Examples with SubstanceURIReporter ambit2.rest.substance.SubstanceURIReporter used on opensource projects

Example 1 with SubstanceURIReporter

use of ambit2.rest.substance.SubstanceURIReporter 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 2 with SubstanceURIReporter

use of ambit2.rest.substance.SubstanceURIReporter in project ambit-mirror by ideaconsult.

the class UIResource method uploadsubstance.

@Override
protected Representation uploadsubstance(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 && 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());
            StringBuilder json = new StringBuilder();
            json.append("{\"files\": [");
            String delimiter = "";
            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) {
                        }
            }
            for (FileItem file : items) {
                if (file.isFormField())
                    continue;
                json.append(delimiter);
                json.append("\n{\n");
                json.append("\"name\":");
                json.append(JSONUtils.jsonQuote(JSONUtils.jsonEscape(file.getName())));
                json.append(",\n\"size\":");
                json.append(file.getSize());
                String ext = file.getName().toLowerCase();
                if (ext.endsWith(".i5z") || ext.endsWith(".i6z") || ext.endsWith(".csv") || ext.endsWith(".rdf") || ext.endsWith(".ttl") || ext.endsWith(".json")) {
                    String img = "i5z.png";
                    if (ext.endsWith(".csv"))
                        img = "csv64.png";
                    else if (ext.endsWith(".xlsx"))
                        img = "xlsx.png";
                    else if (ext.endsWith(".rdf"))
                        img = "rdf64.png";
                    else if (ext.endsWith(".ttl"))
                        img = "rdf64.png";
                    else if (ext.endsWith(".json"))
                        img = "json64.png";
                    else if (ext.endsWith(".i6z"))
                        img = "i6z.png";
                    try {
                        List<FileItem> item = new ArrayList<FileItem>();
                        item.add(file);
                        CallableSubstanceImporter<String> callable = new CallableSubstanceImporter<String>(item, CallableFileUpload.field_files, CallableFileUpload.field_config, getRootRef(), getContext(), new SubstanceURIReporter(getRequest().getRootRef()), new DatasetURIReporter(getRequest().getRootRef()), null, getRequest().getResourceRef().toString(), getClientInfo());
                        callable.setClearComposition(clearComposition);
                        callable.setClearMeasurements(clearMeasurements);
                        callable.setQASettings(qa);
                        ITaskResult result = callable.call();
                        json.append(",\n\"url\":");
                        json.append(JSONUtils.jsonQuote(JSONUtils.jsonEscape(result.getReference().toString())));
                        json.append(",\n\"thumbnailUrl\":");
                        json.append(JSONUtils.jsonQuote(JSONUtils.jsonEscape(String.format("%s/images/%s", getRequest().getRootRef(), img))));
                        json.append(",\n\"deleteUrl\":");
                        json.append(JSONUtils.jsonQuote(JSONUtils.jsonEscape(result.getReference().toString())));
                        json.append(",\n\"deleteType\":");
                        json.append("\"Delete\"");
                    } catch (Exception x) {
                        json.append(",\n\"error\":");
                        json.append(JSONUtils.jsonQuote(JSONUtils.jsonEscape(x.getMessage())));
                    } finally {
                    }
                } else {
                    json.append(",\n\"error\":");
                    json.append(JSONUtils.jsonQuote(JSONUtils.jsonEscape("File type not allowed!")));
                }
                json.append("\n}");
            }
            json.append("\n]}");
            getResponse().setStatus(Status.SUCCESS_OK);
            return new StringRepresentation(json.toString(), MediaType.APPLICATION_JSON);
        } catch (FileUploadException x) {
            throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, x);
        }
    } else
        throw new ResourceException(Status.CLIENT_ERROR_UNSUPPORTED_MEDIA_TYPE);
}

Example 3 with SubstanceURIReporter

use of ambit2.rest.substance.SubstanceURIReporter 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 SubstanceURIReporter

use of ambit2.rest.substance.SubstanceURIReporter in project ambit-mirror by ideaconsult.

the class BundleSubstanceResource method createCallable.

@Override
protected CallableProtectedTask<String> createCallable(Method method, Form form, SubstanceRecord item) throws ResourceException {
    SubstanceEndpointsBundle bundle = null;
    Object id = getRequest().getAttributes().get(OpenTox.URI.bundle.getKey());
    if ((id != null))
        try {
            bundle = new SubstanceEndpointsBundle(new Integer(Reference.decode(id.toString())));
        } catch (Exception x) {
        }
    Connection conn = null;
    try {
        SubstanceURIReporter<IQueryRetrieval<SubstanceRecord>> r = new SubstanceURIReporter<IQueryRetrieval<SubstanceRecord>>(getRequest());
        DBConnection dbc = new DBConnection(getApplication().getContext(), getConfigFile());
        conn = dbc.getConnection(30, true, 8);
        return new CallableSubstanceBundle(bundle, r, method, form, conn, getToken());
    } catch (Exception x) {
        try {
            conn.close();
        } catch (Exception xx) {
        }
        throw new ResourceException(Status.SERVER_ERROR_INTERNAL, x);
    }
}

Example 5 with SubstanceURIReporter

use of ambit2.rest.substance.SubstanceURIReporter in project ambit-mirror by ideaconsult.

the class CallableStudyBundleImporterTest method test.

@Test
public void test() throws Exception {
    setUpDatabase(dbFile);
    IDatabaseConnection c = getConnection();
    IDatabaseConnection c1 = getConnection();
    Form form = new Form();
    form.add("substance_uri", "http://localhost:8081/ambit2/substance/IUC4-efdb21bb-e79f-3286-a988-b6f6944d3734");
    form.add("tag", "CM");
    form.add("remarks", "remark");
    try {
        String ref = "http://localhost:8081/ambit2";
        Reference rootref = new Reference(ref);
        SubstanceEndpointsBundle bundle = new SubstanceEndpointsBundle(1);
        SubstanceURIReporter<IQueryRetrieval<SubstanceRecord>> reporter = new SubstanceURIReporter<IQueryRetrieval<SubstanceRecord>>(rootref);
        DatasetURIReporter dreporter = new DatasetURIReporter(rootref);
        File file = new File(getClass().getClassLoader().getResource("matrixvalue_delete.json").getFile());
        CallableStudyBundleImporter callable = new CallableStudyBundleImporter(_mode.matrixvaluedelete, file, rootref, null, reporter, dreporter, null, ref, null);
        TaskResult task = callable.call();
        ITable table = c1.createQueryTable("EXPECTED", String.format("SELECT idbundle,idsubstance,tag,remarks from bundle_substance"));
        Assert.assertEquals(1, table.getRowCount());
        Assert.assertEquals("CM", table.getValue(0, "tag"));
        Assert.assertEquals("remark", table.getValue(0, "remarks"));
    } catch (Exception x) {
        throw x;
    } finally {
        try {
            c.close();
        } catch (Exception x) {
        }
        try {
            c1.close();
        } catch (Exception x) {
        }
    }
}