diff --git a/model/src/main/java/lcsb/mapviewer/model/map/Comment.java b/model/src/main/java/lcsb/mapviewer/model/map/Comment.java
index 8747682ed2c6b92c52969cf4b2e2a76ab5f3eebb..6bfd0f17db55b671a201861e6e9f324f561dc773 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/Comment.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/Comment.java
@@ -50,15 +50,9 @@ public class Comment implements Serializable {
/**
* The model that was commented.
*/
- @ManyToOne(fetch = FetchType.LAZY)
+ @ManyToOne(fetch = FetchType.LAZY, optional=false)
private ModelData model;
- /**
- * The model that was commented.
- */
- @ManyToOne(fetch = FetchType.LAZY)
- private ModelData submodel;
-
/**
* User who gave the feedback (if logged in).
*/
@@ -314,38 +308,4 @@ public class Comment implements Serializable {
this.model = model2;
}
- /**
- * @return the submodel
- * @see #submodel
- */
- public ModelData getSubmodelData() {
- return submodel;
- }
-
- /**
- * @param submodel
- * the submodel to set
- * @see #submodel
- */
- public void setSubmodelData(ModelData submodel) {
- this.submodel = submodel;
- }
-
- /**
- * @return the submodel
- * @see #submodel
- */
- public Model getSubmodel() {
- return this.submodel.getModel();
- }
-
- /**
- * @param submodel
- * the submodel to set
- * @see #submodel
- */
- public void setSubmodel(Model submodel) {
- this.submodel = submodel.getModelData();
- }
-
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/CommentTest.java b/model/src/test/java/lcsb/mapviewer/model/map/CommentTest.java
index b21e990c59062428a580d527b0aed0eac177d6db..5e4044e69d4e5ff96a41b2a2b0094e95538412ff 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/CommentTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/CommentTest.java
@@ -64,10 +64,6 @@ public class CommentTest extends ModelTestFunctions {
assertEquals(pinned, comment.isPinned());
comment.setRemoveReason(removeReason);
assertEquals(removeReason, comment.getRemoveReason());
- comment.setSubmodel(submodel);
- assertEquals(submodel, comment.getSubmodel());
- comment.setSubmodelData(submodel.getModelData());
- assertEquals(submodel.getModelData(), comment.getSubmodelData());
comment.setTableId(tableId);
assertEquals(tableId, comment.getTableId());
comment.setTableName(tableName);
diff --git a/persist/src/main/resources/db/migration/14.0.0~alpha.0/V14.0.0.20190725__comment_submodel_column_is_removed.sql b/persist/src/main/resources/db/migration/14.0.0~alpha.0/V14.0.0.20190725__comment_submodel_column_is_removed.sql
new file mode 100644
index 0000000000000000000000000000000000000000..25aa099906e0391bd144399080a5943902ffc554
--- /dev/null
+++ b/persist/src/main/resources/db/migration/14.0.0~alpha.0/V14.0.0.20190725__comment_submodel_column_is_removed.sql
@@ -0,0 +1,11 @@
+--remove submodel_id column
+update comment_table set model_id = submodel_id where submodel_id is not null;
+ALTER TABLE comment_table drop COLUMN submodel_id;
+
+--comment must be attached to a model
+delete from comment_table where model_id is null;
+ALTER TABLE comment_table ALTER COLUMN model_id SET NOT NULL;
+
+-- pinned should be not null
+update comment_table set pinned = false where pinned is null;
+ALTER TABLE comment_table ALTER COLUMN pinned SET NOT NULL;
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/graphics/PolylineDataTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/graphics/PolylineDataTest.java
index c483920daa3f78be2ec3f72e76343fe55a7a3d73..84914165c61694d8139e5fd56aaf7be8ba7efdd4 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/graphics/PolylineDataTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/graphics/PolylineDataTest.java
@@ -2,7 +2,7 @@ package lcsb.mapviewer.persist.dao.graphics;
import static org.junit.Assert.*;
-import java.awt.*;
+import java.awt.Color;
import java.awt.geom.Point2D;
import org.junit.*;
@@ -26,40 +26,34 @@ public class PolylineDataTest extends PersistTestFunctions {
@Test
public void test() {
- try {
- PolylineData pd = new PolylineData();
- pd.getBeginAtd().setArrowType(ArrowType.BLANK_CROSSBAR);
- pd.getBeginAtd().setArrowLineType(LineType.DASHED);
- pd.getBeginAtd().setLen(102);
- pd.setColor(Color.CYAN);
- pd.setType(LineType.SOLID_BOLD);
- pd.setWidth(2);
- pd.getPoints().add(new Point2D.Double(1, 1));
- pd.getPoints().add(new Point2D.Double(2, 3));
- pd.getPoints().add(new Point2D.Double(10, 11));
- polylineDao.add(pd);
- assertNotNull(pd.getId());
- PolylineData pd2 = polylineDao.getById(pd.getId());
- assertNotNull(pd2);
-
- assertEquals(ArrowType.BLANK_CROSSBAR, pd2.getBeginAtd().getArrowType());
- assertEquals(LineType.DASHED, pd2.getBeginAtd().getArrowLineType());
- assertEquals(102, pd2.getBeginAtd().getLen(), EPSILON);
- assertEquals(Color.CYAN, pd2.getColor());
- assertEquals(LineType.SOLID_BOLD, pd2.getType());
- assertEquals(2, pd2.getWidth(), EPSILON);
- assertEquals(0, pd2.getPoints().get(0).distance(new Point2D.Double(1, 1)), EPSILON);
- assertEquals(0, pd2.getPoints().get(1).distance(new Point2D.Double(2, 3)), EPSILON);
- assertEquals(0, pd2.getPoints().get(2).distance(new Point2D.Double(10, 11)), EPSILON);
-
- polylineDao.delete(pd);
- pd2 = polylineDao.getById(pd.getId());
- assertNull(pd2);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
+ PolylineData pd = new PolylineData();
+ pd.getBeginAtd().setArrowType(ArrowType.BLANK_CROSSBAR);
+ pd.getBeginAtd().setArrowLineType(LineType.DASHED);
+ pd.getBeginAtd().setLen(102);
+ pd.setColor(Color.CYAN);
+ pd.setType(LineType.SOLID_BOLD);
+ pd.setWidth(2);
+ pd.getPoints().add(new Point2D.Double(1, 1));
+ pd.getPoints().add(new Point2D.Double(2, 3));
+ pd.getPoints().add(new Point2D.Double(10, 11));
+ polylineDao.add(pd);
+ assertNotNull(pd.getId());
+ PolylineData pd2 = polylineDao.getById(pd.getId());
+ assertNotNull(pd2);
+
+ assertEquals(ArrowType.BLANK_CROSSBAR, pd2.getBeginAtd().getArrowType());
+ assertEquals(LineType.DASHED, pd2.getBeginAtd().getArrowLineType());
+ assertEquals(102, pd2.getBeginAtd().getLen(), EPSILON);
+ assertEquals(Color.CYAN, pd2.getColor());
+ assertEquals(LineType.SOLID_BOLD, pd2.getType());
+ assertEquals(2, pd2.getWidth(), EPSILON);
+ assertEquals(0, pd2.getPoints().get(0).distance(new Point2D.Double(1, 1)), EPSILON);
+ assertEquals(0, pd2.getPoints().get(1).distance(new Point2D.Double(2, 3)), EPSILON);
+ assertEquals(0, pd2.getPoints().get(2).distance(new Point2D.Double(10, 11)), EPSILON);
+
+ polylineDao.delete(pd);
+ pd2 = polylineDao.getById(pd.getId());
+ assertNull(pd2);
}
}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/CommentDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/CommentDaoTest.java
index 4a0e19615c699f017b3d43bb797e028cc756c74a..1b4f4edd7efd4bac7e5320b19951a686128f547a 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/CommentDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/CommentDaoTest.java
@@ -48,9 +48,15 @@ public class CommentDaoTest extends PersistTestFunctions {
@Test
public void testGetById() throws Exception {
+ Model model = createModel();
+ project.addModel(model);
+ modelDao.add(model);
+ projectDao.update(project);
+
int counter = (int) commentDao.getCount();
Comment comment = new Comment();
comment.setUser(user);
+ comment.setModel(model);
commentDao.add(comment);
int counter2 = (int) commentDao.getCount();
assertEquals(counter + 1, counter2);
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/user/UserDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/user/UserDaoTest.java
index 363cb67214134b3c0516f48ab2a93b5ba39be268..b7192d734458a67690ce1df71c59c22845b7a5a9 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/user/UserDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/user/UserDaoTest.java
@@ -38,298 +38,233 @@ public class UserDaoTest extends PersistTestFunctions {
@Test
public void testAddUpdateDelete() {
- try {
- User user = userDao.getUserByLogin(testLogin);
- assertNull(user);
+ User user = userDao.getUserByLogin(testLogin);
+ assertNull(user);
- long counter = userDao.getCount();
+ long counter = userDao.getCount();
- user = new User();
- user.setCryptedPassword("");
- user.setLogin(testLogin);
- user.addPrivilege(new Privilege(PrivilegeType.CAN_CREATE_OVERLAYS));
- userDao.add(user);
+ user = new User();
+ user.setCryptedPassword("");
+ user.setLogin(testLogin);
+ user.addPrivilege(new Privilege(PrivilegeType.CAN_CREATE_OVERLAYS));
+ userDao.add(user);
- long counter2 = userDao.getCount();
- assertEquals(counter + 1, counter2);
+ long counter2 = userDao.getCount();
+ assertEquals(counter + 1, counter2);
- user.setLogin(testLogin2);
- userDao.update(user);
+ user.setLogin(testLogin2);
+ userDao.update(user);
- User user2 = userDao.getUserByLogin(testLogin2);
- assertNotNull(user2);
+ User user2 = userDao.getUserByLogin(testLogin2);
+ assertNotNull(user2);
- userDao.delete(user);
+ userDao.delete(user);
- user2 = userDao.getUserByLogin(testLogin2);
- assertNull(user2);
- counter2 = userDao.getCount();
- assertEquals(counter, counter2);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
+ user2 = userDao.getUserByLogin(testLogin2);
+ assertNull(user2);
+ counter2 = userDao.getCount();
+ assertEquals(counter, counter2);
}
@Test(expected = PropertyValueException.class)
public void testTryUserWithNullPassword() {
- try {
- User user = new User();
- user.setLogin(testLogin);
- userDao.add(user);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
+ User user = new User();
+ user.setLogin(testLogin);
+ userDao.add(user);
}
@Test(expected = PropertyValueException.class)
public void testTryUserWithNullLogin() {
- try {
- User user = new User();
- user.setCryptedPassword("ZX");
- userDao.add(user);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
+ User user = new User();
+ user.setCryptedPassword("ZX");
+ userDao.add(user);
}
@Test(expected = ConstraintViolationException.class)
public void testTryUserWithExistingLogin() {
- try {
- User user = new User();
- user.setLogin(testLogin);
- user.setCryptedPassword("");
- userDao.add(user);
-
- User user2 = new User();
- user2.setLogin(testLogin);
- user2.setCryptedPassword("");
- userDao.add(user2);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
+ User user = new User();
+ user.setLogin(testLogin);
+ user.setCryptedPassword("");
+ userDao.add(user);
+
+ User user2 = new User();
+ user2.setLogin(testLogin);
+ user2.setCryptedPassword("");
+ userDao.add(user2);
}
@Test
public void testAddDeleteAdd() {
- try {
- User user = userDao.getUserByLogin(testLogin);
- assertNull(user);
-
- long counter = userDao.getCount();
+ User user = userDao.getUserByLogin(testLogin);
+ assertNull(user);
- user = new User();
- user.setLogin(testLogin);
- user.setCryptedPassword("");
- userDao.add(user);
+ long counter = userDao.getCount();
- long counter2 = userDao.getCount();
- assertEquals(counter + 1, counter2);
+ user = new User();
+ user.setLogin(testLogin);
+ user.setCryptedPassword("");
+ userDao.add(user);
- userDao.delete(user);
+ long counter2 = userDao.getCount();
+ assertEquals(counter + 1, counter2);
- User user2 = userDao.getUserByLogin(testLogin);
- assertNull(user2);
+ userDao.delete(user);
- user2 = new User();
- user2.setCryptedPassword("");
- user2.setLogin(testLogin);
- userDao.add(user2);
+ User user2 = userDao.getUserByLogin(testLogin);
+ assertNull(user2);
- assertNotNull(userDao.getUserByLogin(testLogin));
+ user2 = new User();
+ user2.setCryptedPassword("");
+ user2.setLogin(testLogin);
+ userDao.add(user2);
- userDao.delete(user2);
+ assertNotNull(userDao.getUserByLogin(testLogin));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
+ userDao.delete(user2);
}
@Test
public void testGetUserByLogin() throws Exception {
- try {
- User user = new User();
- user.setCryptedPassword(testPasswd);
- user.setLogin(testLogin);
- userDao.add(user);
- User user2 = userDao.getUserByLogin(testLogin);
- assertNotNull(user2);
- assertEquals(user2.getId(), user.getId());
- assertEquals(user2.getLogin(), user.getLogin());
- assertEquals(user2.getCryptedPassword(), user.getCryptedPassword());
- user2 = userDao.getUserByLogin(testLogin2);
- assertNull(user2);
- userDao.delete(user);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
+ User user = new User();
+ user.setCryptedPassword(testPasswd);
+ user.setLogin(testLogin);
+ userDao.add(user);
+ User user2 = userDao.getUserByLogin(testLogin);
+ assertNotNull(user2);
+ assertEquals(user2.getId(), user.getId());
+ assertEquals(user2.getLogin(), user.getLogin());
+ assertEquals(user2.getCryptedPassword(), user.getCryptedPassword());
+ user2 = userDao.getUserByLogin(testLogin2);
+ assertNull(user2);
+ userDao.delete(user);
}
@Test
public void testGetUserByEmail() throws Exception {
- try {
- User user = new User();
- user.setCryptedPassword(testPasswd);
- user.setLogin(testLogin);
- user.setEmail(testEmail);
- user.addPrivilege(new Privilege(PrivilegeType.CAN_CREATE_OVERLAYS));
- userDao.add(user);
- User user2 = userDao.getUserByEmail(testEmail);
- assertNotNull(user2);
- assertEquals(user2.getId(), user.getId());
- assertEquals(user2.getLogin(), user.getLogin());
- assertEquals(user2.getCryptedPassword(), user.getCryptedPassword());
- user2 = userDao.getUserByEmail(testEmail + "sadas");
- assertNull(user2);
- userDao.delete(user);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
+ User user = new User();
+ user.setCryptedPassword(testPasswd);
+ user.setLogin(testLogin);
+ user.setEmail(testEmail);
+ user.addPrivilege(new Privilege(PrivilegeType.CAN_CREATE_OVERLAYS));
+ userDao.add(user);
+ User user2 = userDao.getUserByEmail(testEmail);
+ assertNotNull(user2);
+ assertEquals(user2.getId(), user.getId());
+ assertEquals(user2.getLogin(), user.getLogin());
+ assertEquals(user2.getCryptedPassword(), user.getCryptedPassword());
+ user2 = userDao.getUserByEmail(testEmail + "sadas");
+ assertNull(user2);
+ userDao.delete(user);
}
@Test
public void testGetAll() throws Exception {
- try {
- assertTrue(userDao.getAll().size() > 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
+ assertTrue(userDao.getAll().size() > 0);
}
@Test
public void testUserWithAnnotatorSchema() throws Exception {
- try {
- User user = new User();
- user.setLogin(testLogin);
- user.setCryptedPassword("");
- UserAnnotationSchema uas = new UserAnnotationSchema();
- uas.setValidateMiriamTypes(true);
- UserClassAnnotators ca = new UserClassAnnotators();
- ca.setClassName(Species.class);
- AnnotatorData annotatorData = new AnnotatorData(String.class);
- ca.addAnnotator(annotatorData);
- uas.addClassAnnotator(ca);
- uas.addClassAnnotator(new UserClassAnnotators(String.class, new ArrayList<>()));
- UserClassValidAnnotations cva = new UserClassValidAnnotations();
- cva.setClassName(Reaction.class);
- cva.addValidMiriamType(MiriamType.HGNC);
- cva.addValidMiriamType(MiriamType.HGNC_SYMBOL);
- uas.addClassValidAnnotations(cva);
- uas.addClassValidAnnotations(new UserClassValidAnnotations(String.class, new ArrayList<>()));
- uas.addClassValidAnnotations(new UserClassValidAnnotations(Integer.class, new ArrayList<>()));
- user.setAnnotationSchema(uas);
- userDao.add(user);
- userDao.evict(user);
- User user2 = userDao.getById(user.getId());
- assertNotNull(user2);
- UserAnnotationSchema uas2 = user2.getAnnotationSchema();
- assertNotNull(uas2);
- assertEquals(2, uas2.getClassAnnotators().size());
- assertEquals(3, uas2.getClassValidAnnotators().size());
- assertEquals(Species.class.getCanonicalName(), uas.getClassAnnotators().get(0).getClassName());
- assertEquals(annotatorData, uas.getClassAnnotators().get(0).getAnnotators().get(0));
- assertEquals(Reaction.class.getCanonicalName(), uas.getClassValidAnnotators().get(0).getClassName());
- assertEquals(MiriamType.HGNC, uas.getClassValidAnnotators().get(0).getValidMiriamTypes().get(0));
- assertEquals(MiriamType.HGNC_SYMBOL, uas.getClassValidAnnotators().get(0).getValidMiriamTypes().get(1));
-
- userDao.delete(user2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
+ User user = new User();
+ user.setLogin(testLogin);
+ user.setCryptedPassword("");
+ UserAnnotationSchema uas = new UserAnnotationSchema();
+ uas.setValidateMiriamTypes(true);
+ UserClassAnnotators ca = new UserClassAnnotators();
+ ca.setClassName(Species.class);
+ AnnotatorData annotatorData = new AnnotatorData(String.class);
+ ca.addAnnotator(annotatorData);
+ uas.addClassAnnotator(ca);
+ uas.addClassAnnotator(new UserClassAnnotators(String.class, new ArrayList<>()));
+ UserClassValidAnnotations cva = new UserClassValidAnnotations();
+ cva.setClassName(Reaction.class);
+ cva.addValidMiriamType(MiriamType.HGNC);
+ cva.addValidMiriamType(MiriamType.HGNC_SYMBOL);
+ uas.addClassValidAnnotations(cva);
+ uas.addClassValidAnnotations(new UserClassValidAnnotations(String.class, new ArrayList<>()));
+ uas.addClassValidAnnotations(new UserClassValidAnnotations(Integer.class, new ArrayList<>()));
+ user.setAnnotationSchema(uas);
+ userDao.add(user);
+ userDao.evict(user);
+ User user2 = userDao.getById(user.getId());
+ assertNotNull(user2);
+ UserAnnotationSchema uas2 = user2.getAnnotationSchema();
+ assertNotNull(uas2);
+ assertEquals(2, uas2.getClassAnnotators().size());
+ assertEquals(3, uas2.getClassValidAnnotators().size());
+ assertEquals(Species.class.getCanonicalName(), uas.getClassAnnotators().get(0).getClassName());
+ assertEquals(annotatorData, uas.getClassAnnotators().get(0).getAnnotators().get(0));
+ assertEquals(Reaction.class.getCanonicalName(), uas.getClassValidAnnotators().get(0).getClassName());
+ assertEquals(MiriamType.HGNC, uas.getClassValidAnnotators().get(0).getValidMiriamTypes().get(0));
+ assertEquals(MiriamType.HGNC_SYMBOL, uas.getClassValidAnnotators().get(0).getValidMiriamTypes().get(1));
+
+ userDao.delete(user2);
}
@Test
public void testUserWithAnnotatorSchemaGuiPreferences() throws Exception {
- try {
- User user = new User();
- user.setLogin(testLogin);
- user.setCryptedPassword("");
- UserAnnotationSchema uas = new UserAnnotationSchema();
- user.setAnnotationSchema(uas);
- UserGuiPreference option = new UserGuiPreference();
- option.setKey("key");
- option.setValue("val");
- uas.addGuiPreference(option);
- userDao.add(user);
- userDao.evict(user);
- User user2 = userDao.getById(user.getId());
- assertNotNull(user2);
- UserAnnotationSchema uas2 = user2.getAnnotationSchema();
- assertNotNull(uas2);
- assertEquals(1, uas2.getGuiPreferences().size());
-
- userDao.delete(user2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
+ User user = new User();
+ user.setLogin(testLogin);
+ user.setCryptedPassword("");
+ UserAnnotationSchema uas = new UserAnnotationSchema();
+ user.setAnnotationSchema(uas);
+ UserGuiPreference option = new UserGuiPreference();
+ option.setKey("key");
+ option.setValue("val");
+ uas.addGuiPreference(option);
+ userDao.add(user);
+ userDao.evict(user);
+ User user2 = userDao.getById(user.getId());
+ assertNotNull(user2);
+ UserAnnotationSchema uas2 = user2.getAnnotationSchema();
+ assertNotNull(uas2);
+ assertEquals(1, uas2.getGuiPreferences().size());
+
+ userDao.delete(user2);
}
@Test
public void testUserWithAnnotatorSchemaRequiredAnnotations() throws Exception {
- try {
- User user = new User();
- user.setLogin(testLogin);
- user.setCryptedPassword("");
- UserAnnotationSchema uas = new UserAnnotationSchema();
- user.setAnnotationSchema(uas);
- uas.addClassRequiredAnnotations(
- new UserClassRequiredAnnotations(String.class, new MiriamType[] { MiriamType.WIKIPEDIA }));
- userDao.add(user);
- userDao.evict(user);
- User user2 = userDao.getById(user.getId());
- assertNotNull(user2);
- UserAnnotationSchema uas2 = user2.getAnnotationSchema();
- assertNotNull(uas2);
- assertEquals(1, uas2.getClassRequiredAnnotators().size());
-
- userDao.delete(user2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
+ User user = new User();
+ user.setLogin(testLogin);
+ user.setCryptedPassword("");
+ UserAnnotationSchema uas = new UserAnnotationSchema();
+ user.setAnnotationSchema(uas);
+ uas.addClassRequiredAnnotations(
+ new UserClassRequiredAnnotations(String.class, new MiriamType[] { MiriamType.WIKIPEDIA }));
+ userDao.add(user);
+ userDao.evict(user);
+ User user2 = userDao.getById(user.getId());
+ assertNotNull(user2);
+ UserAnnotationSchema uas2 = user2.getAnnotationSchema();
+ assertNotNull(uas2);
+ assertEquals(1, uas2.getClassRequiredAnnotators().size());
+
+ userDao.delete(user2);
}
@Test
public void testUserWithAnnotatorParams() throws Exception {
- try {
- User user = new User();
- user.setLogin(testLogin);
- user.setCryptedPassword("");
- UserAnnotationSchema uas = new UserAnnotationSchema();
- user.setAnnotationSchema(uas);
- UserClassAnnotators classAnnotators = new UserClassAnnotators(Integer.class);
- AnnotatorData annotatorData = new AnnotatorData(String.class);
- classAnnotators.addAnnotator(annotatorData);
- uas.addClassAnnotator(classAnnotators);
- AnnotatorConfigParameter param = new AnnotatorConfigParameter(AnnotatorParamDefinition.KEGG_ORGANISM_IDENTIFIER,
- "val");
- annotatorData.addAnnotatorParameter(param);
- userDao.add(user);
- userDao.evict(user);
- User user2 = userDao.getById(user.getId());
- assertNotNull(user2);
- UserAnnotationSchema uas2 = user2.getAnnotationSchema();
- assertNotNull(uas2);
- assertEquals(1, uas2.getClassAnnotators().get(0).getAnnotators().get(0).getAnnotatorParams().size());
-
- userDao.delete(user2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
+ User user = new User();
+ user.setLogin(testLogin);
+ user.setCryptedPassword("");
+ UserAnnotationSchema uas = new UserAnnotationSchema();
+ user.setAnnotationSchema(uas);
+ UserClassAnnotators classAnnotators = new UserClassAnnotators(Integer.class);
+ AnnotatorData annotatorData = new AnnotatorData(String.class);
+ classAnnotators.addAnnotator(annotatorData);
+ uas.addClassAnnotator(classAnnotators);
+ AnnotatorConfigParameter param = new AnnotatorConfigParameter(AnnotatorParamDefinition.KEGG_ORGANISM_IDENTIFIER,
+ "val");
+ annotatorData.addAnnotatorParameter(param);
+ userDao.add(user);
+ userDao.evict(user);
+ User user2 = userDao.getById(user.getId());
+ assertNotNull(user2);
+ UserAnnotationSchema uas2 = user2.getAnnotationSchema();
+ assertNotNull(uas2);
+ assertEquals(1, uas2.getClassAnnotators().get(0).getAnnotators().get(0).getAnnotatorParams().size());
+
+ userDao.delete(user2);
}
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/comments/CommentRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/comments/CommentRestImpl.java
index 5527253a14d4d328ddd33a5ac23ca4757427958a..24dad6f4343cf5e1313f677f2c9d2a25273f674f 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/comments/CommentRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/comments/CommentRestImpl.java
@@ -107,7 +107,7 @@ public class CommentRestImpl extends BaseRestImpl {
value = getId(comment);
break;
case "modelid":
- value = comment.getSubmodelData().getId();
+ value = comment.getModelData().getId();
break;
case "title":
value = getTitle(comment);
@@ -279,7 +279,7 @@ public class CommentRestImpl extends BaseRestImpl {
throw new QueryException("Unknown type of commented object: " + elementType);
}
- Comment comment = commentService.addComment(name, email, content, model, pointCoordinates, commentedObject, pinned,
+ Comment comment = commentService.addComment(name, email, content, pointCoordinates, commentedObject, pinned,
submodel);
return preparedComment(comment, createCommentColumnSet(""));
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/CommentService.java b/service/src/main/java/lcsb/mapviewer/services/impl/CommentService.java
index 3e4268803ee4c25d8277a52c199794bf7a2a5133..3d17c570b6c3293adcc11ada0f4f74552128433b 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/CommentService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/CommentService.java
@@ -12,13 +12,9 @@ import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;
import lcsb.mapviewer.common.ObjectUtils;
-import lcsb.mapviewer.common.exception.InvalidClassException;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.Comment;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelData;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.model.*;
import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.persist.dao.map.CommentDao;
import lcsb.mapviewer.services.interfaces.*;
@@ -79,35 +75,37 @@ public class CommentService implements ICommentService {
}
@Override
- public Comment addComment(String name, String email, String content, Model model, Point2D coordinates, Object object,
+ public Comment addComment(String name, String email, String content, Point2D coordinates, Object object,
boolean pinned, Model submodel) {
Comment comment = new Comment();
comment.setName(name);
comment.setEmail(email);
comment.setContent(content);
- comment.setModel(model);
+ comment.setModel(submodel);
comment.setCoordinates(coordinates);
if (object != null) {
comment.setTableName(object.getClass());
comment.setTableId(ObjectUtils.getIdOfObject(object));
- if (object instanceof Element) {
- comment.setSubmodel(((Element) object).getModel());
- } else if (object instanceof Reaction) {
- comment.setSubmodel(((Reaction) object).getModel());
- } else {
- throw new InvalidClassException("Cannot comment on object of class: " + object.getClass());
- }
- } else {
- comment.setSubmodel(submodel);
}
comment.setUser(null);
comment.setPinned(pinned);
commentDao.add(comment);
try {
+ Project project = submodel.getProject();
+ if (project == null) {
+ for (SubmodelConnection sc : submodel.getParentModels()) {
+ if (sc instanceof ModelSubmodelConnection) {
+ project = ((ModelSubmodelConnection) sc).getParentModel().getModel().getProject();
+ if (project != null) {
+ break;
+ }
+ }
+ }
+ }
+
EmailSender emailSender = new EmailSender(configurationService);
- emailSender.sendEmail("New comment appeard in the " + model.getProject().getProjectId(), content,
- model.getProject().getNotifyEmail());
+ emailSender.sendEmail("New comment appeard in the " + project.getProjectId(), content, project.getNotifyEmail());
} catch (MessagingException e) {
logger.error("Problem with sending email.", e);
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/UserService.java b/service/src/main/java/lcsb/mapviewer/services/impl/UserService.java
index 6d060e5578398e83dc55d225111990676a5acd1d..37f5050da1ccba7a7dafe49278fc3d518bd52777 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/UserService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/UserService.java
@@ -75,24 +75,28 @@ public class UserService implements IUserService {
@Override
public void grantUserPrivilege(User user, PrivilegeType type) {
+ user = getUserByLogin(user.getLogin());
user.addPrivilege(privilegeService.getPrivilege(type));
userDao.update(user);
}
@Override
public void grantUserPrivilege(User user, PrivilegeType type, String objectId) {
+ user = getUserByLogin(user.getLogin());
user.addPrivilege(privilegeService.getPrivilege(type, objectId));
userDao.update(user);
}
@Override
public void revokeUserPrivilege(User user, PrivilegeType type) {
+ user = getUserByLogin(user.getLogin());
user.removePrivilege(privilegeService.getPrivilege(type));
userDao.update(user);
}
@Override
public void revokeUserPrivilege(User user, PrivilegeType type, String objectId) {
+ user = getUserByLogin(user.getLogin());
user.removePrivilege(privilegeService.getPrivilege(type, objectId));
userDao.update(user);
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/ICommentService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/ICommentService.java
index 913e4340daa2c7dd827589b6c67b1af82d78a248..1f0b0ee31fc98c472294bde18566dad0c0a8c8d7 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/ICommentService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/ICommentService.java
@@ -30,8 +30,6 @@ public interface ICommentService {
* email of the person that comments
* @param content
* content of the comment
- * @param model
- * which map we comment on
* @param submodel
* on which submodel we comment on
* @param coordinates
@@ -39,7 +37,7 @@ public interface ICommentService {
*
* @return comment object created based on the data provided as parameters
*/
- Comment addComment(String name, String email, String content, Model model, Point2D coordinates, Object object,
+ Comment addComment(String name, String email, String content, Point2D coordinates, Object object,
boolean pinned, Model submodel);
/**
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
index 2f5ba0faa2bdd1f03652d5844cbecdb91f837a07..af525309e8582bc2d4dc5f58c798b457c04f3be2 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
@@ -820,13 +820,28 @@ public class ColorSchemaReader {
}
String[] columns = line.split("\t");
if (columns.length > 1) {
+ ColorSchemaType type = overlay.getColorSchemaType();
+ if (type == null) {
+ Map<String, String> params = TextFileUtils
+ .getHeaderParametersFromFile(new ByteArrayInputStream(overlay.getInputData().getFileContent()));
+ String typeString = params.get(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE);
+ if (typeString != null) {
+ type = ColorSchemaType.valueOf(typeString);
+ } else {
+ logger.warn("Undefined color schema type for overlay: " + overlay.getId());
+ type = ColorSchemaType.GENERIC;
+ }
+ }
Map<ColorSchemaColumn, Integer> schemaColumns = new HashMap<>();
- parseColumns(columns, schemaColumns, ColorSchemaType.GENERIC);
+ parseColumns(columns, schemaColumns, type);
for (ColorSchemaColumn column : schemaColumns.keySet()) {
try {
Field f = ColorSchemaColumn.class.getField(column.name());
- if (column.getDepractedColumnName() != null || f.isAnnotationPresent(Deprecated.class)) {
+ if (f.isAnnotationPresent(Deprecated.class)) {
+ result.add(column);
+ } else if (column.getDepractedColumnName() != null
+ && column.getDepractedColumnName().equalsIgnoreCase(columns[schemaColumns.get(column)])) {
result.add(column);
}
} catch (NoSuchFieldException | SecurityException e) {
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/CommentServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/CommentServiceTest.java
index 83363c520ecde7089f58c73fc904db25dfae170d..0e3c1dfd79abe9fe3cd516720a170dbad8204da5 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/CommentServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/CommentServiceTest.java
@@ -62,16 +62,11 @@ public class CommentServiceTest extends ServiceTestFunctions {
@Test
public void testGetAgregatedComments() throws Exception {
- commentService.addComment("John Doe", "a@a.pl", "Conteneta 1", model, new Point2D.Double(0, 1), alias, false,
- model);
- commentService.addComment("John Doe", "a@a.pl", "Contenetb 2", model, new Point2D.Double(0, 2), alias, false,
- model);
- commentService.addComment("John Doe", "a@a.pl", "Contenetc 3", model, new Point2D.Double(0, 3), alias2, false,
- model);
- commentService.addComment("John Doe", "a@a.pl", "Contenetc 4", model, new Point2D.Double(0, 4), null, false,
- model);
- commentService.addComment("John Doe", "a@a.pl", "Contenetc 5", model, new Point2D.Double(0, 5), null, false,
- model);
+ commentService.addComment("John Doe", "a@a.pl", "Conteneta 1", new Point2D.Double(0, 1), alias, false, model);
+ commentService.addComment("John Doe", "a@a.pl", "Contenetb 2", new Point2D.Double(0, 2), alias, false, model);
+ commentService.addComment("John Doe", "a@a.pl", "Contenetc 3", new Point2D.Double(0, 3), alias2, false, model);
+ commentService.addComment("John Doe", "a@a.pl", "Contenetc 4", new Point2D.Double(0, 4), null, false, model);
+ commentService.addComment("John Doe", "a@a.pl", "Contenetc 5", new Point2D.Double(0, 5), null, false, model);
CommentService service = new CommentService(null, null, null, null);
service.setCommentDao(commentDao);
List<List<Comment>> comments = service.getAgregatedComments(model, null);
@@ -92,7 +87,7 @@ public class CommentServiceTest extends ServiceTestFunctions {
@Test
public void testAddComment() throws Exception {
long counter = commentService.getCommentCount();
- Comment feedback = commentService.addComment("a", "b", "c", model, new Point2D.Double(0, 0), null, false, model);
+ Comment feedback = commentService.addComment("a", "b", "c", new Point2D.Double(0, 0), null, false, model);
long counter2 = commentService.getCommentCount();
assertEquals(counter + 1, counter2);
commentDao.delete(feedback);
@@ -101,7 +96,7 @@ public class CommentServiceTest extends ServiceTestFunctions {
@Test
public void testAddCommentForReaction() throws Exception {
long counter = commentService.getCommentCount();
- Comment feedback = commentService.addComment("a", "b", "c", model, new Point2D.Double(0, 0),
+ Comment feedback = commentService.addComment("a", "b", "c", new Point2D.Double(0, 0),
model.getReactions().iterator().next(), false, model);
long counter2 = commentService.getCommentCount();
assertEquals(counter + 1, counter2);
@@ -112,7 +107,7 @@ public class CommentServiceTest extends ServiceTestFunctions {
public void testAddCommentForAlias() throws Exception {
Element alias = model.getElementByElementId("sa1");
long counter = commentService.getCommentCount();
- Comment feedback = commentService.addComment("a", "b", "c", model, new Point2D.Double(0, 0), alias, false, model);
+ Comment feedback = commentService.addComment("a", "b", "c", new Point2D.Double(0, 0), alias, false, model);
long counter2 = commentService.getCommentCount();
assertEquals(counter + 1, counter2);
commentDao.delete(feedback);
diff --git a/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java b/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
index f58cdd4923d1c5f3925ef44e0e9d83d14ae58f22..e97c9420f00cd4570dca48c15b4cc2777135d124 100644
--- a/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
@@ -15,12 +15,14 @@ import org.junit.*;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.commands.ColorModelCommand;
import lcsb.mapviewer.common.TextFileUtils;
+import lcsb.mapviewer.converter.zip.ZipEntryFileFactory;
import lcsb.mapviewer.model.cache.UploadedFileEntry;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.layout.*;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.ServiceTestFunctions;
+import lcsb.mapviewer.services.utils.data.ColorSchemaColumn;
public class ColorSchemaReaderTest extends ServiceTestFunctions {
Logger logger = LogManager.getLogger(ColorSchemaReaderTest.class);
@@ -334,4 +336,35 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
overlay.setInputData(file);
assertEquals(0, reader.getDeprecatedColumns(overlay).size());
}
+
+ @Test
+ public void testGetDeprecatedColumnsForValidGeneticColumns() throws Exception {
+ Layout overlay = new Layout();
+ overlay.setColorSchemaType(ColorSchemaType.GENETIC_VARIANT);
+ UploadedFileEntry file = new UploadedFileEntry();
+ file.setFileContent((ColorSchemaColumn.POSITION.name() + "\tgene_name\n").getBytes("UTF-8"));
+ overlay.setInputData(file);
+ assertEquals(0, reader.getDeprecatedColumns(overlay).size());
+ }
+
+ @Test
+ public void testGetDeprecatedColumnsForDeprecatedGeneticColumns() throws Exception {
+ Layout overlay = new Layout();
+ overlay.setColorSchemaType(ColorSchemaType.GENETIC_VARIANT);
+ UploadedFileEntry file = new UploadedFileEntry();
+ file.setFileContent((ColorSchemaColumn.POSITION.name() + "\tname\n").getBytes("UTF-8"));
+ overlay.setInputData(file);
+ assertEquals(1, reader.getDeprecatedColumns(overlay).size());
+ }
+
+ @Test
+ public void testGetDeprecatedColumnsForOverlayWithHeader() throws Exception {
+ Layout overlay = new Layout();
+ UploadedFileEntry file = new UploadedFileEntry();
+ String content = "#" + ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE + "=" + ColorSchemaType.GENERIC + "\n" +
+ ColorSchemaColumn.VALUE.name() + "\tname\n";
+ file.setFileContent((content).getBytes("UTF-8"));
+ overlay.setInputData(file);
+ assertEquals(0, reader.getDeprecatedColumns(overlay).size());
+ }
}
diff --git a/web/src/test/java/lcsb/mapviewer/web/AllIntegrationTests.java b/web/src/test/java/lcsb/mapviewer/web/AllIntegrationTests.java
index 432add8ee7a07f2b3cb912dcc9ba3ffbb8b6727c..a7e43f53026a8724d59ac18b4d12f88e60a7a0b6 100644
--- a/web/src/test/java/lcsb/mapviewer/web/AllIntegrationTests.java
+++ b/web/src/test/java/lcsb/mapviewer/web/AllIntegrationTests.java
@@ -20,6 +20,7 @@ import org.junit.runners.Suite.SuiteClasses;
PluginControllerIntegrationTest.class,
ProjectControllerIntegrationTest.class,
ProjectControllerIntegrationTestForAsyncCalls.class,
+ ProjectControllerIntegrationTestWithoutTransaction.class,
PublicationsControllerIntegrationTest.class,
ReactionControllerIntegrationTest.class,
SpringSecurityGeneralIntegrationTest.class,
diff --git a/web/src/test/java/lcsb/mapviewer/web/CommentControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/CommentControllerIntegrationTest.java
index 1fb757ca94e00f52aea0065947afaafe84e7c276..50e40f3869a52fd8077280bb9780cd711272dd0b 100644
--- a/web/src/test/java/lcsb/mapviewer/web/CommentControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/CommentControllerIntegrationTest.java
@@ -702,7 +702,6 @@ public class CommentControllerIntegrationTest extends ControllerIntegrationTest
private Comment createComment() {
Comment comment = new Comment();
- comment.setSubmodelData(map);
comment.setModel(map);
comment.setCoordinates(new Point2D.Double(10, 20));
return comment;
diff --git a/web/src/test/java/lcsb/mapviewer/web/ControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/ControllerIntegrationTest.java
index df0d467a514896a88b06580bb23adf5e97f8df7c..769bfcf888e2a142499d003977ee61c13db8fa77 100644
--- a/web/src/test/java/lcsb/mapviewer/web/ControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/ControllerIntegrationTest.java
@@ -27,6 +27,7 @@ import org.springframework.web.context.WebApplicationContext;
import lcsb.mapviewer.common.MinervaLoggerAppender;
import lcsb.mapviewer.common.UnitTestFailedWatcher;
import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.ProjectStatus;
import lcsb.mapviewer.model.cache.UploadedFileEntry;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.model.ModelData;
@@ -232,4 +233,33 @@ abstract public class ControllerIntegrationTest {
});
}
+ protected UploadedFileEntry createFileInSeparateThread(String content, User user) throws Exception {
+ return callInSeparateThread(() -> {
+ return createFile(content, user);
+ });
+ }
+
+ protected void waitForProjectToFinishLoading(String projectId) throws InterruptedException {
+ Project project;
+ do {
+ project = projectDao.getProjectByProjectId(projectId);
+ projectDao.evict(project);
+ Thread.sleep(100);
+ } while (project.getStatus() != ProjectStatus.DONE);
+ }
+
+ public void removeProjectInSeparateThread(Project project) throws Exception {
+ removeProjectInSeparateThread(project.getProjectId());
+ }
+
+ public void removeProjectInSeparateThread(String projectId) throws Exception {
+ callInSeparateThread(() -> {
+ Project project = projectDao.getProjectByProjectId(projectId);
+ if (project != null) {
+ projectDao.delete(project);
+ }
+ return null;
+ });
+ }
+
}
diff --git a/web/src/test/java/lcsb/mapviewer/web/ProjectControllerIntegrationTestForAsyncCalls.java b/web/src/test/java/lcsb/mapviewer/web/ProjectControllerIntegrationTestForAsyncCalls.java
index 607a27e11b64605c7fe5d89ddb0815f0d18219cb..c779a724e2f144891caba5b6aac1747e5c60cfc0 100644
--- a/web/src/test/java/lcsb/mapviewer/web/ProjectControllerIntegrationTestForAsyncCalls.java
+++ b/web/src/test/java/lcsb/mapviewer/web/ProjectControllerIntegrationTestForAsyncCalls.java
@@ -101,15 +101,6 @@ public class ProjectControllerIntegrationTestForAsyncCalls extends ControllerInt
}
}
- private void waitForProjectToFinishLoading(String projectId) throws InterruptedException {
- Project project;
- do {
- project = projectDao.getProjectByProjectId(projectId);
- projectDao.evict(project);
- Thread.sleep(100);
- } while (project.getStatus() != ProjectStatus.DONE);
- }
-
private void waitForProjectToFinishRemoving(String projectId) throws InterruptedException {
Project project;
do {
@@ -377,11 +368,6 @@ public class ProjectControllerIntegrationTestForAsyncCalls extends ControllerInt
}
}
- private UploadedFileEntry createFileInSeparateThread(String content, User user) throws Exception {
- return callInSeparateThread(() -> {
- return createFile(content, user);
- });
- }
private User createCuratorInSeparateThread(String login, String password) throws Exception {
return callInSeparateThread(() -> {
@@ -401,18 +387,4 @@ public class ProjectControllerIntegrationTestForAsyncCalls extends ControllerInt
});
}
- private void removeProjectInSeparateThread(Project project) throws Exception {
- removeProjectInSeparateThread(project.getProjectId());
- }
-
- private void removeProjectInSeparateThread(String projectId) throws Exception {
- callInSeparateThread(() -> {
- Project project = projectDao.getProjectByProjectId(projectId);
- if (project != null) {
- projectDao.delete(project);
- }
- return null;
- });
- }
-
}
diff --git a/web/src/test/java/lcsb/mapviewer/web/ProjectControllerIntegrationTestWithoutTransaction.java b/web/src/test/java/lcsb/mapviewer/web/ProjectControllerIntegrationTestWithoutTransaction.java
new file mode 100644
index 0000000000000000000000000000000000000000..a1f33cbaa925c2109e3bba25c974a688a5d8518f
--- /dev/null
+++ b/web/src/test/java/lcsb/mapviewer/web/ProjectControllerIntegrationTestWithoutTransaction.java
@@ -0,0 +1,77 @@
+package lcsb.mapviewer.web;
+
+import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.post;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
+
+import java.nio.file.Files;
+import java.nio.file.Paths;
+import java.util.Arrays;
+
+import org.apache.http.client.entity.UrlEncodedFormEntity;
+import org.apache.http.message.BasicNameValuePair;
+import org.apache.http.util.EntityUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.junit.Before;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.MediaType;
+import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
+import org.springframework.test.web.servlet.RequestBuilder;
+
+import lcsb.mapviewer.model.cache.UploadedFileEntry;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.services.interfaces.IUserService;
+
+@RunWith(SpringJUnit4ClassRunner.class)
+public class ProjectControllerIntegrationTestWithoutTransaction extends ControllerIntegrationTest {
+
+ private static final String BUILT_IN_ADMIN_PASSWORD = "admin";
+ private static final String BUILT_IN_ADMIN_LOGIN = "admin";
+
+ private static final String TEST_PROJECT = "test_project";
+
+ Logger logger = LogManager.getLogger();
+ @Autowired
+ private IUserService userService;
+
+ @Before
+ public void setup() {
+ }
+
+ @Test
+ public void addProjectAsCurator() throws Exception {
+ User admin = userService.getUserByLogin(BUILT_IN_ADMIN_LOGIN);
+ try {
+ UploadedFileEntry fileEntry = createFileInSeparateThread(
+ new String(Files.readAllBytes(Paths.get("./src/test/resources/generic.xml")), "UTF-8"),
+ admin);
+
+ String body = EntityUtils.toString(new UrlEncodedFormEntity(Arrays.asList(
+ new BasicNameValuePair("file-id", String.valueOf(fileEntry.getId())),
+ new BasicNameValuePair("mapCanvasType", "OPEN_LAYERS"),
+ new BasicNameValuePair("parser",
+ "lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser"))));
+
+ RequestBuilder request = post("/projects/" + TEST_PROJECT)
+ .contentType(MediaType.APPLICATION_FORM_URLENCODED)
+ .content(body)
+ .session(createSession(BUILT_IN_ADMIN_LOGIN, BUILT_IN_ADMIN_PASSWORD));
+
+ mockMvc.perform(request).andExpect(status().is2xxSuccessful());
+
+ } finally {
+ callInSeparateThread(()->{
+ try {
+ waitForProjectToFinishLoading(TEST_PROJECT);
+ } catch (InterruptedException e) {
+ e.printStackTrace();
+ }
+ return null;
+ });
+ removeProjectInSeparateThread(TEST_PROJECT);
+ }
+ }
+
+}