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lgallgal
lgal
authored and
lgal
committed
SORMAS-Foundation#3610 WIP rest endpoint for BAG export cases
1 parent eca4173 commit 33e06eb

6 files changed

Lines changed: 303 additions & 135 deletions

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‎sormas-api/src/main/java/de/symeda/sormas/api/user/UserRole.java‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -61,7 +61,8 @@ public enum UserRole
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IMPORT_USER(false, false, false, false, JurisdictionLevel.NONE),
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REST_EXTERNAL_VISITS_USER(false, false, false, false, JurisdictionLevel.NONE),
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REST_USER(false, false, false, false, JurisdictionLevel.NONE),
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SORMAS_TO_SORMAS_CLIENT(false, false, false, false, JurisdictionLevel.NONE);
64+
SORMAS_TO_SORMAS_CLIENT(false, false, false, false, JurisdictionLevel.NONE),
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BAG_USER(false, false, false, false, JurisdictionLevel.NONE);
6566

6667
/*
6768
* Hint for SonarQube issues:

‎sormas-api/src/main/java/de/symeda/sormas/api/utils/CsvStreamUtils.java‎

Lines changed: 196 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,196 @@
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/*
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* SORMAS® - Surveillance Outbreak Response Management & Analysis System
3+
* Copyright © 2016-2020 Helmholtz-Zentrum für Infektionsforschung GmbH (HZI)
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* This program is free software: you can redistribute it and/or modify
5+
* it under the terms of the GNU General Public License as published by
6+
* the Free Software Foundation, either version 3 of the License, or
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* (at your option) any later version.
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* This program is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
10+
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
11+
* GNU General Public License for more details.
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* You should have received a copy of the GNU General Public License
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* along with this program. If not, see <https://www.gnu.org/licenses/>.
14+
*/
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package de.symeda.sormas.api.utils;
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import java.io.OutputStream;
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import java.io.OutputStreamWriter;
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import java.lang.reflect.InvocationTargetException;
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import java.lang.reflect.Method;
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import java.nio.charset.StandardCharsets;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Collections;
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import java.util.Comparator;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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import org.apache.commons.collections.CollectionUtils;
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import org.apache.commons.collections.Predicate;
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import com.opencsv.CSVWriter;
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import de.symeda.sormas.api.ConfigFacade;
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import de.symeda.sormas.api.EntityDto;
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import de.symeda.sormas.api.importexport.ExportConfigurationDto;
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import de.symeda.sormas.api.importexport.ExportProperty;
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import de.symeda.sormas.api.utils.fieldvisibility.checkers.CountryFieldVisibilityChecker;
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public class CsvStreamUtils {
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public static final int STEP_SIZE = 50;
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public static <T> void writeCsvContentToStream(
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Class<T> csvRowClass,
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SupplierBiFunction<Integer, Integer, List<T>> exportRowsSupplier,
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SupplierBiFunction<String, Class<?>, String> propertyIdCaptionSupplier,
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ExportConfigurationDto exportConfiguration,
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final Predicate redMethodFilter,
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ConfigFacade configFacade,
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OutputStream out) {
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try (
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CSVWriter writer = CSVUtils.createCSVWriter(new OutputStreamWriter(out, StandardCharsets.UTF_8.name()), configFacade.getCsvSeparator())) {
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// 1. fields in order of declaration - not using Introspector here, because it gives properties in alphabetical order
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List<Method> readMethods =
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getExportRowClassReadMethods(csvRowClass, exportConfiguration, redMethodFilter, configFacade.getCountryLocale());
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// 2. replace entity fields with all the columns of the entity
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Map<Method, SubEntityProvider<T>> subEntityProviders = new HashMap<Method, SubEntityProvider<T>>();
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for (int i = 0; i < readMethods.size(); i++) {
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final Method method = readMethods.get(i);
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if (EntityDto.class.isAssignableFrom(method.getReturnType())) {
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// allows us to access the sub entity
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SubEntityProvider<T> subEntityProvider = new SubEntityProvider<T>() {
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@Override
72+
public Object get(T o) {
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try {
74+
return method.invoke(o);
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} catch (IllegalAccessException | IllegalArgumentException | InvocationTargetException e) {
76+
throw new RuntimeException(e);
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}
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}
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};
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// remove entity field
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readMethods.remove(i);
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// add columns of the entity
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List<Method> subReadMethods = getReadMethods(method.getReturnType(), null);
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readMethods.addAll(i, subReadMethods);
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i--;
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for (Method subReadMethod : subReadMethods) {
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subEntityProviders.put(subReadMethod, subEntityProvider);
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}
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}
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}
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String[] fieldValues = new String[readMethods.size()];
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for (int i = 0; i < readMethods.size(); i++) {
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final Method method = readMethods.get(i);
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// field caption
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String propertyId = method.getName().startsWith("get") ? method.getName().substring(3) : method.getName().substring(2);
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if (method.isAnnotationPresent(ExportProperty.class)) {
101+
// TODO not sure why we are using the export property name to get the caption here
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final ExportProperty exportProperty = method.getAnnotation(ExportProperty.class);
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if (!exportProperty.combined()) {
104+
propertyId = exportProperty.value();
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}
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}
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propertyId = Character.toLowerCase(propertyId.charAt(0)) + propertyId.substring(1);
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fieldValues[i] = propertyIdCaptionSupplier.apply(propertyId, method.getReturnType());
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}
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writer.writeNext(fieldValues);
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int startIndex = 0;
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List<T> exportRows = exportRowsSupplier.apply(startIndex, STEP_SIZE);
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while (!exportRows.isEmpty()) {
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try {
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for (T exportRow : exportRows) {
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for (int i = 0; i < readMethods.size(); i++) {
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Method method = readMethods.get(i);
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SubEntityProvider<T> subEntityProvider = subEntityProviders.get(method);
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Object entity = subEntityProvider != null ? subEntityProvider.get(exportRow) : exportRow;
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// Sub entity might be null
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Object value = entity != null ? method.invoke(entity) : null;
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fieldValues[i] = DataHelper.valueToString(value);
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}
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writer.writeNext(fieldValues);
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} ;
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} catch (InvocationTargetException | IllegalAccessException | IllegalArgumentException e) {
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throw new RuntimeException(e);
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}
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writer.flush();
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startIndex += STEP_SIZE;
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exportRows = exportRowsSupplier.apply(startIndex, STEP_SIZE);
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}
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} catch (Exception e) {
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throw new RuntimeException(e);
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}
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}
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private static <T> List<Method> getExportRowClassReadMethods(
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Class<T> exportRowClass,
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final ExportConfigurationDto exportConfiguration,
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final Predicate redMethodFilter,
145+
String countryLocale) {
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final CountryFieldVisibilityChecker countryFieldVisibilityChecker = new CountryFieldVisibilityChecker(countryLocale);
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return getReadMethods(exportRowClass, new Predicate() {
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@Override
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public boolean evaluate(Object o) {
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Method m = (Method) o;
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return (countryFieldVisibilityChecker.isVisible(m))
154+
&& (redMethodFilter == null || redMethodFilter.evaluate(o))
155+
&& (exportConfiguration == null || exportConfiguration.getProperties().contains(m.getAnnotation(ExportProperty.class).value()));
156+
}
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});
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}
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160+
private static List<Method> getReadMethods(Class<?> clazz, final Predicate filters) {
161+
ArrayList<Method> readMethods = new ArrayList<>(Arrays.asList(clazz.getDeclaredMethods()));
162+
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CollectionUtils.filter(readMethods, new Predicate() {
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@Override
166+
public boolean evaluate(Object o) {
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Method m = (Method) o;
168+
return (m.getName().startsWith("get") || m.getName().startsWith("is"))
169+
&& m.isAnnotationPresent(Order.class)
170+
&& (filters == null || filters.evaluate(o));
171+
}
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});
173+
Collections.sort(readMethods, new Comparator<Method>() {
174+
175+
@Override
176+
public int compare(Method m1, Method m2) {
177+
int o1 = m1.getAnnotation(Order.class).value();
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int o2 = m2.getAnnotation(Order.class).value();
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return o1 - o2;
181+
}
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});
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184+
return readMethods;
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}
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public interface SupplierBiFunction<T, U, R> {
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189+
R apply(T t, U u);
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}
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private interface SubEntityProvider<T> {
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Object get(T parent);
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}
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}

‎sormas-rest/src/main/java/de/symeda/sormas/rest/BAGExportResource.java‎

Lines changed: 67 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,67 @@
1+
/*
2+
* SORMAS® - Surveillance Outbreak Response Management & Analysis System
3+
* Copyright © 2016-2020 Helmholtz-Zentrum für Infektionsforschung GmbH (HZI)
4+
* This program is free software: you can redistribute it and/or modify
5+
* it under the terms of the GNU General Public License as published by
6+
* the Free Software Foundation, either version 3 of the License, or
7+
* (at your option) any later version.
8+
* This program is distributed in the hope that it will be useful,
9+
* but WITHOUT ANY WARRANTY; without even the implied warranty of
10+
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
11+
* GNU General Public License for more details.
12+
* You should have received a copy of the GNU General Public License
13+
* along with this program. If not, see <https://www.gnu.org/licenses/>.
14+
*/
15+
16+
package de.symeda.sormas.rest;
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18+
import java.io.ByteArrayOutputStream;
19+
import java.util.Date;
20+
21+
import javax.annotation.security.RolesAllowed;
22+
import javax.ws.rs.Consumes;
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import javax.ws.rs.GET;
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import javax.ws.rs.Path;
25+
import javax.ws.rs.Produces;
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import javax.ws.rs.core.MediaType;
27+
import javax.ws.rs.core.Response;
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import de.symeda.sormas.api.FacadeProvider;
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import de.symeda.sormas.api.bagexport.BAGExportCaseDto;
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import de.symeda.sormas.api.i18n.I18nProperties;
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import de.symeda.sormas.api.utils.CsvStreamUtils;
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import de.symeda.sormas.api.utils.DateFormatHelper;
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@Path("/bagexport")
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@Produces(MediaType.APPLICATION_OCTET_STREAM)
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@Consumes(MediaType.APPLICATION_JSON + "; charset=UTF-8")
38+
@RolesAllowed({
39+
"BAG_USER" })
40+
public class BAGExportResource {
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42+
@GET
43+
@Path("/cases")
44+
public Response exportCases(String file) {
45+
ByteArrayOutputStream baos = new ByteArrayOutputStream();
46+
47+
CsvStreamUtils.writeCsvContentToStream(
48+
BAGExportCaseDto.class,
49+
(from, to) -> FacadeProvider.getBAGExportFacade().getCaseExportList(from, to),
50+
(propertyId, type) -> {
51+
String caption = I18nProperties.findPrefixCaption(propertyId);
52+
if (Date.class.isAssignableFrom(type)) {
53+
caption += " (" + DateFormatHelper.getDateFormatPattern() + ")";
54+
}
55+
return caption;
56+
},
57+
null,
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null,
59+
FacadeProvider.getConfigFacade(),
60+
baos);
61+
62+
Response.ResponseBuilder response = Response.ok(baos);
63+
response.header("Content-Disposition", "attachment;filename=test.csv");
64+
65+
return response.build();
66+
}
67+
}

‎sormas-rest/src/main/webapp/WEB-INF/glassfish-web.xml‎

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -50,4 +50,8 @@
5050
<role-name>SORMAS_TO_SORMAS_CLIENT</role-name>
5151
<group-name>SORMAS_TO_SORMAS_CLIENT</group-name>
5252
</security-role-mapping>
53+
<security-role-mapping>
54+
<role-name>BAG_USER</role-name>
55+
<group-name>BAG_USER</group-name>
56+
</security-role-mapping>
5357
</glassfish-web-app>

‎sormas-rest/src/main/webapp/WEB-INF/web.xml‎

Lines changed: 3 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -31,5 +31,8 @@
3131
<security-role>
3232
<role-name>SORMAS_TO_SORMAS_CLIENT</role-name>
3333
</security-role>
34+
<security-role>
35+
<role-name>BAG_USER</role-name>
36+
</security-role>
3437

3538
</web-app>

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