Examples with CallableSubstanceI5Query ambit2.db.processors.CallableSubstanceI5Query used on opensource projects

Example 1 with CallableSubstanceI5Query

use of ambit2.db.processors.CallableSubstanceI5Query 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);
}