16.png")));
- for (
- int x = 0; x < hierarchy.length(); x++) {
- XSSFRow r = sheetOntohierarchy.createRow(compteur++);
- JSONArray arrayDesc = (JSONArray) hierarchy.get(x);
- for (int j = 0; j < arrayDesc.length(); j++) {
- r.createCell(j).setCellValue((String) arrayDesc.get(j));
- maxColumn = Math.max(maxColumn, j);
- }
- }
- Tools.autoResize(sheetOntohierarchy, maxColumn);
- }
- return true;
- }
- };
- taskExport.setOnSucceeded(workerStateEvent -> {
- FileChooser fileChooser = new FileChooser();
- fileChooser.setTitle("Export file");
- fileChooser.setInitialFileName(file.getFileName()+".xlsx");
- File fileExport = fileChooser.showSaveDialog(MainApp.primaryStage);
- if (fileExport != null) {
- try {
- FileOutputStream fout = new FileOutputStream(fileExport, false);
- book.write(fout);
- fout.close();
- } catch (IOException ex) {
- MainApp.logger.error(ex.getMessage());
- }
- }
- });
- new Thread(taskExport).start();
- }
- }
- });
- menu.getItems().add(exportObs);
-
- MenuItem importObs = new MenuItem("Import Observation");
- importObs.setGraphic(new ImageView(UITools.getImage("resources/images/file-import-16.png")));
- importObs.disableProperty().bind(Bindings.not(mainApp.getEditProperty()));
- importObs.setOnAction(event -> {
- ObservationFile file = (ObservationFile) item.getFile();
- File fileImport = getFile(mainApp.primaryStage);
- if (fileImport != null) {
- MainApp.logger.info("start importing/update file " + fileImport.getName());
- // temp obs file
- ObservationFile tempF = null;
- if(file.getStepFile() != null) {
- Report r = file.getStepFile().checkUpdateObservationFromXLSX(fileImport, file);
- if(r.success()) {
- file.getStepFile().updateObservationFromXLSX(fileImport, file);
- MainApp.getDataControler().refreshTree();
- MainApp.getDataControler().showNodeDetails(file, file);
- MainApp.logger.info("import done with sucess");
- } else {
- showErrorImportAlert(r.prettyPrintError());
- }
- }
- if(file.getItineraryFile() != null) {
- Report r = file.getItineraryFile().checkUpdateObservationFromXLSX(fileImport, file);
- if(r.success()) {
- file.getItineraryFile().updateObservationFromXLSX(fileImport, file);
- MainApp.getDataControler().refreshTree();
- MainApp.getDataControler().showNodeDetails(file, file);
- MainApp.logger.info("import done with sucess");
- } else {
- showErrorImportAlert(r.prettyPrintError());
- }
- }
- }
- });
- menu.getItems().add(importObs);
+ MenuItem importCurRep = new MenuItem("for current replicate");
+ importCurRep.disableProperty().bind(Bindings.not(mainApp.getEditProperty()));
+ GeneralFile finalProcessFile = processFile;
+ importCurRep.setOnAction(event -> {
+ importObservation(obsFile, finalProcessFile.getCurrentReplicate().getId());
+ });
+ MenuItem importAllRep = new MenuItem("for all replicates");
+ importAllRep.disableProperty().bind(Bindings.not(mainApp.getEditProperty()));
+ importAllRep.setOnAction(event -> {
+ importObservation(obsFile, -1);
+ });
+
+ importObs.getItems().add(importCurRep);
+ importObs.getItems().add(importAllRep);
+ menu.getItems().add(importObs);
+ } else {
+ MenuItem importObs = new MenuItem("Import Observation");
+ importObs.disableProperty().bind(Bindings.not(mainApp.getEditProperty()));
+ importObs.setGraphic(new ImageView(UITools.getImage("resources/images/file-import-16.png")));
+ importObs.setOnAction(event -> {
+ importObservation(obsFile, 0);
+ });
+ menu.getItems().add(importObs);
+ }
MenuItem moveObs = new MenuItem("Move Observation");
moveObs.setGraphic(new ImageView(UITools.getImage("resources/images/move_16.png")));
moveObs.disableProperty().bind(Bindings.not(mainApp.getEditProperty()));
menu.getItems().add(moveObs);
+ GeneralFile finalProcessFile2 = processFile;
moveObs.setOnAction(event -> {
- ObservationFile obsFile = (ObservationFile) item.getFile();
- GeneralFile processFile = null;
- if(obsFile.getStepFile() != null) {
- processFile = obsFile.getStepFile().getGeneralFile();
- } else {
- processFile = obsFile.getItineraryFile().getProcessFile();
- }
Dialog<ButtonType> moveObsDiag = new Dialog<>();
moveObsDiag.getDialogPane().setPrefSize(500, 400);
moveObsDiag.initModality(Modality.WINDOW_MODAL);
@@ -970,7 +1323,7 @@ public class DataTreeCell extends TextFieldTreeCell<DataNode> {
treeStep.setCellFactory(factory -> new TextFieldTreeCell<>(){});
treeStep.setShowRoot(false);
- processFile.getItinerary().forEach(itiFile -> {
+ finalProcessFile2.getItinerary().forEach(itiFile -> {
TreeItem<GenericFile> ckIti = new TreeItem<>(itiFile);
fakeRoot.getChildren().add(ckIti);
itiFile.getListStep().forEach(step -> {
@@ -1044,7 +1397,7 @@ public class DataTreeCell extends TextFieldTreeCell<DataNode> {
case STEP:
StepFile s = (StepFile) item.getFile();
-
+ processFile = s.getGeneralFile();
Menu newSubStep = new Menu("New SubStep");
newSubStep.setGraphic(new ImageView(UITools.getImage("resources/images/treeview/step.png")));
newSubStep.disableProperty().bind(Bindings.not(mainApp.getEditProperty()));
@@ -1067,7 +1420,7 @@ public class DataTreeCell extends TextFieldTreeCell<DataNode> {
addProcessSubStepFromCSV.setGraphic(new ImageView(UITools.getImage("resources/images/treeview/step_csv.png")));
addProcessSubStepFromCSV.disableProperty().bind(Bindings.not(mainApp.getEditProperty()));
addProcessSubStepFromCSV.setOnAction(event -> {
- newStepImport(item.getItineraryFile(), s);
+ newStepImport(item.getItineraryFile(), s, -1);
});
newSubStep.getItems().add(newSubStepFC);
@@ -1098,7 +1451,7 @@ public class DataTreeCell extends TextFieldTreeCell<DataNode> {
addNewStepObservationFromCsv.setGraphic(new ImageView(UITools.getImage("resources/images/treeview/observation_csv.png")));
addNewStepObservationFromCsv.disableProperty().bind(Bindings.not(mainApp.getEditProperty()));
addNewStepObservationFromCsv.setOnAction(event -> {
- newStepObsImport(s);
+ newStepObsImport(s, -1);
});
newObs.getItems().add(newObsFC);
@@ -1210,9 +1563,10 @@ public class DataTreeCell extends TextFieldTreeCell<DataNode> {
moveStep.setDisable(false);
moveStep.disableProperty().bind(Bindings.not(mainApp.getEditProperty()));
moveStep.setGraphic(new ImageView(UITools.getImage("resources/images/move_16.png")));
+ GeneralFile finalProcessFile1 = processFile;
moveStep.setOnAction(event -> {
StepFile stepFile = (StepFile) item.getFile();
- GeneralFile processFile = stepFile.getGeneralFile();
+// GeneralFile processFile = stepFile.getGeneralFile();
Dialog<ButtonType> moveStepDiag = new Dialog<>();
moveStepDiag.getDialogPane().setPrefSize(500, 400);
@@ -1227,7 +1581,7 @@ public class DataTreeCell extends TextFieldTreeCell<DataNode> {
treeStep.setCellFactory(factory -> new TextFieldTreeCell<>(){});
treeStep.setShowRoot(false);
- processFile.getItinerary().forEach(itiFile -> {
+ finalProcessFile1.getItinerary().forEach(itiFile -> {
TreeItem<GenericFile> ckIti = new TreeItem<>(itiFile);
fakeRoot.getChildren().add(ckIti);
itiFile.getListStep().forEach(step -> {
@@ -1268,12 +1622,12 @@ public class DataTreeCell extends TextFieldTreeCell<DataNode> {
if(moveTo instanceof StepFile) {
StepFile stepFileFather = (StepFile) moveTo;
stepFileFather.addSubStep(stepFile);
- for(ItineraryFile iti : processFile.getItinerary()) {
+ for(ItineraryFile iti : finalProcessFile1.getItinerary()) {
if(iti.contains(stepFileFather)) {
iti.addStep(stepFile);
}
}
- MainApp.getDataControler().buildProcessTree(processFile);
+ MainApp.getDataControler().buildProcessTree(finalProcessFile1);
}
MainApp.getDataControler().selectNode(stepFile);
}
@@ -1284,154 +1638,59 @@ public class DataTreeCell extends TextFieldTreeCell<DataNode> {
menu.getItems().add(moveStep);
- MenuItem exportStep = new MenuItem("Export Step");
- exportStep.setDisable(false);
- exportStep.setGraphic(new ImageView(UITools.getImage("resources/images/file-export-16.png")));
- exportStep.setOnAction(event -> {
- List<String> choices = new ArrayList<>();
- choices.add("with ontology");
- choices.add("without ontology");
- ChoiceDialog<String> dialog = new ChoiceDialog<>("without ontology", choices);
- dialog.setTitle("Export Step");
- dialog.setHeaderText(null);
- dialog.setContentText("Export step data ");
- dialog.initModality(Modality.WINDOW_MODAL);
- dialog.initOwner(MainApp.primaryStage);
- Boolean exportOnto = false;
- Optional<String> result = dialog.showAndWait();
-
- if (result.isPresent() ) {
- exportOnto = result.get().equals("with ontology");
- if(exportOnto && mainApp.getOntologyControler().getCurrentOntology() == null) {
- Alert noOntology = new Alert(Alert.AlertType.ERROR);
- noOntology.setTitle("No ontology loaded");
- noOntology.setHeaderText("Please load an ontology");
- noOntology.setContentText("In order to create an export file, please load the corresponding ontology");
- noOntology.initOwner(MainApp.primaryStage);
- noOntology.initModality(Modality.APPLICATION_MODAL);
- noOntology.showAndWait();
- } else {
- XSSFWorkbook book = new XSSFWorkbook();
- Boolean finalExportOnto = exportOnto;
- Task<Boolean> taskExport = new Task<Boolean>() {
- @Override
- protected Boolean call() throws Exception {
- XSSFSheet sheet = Tools.createSheet(book,"step|"+ DigestUtils.md5Hex(s.getNameProperty().getValue()));
-
- Integer compteur = 0;
- Integer maxColumn = 0;
-
- for (LinkedList<String> line : s.getDataForExcel(true)) {
- XSSFRow r = sheet.createRow(compteur++);
- Integer compteurCell = 0;
- for (String val : line) {
- r.createCell(compteurCell++).setCellValue(val);
- maxColumn = Math.max(maxColumn, compteurCell);
- }
- }
-
-
- // composition
- for (Map.Entry<CompositionFile, Boolean> entry : s.getCompositionFile().entrySet()) {
- XSSFSheet sheetCompo = Tools.createSheet(book,"compo-"+(entry.getValue() ? "input" : "output")+"|"+Tools.removeNonAlphaNumChar(entry.getKey().getCompositionID().getValue().get()));
- Integer compteurCompo = 0;
- Integer maxColumnCompo = 0;
- for (LinkedList<String> line : entry.getKey().getDataForExcel()) {
- XSSFRow r = sheetCompo.createRow(compteurCompo++);
- Integer compteurCell = 0;
- for (String val : line) {
- r.createCell(compteurCell++).setCellValue(val);
- maxColumnCompo = Math.max(maxColumnCompo, compteurCell);
- }
- }
- Tools.autoResize(sheetCompo, maxColumnCompo);
- }
-
-
+ if(processFile.getListReplicate().size() > 1) {
+ Menu exportStep = new Menu("Export Step");
+ exportStep.setGraphic(new ImageView(UITools.getImage("resources/images/file-export-16.png")));
- Tools.autoResize(sheet, maxColumn);
-
- for(ObservationFile obs : s.getObservationFiles()) {
- XSSFSheet sheetObs = Tools.createSheet(book,"obs|"+Tools.removeNonAlphaNumChar(obs.getCID().getValue().get()));
-
- Integer compteurObs = 0;
- Integer maxColumnObs = 0;
- for (LinkedList<String> line : obs.getDataForExcel()) {
- XSSFRow r = sheetObs.createRow(compteurObs++);
- Integer compteurCell = 0;
- for (String val : line) {
- r.createCell(compteurCell++).setCellValue(val);
- maxColumnObs = Math.max(maxColumnObs, compteurCell);
- }
- }
- Tools.autoResize(sheetObs, maxColumnObs);
- }
+ MenuItem exportCurRep = new MenuItem("for current replicate");
+ GeneralFile finalProcessFile = processFile;
+ exportCurRep.setOnAction(event -> {
+ exportStepFile(s, finalProcessFile.getCurrentReplicate().getId());
+ });
+ MenuItem exportAllRep = new MenuItem("for all replicates");
+ exportAllRep.setOnAction(event -> {
+ exportStepFile(s, -1);
+ });
- if(finalExportOnto) {
-
- JSONObject hierarchyVocab = mainApp.getOntologyControler().getHierarchyVocabJSON();
- // Récupération de l'ontology au format JSON
- XSSFSheet sheetOntoVocab = Tools.createSheet(book,"onto-vocab|" + Tools.removeNonAlphaNumChar(mainApp.getOntologyControler().getCurrentOntology().getName().getValue()));
- JSONArray vocab = (JSONArray) hierarchyVocab.get("vocabulary");
-
- compteur = 0;
- maxColumn = 0;
- for (int i = 0; i < vocab.length(); i++) {
- JSONArray array = (JSONArray) vocab.get(i);
- XSSFRow r = sheetOntoVocab.createRow(compteur++);
- for (int j = 0; j < array.length(); j++) {
- r.createCell(j).setCellValue((String) array.get(j));
- maxColumn = Math.max(maxColumn, j);
- }
- }
- Tools.autoResize(sheetOntoVocab, maxColumn);
+ exportStep.getItems().add(exportCurRep);
+ exportStep.getItems().add(exportAllRep);
+ menu.getItems().add(exportStep);
+ } else {
+ MenuItem exportStep = new MenuItem("Export Step");
+ exportStep.setGraphic(new ImageView(UITools.getImage("resources/images/file-export-16.png")));
+ exportStep.setOnAction(event -> {
+ exportStepFile(s, 0);
+ });
+ menu.getItems().add(exportStep);
+ }
- XSSFSheet sheetOntohierarchy = Tools.createSheet(book,"onto-hierarchy|" + Tools.removeNonAlphaNumChar(mainApp.getOntologyControler().getCurrentOntology().getName().getValue()));
- JSONArray hierarchy = (JSONArray) hierarchyVocab.get("hierarchy");
+ if(processFile.getListReplicate().size() > 1) {
+ Menu importStep = new Menu("Import Step");
+ importStep.setGraphic(new ImageView(UITools.getImage("resources/images/file-import-16.png")));
- compteur = 0;
- maxColumn = 0;
+ MenuItem importCurRep = new MenuItem("for current replicate");
+ GeneralFile finalProcessFile = processFile;
+ importCurRep.setOnAction(event -> {
+ stepImport(s, false, finalProcessFile.getCurrentReplicate().getId());
+ });
+ MenuItem importAllRep = new MenuItem("for all replicates");
+ importAllRep.setOnAction(event -> {
+ stepImport(s, false, -1);
+ });
- for (int x = 0; x < hierarchy.length(); x++) {
- XSSFRow r = sheetOntohierarchy.createRow(compteur++);
- JSONArray arrayDesc = (JSONArray) hierarchy.get(x);
- for (int j = 0; j < arrayDesc.length(); j++) {
- r.createCell(j).setCellValue((String) arrayDesc.get(j));
- maxColumn = Math.max(maxColumn, j);
- }
- }
- Tools.autoResize(sheetOntohierarchy, maxColumn);
- }
- return true;
- }
- };
- taskExport.setOnSucceeded(workerStateEvent -> {
- FileChooser fileChooser = new FileChooser();
- fileChooser.setTitle("Export file");
- fileChooser.setInitialFileName(s.getNameProperty().getValue()+".xlsx");
- File fileExport = fileChooser.showSaveDialog(MainApp.primaryStage);
- if (fileExport != null) {
- try {
- FileOutputStream fout = new FileOutputStream(fileExport, false);
- book.write(fout);
- fout.close();
- } catch (IOException ex) {
- MainApp.logger.error(ex.getMessage());
- }
- }
- });
- new Thread(taskExport).start();
- }
- }
- });
- menu.getItems().add(exportStep);
+ importStep.getItems().add(importCurRep);
+ importStep.getItems().add(importAllRep);
+ menu.getItems().add(importStep);
+ } else {
+ MenuItem importStep = new MenuItem("Export Step");
+ importStep.setGraphic(new ImageView(UITools.getImage("resources/images/file-export-16.png")));
+ importStep.setOnAction(event -> {
+ stepImport(s, false, 0);
+ });
+ menu.getItems().add(importStep);
+ }
- MenuItem importStep = new MenuItem("Import Step");
- importStep.setGraphic(new ImageView(UITools.getImage("resources/images/file-import-16.png")));
- importStep.disableProperty().bind(Bindings.not(mainApp.getEditProperty()));
- importStep.setOnAction(event -> stepImport((StepFile) item.getFile(), false));
- menu.getItems().add(importStep);
MenuItem deleteStepButton = new MenuItem("Delete Step");
deleteStepButton.setGraphic(new ImageView(UITools.getImage("resources/images/del_16.png")));
@@ -1537,7 +1796,7 @@ public class DataTreeCell extends TextFieldTreeCell<DataNode> {
addProcessStepFromCSV.disableProperty().bind(Bindings.not(mainApp.getEditProperty()));
addProcessStepFromCSV.setOnAction(event -> {
ItineraryFile iti = (ItineraryFile) item.getFile();
- newStepImport(iti, null);
+ newStepImport(iti, null, -1);
});
newStep.getItems().add(addProcessStep);
@@ -1573,7 +1832,7 @@ public class DataTreeCell extends TextFieldTreeCell<DataNode> {
addNewItineraryObservationFromCsv.disableProperty().bind(Bindings.not(mainApp.getEditProperty()));
addNewItineraryObservationFromCsv.setOnAction(event -> {
ItineraryFile iti = (ItineraryFile) item.getFile();
- newItineraryObsImport(iti);
+ newItineraryObsImport(iti, -1);
});
newObsIti.getItems().add(newObsItiFC);
@@ -1593,136 +1852,4 @@ public class DataTreeCell extends TextFieldTreeCell<DataNode> {
this.setContextMenu(menu);
}
}
-
- private static void stepImport(StepFile file, boolean isNewStep) {
- File fileImport = getFile(MainApp.primaryStage);
- if (fileImport != null) {
- MainApp.logger.info("start importing file " + fileImport.getName());
- ImportReport importReport = file.realPreConst(fileImport, isNewStep);
- if(importReport.success()) {
-
- // validation de l'import par l'utilisateur
- Dialog<ButtonType> validateImport = new Dialog();
- validateImport.setTitle("import validation");
- validateImport.initOwner(MainApp.primaryStage);
- validateImport.initModality(Modality.WINDOW_MODAL);
- ButtonType importButtonType = new ButtonType("Import", ButtonBar.ButtonData.OK_DONE);
- validateImport.getDialogPane().getButtonTypes().addAll(importButtonType, ButtonType.CANCEL);
-
- GridPane paneImport = new GridPane();
- paneImport.setHgap(20);
- paneImport.setVgap(20);
-
- Integer comptLine = 0;
- Text stepText = new Text(file.getNameProperty().getValue());
- Text sepa = new Text(" : ");
- paneImport.add(new ImageView(UITools.getImage("resources/images/treeview/step.png")), 0, comptLine);
- paneImport.add(stepText, 1, comptLine);
- paneImport.add(sepa, 2, comptLine);
- paneImport.add(new ImageView(UITools.getImage("resources/images/update_30.png")), 3, comptLine);
-
- comptLine++;
-
-
- for (ObservationFile obsF : file.getObservationFiles()) {
- Text obsText = new Text(obsF.getCID().getValue().get());
- Text sepa2 = new Text(" : ");
- paneImport.add(new ImageView(UITools.getImage("resources/images/treeview/observation.png")), 0, comptLine);
- paneImport.add(obsText, 1, comptLine);
- paneImport.add(sepa2, 2, comptLine);
- if (importReport.getObsMapping().containsValue(obsF)) {
- paneImport.add(new ImageView(UITools.getImage("resources/images/update_30.png")), 3, comptLine);
- } else {
- paneImport.add(new ImageView(UITools.getImage("resources/images/del_30.png")), 3, comptLine);
- }
- comptLine++;
- }
-
- for(XSSFSheet oo : importReport.getObsMapping().keySet()) {
- if(importReport.getObsMapping().get(oo) == null) { // new obs
- Text obsText = new Text(oo.getSheetName());
- Text sepa2 = new Text(" : ");
- paneImport.add(new ImageView(UITools.getImage("resources/images/treeview/observation.png")), 0, comptLine);
- paneImport.add(obsText, 1, comptLine);
- paneImport.add(sepa2, 2, comptLine);
- paneImport.add(new ImageView(UITools.getImage("resources/images/add_30.png")), 3, comptLine);
- comptLine++;
- }
- }
-
- for (CompositionFile compoF : file.getCompositionFile().keySet()) {
- Text compoText = new Text(compoF.getCompositionID().getValue().get());
- Text sepa2 = new Text(" : ");
- paneImport.add(new ImageView(UITools.getImage("resources/images/treeview/composition.png")), 0, comptLine);
- paneImport.add(compoText, 1, comptLine);
- paneImport.add(sepa2, 2, comptLine);
- if(importReport.getCompoMapping().values().stream().map(org.apache.commons.lang3.tuple.Pair::getLeft).noneMatch(c -> c.equals(compoF))) {
- paneImport.add(new ImageView(UITools.getImage("resources/images/del_30.png")), 3, comptLine);
- } else {
- paneImport.add(new ImageView(UITools.getImage("resources/images/update_30.png")), 3, comptLine);
- }
- comptLine++;
- }
-
- for(XSSFSheet oo : importReport.getCompoMapping().keySet()) {
- if(importReport.getCompoMapping().get(oo).getLeft() == null) { // new Compo
- Text compoText = new Text(oo.getSheetName());
- Text sepa2 = new Text(" : ");
- paneImport.add(new ImageView(UITools.getImage("resources/images/treeview/composition.png")), 0, comptLine);
- paneImport.add(compoText, 1, comptLine);
- paneImport.add(sepa2, 2, comptLine);
- paneImport.add(new ImageView(UITools.getImage("resources/images/add_30.png")), 3, comptLine);
- comptLine++;
- }
- }
-
- validateImport.getDialogPane().setContent(paneImport);
- Optional<ButtonType> result = Optional.empty();
- if(!isNewStep) {
- result = validateImport.showAndWait();
- }
- if (isNewStep || result.isPresent() && result.get() == importButtonType) {
- // l'utilisateur valide la la mise à jour
- Report report = file.constructDataFromImport(fileImport, isNewStep);
- handleInterfaceUpdate(file.getGeneralFile(), report.success(), report.toString());
- MainApp.getDataControler().selectNode(file);
- }
-
- } else {
- showErrorImportAlert(importReport.toString());
- }
- } else {
- }
- }
-
- private static void handleInterfaceUpdate(GeneralFile file, boolean reportBoolean, String reportString) {
- if(reportBoolean) {
- MainApp.getDataControler().buildProcessTree(file);
- showOkImportAlert();
- } else {
- showErrorImportAlert(reportString);
- }
- }
-
- private static void showErrorImportAlert(String report) {
- Alert errorImport = new Alert(Alert.AlertType.ERROR);
- errorImport.setTitle("Import error");
- errorImport.setContentText(report);
- errorImport.initModality(Modality.APPLICATION_MODAL);
- errorImport.initOwner(MainApp.primaryStage);
- errorImport.showAndWait();
- }
-
- private static void showOkImportAlert() {
- Alert okImport = new Alert(Alert.AlertType.INFORMATION);
- okImport.setGraphic(new ImageView(UITools.getImage("resources/images/valid.png")));
- okImport.setHeaderText(null);
- okImport.setTitle("Successful import");
- okImport.setContentText("Successful import");
- okImport.initModality(Modality.APPLICATION_MODAL);
- okImport.initOwner(MainApp.primaryStage);
- okImport.showAndWait();
- }
-
-
}
diff --git a/src/main/java/fr/inra/po2vocabmanager/utils/UITools.java b/src/main/java/fr/inra/po2vocabmanager/utils/UITools.java
index d4ed78b183fd82f9b0180e7da7ea8914797c7031..a087e37f7f999465d4ea4ad978df17a7e26e4dae 100644
--- a/src/main/java/fr/inra/po2vocabmanager/utils/UITools.java
+++ b/src/main/java/fr/inra/po2vocabmanager/utils/UITools.java
@@ -20,9 +20,7 @@ package fr.inra.po2vocabmanager.utils;
import fr.inra.po2vocabmanager.MainApp;
import fr.inrae.po2engine.externalTools.CloudConnector;
-import fr.inrae.po2engine.model.ComplexField;
-import fr.inrae.po2engine.model.Ontology;
-import fr.inrae.po2engine.model.VocabConcept;
+import fr.inrae.po2engine.model.*;
import fr.inrae.po2engine.model.dataModel.KeyWords;
import fr.inrae.po2engine.model.partModel.ComplexTable;
import fr.inrae.po2engine.model.partModel.GenericTable;
@@ -39,10 +37,12 @@ import javafx.beans.property.ObjectProperty;
import javafx.beans.property.SimpleObjectProperty;
import javafx.beans.property.SimpleStringProperty;
import javafx.beans.property.StringProperty;
+import javafx.beans.value.ChangeListener;
import javafx.beans.value.ObservableValue;
import javafx.collections.FXCollections;
import javafx.collections.MapChangeListener;
import javafx.collections.ObservableList;
+import javafx.collections.ObservableMap;
import javafx.collections.transformation.FilteredList;
import javafx.concurrent.Task;
import javafx.event.ActionEvent;
@@ -562,13 +562,26 @@ public class UITools {
tField.styleProperty().bind(Bindings.when(cField.stateProperty().isEqualTo(FieldState.WARNING)).then("-fx-border-color: orange;").otherwise(Bindings.when(cField.stateProperty().isEqualTo(FieldState.ERROR)).then("-fx-border-color: red;").otherwise("")));
}
public static void simpleBindValue(ComplexField cField, TextField tField) {
- cField.getValue().unbind();
+ cField.unbindReplicatesValues();
tField.setText(cField.getValue().getValue());
cField.getValue().bind(tField.textProperty());
tField.styleProperty().unbind();
tField.styleProperty().bind(Bindings.when(cField.stateProperty().isEqualTo(FieldState.WARNING)).then("-fx-border-color: orange;").otherwise(Bindings.when(cField.stateProperty().isEqualTo(FieldState.ERROR)).then("-fx-border-color: red;").otherwise("")));
}
+ public static void simpleBindValue(ComplexField cField, Replicate replicate, TextField tField) {
+ cField.unbindReplicatesValues();
+ int replicateID = replicate != null ? replicate.getId() : 0;
+ tField.setText(cField.getValueWithReplicate(replicateID).getValue());
+ cField.getValueWithReplicate(replicateID).bind(tField.textProperty());
+ tField.styleProperty().unbind();
+ if(replicate == null) {
+ tField.styleProperty().bind(Bindings.when(cField.stateProperty().isEqualTo(FieldState.WARNING)).then("-fx-border-color: orange;").otherwise(Bindings.when(cField.stateProperty().isEqualTo(FieldState.ERROR)).then("-fx-border-color: red;").otherwise("")));
+ } else {
+ tField.styleProperty().bind(Bindings.when(cField.stateProperty().isEqualTo(FieldState.WARNING)).then("-fx-border-color: orange;").otherwise(Bindings.when(cField.stateProperty().isEqualTo(FieldState.ERROR)).then("-fx-border-color: red;").otherwise("-fx-border-color: DarkSlateBlue;")));
+ }
+ }
+
public static void simpleBindValue(ComplexField cField, TextArea tField) {
cField.getValue().unbind();
tField.setText(cField.getValue().getValue());
@@ -577,6 +590,68 @@ public class UITools {
tField.styleProperty().bind(Bindings.when(cField.stateProperty().isEqualTo(FieldState.WARNING)).then("-fx-border-color: orange;").otherwise(Bindings.when(cField.stateProperty().isEqualTo(FieldState.ERROR)).then("-fx-border-color: red;").otherwise("")));
}
+ public static void bindComboBoxAgent(ObservableMap<Integer, ObjectProperty<HashMap<KeyWords, ComplexField>>> agentProp, ObservableList<HashMap<KeyWords, ComplexField>> list, Replicate replicate, ComboBox<HashMap<KeyWords, ComplexField>> comboField) {
+ int replicateID = replicate != null ? replicate.getId() : 0;
+ comboField.setConverter(new StringConverter<HashMap<KeyWords, ComplexField>>() {
+ @Override
+ public String toString(HashMap<KeyWords, ComplexField> keyWordsComplexFieldHashMap) {
+ if (keyWordsComplexFieldHashMap == null){
+ return null;
+ } else {
+ return Tools.agentToString(keyWordsComplexFieldHashMap);
+ }
+ }
+
+ @Override
+ public HashMap<KeyWords, ComplexField> fromString(String s) {
+ HashMap<KeyWords, ComplexField> val = list.stream().filter(keyWordsComplexFieldHashMap -> {
+ return s.equalsIgnoreCase(Tools.agentToString(keyWordsComplexFieldHashMap));
+ }).findFirst().orElse(null);
+ return val;
+ }
+ });
+ comboField.setCellFactory(p -> {
+ return new ListCell<HashMap<KeyWords, ComplexField>>() {
+
+ @Override
+ protected void updateItem(HashMap<KeyWords, ComplexField> item, boolean empty) {
+ super.updateItem(item, empty);
+ if (item == null || empty) {
+ setGraphic(null);
+ setText("");
+ } else {
+ setGraphic(null);
+ setText(Tools.agentToString(item));
+ }
+ }
+ };
+ });
+
+ comboField.setValue(null);
+ ObservableList<HashMap<KeyWords, ComplexField>> listCopy = FXCollections.observableArrayList();
+ listCopy.add(Tools.createFakeAgentFromString(""));
+
+ agentProp.computeIfAbsent(replicateID, k -> {
+ SimpleObjectProperty sop = new SimpleObjectProperty<>();
+ sop.addListener(Data.changeListener);
+ return sop;
+ } );
+
+ if(!list.contains(agentProp.get(replicateID).getValue())) {
+ if(!Tools.agentToString(agentProp.get(replicateID).getValue()).isBlank()) {
+ listCopy.add(agentProp.get(replicateID).getValue());
+ }
+ }
+ listCopy.addAll(list);
+ comboField.setItems(listCopy);
+ comboField.setValue(agentProp.get(replicateID).getValue());
+ agentProp.get(replicateID).bind(comboField.valueProperty());
+
+ comboField.styleProperty().unbind();
+ BooleanBinding containAgent = Bindings.createBooleanBinding( () -> list.contains( agentProp.get(replicateID).getValue() ) || Tools.agentToString(agentProp.get(replicateID).getValue()).isEmpty(), list, agentProp );
+ comboField.styleProperty().bind(Bindings.when(containAgent).then("-fx-border-color: DarkSlateBlue;").otherwise("-fx-border-color: red;"));
+ }
+
public static void bindComboBoxAgent(ObjectProperty<HashMap<KeyWords, ComplexField>> agentProp, ObservableList<HashMap<KeyWords, ComplexField>> list, ComboBox<HashMap<KeyWords, ComplexField>> comboField) {
comboField.setConverter(new StringConverter<HashMap<KeyWords, ComplexField>>() {
@Override
@@ -631,18 +706,22 @@ public class UITools {
comboField.styleProperty().bind(Bindings.when(containAgent).then("").otherwise("-fx-border-color: red;"));
}
- public static void bindTable(GenericTable table, TableView tableView) {
+ public static void bindTable(GenericTable table, Replicate replicate, TableView tableView) {
if(table instanceof SimpleTable) {
- bindSimpleTable((SimpleTable) table, tableView);
+ bindSimpleTable((SimpleTable) table, replicate, tableView);
}
if(table instanceof ComplexTable) {
- bindComplexTable((ComplexTable) table, tableView);
+ bindComplexTable((ComplexTable) table, replicate, tableView);
}
}
- public static void bindComplexTable(ComplexTable complexTable, TableView tableView) {
+ public static void bindComplexTable(ComplexTable complexTable, Replicate replicate, TableView tableView) {
+ ChangeListener changeListener = (observable, oldValue, newValue) -> {
+ complexTable.getData().setModified(true);
+ };
tableView.getColumns().clear();
tableView.setTableMenuButtonVisible(true);
+ int replicateID = replicate != null ? replicate.getId() : 0;
Button addLine = new Button("New line ");
addLine.disableProperty().bind(tableView.editableProperty().not());
@@ -688,7 +767,7 @@ public class UITools {
colAdd.setGraphic(new ImageView(UITools.getImage("resources/images/add_col-16.png")));
colAdd.setOnAction(actionEvent -> {
complexTable.addColumn(-1);
- UITools.bindComplexTable(complexTable, tableView);
+ UITools.bindComplexTable(complexTable, replicate, tableView);
});
colAdd.disableProperty().bind(tableView.editableProperty().not());
colAction.setGraphic(colAdd);
@@ -738,7 +817,7 @@ public class UITools {
};
});
- for(ComplexField c : complexTable.getTableHeader()) {
+ for(ComplexField c : complexTable.getTableHeader()) {
if(!c.equals(ComplexTable.numC) && !c.equals(ComplexTable.actionC)) {
TableColumn<Map<ComplexField, ComplexField>, ComplexField> colType = new TableColumn();
tableView.getColumns().add(colType);
@@ -748,7 +827,7 @@ public class UITools {
delete.setOnAction(event -> {
complexTable.deleteColumn(c);
complexTable.getData().setModified(true);
- UITools.bindComplexTable(complexTable, tableView);
+ UITools.bindComplexTable(complexTable, replicate, tableView);
});
Button edit = new Button("");
edit.disableProperty().bind(tableView.editableProperty().not());
@@ -938,10 +1017,10 @@ public class UITools {
TextField text = new TextField();
text.editableProperty().bind(tableView.editableProperty());
text.styleProperty().bind(item.styleProperty());
- item.getValue().unbind();
- text.setText(item.getValue().get());
- item.getValue().bind(text.textProperty());
-
+ item.unbindReplicatesValues();
+ text.setText(item.getValueWithReplicate(replicateID).get());
+ item.getValueWithReplicate(replicateID).bind(text.textProperty());
+ item.setValuesListener(changeListener);
text.setOnMouseClicked(event -> {
if(text.isEditable() && event.getClickCount() == 2) {
@@ -1002,9 +1081,6 @@ public class UITools {
}
});
setGraphic(text);
- item.getValue().addListener((observable, oldValue, newValue) -> {
- complexTable.getData().setModified(true);
- });
}
}
};
@@ -1020,7 +1096,11 @@ public class UITools {
tableView.setColumnResizePolicy(TableView.CONSTRAINED_RESIZE_POLICY);
}
- public static void bindSimpleTable(SimpleTable simpleTable, TableView tableView) {
+ public static void bindSimpleTable(SimpleTable simpleTable, Replicate replicate, TableView tableView) {
+ ChangeListener changeListener = (observable, oldValue, newValue) -> {
+ simpleTable.getData().setModified(true);
+ };
+
tableView.setColumnResizePolicy(TableView.CONSTRAINED_RESIZE_POLICY);
tableView.setTableMenuButtonVisible(true);
Button addLine = new Button("New line ");
@@ -1150,10 +1230,7 @@ public class UITools {
UITools.addAutoComplete(combo, item.getListConstraint());
// UITools.addPopOver(combo, Ontology.Attribut);
item.getValue().bind(combo.textProperty());
-
- item.getValue().addListener((observable, oldValue, newValue) -> {
- simpleTable.getData().setModified(true);
- });
+ item.setValuesListener(changeListener);
combo.styleProperty().bind(item.styleProperty());
setGraphic(combo);
} else {
@@ -1319,10 +1396,7 @@ public class UITools {
UITools.addAutoComplete(combo, item.getListConstraint());
// UITools.addPopOver(combo, Ontology.Component);
item.getValue().bind(combo.textProperty());
-
- item.getValue().addListener((observable, oldValue, newValue) -> {
- simpleTable.getData().setModified(true);
- });
+ item.setValuesListener(changeListener);
combo.styleProperty().bind(item.styleProperty());
setGraphic(combo);
} else {
@@ -1356,10 +1430,11 @@ public class UITools {
TextField text = new TextField();
text.editableProperty().bind(tableView.editableProperty());
text.styleProperty().bind(item.styleProperty());
- item.getValue().unbind();
- text.setText(item.getValue().get());
- item.getValue().bind(text.textProperty());
-
+ item.unbindReplicatesValues();
+ int replicateID = replicate != null ? replicate.getId() : 0;
+ text.setText(item.getValueWithReplicate(replicateID).getValue());
+ item.getValueWithReplicate(replicateID).bind(text.textProperty());
+ item.setValuesListener(changeListener);
text.setOnMouseClicked(event -> {
if (text.isEditable() && event.getClickCount() == 2) {
@@ -1421,13 +1496,10 @@ public class UITools {
});
setGraphic(text);
- item.getValue().addListener((observable, oldValue, newValue) -> {
- simpleTable.getData().setModified(true);
- });
} else {
TextField combo = new TextField();
combo.maxWidthProperty().bind(widthProperty());
- item.getValue().unbind();
+ item.unbindReplicatesValues();
if (item.isEditable()) {
combo.editableProperty().bind(tableView.editableProperty());
} else {
@@ -1436,17 +1508,12 @@ public class UITools {
combo.disableProperty().bind(combo.editableProperty().not());
combo.setText(item.getValue().get());
UITools.addAutoComplete(combo, item.getListConstraint());
-// if(item.getConceptConstraint() != null && item.getConceptConstraint().size() > 0) {
-// UITools.addPopOver(combo, item.getConceptConstraint().toArray(new String[0]));
-// }
- item.getValue().bind(combo.textProperty());
+ int replicateID = replicate != null ? replicate.getId() : 0;
+ item.getValueWithReplicate(replicateID).bind(combo.textProperty());
combo.styleProperty().bind(item.styleProperty());
setGraphic(combo);
- item.getValue().addListener((observable, oldValue, newValue) -> {
- simpleTable.getData().setModified(true);
- });
-
+ item.setValuesListener(changeListener);
}
}
}
@@ -1470,11 +1537,8 @@ public class UITools {
item.getValue().unbind();
text.setText(item.getValue().get());
item.getValue().bind(text.textProperty());
-
+ item.setValuesListener(changeListener);
setGraphic(text);
- item.getValue().addListener((observable, oldValue, newValue) -> {
- simpleTable.getData().setModified(true);
- });
}
}
};
diff --git a/src/main/java/fr/inra/po2vocabmanager/view/dataView/DataOverviewController.java b/src/main/java/fr/inra/po2vocabmanager/view/dataView/DataOverviewController.java
index 8f86f5dc0f1653beb59c14816715c02f9dc35ad1..66b40f84f1f72d09a2767911d4969da03350160a 100644
--- a/src/main/java/fr/inra/po2vocabmanager/view/dataView/DataOverviewController.java
+++ b/src/main/java/fr/inra/po2vocabmanager/view/dataView/DataOverviewController.java
@@ -287,13 +287,13 @@ public class DataOverviewController {
case STEP:
newNode.getFile().setSelectedInTree(true);
stepControler.setMainApp(this.mainApp);
- stepControler.showNodeDetails(newNode);
+ stepControler.showNodeDetails(newNode, newNode.getItineraryFile().getProcessFile().getCurrentReplicate());
infoPane.getChildren().add(stepOverview);
break;
case OBSERVATION:
newNode.getFile().setSelectedInTree(true);
observationControler.setMainApp(this.mainApp);
- observationControler.showNodeDetails(newNode);
+ observationControler.showNodeDetails(newNode, newNode.getItineraryFile().getProcessFile().getCurrentReplicate());
infoPane.getChildren().add(observationOverview);
break;
case ITINERARY:
@@ -521,6 +521,12 @@ public class DataOverviewController {
}
listDataNode.get(file).add(node);
node.setFile(file);
+ if(node.getType().equals(DataNodeType.ITINERARY)) {
+ node.setItineraryFile((ItineraryFile) file);
+ }
+ if(father != null && father.getItineraryFile() != null) {
+ node.setItineraryFile(father.getItineraryFile());
+ }
node.nameProperty().bindBidirectional(file.getNameProperty());
if(father != null) {
father.addSubNode(node);
diff --git a/src/main/java/fr/inra/po2vocabmanager/view/dataView/MaterialMethodLinkOverviewController.java b/src/main/java/fr/inra/po2vocabmanager/view/dataView/MaterialMethodLinkOverviewController.java
index 09517f7781db13f307ee939a620271d5aa977b89..ba2fecc1f2d813f382be353ab4a5538fbdeae449 100644
--- a/src/main/java/fr/inra/po2vocabmanager/view/dataView/MaterialMethodLinkOverviewController.java
+++ b/src/main/java/fr/inra/po2vocabmanager/view/dataView/MaterialMethodLinkOverviewController.java
@@ -325,7 +325,7 @@ public class MaterialMethodLinkOverviewController {
TableView tableConsign = new TableView();
tableConsign.editableProperty().bind(mainApp.getEditProperty());
- UITools.bindSimpleTable(newValue.getConsignPart().getDataTable(), tableConsign);
+ UITools.bindSimpleTable(newValue.getConsignPart().getDataTable(), null, tableConsign);
grid.add(tableConsign, 0, 1);
GridPane.setFillWidth(tableConsign, true);
grid.getColumnConstraints().addAll(c);
diff --git a/src/main/java/fr/inra/po2vocabmanager/view/dataView/MaterialMethodOverviewController.java b/src/main/java/fr/inra/po2vocabmanager/view/dataView/MaterialMethodOverviewController.java
index ba314ab12135f6c033554e48c103b4cec12e9bbe..7d53888f193f3838b8cce75bfe151071feb5a1e1 100644
--- a/src/main/java/fr/inra/po2vocabmanager/view/dataView/MaterialMethodOverviewController.java
+++ b/src/main/java/fr/inra/po2vocabmanager/view/dataView/MaterialMethodOverviewController.java
@@ -318,7 +318,7 @@ public class MaterialMethodOverviewController {
// addLine.setOnMouseClicked(event -> newValue.addLine());
TableView tableView = new TableView();
tableView.editableProperty().bind(mainApp.getEditProperty());
- UITools.bindSimpleTable(newValue.getDataTable(), tableView);
+ UITools.bindSimpleTable(newValue.getDataTable(), null, tableView);
// newValue.bindData(tableView);
// grid.add(tableView, 0, 0);
// grid.add(addLine, 0, 1);
diff --git a/src/main/java/fr/inra/po2vocabmanager/view/dataView/ObservationOverviewController.java b/src/main/java/fr/inra/po2vocabmanager/view/dataView/ObservationOverviewController.java
index 4f593653190f24cbadea601896093ae2d51ac42f..2409e55faf685b7e6f5bad4644a268d39d18ecb1 100644
--- a/src/main/java/fr/inra/po2vocabmanager/view/dataView/ObservationOverviewController.java
+++ b/src/main/java/fr/inra/po2vocabmanager/view/dataView/ObservationOverviewController.java
@@ -22,6 +22,7 @@ import fr.inra.po2vocabmanager.MainApp;
import fr.inra.po2vocabmanager.model.DataNode;
import fr.inra.po2vocabmanager.utils.UITools;
import fr.inrae.po2engine.model.ComplexField;
+import fr.inrae.po2engine.model.Replicate;
import fr.inrae.po2engine.model.dataModel.CompositionFile;
import fr.inrae.po2engine.model.dataModel.KeyWords;
import fr.inrae.po2engine.model.dataModel.ObservationFile;
@@ -135,22 +136,26 @@ public class ObservationOverviewController {
}
- public void showNodeDetails(DataNode node) {
+ public void showNodeDetails(DataNode node, Replicate replicate) {
ToggleGroup groupFOI = new ToggleGroup();
-
file = (ObservationFile) node.getFile();
file.checkValue();
+ if(replicate != null) {
+ observationPanel.setText("Observation (replicate : " + replicate.getName() + ")");
+ } else {
+ observationPanel.setText("Observation");
+ }
UITools.simpleBindValue(file.getCName(), observationType);
UITools.simpleBindValue(file.getCID(), observationName);
- UITools.simpleBindValue(file.getCDate(), observationDate);
- UITools.simpleBindValue(file.getCDuree(), observationTimeD);
- UITools.simpleBindValue(file.getCHeure(), observationTime);
+ UITools.simpleBindValue(file.getCDate(),replicate, observationDate);
+ UITools.simpleBindValue(file.getCDuree(),replicate, observationTimeD);
+ UITools.simpleBindValue(file.getCHeure(),replicate,observationTime);
UITools.simpleBindValue(file.getCDescrition(), observationDesc);
UITools.simpleBindValue(file.getCScale(), observationScale);
- UITools.bindComboBoxAgent(file.getAgentProperty(),file.getData().getProjectFile().getListAgent(), orgAgent);
+ UITools.bindComboBoxAgent(file.getAgentsMap(),file.getData().getProjectFile().getListAgent(), replicate, orgAgent);
UITools.addAutoComplete(observationScale, file.getCScale().getListConstraint());
@@ -165,7 +170,7 @@ public class ObservationOverviewController {
listItem.add(new MutablePair<>("Step - " + file.getStepFile().getId(), new MutablePair<>("step", new SimpleBooleanProperty(false))));
for (CompositionFile comp : file.getStepFile().getCompositionFile().keySet()) {
- String inout = file.getStepFile().getCompositionFile().get(comp) ? "Input" : "Output";
+ String inout = Boolean.TRUE.equals(file.getStepFile().getCompositionFile().get(comp)) ? "Input" : "Output";
listItem.add(new MutablePair<>(inout+" - " + comp.getHeaderPart().getCompositionID() , new MutablePair<>(comp.getFileName(), new SimpleBooleanProperty(false))));
}
@@ -208,36 +213,6 @@ public class ObservationOverviewController {
return cell;
});
- Label titlePane = new Label("Observation");
- titlePane.setAlignment(Pos.CENTER_LEFT);
-// Button exportExcel = new Button(null, new ImageView(UITools.getImage("resources/images/file-export-16.png")));
-// exportExcel.setTooltip(new Tooltip("Export Observation"));
-// exportExcel.setOnMouseClicked(event -> {
-// // Export des données.
-//
-// });
- Button importExcel = new Button(null, new ImageView(UITools.getImage("resources/images/file-import-16.png")));
- importExcel.setTooltip(new Tooltip("Export Observation"));
- importExcel.setOnMouseClicked(event -> {
-
- });
-
-
-
-
- importExcel.disableProperty().bind(this.mainApp.getEditProperty().not());
-
- Label emptyLabelTitle = new Label(" ");
- emptyLabelTitle.setMaxWidth(Double.MAX_VALUE);
- HBox bbT = new HBox();
- bbT.setAlignment(Pos.CENTER_RIGHT);
- bbT.getChildren().addAll(titlePane,emptyLabelTitle/*, exportExcel, importExcel*/);
- HBox.setHgrow(emptyLabelTitle, Priority.ALWAYS);
- bbT.setPadding(new Insets(0,3,0,0));
- bbT.minWidthProperty().bind(observationPanel.widthProperty().subtract(25));
-
- observationPanel.setGraphic(bbT);
-
boxContent.getChildren().retainAll(observationPanel);
TitledPane matMetPane = new TitledPane();
@@ -268,7 +243,7 @@ public class ObservationOverviewController {
TableView table = new TableView();
table.setMinHeight(200);
table.editableProperty().bind(this.mainApp.getEditProperty());
- UITools.bindTable(tablePart.getTable(), table);
+ UITools.bindTable(tablePart.getTable(), replicate, table);
tablePane.setContent(table);
boxContent.getChildren().add(tablePane);
@@ -304,7 +279,7 @@ public class ObservationOverviewController {
Optional<ButtonType> res = a.showAndWait();
if(res.get() == ButtonType.OK) {
file.removeTablePart(tablePart);
- showNodeDetails(node);
+ showNodeDetails(node, replicate);
}
});
diff --git a/src/main/java/fr/inra/po2vocabmanager/view/dataView/ProcessOverviewController.java b/src/main/java/fr/inra/po2vocabmanager/view/dataView/ProcessOverviewController.java
index fb9108daa337a9e7ef519bb4d648a76adb3a096c..530d629bfb99c63993fdaffcfc60326bd4dbd391 100644
--- a/src/main/java/fr/inra/po2vocabmanager/view/dataView/ProcessOverviewController.java
+++ b/src/main/java/fr/inra/po2vocabmanager/view/dataView/ProcessOverviewController.java
@@ -22,12 +22,15 @@ import fr.inra.po2vocabmanager.MainApp;
import fr.inra.po2vocabmanager.model.DataNode;
import fr.inra.po2vocabmanager.utils.UITools;
import fr.inra.po2vocabmanager.utils.XCell;
+import fr.inrae.po2engine.model.Replicate;
import fr.inrae.po2engine.model.dataModel.GeneralFile;
import fr.inrae.po2engine.model.dataModel.StepFile;
import javafx.animation.TranslateTransition;
import javafx.beans.binding.Bindings;
+import javafx.beans.property.SimpleIntegerProperty;
import javafx.beans.property.SimpleObjectProperty;
import javafx.beans.property.SimpleStringProperty;
+import javafx.beans.value.ChangeListener;
import javafx.collections.FXCollections;
import javafx.collections.ListChangeListener;
import javafx.collections.ObservableList;
@@ -44,6 +47,7 @@ import org.controlsfx.control.textfield.AutoCompletionBinding;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Optional;
+import java.util.concurrent.atomic.AtomicReference;
import java.util.stream.Collectors;
public class ProcessOverviewController {
@@ -59,6 +63,8 @@ public class ProcessOverviewController {
@FXML
TitledPane stepAvailable;
@FXML
+ TitledPane replicatesPane;
+ @FXML
TextArea description;
@FXML
Label linksLabel;
@@ -70,6 +76,12 @@ public class ProcessOverviewController {
TreeTableColumn<StepFile, String> colIti;
TreeTableColumn<StepFile, StepFile> colDel;
+ TableView<Replicate> replicateTable;
+ TableColumn<Replicate, Replicate> colRepName;
+ TableColumn<Replicate, Integer> colRepId;
+ TableColumn<Replicate, Replicate> colRepDesc;
+ TableColumn<Replicate, Replicate> colRepDel;
+
TreeItem<StepFile> rootTree;
@@ -89,7 +101,6 @@ public class ProcessOverviewController {
endDate.editableProperty().bind(mainApp.getEditProperty());
processType.editableProperty().bind(mainApp.getEditProperty());
description.editableProperty().bind(mainApp.getEditProperty());
-
}
private TranslateTransition createTranslateTransition(final Shape group) {
@@ -135,6 +146,9 @@ public class ProcessOverviewController {
generalFile.unbind();
generalFile.checkValue();
+ ChangeListener changeListener = (observable, oldValue, newValue) -> {
+ generalFile.getData().setModified(true);
+ };
UITools.simpleBindValue(generalFile.getCTitle(), processTitle);
UITools.simpleBindValue(generalFile.getCStartDate(), startDate);
@@ -145,7 +159,7 @@ public class ProcessOverviewController {
UITools.simpleBindValue(generalFile.getCDescription(), description);
listAutoCompletion.add(UITools.addAutoComplete(processType, generalFile.getCType().getListConstraint()));
-
+ generalFile.getListReplicate().forEach(r -> r.setValuesListener(changeListener));
ArrayList<String> ls = generalFile.getExternalLinks();
String[] arrayLink = new String [ls.size()];
@@ -248,6 +262,109 @@ public class ProcessOverviewController {
stepAvailable.setContent(treeTableView);
+ replicateTable = new TableView<>();
+ replicateTable.setColumnResizePolicy(TableView.CONSTRAINED_RESIZE_POLICY);
+ replicateTable.editableProperty().bind(mainApp.getEditProperty());
+ colRepId = new TableColumn<>("id");
+ colRepId.setCellValueFactory(cellData -> new SimpleIntegerProperty(cellData.getValue().getId()).asObject());
+ colRepId.setMaxWidth(60);
+ colRepId.setMinWidth(60);
+ colRepId.setPrefWidth(60);
+
+ colRepName = new TableColumn<>("Name");
+ colRepName.setCellValueFactory(cellData -> new SimpleObjectProperty<>(cellData.getValue()));
+ colRepName.setCellFactory(param -> {
+ return new TableCell<Replicate, Replicate>() {
+ @Override
+ public void updateItem(Replicate item, boolean empty) {
+ super.updateItem(item, empty);
+ TextField text = new TextField();
+ if (item != null && !empty) {
+ text.editableProperty().bind(replicateTable.editableProperty());
+ item.nameProperty().unbind();
+ text.setText(item.getName());
+ item.nameProperty().bind(text.textProperty());
+ setGraphic(text);
+ } else {
+ setText(null);
+ setStyle(null);
+ setGraphic(null);
+ }
+ }
+ };
+ });
+
+ colRepDesc = new TableColumn<>("Description");
+ colRepDesc.setCellValueFactory(cellData -> new SimpleObjectProperty<>(cellData.getValue()));
+ colRepDesc.setCellFactory(param -> {
+ return new TableCell<Replicate, Replicate>() {
+ @Override
+ public void updateItem(Replicate item, boolean empty) {
+ super.updateItem(item, empty);
+ TextField text = new TextField();
+ if (item != null && !empty) {
+ text.editableProperty().bind(replicateTable.editableProperty());
+ item.descriptionProperty().unbind();
+ text.setText(item.getDescription());
+ item.descriptionProperty().bind(text.textProperty());
+ setGraphic(text);
+ } else {
+ setText(null);
+ setStyle(null);
+ setGraphic(null);
+ }
+ }
+ };
+ });
+
+ colRepDel = new TableColumn<>();
+ colRepDel.setCellValueFactory(cellData -> new SimpleObjectProperty<>(cellData.getValue()));
+ colRepDel.setMaxWidth(60);
+ colRepDel.setMinWidth(60);
+ colRepDel.setPrefWidth(60);
+ AtomicReference<GeneralFile> currentGF = new AtomicReference<>(generalFile);
+
+ colRepDel.setCellFactory(cell -> {
+
+ return new TableCell<>(){
+ @Override
+ protected void updateItem(Replicate replicate, boolean b) {
+ super.updateItem(replicate, b);
+
+ if(replicate == null || b) {
+ setGraphic(null);
+ } else {
+ Button buttonDel = new Button();
+ buttonDel.setGraphic(new ImageView(UITools.getImage("resources/images/del_16.png")));
+ if(replicate.getId() == 0) {
+ buttonDel.setDisable(true);
+ } else {
+ buttonDel.disableProperty().bind(Bindings.not(mainApp.getEditProperty()));
+ }
+ buttonDel.setOnAction(event -> {
+ Alert a = new Alert(Alert.AlertType.CONFIRMATION);
+ a.setTitle("Delete Replicate");
+ a.setHeaderText("Delete Replicate " + replicate.getName());
+ a.initModality(Modality.WINDOW_MODAL);
+ a.initOwner(MainApp.primaryStage);
+ Optional<ButtonType> res = a.showAndWait();
+ if (res.get() == ButtonType.OK) {
+ GeneralFile gf = currentGF.get();
+ gf.removeReplicate(replicate);
+ gf.getData().setModified(true);
+ }
+ });
+ setGraphic(buttonDel);
+ }
+ }
+ };
+ });
+
+ replicateTable.getColumns().addAll(colRepId, colRepName, colRepDesc, colRepDel);
+
+ replicatesPane.setContent(replicateTable);
+ replicateTable.setItems(generalFile.getListReplicate());
+
}
private void updateListLink() {
diff --git a/src/main/java/fr/inra/po2vocabmanager/view/dataView/StepOverviewController.java b/src/main/java/fr/inra/po2vocabmanager/view/dataView/StepOverviewController.java
index b8b498c4f07b276e858a0db60d23169c833a944e..208ca9da8add26d8c107531d7146135c5f6de548 100644
--- a/src/main/java/fr/inra/po2vocabmanager/view/dataView/StepOverviewController.java
+++ b/src/main/java/fr/inra/po2vocabmanager/view/dataView/StepOverviewController.java
@@ -22,6 +22,7 @@ import fr.inra.po2vocabmanager.MainApp;
import fr.inra.po2vocabmanager.model.DataNode;
import fr.inra.po2vocabmanager.utils.UITools;
import fr.inrae.po2engine.model.ComplexField;
+import fr.inrae.po2engine.model.Replicate;
import fr.inrae.po2engine.model.dataModel.CompositionFile;
import fr.inrae.po2engine.model.dataModel.KeyWords;
import fr.inrae.po2engine.model.dataModel.StepFile;
@@ -108,19 +109,26 @@ public class StepOverviewController {
scale.disableProperty().bind(this.mainApp.getEditProperty().not());
}
- public void showNodeDetails(DataNode node) {
+ public void showNodeDetails(DataNode node, Replicate replicate) {
for(AutoCompletionBinding auto : listAutoCompletion) {
auto.dispose();
}
f = (StepFile) node.getFile();
f.checkValue();
+
+ if(replicate != null) {
+ stepPanel.setText("Step (replicate : " + replicate.getName() + ")");
+ } else {
+ stepPanel.setText("Step");
+ }
+
UITools.simpleBindValue(f.getCType(), stepTitle);
UITools.simpleBindValue(f.getCId(), stepID);
UITools.simpleBindValue(f.getCDescrition(), description);
- UITools.simpleBindValue(f.getCDate(), date);
- UITools.simpleBindValue(f.getCTime(), time);
- UITools.simpleBindValue(f.getCDuration(), duree);
- UITools.bindComboBoxAgent(f.getAgentProperty(),f.getData().getProjectFile().getListAgent(), orgAgent);
+ UITools.simpleBindValue(f.getCDate(), replicate, date);
+ UITools.simpleBindValue(f.getCTime(), replicate, time);
+ UITools.simpleBindValue(f.getCDuration(), replicate, duree);
+ UITools.bindComboBoxAgent(f.getAgentsMap(),f.getData().getProjectFile().getListAgent(), replicate, orgAgent);
UITools.simpleBindValue(f.getCScale(), scale);
listAutoCompletion.add(UITools.addAutoComplete(scale, f.getCScale().getListConstraint()));
@@ -216,7 +224,7 @@ public class StepOverviewController {
Optional<ButtonType> res = a.showAndWait();
if(res.get() == ButtonType.OK) {
f.removeCompositionFile(compoFile);
- showNodeDetails(node);
+ showNodeDetails(node, replicate);
}
});
diff --git a/src/main/resources/fr/inra/po2vocabmanager/view/dataView/ProcessOverview.fxml b/src/main/resources/fr/inra/po2vocabmanager/view/dataView/ProcessOverview.fxml
index ef01250e85cc3bff006a9a3a4a44cc524a8bc05c..43ecc3bcb3b6b452edbb8ee8487e180ae2fe786e 100644
--- a/src/main/resources/fr/inra/po2vocabmanager/view/dataView/ProcessOverview.fxml
+++ b/src/main/resources/fr/inra/po2vocabmanager/view/dataView/ProcessOverview.fxml
@@ -91,6 +91,7 @@
</TitledPane>
<TitledPane fx:id="stepAvailable" maxHeight="Infinity" prefHeight="428.0" prefWidth="718.0" text="Steps available" VBox.vgrow="ALWAYS" />
+ <TitledPane fx:id="replicatesPane" animated="false" text="Replicates" />
</children>
</VBox>
</children>