documentation for get publication list API call added

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java

@@ -22,7 +22,6 @@ import lcsb.mapviewer.converter.ConverterParams;
 import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
 import lcsb.mapviewer.model.graphics.PolylineData;
 import lcsb.mapviewer.model.graphics.PolylineDataComparator;
-import lcsb.mapviewer.model.map.InconsistentModelException;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.model.*;
 import lcsb.mapviewer.model.map.reaction.*;

rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectController.java

@@ -6,8 +6,6 @@ import java.util.Map;
 
 import javax.servlet.ServletContext;
 
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.MediaType;
 import org.springframework.http.ResponseEntity;

web/src/main/asciidoc/projects/project_data.adoc

@@ -140,3 +140,21 @@ include::{snippets}/projects/project_data/get_project_statistics/curl-request.ad
 === Sample Response
 include::{snippets}/projects/project_data/get_project_statistics/response-body.adoc[]
 
+== Get publications
+Gets publication list used in the project.
+
+=== Path Parameters
+include::{snippets}/projects/project_data/get_publications/path-parameters.adoc[]
+
+=== Request Parameters
+include::{snippets}/projects/project_data/get_project_logs/request-parameters.adoc[]
+
+=== Response Fields
+include::{snippets}/projects/project_data/get_publications/response-fields.adoc[]
+
+=== CURL sample
+include::{snippets}/projects/project_data/get_publications/curl-request.adoc[]
+
+=== Sample Response
+include::{snippets}/projects/project_data/get_publications/response-body.adoc[]
+

web/src/test/java/lcsb/mapviewer/web/ControllerIntegrationTest.java

@@ -246,6 +246,7 @@ abstract public class ControllerIntegrationTest {
     Reaction reaction = new TransportReaction("re1");
     reaction.setZ(2);
     reaction.setLine(new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 0)));
+    reaction.addMiriamData(new MiriamData(MiriamType.PUBMED, "28725475"));
     map.addReaction(reaction);
     Element element = new GenericProtein("p1");
     element.setWidth(100.0);

web/src/test/java/lcsb/mapviewer/web/ProjectControllerIntegrationTest.java

@@ -153,13 +153,13 @@ public class ProjectControllerIntegrationTest extends ControllerIntegrationTest
     mockMvc.perform(request)
         .andDo(document("projects/project_data/get_project_logs",
             requestParameters(
-                parameterWithName("start").description("number of first entry in this response"),
+                parameterWithName("start").description("number of first entry in this response").optional(),
                 parameterWithName("sortColumn")
-                    .description("log entry column that should be used for sorting (default: id)"),
-                parameterWithName("sortOrder").description("log entry sort order (asc, desc)"),
-                parameterWithName("level").description("level of log entry (warning, error)"),
-                parameterWithName("length").description("number of log entres we want to obtain"),
-                parameterWithName("search").description("search query used for filtering")),
+                    .description("log entry column that should be used for sorting (default: id)").optional(),
+                parameterWithName("sortOrder").description("log entry sort order (asc, desc)").optional(),
+                parameterWithName("level").description("level of log entry (warning, error)").optional(),
+                parameterWithName("length").description("number of log entres we want to obtain").optional(),
+                parameterWithName("search").description("search query used for filtering").optional()),
             pathParameters(parameterWithName("projectId").description("project identifier")),
             responseFields(
                 subsectionWithPath("data")

web/src/test/java/lcsb/mapviewer/web/PublicationsControllerIntegrationTest.java

 package lcsb.mapviewer.web;
 
-import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get;
+import static org.springframework.restdocs.mockmvc.MockMvcRestDocumentation.document;
+import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.get;
+import static org.springframework.restdocs.payload.PayloadDocumentation.*;
+import static org.springframework.restdocs.request.RequestDocumentation.*;
 import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
 
 import org.apache.logging.log4j.LogManager;
@@ -8,36 +11,28 @@ import org.apache.logging.log4j.Logger;
 import org.junit.*;
 import org.junit.runner.RunWith;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.MediaType;
 import org.springframework.mock.web.MockHttpSession;
 import org.springframework.test.annotation.Rollback;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 import org.springframework.test.web.servlet.RequestBuilder;
 import org.springframework.transaction.annotation.Transactional;
 
-import lcsb.mapviewer.common.Configuration;
 import lcsb.mapviewer.model.Project;
 import lcsb.mapviewer.model.map.model.ModelData;
-import lcsb.mapviewer.model.security.PrivilegeType;
-import lcsb.mapviewer.model.user.User;
 import lcsb.mapviewer.persist.dao.ProjectDao;
-import lcsb.mapviewer.services.interfaces.IUserService;
 
 @RunWith(SpringJUnit4ClassRunner.class)
 @Transactional
 @Rollback
 public class PublicationsControllerIntegrationTest extends ControllerIntegrationTest {
 
-  Logger logger = LogManager.getLogger();
+  private static final String TEST_PROJECT = "test_project";
 
-  @Autowired
-  private IUserService userService;
+  Logger logger = LogManager.getLogger();
 
   @Autowired
   private ProjectDao projectDao;
 
-  private User anonymous;
-
   private Project project;
   private ModelData map;
 
@@ -45,7 +40,6 @@ public class PublicationsControllerIntegrationTest extends ControllerIntegration
   public void setup() {
     project = projectDao.getProjectByProjectId(BUILT_IN_PROJECT);
     map = project.getModels().iterator().next();
-    anonymous = userService.getUserByLogin(Configuration.ANONYMOUS_LOGIN);
   }
 
   @After
@@ -54,12 +48,41 @@ public class PublicationsControllerIntegrationTest extends ControllerIntegration
 
   @Test
   public void testGetPublicationsForMap() throws Exception {
-    userService.grantUserPrivilege(anonymous, PrivilegeType.READ_PROJECT, BUILT_IN_PROJECT);
+    MockHttpSession session = createSession(ControllerIntegrationTest.BUILT_IN_TEST_ADMIN_LOGIN,
+        ControllerIntegrationTest.BUILT_IN_TEST_ADMIN_PASSWORD);
+    project = createProject(TEST_PROJECT);
+    map = project.getModels().iterator().next();
 
-    RequestBuilder request = get("/projects/" + BUILT_IN_PROJECT + "/models/" + map.getId() + "/publications/")
-        .contentType(MediaType.APPLICATION_FORM_URLENCODED);
+    RequestBuilder request = get("/projects/{projectId}/models/{mapId}/publications/", TEST_PROJECT, map.getId())
+        .session(session);
 
     mockMvc.perform(request)
+        .andDo(document("projects/project_data/get_publications",
+            requestParameters(
+                parameterWithName("start").description("number of first entry in this response").optional(),
+                parameterWithName("sortColumn")
+                    .description("entry column that should be used for sorting (default: pubmedId)").optional(),
+                parameterWithName("sortOrder").description("entry sort order (asc, desc)").optional(),
+                parameterWithName("length").description("number of entres we want to obtain").optional(),
+                parameterWithName("search").description("search query used for filtering").optional()),
+            pathParameters(parameterWithName("projectId").description("project identifier"),
+                parameterWithName("mapId").description("submap identifier (use '*' to indicate all maps)")),
+            responseFields(
+                subsectionWithPath("data")
+                    .description("list of publications")
+                    .type("Array<Article>"),
+                fieldWithPath("filteredSize")
+                    .description("number of entries that match filter criteria")
+                    .type("number"),
+                fieldWithPath("length")
+                    .description("number of entries in this response")
+                    .type("number"),
+                fieldWithPath("start")
+                    .description("number of first entry in this response")
+                    .type("number"),
+                fieldWithPath("totalSize")
+                    .description("number of all log entries")
+                    .type("number"))))
         .andExpect(status().is2xxSuccessful());
   }
 
@@ -69,7 +92,6 @@ public class PublicationsControllerIntegrationTest extends ControllerIntegration
         ControllerIntegrationTest.BUILT_IN_TEST_ADMIN_PASSWORD);
 
     RequestBuilder request = get("/projects/*/models/" + map.getId() + "/publications/")
-        .contentType(MediaType.APPLICATION_FORM_URLENCODED)
         .session(session);
 
     mockMvc.perform(request)