SQL API added

opal-core-api/src/main/java/org/obiba/opal/core/service/SQLException.java

@@ -0,0 +1,22 @@
+/*
+ * Copyright (c) 2021 OBiBa. All rights reserved.
+ *
+ * This program and the accompanying materials
+ * are made available under the terms of the GNU Public License v3.0.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package org.obiba.opal.core.service;
+
+public class SQLException extends RuntimeException {
+
+  public SQLException(String message) {
+    super(message);
+  }
+
+  public SQLException(Throwable throwable) {
+    super(throwable.getMessage(), throwable);
+  }
+}

opal-core-api/src/main/java/org/obiba/opal/core/service/SQLService.java

@@ -0,0 +1,41 @@
+/*
+ * Copyright (c) 2021 OBiBa. All rights reserved.
+ *
+ * This program and the accompanying materials
+ * are made available under the terms of the GNU Public License v3.0.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package org.obiba.opal.core.service;
+
+import java.io.File;
+
+/**
+ * A service for executing SQL queries on a project's tables.
+ */
+public interface SQLService extends SystemService {
+
+  /**
+   * Execute a SQL query in the context of a datasource and output result as a JSON object.
+   *
+   * @param datasource
+   * @param query
+   * @param idName
+   * @return
+   */
+  File executeToJSON(String datasource, String query, String idName);
+
+  /**
+   * Execute a SQL query in the context of a datasource and dump output to a temporary
+   * CSV file.
+   *
+   * @param datasource
+   * @param query
+   * @param idName
+   * @return
+   */
+  File executeToCSV(String datasource, String query, String idName);
+
+}

opal-core-ws/src/main/java/org/obiba/opal/core/security/DatasourcePermissionConverter.java

@@ -41,6 +41,7 @@ public enum Permission {
       public Iterable<String> convert(String node) {
         String[] args = args(node, "/datasource/(.+)");
         return Lists.newArrayList(toRest("/datasource/{0}", "*:GET/*", args),
+            toRest("/datasource/{0}/_sql", "POST:GET", args),
             toRest("/identifiers/mappings", "GET"),
             toRest("/datasource-plugin", "GET:GET/GET"),
             toRest("/project/{0}", "GET:GET", args),
@@ -66,6 +67,7 @@ public Iterable<String> convert(String node) {
       public Iterable<String> convert(String node) {
         String[] args = args(node, "/datasource/(.+)");
         return Lists.newArrayList(toRest("/datasource/{0}/tables", "GET:GET", args),
+            toRest("/datasource/{0}/_sql", "POST:GET", args),
             toRest("/datasource/{0}/tables", "POST:GET", args),
             toRest("/datasource/{0}/tables", "DELETE", args),
             toRest("/datasource/{0}/views", "POST:GET", args),
@@ -91,6 +93,7 @@ public Iterable<String> convert(String node) {
       public Iterable<String> convert(String node) {
         String[] args = args(node, "/datasource/(.+)");
         return Lists.newArrayList(toRest("/datasource/{0}", "GET:GET/GET", args),
+            toRest("/datasource/{0}/_sql", "POST:GET", args),
             toRest("/project/{0}/commands/_analyse", "POST:GET", args),
             toRest("/project/{0}/commands/_export", "POST:GET", args),
             toRest("/project/{0}/commands/_copy", "POST:GET", args),

opal-core-ws/src/main/java/org/obiba/opal/core/security/TablePermissionConverter.java

@@ -46,6 +46,7 @@ public Iterable<String> convert(String node) {
         String[] args = isView ? args(node, "/datasource/(.+)/view/(.+)") : args(node, "/datasource/(.+)/table/(.+)");
 
         List<String> perms = Lists.newArrayList(toRest("/datasource/{0}/table/{1}", "*:GET/*", args),
+            toRest("/datasource/{0}/_sql", "POST:GET", args),
             toRest("/project/{0}/commands/_export", "POST:GET", args),
             toRest("/project/{0}/commands/_copy", "POST:GET", args),
             toRest("/project/{0}/commands/_refresh", "POST:GET", args),
@@ -104,6 +105,7 @@ public Iterable<String> convert(String node) {
             toRest("/datasource/{0}/table/{1}/index/_search", "GET", args),
             toRest("/datasource/{0}/table/{1}/index/_search", "POST", args),
             toRest("/datasource/{0}/table/{1}/index/_schema", "GET", args),
+            toRest("/datasource/{0}/_sql", "POST:GET", args),
             toRest("/project/{0}/commands/_analyse", "POST:GET", args),
             toRest("/project/{0}/commands/_export", "POST:GET", args),
             toRest("/project/{0}/commands/_copy", "POST:GET", args),
@@ -148,6 +150,7 @@ public Iterable<String> convert(String node) {
         }
 
         perms.addAll(Lists.newArrayList(toRest("/datasource/{0}/table/{1}/index", "GET:GET", args),
+            toRest("/datasource/{0}/_sql", "POST:GET", args),
             toRest("/datasource/{0}/table/{1}/index/schedule", "GET:GET", args),
             toRest("/files/projects/{0}", "GET:GET/*", args),
             toRest("/files/projects/{0}", "POST:GET/*", args),

opal-core-ws/src/main/java/org/obiba/opal/web/magma/DatasourceResource.java

@@ -13,6 +13,8 @@
 import com.google.common.eventbus.EventBus;
 import com.googlecode.protobuf.format.JsonFormat;
 import java.io.BufferedOutputStream;
+import java.io.File;
+import java.nio.file.Files;
 import java.util.Date;
 import java.util.List;
 import java.util.stream.Collectors;
@@ -29,6 +31,7 @@
 import org.obiba.opal.core.event.ValueTableAddedEvent;
 import org.obiba.opal.core.security.OpalPermissions;
 import org.obiba.opal.core.service.OpalGeneralConfigService;
+import org.obiba.opal.core.service.SQLService;
 import org.obiba.opal.search.IndexManagerConfigurationService;
 import org.obiba.opal.search.Schedule;
 import org.obiba.opal.web.magma.view.ViewDtos;
@@ -80,6 +83,9 @@ public class DatasourceResource {
   @Autowired
   private EventBus eventBus;
 
+  @Autowired
+  private SQLService sqlService;
+
   public void setName(String name) {
     this.name = name;
   }
@@ -253,6 +259,38 @@ public Iterable<LocaleDto> getLocales(@QueryParam("locale") String displayLocale
     return localeDtos;
   }
 
+  @POST
+  @Path("/_sql")
+  @Consumes(MediaType.TEXT_PLAIN)
+  @Produces(MediaType.APPLICATION_JSON)
+  public Response executeSQLToJSON(String query, @QueryParam("id") @DefaultValue("_id") String idName) {
+    final File output = sqlService.executeToJSON(name, query, idName);
+    StreamingOutput stream = os -> {
+      Files.copy(output.toPath(), os);
+      output.delete();
+    };
+
+    return Response.ok(stream, MediaType.APPLICATION_JSON_TYPE)
+        .header("Content-Disposition", "attachment; filename=\"" + output.getName() + "\"").build();
+//    return Response.ok().type(MediaType.APPLICATION_JSON_TYPE)
+//        .entity(sqlService.executeToJSON(name, query, idName)).build();
+  }
+
+  @POST
+  @Path("/_sql")
+  @Consumes(MediaType.APPLICATION_FORM_URLENCODED)
+  @Produces("text/csv")
+  public Response executeSQLToCSV(@FormParam("query") String query, @FormParam("id") @DefaultValue("_id") String idName) {
+    final File output = sqlService.executeToCSV(name, query, idName);
+    StreamingOutput stream = os -> {
+      Files.copy(output.toPath(), os);
+      output.delete();
+    };
+
+    return Response.ok(stream, "text/csv")
+        .header("Content-Disposition", "attachment; filename=\"" + output.getName() + "\"").build();
+  }
+
   Datasource getDatasource() {
     return MagmaEngine.get().hasDatasource(name)
         ? MagmaEngine.get().getDatasource(name)

opal-core-ws/src/main/java/org/obiba/opal/web/provider/SQLExceptionMapper.java

@@ -0,0 +1,43 @@
+/*
+ * Copyright (c) 2020 OBiBa. All rights reserved.
+ *
+ * This program and the accompanying materials
+ * are made available under the terms of the GNU Public License v3.0.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package org.obiba.opal.web.provider;
+
+import com.google.protobuf.GeneratedMessage;
+import org.obiba.opal.core.service.SQLException;
+import org.obiba.opal.web.magma.ClientErrorDtos;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.stereotype.Component;
+
+import javax.ws.rs.BadRequestException;
+import javax.ws.rs.core.Response;
+import javax.ws.rs.ext.Provider;
+
+import static javax.ws.rs.core.Response.Status.BAD_REQUEST;
+
+@Component
+@Provider
+public class SQLExceptionMapper extends ErrorDtoExceptionMapper<SQLException> {
+
+  private static final Logger log = LoggerFactory.getLogger(SQLExceptionMapper.class);
+
+  @Override
+  protected Response.Status getStatus() {
+    return BAD_REQUEST;
+  }
+
+  @Override
+  protected GeneratedMessage.ExtendableMessage<?> getErrorDto(SQLException exception) {
+    log.debug("SQL exception", exception);
+    return ClientErrorDtos.getErrorMessage(getStatus(), "SQLError", exception);
+  }
+
+}

opal-core-ws/src/test/java/org/obiba/opal/core/security/DatasourcePermissionConverterTest.java

@@ -21,6 +21,7 @@ public class DatasourcePermissionConverterTest
   public void testDatasourceAll() {
     testConversion("/datasource/patate", DatasourcePermissionConverter.Permission.DATASOURCE_ALL,
         "rest:/datasource/patate:*:GET/*",
+        "rest:/datasource/patate/_sql:POST:GET",
         "rest:/identifiers/mappings:GET",
         "rest:/datasource-plugin:GET:GET/GET",
         "rest:/project/patate:GET:GET",
@@ -44,6 +45,7 @@ public void testDatasourceAll() {
   public void testDatasourceView() {
     testConversion("/datasource/patate", DatasourcePermissionConverter.Permission.DATASOURCE_VIEW,
         "rest:/datasource/patate:GET:GET/GET",
+        "rest:/datasource/patate/_sql:POST:GET",
         "rest:/project/patate/commands/_analyse:POST:GET",
         "rest:/project/patate/commands/_export:POST:GET",
         "rest:/project/patate/commands/_copy:POST:GET",
@@ -60,6 +62,7 @@ public void testDatasourceView() {
   public void testCreateTable() {
     testConversion("/datasource/patate", DatasourcePermissionConverter.Permission.TABLE_ADD,
         "rest:/datasource/patate/tables:GET:GET",
+        "rest:/datasource/patate/_sql:POST:GET",
         "rest:/datasource/patate/tables:POST:GET",
         "rest:/datasource/patate/tables:DELETE",
         "rest:/datasource/patate/views:POST:GET",

opal-core-ws/src/test/java/org/obiba/opal/core/security/TablePermissionConverterTest.java

@@ -31,6 +31,7 @@ public void testArgs() {
   public void testTableAll() {
     testConversion("/datasource/patate/table/pwel", TablePermissionConverter.Permission.TABLE_ALL,
         "rest:/datasource/patate/table/pwel:*:GET/*",
+        "rest:/datasource/patate/_sql:POST:GET",
         "rest:/project/patate/commands/_export:POST:GET",
         "rest:/project/patate/commands/_copy:POST:GET",
         "rest:/project/patate/commands/_refresh:POST:GET",
@@ -51,6 +52,7 @@ public void testTableAll() {
   public void testTableAllOnView() {
     testConversion("/datasource/patate/view/pwel", TablePermissionConverter.Permission.TABLE_ALL,
         "rest:/datasource/patate/table/pwel:*:GET/*",
+        "rest:/datasource/patate/_sql:POST:GET",
         "rest:/project/patate/commands/_export:POST:GET",
         "rest:/project/patate/commands/_copy:POST:GET",
         "rest:/project/patate/commands/_refresh:POST:GET",
@@ -75,6 +77,7 @@ public void testTableEdit() {
         "rest:/datasource/patate/table/pwel/variables:POST:GET/*",
         "rest:/datasource/patate/table/pwel/variables:DELETE:GET",
         "rest:/datasource/patate/table/pwel/index:GET:GET",
+        "rest:/datasource/patate/_sql:POST:GET",
         "rest:/datasource/patate/table/pwel/index/schedule:GET:GET",
         "rest:/files/projects/patate:GET:GET/*",
         "rest:/files/projects/patate:POST:GET/*",
@@ -102,6 +105,7 @@ public void testTableValuesEdit() {
         "rest:/datasource/patate/table/pwel/index/_search:GET",
         "rest:/datasource/patate/table/pwel/index/_search:POST",
         "rest:/datasource/patate/table/pwel/index/_schema:GET",
+        "rest:/datasource/patate/_sql:POST:GET",
         "rest:/project/patate/commands/_analyse:POST:GET",
         "rest:/project/patate/commands/_export:POST:GET",
         "rest:/project/patate/commands/_copy:POST:GET",
@@ -132,6 +136,7 @@ public void testTableValuesEdit() {
         "rest:/datasource/patate/table/pwel/variables:POST:GET/*",
         "rest:/datasource/patate/table/pwel/variables:DELETE:GET",
         "rest:/datasource/patate/table/pwel/index:GET:GET",
+        "rest:/datasource/patate/_sql:POST:GET",
         "rest:/datasource/patate/table/pwel/index/schedule:GET:GET",
         "rest:/files/projects/patate:GET:GET/*",
         "rest:/files/projects/patate:POST:GET/*",
@@ -177,6 +182,7 @@ public void testTableValuesOnView() {
         "rest:/datasource/patate/table/pwel/index/_search:GET",
         "rest:/datasource/patate/table/pwel/index/_search:POST",
         "rest:/datasource/patate/table/pwel/index/_schema:GET",
+        "rest:/datasource/patate/_sql:POST:GET",
         "rest:/project/patate/commands/_analyse:POST:GET",
         "rest:/project/patate/commands/_export:POST:GET",
         "rest:/project/patate/commands/_copy:POST:GET",

opal-gwt-client/src/main/java/org/obiba/opal/web/gwt/app/client/i18n/Translations.java

@@ -756,7 +756,8 @@ public interface Translations extends Constants {
       "NameMustBeUnique", "Name must be unique.",
       "GHOrganizationIsRequired", "GitHub user or organization name is required",
       "ResourceAssignSuccess", "Resource assignment in R was successful.",
-      "ResourceAssignFailed", "Resource assignment in R has failed: "
+      "ResourceAssignFailed", "Resource assignment in R has failed: ",
+      "SQLError", "{0}"
   })
   Map<String, String> userMessageMap();
 

opal-gwt-client/src/main/java/org/obiba/opal/web/gwt/app/client/magma/MagmaModule.java

@@ -33,6 +33,8 @@
 import org.obiba.opal.web.gwt.app.client.magma.presenter.VariablePresenter;
 import org.obiba.opal.web.gwt.app.client.magma.presenter.VariableVcsCommitHistoryPresenter;
 import org.obiba.opal.web.gwt.app.client.magma.presenter.VcsCommitHistoryModalPresenter;
+import org.obiba.opal.web.gwt.app.client.magma.sql.SQLPresenter;
+import org.obiba.opal.web.gwt.app.client.magma.sql.SQLView;
 import org.obiba.opal.web.gwt.app.client.magma.table.presenter.TablePropertiesModalPresenter;
 import org.obiba.opal.web.gwt.app.client.magma.table.presenter.ViewModalPresenter;
 import org.obiba.opal.web.gwt.app.client.magma.table.presenter.ViewWhereModalPresenter;
@@ -101,7 +103,7 @@ private void configureMagma() {
         VariableTaxonomyModalView.class);
     bindPresenterWidget(AddVariablesModalPresenter.class, AddVariablesModalPresenter.Display.class,
         AddVariablesModalView.class);
-
+    bindPresenterWidget(SQLPresenter.class, SQLPresenter.Display.class, SQLView.class);
   }
 
   private void configureDatasource() {