Examples with UIMAException org.apache.uima.UIMAException used on opensource projects

Example 6 with UIMAException

use of org.apache.uima.UIMAException in project webanno by webanno.

the class ImportExportServiceImpl method exportCasToFile.

/**
 * A new directory is created using UUID so that every exported file will reside in its own
 * directory. This is useful as the written file can have multiple extensions based on the
 * Writer class used.
 */
@Override
public File exportCasToFile(CAS cas, SourceDocument aDocument, String aFileName, @SuppressWarnings("rawtypes") Class aWriter, boolean aStripExtension) throws IOException, UIMAException {
    // Update the source file name in case it is changed for some reason. This is necessary
    // for the writers to create the files under the correct names.
    Project project = aDocument.getProject();
    File currentDocumentUri = new File(dir.getAbsolutePath() + "/" + PROJECT_FOLDER + "/" + project.getId() + "/" + DOCUMENT_FOLDER + "/" + aDocument.getId() + "/" + SOURCE_FOLDER);
    DocumentMetaData documentMetadata = DocumentMetaData.get(cas.getJCas());
    documentMetadata.setDocumentUri(new File(currentDocumentUri, aFileName).toURI().toURL().toExternalForm());
    documentMetadata.setDocumentBaseUri(currentDocumentUri.toURI().toURL().toExternalForm());
    documentMetadata.setCollectionId(currentDocumentUri.toURI().toURL().toExternalForm());
    documentMetadata.setDocumentUri(new File(dir.getAbsolutePath() + "/" + PROJECT_FOLDER + "/" + project.getId() + "/" + DOCUMENT_FOLDER + "/" + aDocument.getId() + "/" + SOURCE_FOLDER + "/" + aFileName).toURI().toURL().toExternalForm());
    // update with the correct tagset name
    List<AnnotationFeature> features = annotationService.listAnnotationFeature(project);
    for (AnnotationFeature feature : features) {
        TagSet tagSet = feature.getTagset();
        if (tagSet == null) {
            continue;
        } else if (!feature.getLayer().getType().equals(WebAnnoConst.CHAIN_TYPE)) {
            updateCasWithTagSet(cas, feature.getLayer().getName(), tagSet.getName());
        }
    }
    File exportTempDir = File.createTempFile("webanno", "export");
    try {
        exportTempDir.delete();
        exportTempDir.mkdirs();
        AnalysisEngineDescription writer;
        if (aWriter.getName().equals("de.tudarmstadt.ukp.clarin.webanno.tsv.WebannoTsv3Writer")) {
            List<AnnotationLayer> layers = annotationService.listAnnotationLayer(aDocument.getProject());
            List<String> slotFeatures = new ArrayList<>();
            List<String> slotTargets = new ArrayList<>();
            List<String> linkTypes = new ArrayList<>();
            Set<String> spanLayers = new HashSet<>();
            Set<String> slotLayers = new HashSet<>();
            for (AnnotationLayer layer : layers) {
                if (layer.getType().contentEquals(WebAnnoConst.SPAN_TYPE)) {
                    // TSV will not use this
                    if (!annotationExists(cas, layer.getName())) {
                        continue;
                    }
                    boolean isslotLayer = false;
                    for (AnnotationFeature f : annotationService.listAnnotationFeature(layer)) {
                        if (MultiValueMode.ARRAY.equals(f.getMultiValueMode()) && LinkMode.WITH_ROLE.equals(f.getLinkMode())) {
                            isslotLayer = true;
                            slotFeatures.add(layer.getName() + ":" + f.getName());
                            slotTargets.add(f.getType());
                            linkTypes.add(f.getLinkTypeName());
                        }
                    }
                    if (isslotLayer) {
                        slotLayers.add(layer.getName());
                    } else {
                        spanLayers.add(layer.getName());
                    }
                }
            }
            spanLayers.addAll(slotLayers);
            List<String> chainLayers = new ArrayList<>();
            for (AnnotationLayer layer : layers) {
                if (layer.getType().contentEquals(WebAnnoConst.CHAIN_TYPE)) {
                    if (!chainAnnotationExists(cas, layer.getName() + "Chain")) {
                        continue;
                    }
                    chainLayers.add(layer.getName());
                }
            }
            List<String> relationLayers = new ArrayList<>();
            for (AnnotationLayer layer : layers) {
                if (layer.getType().contentEquals(WebAnnoConst.RELATION_TYPE)) {
                    // TSV will not use this
                    if (!annotationExists(cas, layer.getName())) {
                        continue;
                    }
                    relationLayers.add(layer.getName());
                }
            }
            writer = createEngineDescription(aWriter, JCasFileWriter_ImplBase.PARAM_TARGET_LOCATION, exportTempDir, JCasFileWriter_ImplBase.PARAM_STRIP_EXTENSION, aStripExtension, "spanLayers", spanLayers, "slotFeatures", slotFeatures, "slotTargets", slotTargets, "linkTypes", linkTypes, "chainLayers", chainLayers, "relationLayers", relationLayers);
        } else {
            writer = createEngineDescription(aWriter, JCasFileWriter_ImplBase.PARAM_TARGET_LOCATION, exportTempDir, JCasFileWriter_ImplBase.PARAM_STRIP_EXTENSION, aStripExtension);
        }
        runPipeline(cas, writer);
        // If the writer produced more than one file, we package it up as a ZIP file
        File exportFile;
        if (exportTempDir.listFiles().length > 1) {
            exportFile = new File(exportTempDir.getAbsolutePath() + ".zip");
            try {
                ZipUtils.zipFolder(exportTempDir, exportFile);
            } catch (Exception e) {
                try (MDC.MDCCloseable closable = MDC.putCloseable(Logging.KEY_PROJECT_ID, String.valueOf(project.getId()))) {
                    log.info("Unable to create zip File");
                }
            }
        } else {
            exportFile = new File(exportTempDir.getParent(), exportTempDir.listFiles()[0].getName());
            FileUtils.copyFile(exportTempDir.listFiles()[0], exportFile);
        }
        return exportFile;
    } finally {
        if (exportTempDir != null) {
            FileUtils.forceDelete(exportTempDir);
        }
    }
}

Example 7 with UIMAException

use of org.apache.uima.UIMAException in project webanno by webanno.

the class CorrectionPage method commonInit.

private void commonInit() {
    setVersioned(false);
    setModel(Model.of(new AnnotatorStateImpl(Mode.CORRECTION)));
    WebMarkupContainer rightSidebar = new WebMarkupContainer("rightSidebar");
    // Override sidebar width from preferences
    rightSidebar.add(new AttributeModifier("style", LambdaModel.of(() -> String.format("flex-basis: %d%%;", getModelObject().getPreferences().getSidebarSize()))));
    rightSidebar.setOutputMarkupId(true);
    add(rightSidebar);
    List<UserAnnotationSegment> segments = new LinkedList<>();
    UserAnnotationSegment userAnnotationSegment = new UserAnnotationSegment();
    if (getModelObject().getDocument() != null) {
        userAnnotationSegment.setSelectionByUsernameAndAddress(annotationSelectionByUsernameAndAddress);
        userAnnotationSegment.setAnnotatorState(getModelObject());
        segments.add(userAnnotationSegment);
    }
    suggestionView = new SuggestionViewPanel("correctionView", new ListModel<>(segments)) {

        private static final long serialVersionUID = 2583509126979792202L;

        @Override
        public void onChange(AjaxRequestTarget aTarget) {
            AnnotatorState state = CorrectionPage.this.getModelObject();
            aTarget.addChildren(getPage(), IFeedback.class);
            try {
                // update begin/end of the curation segment based on bratAnnotatorModel changes
                // (like sentence change in auto-scroll mode,....
                curationContainer.setBratAnnotatorModel(state);
                JCas editorCas = getEditorCas();
                setCurationSegmentBeginEnd(editorCas);
                suggestionView.updatePanel(aTarget, curationContainer, annotationSelectionByUsernameAndAddress, curationSegment);
                annotationEditor.requestRender(aTarget);
                aTarget.add(getOrCreatePositionInfoLabel());
                update(aTarget);
            } catch (UIMAException e) {
                LOG.error("Error: " + e.getMessage(), e);
                error("Error: " + ExceptionUtils.getRootCauseMessage(e));
            } catch (Exception e) {
                LOG.error("Error: " + e.getMessage(), e);
                error("Error: " + e.getMessage());
            }
        }
    };
    suggestionView.setOutputMarkupId(true);
    add(suggestionView);
    rightSidebar.add(detailEditor = createDetailEditor());
    annotationEditor = new BratAnnotationEditor("mergeView", getModel(), detailEditor, this::getEditorCas);
    add(annotationEditor);
    curationContainer = new CurationContainer();
    curationContainer.setBratAnnotatorModel(getModelObject());
    add(documentNamePanel = createDocumentInfoLabel());
    add(getOrCreatePositionInfoLabel());
    add(openDocumentsModal = new OpenDocumentDialog("openDocumentsModal", getModel(), getAllowedProjects()) {

        private static final long serialVersionUID = 5474030848589262638L;

        @Override
        public void onDocumentSelected(AjaxRequestTarget aTarget) {
            // Reload the page using AJAX. This does not add the project/document ID to the URL,
            // but being AJAX it flickers less.
            actionLoadDocument(aTarget);
        }
    });
    add(preferencesModal = new AnnotationPreferencesDialog("preferencesDialog", getModel()));
    preferencesModal.setOnChangeAction(this::actionCompletePreferencesChange);
    add(exportDialog = new ExportDocumentDialog("exportDialog", getModel()));
    add(guidelinesDialog = new GuidelinesDialog("guidelinesDialog", getModel()));
    Form<Void> gotoPageTextFieldForm = new Form<>("gotoPageTextFieldForm");
    gotoPageTextField = new NumberTextField<>("gotoPageText", Model.of(1), Integer.class);
    // FIXME minimum and maximum should be obtained from the annotator state
    gotoPageTextField.setMinimum(1);
    gotoPageTextField.setOutputMarkupId(true);
    gotoPageTextFieldForm.add(gotoPageTextField);
    LambdaAjaxSubmitLink gotoPageLink = new LambdaAjaxSubmitLink("gotoPageLink", gotoPageTextFieldForm, this::actionGotoPage);
    gotoPageTextFieldForm.setDefaultButton(gotoPageLink);
    gotoPageTextFieldForm.add(gotoPageLink);
    add(gotoPageTextFieldForm);
    add(new LambdaAjaxLink("showOpenDocumentModal", this::actionShowOpenDocumentDialog));
    add(new LambdaAjaxLink("showPreferencesDialog", this::actionShowPreferencesDialog));
    add(new ActionBarLink("showGuidelinesDialog", guidelinesDialog::show));
    add(new LambdaAjaxLink("showExportDialog", exportDialog::show) {

        private static final long serialVersionUID = -708400631769656072L;

        {
            setOutputMarkupId(true);
            setOutputMarkupPlaceholderTag(true);
        }

        @Override
        protected void onConfigure() {
            super.onConfigure();
            AnnotatorState state = CorrectionPage.this.getModelObject();
            setVisible(state.getProject() != null && (SecurityUtil.isAdmin(state.getProject(), projectService, state.getUser()) || !state.getProject().isDisableExport()));
        }
    });
    add(new LambdaAjaxLink("showPreviousDocument", t -> actionShowPreviousDocument(t)).add(new InputBehavior(new KeyType[] { KeyType.Shift, KeyType.Page_up }, EventType.click)));
    add(new LambdaAjaxLink("showNextDocument", t -> actionShowNextDocument(t)).add(new InputBehavior(new KeyType[] { KeyType.Shift, KeyType.Page_down }, EventType.click)));
    add(new LambdaAjaxLink("showNext", t -> actionShowNextPage(t)).add(new InputBehavior(new KeyType[] { KeyType.Page_down }, EventType.click)));
    add(new LambdaAjaxLink("showPrevious", t -> actionShowPreviousPage(t)).add(new InputBehavior(new KeyType[] { KeyType.Page_up }, EventType.click)));
    add(new LambdaAjaxLink("showFirst", t -> actionShowFirstPage(t)).add(new InputBehavior(new KeyType[] { KeyType.Home }, EventType.click)));
    add(new LambdaAjaxLink("showLast", t -> actionShowLastPage(t)).add(new InputBehavior(new KeyType[] { KeyType.End }, EventType.click)));
    add(new LambdaAjaxLink("toggleScriptDirection", this::actionToggleScriptDirection));
    add(createOrGetResetDocumentDialog());
    add(createOrGetResetDocumentLink());
    add(finishDocumentDialog = new ConfirmationDialog("finishDocumentDialog", new StringResourceModel("FinishDocumentDialog.title", this, null), new StringResourceModel("FinishDocumentDialog.text", this, null)));
    add(finishDocumentLink = new LambdaAjaxLink("showFinishDocumentDialog", this::actionFinishDocument) {

        private static final long serialVersionUID = 874573384012299998L;

        @Override
        protected void onConfigure() {
            super.onConfigure();
            AnnotatorState state = CorrectionPage.this.getModelObject();
            setEnabled(state.getDocument() != null && !documentService.isAnnotationFinished(state.getDocument(), state.getUser()));
        }
    });
    finishDocumentIcon = new FinishImage("finishImage", getModel());
    finishDocumentIcon.setOutputMarkupId(true);
    finishDocumentLink.add(finishDocumentIcon);
}

Example 8 with UIMAException

use of org.apache.uima.UIMAException in project webanno by webanno.

the class ProjectCasDoctorPanel method actionCheck.

private void actionCheck(AjaxRequestTarget aTarget, Form<?> aForm) throws IOException, UIMAException, ClassNotFoundException {
    casStorageService.disableCache();
    CasDoctor casDoctor = new CasDoctor();
    casDoctor.setApplicationContext(ApplicationContextProvider.getApplicationContext());
    casDoctor.setFatalChecks(false);
    casDoctor.setCheckClasses(CasDoctor.scanChecks());
    Project project = getModelObject();
    formModel.messageSets = new ArrayList<>();
    for (SourceDocument sd : documentService.listSourceDocuments(project)) {
        {
            LogMessageSet messageSet = new LogMessageSet(sd.getName() + " [INITIAL]");
            JCas initialCas;
            try {
                if (documentService.existsInitialCas(sd)) {
                    initialCas = documentService.readInitialCas(sd, false);
                } else {
                    messageSet.messages.add(new LogMessage(getClass(), LogLevel.INFO, "No initial CAS for [" + sd.getName() + "]"));
                    initialCas = documentService.createInitialCas(sd, false);
                }
                casDoctor.analyze(project, initialCas.getCas(), messageSet.messages);
            } catch (Exception e) {
                messageSet.messages.add(new LogMessage(getClass(), LogLevel.ERROR, "Error reading initial CAS for [" + sd.getName() + "]: " + e.getMessage()));
                LOG.error("Error reading initial CAS for [" + sd.getName() + "]", e);
            }
            noticeIfThereAreNoMessages(messageSet);
            formModel.messageSets.add(messageSet);
        }
        for (AnnotationDocument ad : documentService.listAnnotationDocuments(sd)) {
            if (documentService.existsAnnotationCas(ad)) {
                LogMessageSet messageSet = new LogMessageSet(sd.getName() + " [" + ad.getUser() + "]");
                JCas userCas = documentService.readAnnotationCas(ad, false);
                casDoctor.analyze(project, userCas.getCas(), messageSet.messages);
                noticeIfThereAreNoMessages(messageSet);
                formModel.messageSets.add(messageSet);
            }
        }
    }
    aTarget.add(this);
}

Example 9 with UIMAException

use of org.apache.uima.UIMAException in project webanno by webanno.

the class ExportUtil method exportCuratedDocuments.

/**
 * Copy, if exists, curation documents to a folder that will be exported as Zip file
 *
 * @param aCopyDir
 *            The folder where curated documents are copied to be exported as Zip File
 */
public static void exportCuratedDocuments(DocumentService documentService, ImportExportService importExportService, ProjectExportRequest aModel, File aCopyDir, boolean aIncludeInProgress) throws UIMAException, IOException, ClassNotFoundException, ProjectExportException {
    Project project = aModel.project.getObject();
    // Get all the source documents from the project
    List<de.tudarmstadt.ukp.clarin.webanno.model.SourceDocument> documents = documentService.listSourceDocuments(project);
    // Determine which format to use for export.
    Class<?> writer;
    if (FORMAT_AUTO.equals(aModel.format)) {
        writer = WebannoTsv3XWriter.class;
    } else {
        writer = importExportService.getWritableFormats().get(importExportService.getWritableFormatId(aModel.format));
        if (writer == null) {
            writer = WebannoTsv3XWriter.class;
        }
    }
    int initProgress = aModel.progress - 1;
    int i = 1;
    for (de.tudarmstadt.ukp.clarin.webanno.model.SourceDocument sourceDocument : documents) {
        File curationCasDir = new File(aCopyDir + CURATION_AS_SERIALISED_CAS + sourceDocument.getName());
        FileUtils.forceMkdir(curationCasDir);
        File curationDir = new File(aCopyDir + CURATION_FOLDER + sourceDocument.getName());
        FileUtils.forceMkdir(curationDir);
        // finished or also the ones that are in progress
        if ((aIncludeInProgress && SourceDocumentState.CURATION_IN_PROGRESS.equals(sourceDocument.getState())) || SourceDocumentState.CURATION_FINISHED.equals(sourceDocument.getState())) {
            File curationCasFile = documentService.getCasFile(sourceDocument, WebAnnoConst.CURATION_USER);
            if (curationCasFile.exists()) {
                // Copy CAS - this is used when importing the project again
                FileUtils.copyFileToDirectory(curationCasFile, curationCasDir);
                // Copy secondary export format for convenience - not used during import
                try {
                    File curationFile = importExportService.exportAnnotationDocument(sourceDocument, WebAnnoConst.CURATION_USER, writer, WebAnnoConst.CURATION_USER, Mode.CURATION);
                    FileUtils.copyFileToDirectory(curationFile, curationDir);
                    FileUtils.forceDelete(curationFile);
                } catch (Exception e) {
                    // ExceptionUtils.getRootCauseMessage(e) );
                    throw new ProjectExportException("Aborting due to unrecoverable error while exporting!");
                }
            }
        }
        aModel.progress = initProgress + (int) Math.ceil(((double) i) / documents.size() * 10.0);
        i++;
    }
}