From 8e33399aa7c96e343642b3a474b7bdd2d60cce08 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Tue, 8 Aug 2017 13:50:22 +0200
Subject: [PATCH] info about models is returned when accessing models (not a
project)
---
.../java/lcsb/mapviewer/api/BaseRestImpl.java | 22 ++++++-
.../api/projects/ProjectMetaData.java | 39 -------------
.../api/projects/ProjectRestImpl.java | 11 +---
.../api/projects/models/ModelController.java | 40 +++++++++++++
.../projects/{ => models}/ModelMetaData.java | 2 +-
.../api/projects/models/ModelRestImpl.java | 58 +++++++++++++++++++
.../publications/PublicationsRestImpl.java | 3 +-
.../api/projects/ModelMetaDataTest.java | 2 +-
8 files changed, 126 insertions(+), 51 deletions(-)
create mode 100644 rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelController.java
rename rest-api/src/main/java/lcsb/mapviewer/api/projects/{ => models}/ModelMetaData.java (94%)
create mode 100644 rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelRestImpl.java
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
index 56071ddde9..ac78d8b8d3 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
@@ -26,6 +26,7 @@ import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.interfaces.IModelService;
+import lcsb.mapviewer.services.interfaces.IProjectService;
import lcsb.mapviewer.services.interfaces.IUserService;
import lcsb.mapviewer.services.search.ElementMatcher;
import lcsb.mapviewer.services.search.data.ElementIdentifier.ElementIdentifierType;
@@ -33,7 +34,7 @@ import lcsb.mapviewer.services.view.AnnotationView;
@Transactional(value = "txManager")
public abstract class BaseRestImpl {
-
+
/**
* Default class logger.
*/
@@ -42,6 +43,9 @@ public abstract class BaseRestImpl {
@Autowired
private IModelService modelService;
+ @Autowired
+ private IProjectService projectService;
+
@Autowired
private IUserService userService;
@@ -262,4 +266,20 @@ public abstract class BaseRestImpl {
}
}
+ /**
+ * @return the projectService
+ * @see #projectService
+ */
+ public IProjectService getProjectService() {
+ return projectService;
+ }
+
+ /**
+ * @param projectService the projectService to set
+ * @see #projectService
+ */
+ public void setProjectService(IProjectService projectService) {
+ this.projectService = projectService;
+ }
+
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectMetaData.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectMetaData.java
index 8b4e0560e0..58365826a5 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectMetaData.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectMetaData.java
@@ -47,10 +47,6 @@ public class ProjectMetaData implements Serializable {
*/
private String description;
- private ModelMetaData map;
-
- private Integer publicationCount;
-
/**
* List of overview images attached to this model.
*/
@@ -169,23 +165,6 @@ public class ProjectMetaData implements Serializable {
this.projectId = projectId;
}
- /**
- * @return the map
- * @see #map
- */
- public ModelMetaData getMap() {
- return map;
- }
-
- /**
- * @param map
- * the map to set
- * @see #map
- */
- public void setMap(ModelMetaData map) {
- this.map = map;
- }
-
/**
* @return the idObject
* @see #idObject
@@ -236,22 +215,4 @@ public class ProjectMetaData implements Serializable {
public void setOrganism(Map<String, Object> organism) {
this.organism = organism;
}
-
- /**
- * @return the publicationCount
- * @see #publicationCount
- */
- public Integer getPublicationCount() {
- return publicationCount;
- }
-
- /**
- * @param publicationCount
- * the publicationCount to set
- * @see #publicationCount
- */
- public void setPublicationCount(Integer publicationCount) {
- this.publicationCount = publicationCount;
- }
-
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
index a64ef7f781..6f4f9a1d17 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
@@ -129,7 +129,7 @@ public class ProjectRestImpl extends BaseRestImpl {
result.setVersion(model.getMapVersion());
result.setDescription(model.getNotes());
- Set<OverviewImage> set = new HashSet<OverviewImage>();
+ Set<OverviewImage> set = new HashSet<>();
set.addAll(model.getOverviewImages());
for (OverviewImage image : model.getOverviewImages()) {
for (OverviewLink ol : image.getLinks()) {
@@ -144,13 +144,6 @@ public class ProjectRestImpl extends BaseRestImpl {
logger.warn("Cannot determine top level image. Taking first one. " + model.getOverviewImages().get(0).getFilename());
result.setTopOverviewImage(factory.create(model.getOverviewImages().get(0)));
}
- result.setMap(new ModelMetaData(model));
-
- List<Model> models = new ArrayList<>();
- models.add(model);
- models.addAll(model.getSubmodels());
- result.setPublicationCount(publicationsRestImpl.getPublications(models).size());
-
}
return result;
@@ -434,6 +427,8 @@ public class ProjectRestImpl extends BaseRestImpl {
}
result.put("reactionAnnotations", reactionAnnotations);
+
+ result.put("publications", publicationsRestImpl.getPublications(models).size());
return result;
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelController.java
new file mode 100644
index 0000000000..26d0fb353b
--- /dev/null
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelController.java
@@ -0,0 +1,40 @@
+package lcsb.mapviewer.api.projects.models;
+
+import java.util.List;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.MediaType;
+import org.springframework.web.bind.annotation.CookieValue;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RestController;
+
+import lcsb.mapviewer.api.BaseController;
+import lcsb.mapviewer.api.ObjectNotFoundException;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.services.SecurityException;
+
+@RestController
+public class ModelController extends BaseController {
+ @Autowired
+ private ModelRestImpl modelController;
+
+ @RequestMapping(value = "/projects/{projectId:.+}/models/", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public List<ModelMetaData> getModels(//
+ @PathVariable(value = "projectId") String projectId, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, ObjectNotFoundException {
+ return modelController.getModels(projectId, token);
+ }
+
+ @RequestMapping(value = "/projects/{projectId:.+}/models/{modelId:.+}", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public ModelMetaData getModel(//
+ @PathVariable(value = "modelId") String modelId, //
+ @PathVariable(value = "projectId") String projectId, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, ObjectNotFoundException {
+ return modelController.getModel(projectId, modelId, token);
+ }
+
+}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ModelMetaData.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelMetaData.java
similarity index 94%
rename from rest-api/src/main/java/lcsb/mapviewer/api/projects/ModelMetaData.java
rename to rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelMetaData.java
index 273364a57e..62181d0b37 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ModelMetaData.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelMetaData.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.api.projects;
+package lcsb.mapviewer.api.projects.models;
import java.awt.geom.Point2D;
import java.io.Serializable;
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelRestImpl.java
new file mode 100644
index 0000000000..e2a747e997
--- /dev/null
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelRestImpl.java
@@ -0,0 +1,58 @@
+package lcsb.mapviewer.api.projects.models;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.springframework.transaction.annotation.Transactional;
+
+import lcsb.mapviewer.api.BaseRestImpl;
+import lcsb.mapviewer.api.ObjectNotFoundException;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.services.SecurityException;
+import lcsb.mapviewer.services.view.AuthenticationToken;
+
+@Transactional(value = "txManager")
+public class ModelRestImpl extends BaseRestImpl {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(ModelRestImpl.class);
+
+ public List<ModelMetaData> getModels(String projectId, String token) throws SecurityException, ObjectNotFoundException {
+ AuthenticationToken authenticationToken = getUserService().getToken(token);
+ Project project = getProjectService().getProjectByProjectId(projectId, authenticationToken);
+ if (project == null) {
+ throw new ObjectNotFoundException("Project with given id doesn't exist");
+ }
+ List<ModelMetaData> result = createData(project, authenticationToken);
+ return result;
+ }
+
+ public ModelMetaData getModel(String projectId, String modelId, String token) throws SecurityException, ObjectNotFoundException {
+ AuthenticationToken authenticationToken = getUserService().getToken(token);
+ Model model = getModelService().getLastModelByProjectId(projectId, authenticationToken);
+ Model submodel = model.getSubmodelById(modelId);
+ if (submodel == null) {
+ return null;
+ } else {
+ return new ModelMetaData(submodel);
+ }
+ }
+
+ private List<ModelMetaData> createData(Project project, AuthenticationToken token) {
+ List<ModelMetaData> result = new ArrayList<>();
+ Model model = getModelService().getLastModelByProjectId(project.getProjectId(), token);
+
+ List<Model> models = new ArrayList<>();
+ models.add(model);
+ models.addAll(model.getSubmodels());
+ for (Model model2 : models) {
+ result.add(new ModelMetaData(model2));
+ }
+ return result;
+ }
+}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java
index ace3974815..0d3e034912 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.api.projects.models.publications;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.Comparator;
import java.util.HashMap;
import java.util.HashSet;
@@ -56,7 +57,7 @@ public class PublicationsRestImpl extends BaseRestImpl {
@Autowired
private OverviewImageViewFactory factory;
- public SortedMap<MiriamData, List<BioEntity>> getPublications(List<Model> models) {
+ public SortedMap<MiriamData, List<BioEntity>> getPublications(Collection<Model> models) {
SortedMap<MiriamData, List<BioEntity>> publications = new TreeMap<>();
for (Model modelData : models) {
for (Element element : modelData.getElements()) {
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/ModelMetaDataTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/ModelMetaDataTest.java
index 521d3701fe..243de1dad2 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/ModelMetaDataTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/ModelMetaDataTest.java
@@ -9,7 +9,7 @@ import org.junit.Test;
import com.google.gson.Gson;
-import lcsb.mapviewer.api.projects.ModelMetaData;
+import lcsb.mapviewer.api.projects.models.ModelMetaData;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
--
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