Examples with ITask net.idea.restnet.i.task.ITask used on opensource projects

Example 1 with ITask

use of net.idea.restnet.i.task.ITask in project ambit-mirror by ideaconsult.

the class CatalogResource method post.

@Override
protected Representation post(Representation entity, Variant variant) throws ResourceException {
    synchronized (this) {
        Form form = entity.isAvailable() ? new Form(entity) : new Form();
        // models
        Iterator<T> query = queryObject;
        if (query == null)
            throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST);
        ArrayList<UUID> tasks = new ArrayList<UUID>();
        while (query.hasNext()) try {
            T model = query.next();
            Reference reference = getSourceReference(form, model);
            ICallableTask callable = createCallable(form, model);
            ITask<ITaskResult, String> task = ((ITaskApplication) getApplication()).addTask(String.format("Apply %s %s %s", model.toString(), reference == null ? "" : "to", reference == null ? "" : reference), callable, getRequest().getRootRef(), callable instanceof CallablePOST, getToken());
            task.update();
            setStatus(task.isDone() ? Status.SUCCESS_OK : Status.SUCCESS_ACCEPTED);
            tasks.add(task.getUuid());
        } catch (ResourceException x) {
            throw x;
        } catch (Exception x) {
            throw new ResourceException(Status.SERVER_ERROR_INTERNAL, x.getMessage(), x);
        }
        if (tasks.size() == 0)
            throw new ResourceException(Status.CLIENT_ERROR_NOT_FOUND);
        else {
            ITaskStorage storage = ((ITaskApplication) getApplication()).getTaskStorage();
            FactoryTaskConvertor<Object> tc = new FactoryTaskConvertor<Object>(storage);
            if (tasks.size() == 1)
                return tc.createTaskRepresentation(tasks.get(0), variant, getRequest(), getResponse(), null);
            else
                return tc.createTaskRepresentation(tasks.iterator(), variant, getRequest(), getResponse(), null);
        }
    }
}

Example 2 with ITask

use of net.idea.restnet.i.task.ITask in project ambit-mirror by ideaconsult.

the class SubstanceResource method post.

@Override
protected Representation post(Representation entity, Variant variant) throws ResourceException {
    if ((entity == null) || !entity.isAvailable())
        throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, "Empty content");
    if (entity.getMediaType() != null)
        if (MediaType.MULTIPART_FORM_DATA.getName().equals(entity.getMediaType().getName())) {
            DiskFileItemFactory factory = new DiskFileItemFactory();
            RestletFileUpload upload = new RestletFileUpload(factory);
            try {
                List<FileItem> items = upload.parseRequest(getRequest());
                String token = getToken();
                QASettings qa = new QASettings();
                // sets enabled to false and clears all flags
                qa.clear();
                boolean clearMeasurements = false;
                boolean clearComposition = false;
                for (FileItem file : items) {
                    if (file.isFormField()) {
                        if ("qaenabled".equals(file.getFieldName()))
                            try {
                                if ("on".equals(file.getString()))
                                    qa.setEnabled(true);
                                if ("yes".equals(file.getString()))
                                    qa.setEnabled(true);
                                if ("checked".equals(file.getString()))
                                    qa.setEnabled(true);
                            } catch (Exception x) {
                                qa.setEnabled(true);
                            }
                        else if ("clearMeasurements".equals(file.getFieldName())) {
                            try {
                                clearMeasurements = false;
                                String cm = file.getString();
                                if ("on".equals(cm))
                                    clearMeasurements = true;
                                else if ("yes".equals(cm))
                                    clearMeasurements = true;
                                else if ("checked".equals(cm))
                                    clearMeasurements = true;
                            } catch (Exception x) {
                                clearMeasurements = false;
                            }
                        } else if ("clearComposition".equals(file.getFieldName())) {
                            try {
                                clearComposition = false;
                                String cm = file.getString();
                                if ("on".equals(cm))
                                    clearComposition = true;
                                else if ("yes".equals(cm))
                                    clearComposition = true;
                                else if ("checked".equals(cm))
                                    clearComposition = true;
                            } catch (Exception x) {
                                clearComposition = false;
                            }
                        } else
                            for (IQASettings.qa_field f : IQASettings.qa_field.values()) if (f.name().equals(file.getFieldName()))
                                try {
                                    String value = file.getString("UTF-8");
                                    f.addOption(qa, "null".equals(value) ? null : value == null ? null : value.toString());
                                } catch (Exception x) {
                                }
                    } else {
                        String ext = file.getName().toLowerCase().trim();
                        if ("".equals(ext) || ext.endsWith(".i5z") || ext.endsWith(".i6z") || ext.endsWith(".csv") || ext.endsWith(".rdf") || ext.endsWith(".ttl") || ext.endsWith(".json") || ext.endsWith(".xlsx") || ext.endsWith(".xls")) {
                        } else
                            throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, "Unsupported format " + ext);
                    }
                }
                CallableSubstanceImporter<String> callable = new CallableSubstanceImporter<String>(items, CallableFileUpload.field_files, CallableFileUpload.field_config, getRootRef(), getContext(), new SubstanceURIReporter(getRequest().getRootRef()), new DatasetURIReporter(getRequest().getRootRef()), token, getRequest().getResourceRef().toString(), getClientInfo());
                callable.setClearComposition(clearComposition);
                callable.setClearMeasurements(clearMeasurements);
                callable.setQASettings(qa);
                ITask<Reference, Object> task = ((ITaskApplication) getApplication()).addTask("Substance import", callable, getRequest().getRootRef(), token);
                ITaskStorage storage = ((ITaskApplication) getApplication()).getTaskStorage();
                FactoryTaskConvertor<Object> tc = new FactoryTaskConvertor<Object>(storage);
                task.update();
                getResponse().setStatus(task.isDone() ? Status.SUCCESS_OK : Status.SUCCESS_ACCEPTED);
                return tc.createTaskRepresentation(task.getUuid(), variant, getRequest(), getResponse(), null);
            } catch (ResourceException x) {
                throw x;
            } catch (Exception x) {
                throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, x);
            }
        } else if (MediaType.APPLICATION_WWW_FORM.getName().equals(entity.getMediaType().getName())) {
            /*
				 * web form to update substances from IUCLID5 server Expected web form fields :
				 * substance: UUID or query URL type : UUID or query or URL (ambit substance
				 * URL) qa options query : one of {@link QueryToolClient.PredefinedQuery} query
				 * parameters: depend on the query type iuclid5 server; credentials - optional,
				 * use preconfigured if not submitted [(option,UUID), (uuid,ZZZZZZZZZZ),
				 * (extidtype,CompTox), (extidvalue,Ambit Transfer), (i5server,null),
				 * (i5user,null), (i5pass,null)]
				 */
            Form form = new Form(entity);
            String token = getToken();
            CallableSubstanceI5Query<String> callable = new CallableSubstanceI5Query<String>(getRootRef(), form, getContext(), new SubstanceURIReporter(getRequest().getRootRef()), new DatasetURIReporter(getRequest().getRootRef()), token, getRequest().getResourceRef().toString(), getClientInfo());
            ITask<Reference, Object> task = ((ITaskApplication) getApplication()).addTask("Retrieve substance from IUCLID server", callable, getRequest().getRootRef(), token);
            ITaskStorage storage = ((ITaskApplication) getApplication()).getTaskStorage();
            FactoryTaskConvertor<Object> tc = new FactoryTaskConvertor<Object>(storage);
            task.update();
            getResponse().setStatus(task.isDone() ? Status.SUCCESS_OK : Status.SUCCESS_ACCEPTED);
            return tc.createTaskRepresentation(task.getUuid(), variant, getRequest(), getResponse(), null);
        }
    throw new ResourceException(Status.CLIENT_ERROR_UNSUPPORTED_MEDIA_TYPE);
}

Example 3 with ITask

use of net.idea.restnet.i.task.ITask in project ambit-mirror by ideaconsult.

the class BundleMatrixResource method put.

@Override
protected Representation put(Representation entity, Variant variant) throws ResourceException {
    _matrix matrix = getList();
    if ((entity == null) || !entity.isAvailable())
        throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, "Empty content");
    if (entity.getMediaType() != null) {
        if (MediaType.APPLICATION_JSON.getName().equals(entity.getMediaType().getName())) {
            _mode importmode = _mode.studyimport;
            switch(matrix) {
                case deleted_values:
                    {
                        importmode = _mode.matrixvaluedelete;
                        break;
                    }
                case matrix_working:
                    {
                        importmode = _mode.studyimport;
                        break;
                    }
                default:
                    throw new ResourceException(Status.CLIENT_ERROR_METHOD_NOT_ALLOWED);
            }
            try {
                File file = File.createTempFile("_matrix_", ".json");
                file.deleteOnExit();
                DownloadTool.download(entity.getStream(), file);
                String token = getToken();
                QASettings qa = new QASettings();
                // sets enabled to false and clears all flags
                qa.clear();
                CallableStudyBundleImporter<String> callable = new CallableStudyBundleImporter<String>(importmode, file, getRootRef(), getContext(), new SubstanceURIReporter(getRequest().getRootRef()), new DatasetURIReporter(getRequest().getRootRef()), token, getRequest().getResourceRef().toString(), getClientInfo());
                callable.setBundle(bundle);
                callable.setClearComposition(false);
                callable.setClearMeasurements(false);
                callable.setQASettings(qa);
                ITask<Reference, Object> task = ((ITaskApplication) getApplication()).addTask("Substance import", callable, getRequest().getRootRef(), token);
                ITaskStorage storage = ((ITaskApplication) getApplication()).getTaskStorage();
                FactoryTaskConvertor<Object> tc = new FactoryTaskConvertor<Object>(storage);
                task.update();
                getResponse().setStatus(task.isDone() ? Status.SUCCESS_OK : Status.SUCCESS_ACCEPTED);
                return tc.createTaskRepresentation(task.getUuid(), variant, getRequest(), getResponse(), null);
            } catch (Exception x) {
                x.printStackTrace();
            } finally {
                try {
                    entity.getStream().close();
                } catch (Exception xx) {
                }
            }
        } else if (MediaType.MULTIPART_FORM_DATA.getName().equals(entity.getMediaType().getName())) {
            switch(matrix) {
                case matrix_working:
                    {
                        break;
                    }
                default:
                    throw new ResourceException(Status.CLIENT_ERROR_METHOD_NOT_ALLOWED);
            }
            DiskFileItemFactory factory = new DiskFileItemFactory();
            RestletFileUpload upload = new RestletFileUpload(factory);
            try {
                List<FileItem> items = upload.parseRequest(getRequest());
                String token = getToken();
                QASettings qa = new QASettings();
                // sets enabled to false and clears all flags
                qa.clear();
                boolean clearMeasurements = false;
                boolean clearComposition = false;
                for (FileItem file : items) {
                    if (file.isFormField()) {
                    // ignore
                    } else {
                        String ext = file.getName().toLowerCase();
                        if (ext.endsWith(".json")) {
                        } else
                            throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, "Unsupported format " + ext);
                    }
                }
                CallableStudyBundleImporter<String> callable = new CallableStudyBundleImporter<String>(items, CallableFileUpload.field_files, CallableFileUpload.field_config, getRootRef(), getContext(), new SubstanceURIReporter(getRequest().getRootRef()), new DatasetURIReporter(getRequest().getRootRef()), token, getRequest().getResourceRef().toString(), getClientInfo());
                callable.setBundle(bundle);
                callable.setClearComposition(clearComposition);
                callable.setClearMeasurements(clearMeasurements);
                callable.setQASettings(qa);
                ITask<Reference, Object> task = ((ITaskApplication) getApplication()).addTask("Substance import", callable, getRequest().getRootRef(), token);
                ITaskStorage storage = ((ITaskApplication) getApplication()).getTaskStorage();
                FactoryTaskConvertor<Object> tc = new FactoryTaskConvertor<Object>(storage);
                task.update();
                getResponse().setStatus(task.isDone() ? Status.SUCCESS_OK : Status.SUCCESS_ACCEPTED);
                return tc.createTaskRepresentation(task.getUuid(), variant, getRequest(), getResponse(), null);
            } catch (ResourceException x) {
                throw x;
            } catch (Exception x) {
                throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, x);
            }
        }
    }
    throw new ResourceException(Status.CLIENT_ERROR_UNSUPPORTED_MEDIA_TYPE);
}

Example 4 with ITask

use of net.idea.restnet.i.task.ITask in project ambit-mirror by ideaconsult.

the class FileUpload method upload.

public Representation upload(Representation entity, Variant variant, boolean newEntry, boolean propertyOnly, USERID token, String referer, ClientInfo clientInfo) throws ResourceException {
    if ((entity == null) || !entity.isAvailable())
        throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, "Empty content");
    if (MediaType.APPLICATION_WWW_FORM.equals(entity.getMediaType())) {
        // propertyOnly POST:
        boolean clearPreviousContent = !propertyOnly;
        // false, PUT : true
        return copyDatasetToQueryResultsTable(new Form(entity), token, clearPreviousContent, referer, clientInfo);
    } else if (MediaType.MULTIPART_FORM_DATA.equals(entity.getMediaType(), true)) {
        DiskFileItemFactory factory = new DiskFileItemFactory();
        // factory.setSizeThreshold(100);
        RestletFileUpload upload = new RestletFileUpload(factory);
        Connection connection = null;
        try {
            DBConnection dbc = new DBConnection(getApplication().getContext());
            connection = dbc.getConnection(30, true, 8);
            List<FileItem> items = upload.parseRequest(getRequest());
            DatasetURIReporter<IQueryRetrieval<ISourceDataset>, ISourceDataset> reporter = new DatasetURIReporter<IQueryRetrieval<ISourceDataset>, ISourceDataset>(getRequest());
            ConformerURIReporter<IQueryRetrieval<IStructureRecord>> compoundReporter = new ConformerURIReporter<IQueryRetrieval<IStructureRecord>>(getRequest());
            CallableFileImport callable = new CallableFileImport(getRequest().getClientInfo(), dataset, items, fileUploadField, connection, reporter, compoundReporter, firstCompoundOnly, token);
            callable.setPropertyOnly(propertyOnly);
            ITask<Reference, Object> task = ((ITaskApplication) getApplication()).addTask("File import", callable, getRequest().getRootRef(), token);
            ITaskStorage storage = ((ITaskApplication) getApplication()).getTaskStorage();
            FactoryTaskConvertor<Object> tc = new FactoryTaskConvertor<Object>(storage);
            task.update();
            getResponse().setStatus(task.isDone() ? Status.SUCCESS_OK : Status.SUCCESS_ACCEPTED);
            return tc.createTaskRepresentation(task.getUuid(), variant, getRequest(), getResponse(), null);
        } catch (Exception x) {
            try {
                connection.close();
            } catch (Exception xx) {
                xx.printStackTrace();
            }
            throw new ResourceException(Status.SERVER_ERROR_INTERNAL, x);
        }
    } else if (isAllowedMediaType(entity.getMediaType())) {
        Connection connection = null;
        try {
            DBConnection dbc = new DBConnection(getApplication().getContext());
            connection = dbc.getConnection(30, true, 8);
            DatasetURIReporter<IQueryRetrieval<ISourceDataset>, ISourceDataset> reporter = new DatasetURIReporter<IQueryRetrieval<ISourceDataset>, ISourceDataset>(getRequest());
            ConformerURIReporter<IQueryRetrieval<IStructureRecord>> compoundReporter = new ConformerURIReporter<IQueryRetrieval<IStructureRecord>>(getRequest());
            CallableFileImport callable = new CallableFileImport(getRequest().getClientInfo(), dataset, entity, connection, reporter, compoundReporter, firstCompoundOnly, token);
            callable.setPropertyOnly(propertyOnly);
            ITask<ITaskResult, Object> task = ((AmbitApplication) getApplication()).addTask(String.format("File import %s [%d]", entity.getDownloadName() == null ? entity.getMediaType() : entity.getDownloadName(), entity.getSize()), callable, getRequest().getRootRef(), token == null ? null : token.toString());
            ITaskStorage storage = ((ITaskApplication) getApplication()).getTaskStorage();
            FactoryTaskConvertor<Object> tc = new FactoryTaskConvertor<Object>(storage);
            task.update();
            getResponse().setStatus(task.isDone() ? Status.SUCCESS_OK : Status.SUCCESS_ACCEPTED);
            return tc.createTaskRepresentation(task.getUuid(), variant, getRequest(), getResponse(), null);
        } catch (Exception x) {
            try {
                connection.close();
            } catch (Exception xx) {
                xx.printStackTrace();
            }
            throw new ResourceException(Status.SERVER_ERROR_INTERNAL, x);
        }
    } else
        throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, String.format("Unsupported Content-type=%s", entity.getMediaType()));
}