Examples with IOConfiguration eu.esdihumboldt.hale.common.core.io.project.model.IOConfiguration used on opensource projects

Example 1 with IOConfiguration

use of eu.esdihumboldt.hale.common.core.io.project.model.IOConfiguration in project hale by halestudio.

the class TemplateProject method onSuccess.

@Override
protected void onSuccess(Void context, String projectId, File projectFile, Project project, ReportFile reportFile) {
    super.onSuccess(context, projectId, projectFile, project, reportFile);
    // update locations in project file
    LocationUpdater updater = new LocationUpdater(project, projectFile.toURI());
    updater.updateProject(false);
    resources.clear();
    List<Path> invalidSources = new ArrayList<>();
    Path projectFolder = getProjectFolder().toPath();
    // validate resources
    for (IOConfiguration config : project.getResources()) {
        Resource resource = new IOConfigurationResource(config, getProjectFile().toURI());
        // check if file URIs are valid and inside project folder
        URI source = resource.getSource();
        if (source != null) {
            Path path = null;
            if (source.getScheme() == null) {
                // is a relative URI
                path = projectFile.toPath().resolve(source.toString()).normalize();
            } else if ("file".equals(source.getScheme())) {
                // is a file URI
                path = Paths.get(source).normalize();
            }
            if (path != null) {
                if (!path.startsWith(projectFolder) || !Files.exists(path)) {
                    // invalid source
                    invalidSources.add(path);
                }
            }
        }
        resources.put(resource.getActionId(), resource);
    }
    valid = invalidSources.isEmpty();
    if (!valid) {
        StringBuilder builder = new StringBuilder("Files referenced by the project could not be found: ");
        for (int i = 0; i < invalidSources.size(); i++) {
            if (i > 0)
                builder.append(", ");
            Path path = invalidSources.get(i);
            builder.append(path.getFileName().toString());
        }
        notValidMessage = builder.toString();
    } else {
        notValidMessage = "";
    }
    // additionally, try to find out cell count
    definedRelations = 0;
    // check if default alignment file exists
    try {
        File defAlignmentFile = new File(URI.create(projectFile.toURI().toASCIIString() + "." + AlignmentIO.PROJECT_FILE_ALIGNMENT));
        if (defAlignmentFile.exists()) {
            try (InputStream in = new BufferedInputStream(new FileInputStream(defAlignmentFile))) {
                /*
					 * Try loading the file with JAXB - only supports 2.6+
					 * projects.
					 */
                AlignmentType alignment = JaxbToAlignment.load(in, null);
                // XXX ignoring base alignments
                int count = 0;
                for (Object element : alignment.getCellOrModifier()) {
                    if (element instanceof CellType) {
                        count++;
                    }
                }
                definedRelations = count;
            } catch (Exception e) {
            // ignore
            }
        }
    } catch (Exception e) {
    // ignore
    }
}

Example 2 with IOConfiguration

use of eu.esdihumboldt.hale.common.core.io.project.model.IOConfiguration in project hale by halestudio.

the class ProjectServiceImpl method save.

/**
 * @see ProjectService#save()
 */
@Override
public void save() {
    File projectFile;
    IOConfiguration saveConfig;
    synchronized (this) {
        projectFile = this.projectFile;
        saveConfig = main.getSaveConfiguration();
    }
    if (projectFile != null || canSaveTo(projectLocation)) {
        Collection<IOProviderDescriptor> providers = HaleIO.getProviderFactories(ProjectWriter.class);
        // use configuration from previous save if possible
        if (saveConfig != null) {
            // get provider ...
            ProjectWriter writer = null;
            for (IOProviderDescriptor factory : providers) {
                if (factory.getIdentifier().equals(saveConfig.getProviderId())) {
                    /*
						 * Check if the content type the project was loaded with
						 * is supported for saving.
						 * 
						 * Example for a changed content type: A saved project
						 * archive may have been extracted and the internal XML
						 * project file loaded.
						 */
                    if (projectLoadContentType != null) {
                        if (factory.getSupportedTypes() == null || !factory.getSupportedTypes().contains(projectLoadContentType)) {
                            log.warn("Project cannot be saved with the same settings it was originally saved with, as the content type has changed.");
                            break;
                        }
                    }
                    try {
                        writer = (ProjectWriter) factory.createExtensionObject();
                    } catch (Exception e) {
                        log.error("Could not create project writer", e);
                    }
                }
            }
            if (writer != null) {
                // configure provider
                writer.loadConfiguration(saveConfig.getProviderConfiguration());
                // moved externally)
                if (projectFile != null) {
                    writer.setTarget(new FileIOSupplier(projectFile));
                } else {
                    writer.setTarget(new NoStreamOutputSupplier(projectLocation));
                }
                ListenableFuture<IOReport> result = ProjectResourcesUtil.executeProvider(writer, saveProjectAdvisor, true, null);
                PlatformUI.getWorkbench().getDisplay().syncExec(new Runnable() {

                    @Override
                    public void run() {
                        try {
                            IOReport report = result.get();
                            if (!report.isSuccess()) {
                                log.userError("The project could not be saved. Please check the report for more details.");
                            }
                        } catch (InterruptedException | ExecutionException e) {
                            log.userError("The project could not be saved.", e);
                        }
                    }
                });
            } else {
                log.info("The project cannot be saved because the format the project was saved with is not available or has changed.");
                // use save as instead
                saveAs();
            }
        } else if (projectFile != null) {
            // use I/O provider and content type mechanisms to try saving
            // the project file
            ProjectWriter writer = HaleIO.findIOProvider(ProjectWriter.class, new FileIOSupplier(projectFile), projectFile.getAbsolutePath());
            if (writer != null) {
                ProjectResourcesUtil.executeProvider(writer, saveProjectAdvisor, null);
            } else {
                log.error("The project cannot be saved because the format is not available.");
                // use save as instead
                saveAs();
            }
        } else {
            saveAs();
        }
    } else {
        saveAs();
    }
}

Example 3 with IOConfiguration

use of eu.esdihumboldt.hale.common.core.io.project.model.IOConfiguration in project hale by halestudio.

the class ProjectServiceImpl method removeResources.

@Override
public List<? extends Resource> removeResources(String actionId) {
    Builder<Resource> removedBuilder = ImmutableList.builder();
    synchronized (this) {
        Iterator<IOConfiguration> iter = main.getResources().iterator();
        while (iter.hasNext()) {
            IOConfiguration conf = iter.next();
            if (conf.getActionId().equals(actionId)) {
                iter.remove();
                removedBuilder.add(new IOConfigurationResource(conf, projectLocation));
            }
        }
    }
    setChanged();
    List<Resource> removedResources = removedBuilder.build();
    notifyResourcesRemoved(actionId, removedResources);
    return removedResources;
}

Example 4 with IOConfiguration

use of eu.esdihumboldt.hale.common.core.io.project.model.IOConfiguration in project hale by halestudio.

the class IOWizard method performFinish.

/**
 * @see Wizard#performFinish()
 *
 * @return <code>true</code> if executing the I/O provider was successful
 */
@Override
public boolean performFinish() {
    if (getProvider() == null) {
        return false;
    }
    if (!applyConfiguration()) {
        return false;
    }
    // create default report
    IOReporter defReport = provider.createReporter();
    // validate and execute provider
    try {
        // validate configuration
        provider.validate();
        ProjectService ps = PlatformUI.getWorkbench().getService(ProjectService.class);
        URI projectLoc = ps.getLoadLocation() == null ? null : ps.getLoadLocation();
        boolean isProjectResource = false;
        if (actionId != null) {
            // XXX instead move project resource to action?
            ActionUI factory = ActionUIExtension.getInstance().findActionUI(actionId);
            isProjectResource = factory.isProjectResource();
        }
        // prevent loading of duplicate resources
        if (isProjectResource && provider instanceof ImportProvider && !getProviderFactory().allowDuplicateResource()) {
            String currentResource = ((ImportProvider) provider).getSource().getLocation().toString();
            URI currentAbsolute = URI.create(currentResource);
            if (projectLoc != null && !currentAbsolute.isAbsolute()) {
                currentAbsolute = projectLoc.resolve(currentAbsolute);
            }
            for (IOConfiguration conf : ((Project) ps.getProjectInfo()).getResources()) {
                Value otherResourceValue = conf.getProviderConfiguration().get(ImportProvider.PARAM_SOURCE);
                if (otherResourceValue == null) {
                    continue;
                }
                String otherResource = otherResourceValue.as(String.class);
                URI otherAbsolute = URI.create(otherResource);
                if (projectLoc != null && !otherAbsolute.isAbsolute()) {
                    otherAbsolute = projectLoc.resolve(otherAbsolute);
                }
                String action = conf.getActionId();
                // resource is already loaded into the project
                if (currentAbsolute.equals(otherAbsolute) && Objects.equal(actionId, action)) {
                    // check if the resource is loaded with a provider that
                    // allows duplicates
                    boolean allowDuplicate = false;
                    IOProviderDescriptor providerFactory = IOProviderExtension.getInstance().getFactory(conf.getProviderId());
                    if (providerFactory != null) {
                        allowDuplicate = providerFactory.allowDuplicateResource();
                    }
                    if (!allowDuplicate) {
                        log.userError("Resource is already loaded. Loading duplicate resources is aborted!");
                        return false;
                    }
                }
            }
        }
        // enable provider internal caching
        if (isProjectResource && provider instanceof CachingImportProvider) {
            ((CachingImportProvider) provider).setProvideCache();
        }
        IOReport report = execute(provider, defReport);
        if (report != null) {
            // add report to report server
            ReportService repService = PlatformUI.getWorkbench().getService(ReportService.class);
            repService.addReport(report);
            // show message to user
            if (report.isSuccess()) {
                // let advisor handle results
                try {
                    getContainer().run(true, false, new IRunnableWithProgress() {

                        @Override
                        public void run(IProgressMonitor monitor) throws InvocationTargetException, InterruptedException {
                            monitor.beginTask("Completing operation...", IProgressMonitor.UNKNOWN);
                            try {
                                advisor.handleResults(getProvider());
                            } finally {
                                monitor.done();
                            }
                        }
                    });
                } catch (InvocationTargetException e) {
                    log.userError("Error processing results:\n" + e.getCause().getLocalizedMessage(), e.getCause());
                    return false;
                } catch (Exception e) {
                    log.userError("Error processing results:\n" + e.getLocalizedMessage(), e);
                    return false;
                }
                // add to project service if necessary
                if (isProjectResource)
                    ps.rememberIO(actionId, getProviderFactory().getIdentifier(), provider);
                return true;
            } else {
                // error message
                log.userError(report.getSummary() + "\nPlease see the report for details.");
                return false;
            }
        } else
            return true;
    } catch (IOProviderConfigurationException e) {
        // user feedback
        log.userError("Validation of the provider configuration failed:\n" + e.getLocalizedMessage(), e);
        return false;
    }
}

Example 5 with IOConfiguration

use of eu.esdihumboldt.hale.common.core.io.project.model.IOConfiguration in project hale by halestudio.

the class SchemaUpdateComponent method updateSelectedSchema.

/**
 */
protected void updateSelectedSchema() {
    ISelection sel = tableViewer.getSelection();
    if (!sel.isEmpty() && sel instanceof IStructuredSelection) {
        final IOConfiguration selected = (IOConfiguration) ((IStructuredSelection) sel).getFirstElement();
        SchemaImportWizard wizard = new SchemaImportWizard() {

            @Override
            public boolean performFinish() {
                if (!applyConfiguration()) {
                    return false;
                }
                IOConfiguration configuration = new IOConfiguration();
                configuration.setActionId(getActionId());
                configuration.setProviderId(getProviderFactory().getIdentifier());
                getProvider().storeConfiguration(configuration.getProviderConfiguration());
                // replace the previously selected I/O configuration
                int index = configurations.indexOf(selected);
                configurations.set(index, configuration);
                // refresh table viewer to reflect the changes
                tableViewer.refresh(true);
                return true;
            }
        };
        // configure advisor
        // FIXME
        SchemaImportAdvisor advisor = new SchemaImportAdvisor(SchemaSpaceID.TARGET);
        advisor.setServiceProvider(HaleUI.getServiceProvider());
        advisor.setActionId(SchemaIO.ACTION_LOAD_TARGET_SCHEMA);
        wizard.setAdvisor(advisor, actionId);
        // open wizard
        Shell shell = Display.getCurrent().getActiveShell();
        HaleWizardDialog dialog = new HaleWizardDialog(shell, wizard);
        dialog.open();
    }
}