diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java
index 9f8111197fd2cd33ea13978d6f9c2592cb258bd4..f178102c82c2212396c9c6cd62316ea05b26ebf7 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java
@@ -17,15 +17,12 @@ import lcsb.mapviewer.annotation.services.MiriamConnector;
import lcsb.mapviewer.annotation.services.PubmedParser;
import lcsb.mapviewer.annotation.services.PubmedSearchException;
import lcsb.mapviewer.annotation.services.TaxonomyBackend;
-import lcsb.mapviewer.annotation.services.TaxonomySearchException;
-import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
import lcsb.mapviewer.commands.CopyCommand;
import lcsb.mapviewer.common.IProgressUpdater;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.Layout;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
@@ -41,10 +38,8 @@ import lcsb.mapviewer.services.interfaces.IUserService;
import lcsb.mapviewer.services.search.data.LightAliasView;
import lcsb.mapviewer.services.search.data.LightAliasViewFactory;
import lcsb.mapviewer.services.search.data.LightReactionView;
-import lcsb.mapviewer.services.view.LayoutView;
import lcsb.mapviewer.services.view.ModelView;
import lcsb.mapviewer.services.view.ModelViewFactory;
-import lcsb.mapviewer.services.view.ProjectView;
/**
* Implementation of the service that manages models.
@@ -122,7 +117,8 @@ public class ModelService implements IModelService {
private TaxonomyBackend taxonomyBackend;
@Override
- public Model getLastModelByProjectId(String projectName, String token) throws lcsb.mapviewer.services.SecurityException {
+ public Model getLastModelByProjectId(String projectName, String token)
+ throws lcsb.mapviewer.services.SecurityException {
if (projectName == null) {
return null;
}
@@ -235,82 +231,6 @@ public class ModelService implements IModelService {
logger.debug("Caching finished");
}
- @Override
- public void updateModel(ModelData model, ProjectView selectedProject) {
-
- for (Model cachedModel : models.values()) {
- if (cachedModel.getId().equals(selectedProject.getModelId())) {
- setModel(cachedModel.getModelData(), selectedProject);
- }
- }
- setModel(model, selectedProject);
- modelDao.update(model);
- }
-
- /**
- * Sets the data from selectedProject into model.
- *
- * @param model
- * destination of the data
- * @param selectedProject
- * source of the data
- */
- private void setModel(ModelData model, ProjectView selectedProject) {
- model.setNotes(selectedProject.getDescription());
- List<Layout> toRemove = new ArrayList<Layout>();
- for (Layout layout : model.getLayouts()) {
- boolean exists = false;
- for (LayoutView row : selectedProject.getLayouts()) {
- if (layout.getId() == row.getIdObject()) {
- exists = true;
- // don't allow client side to edit layouts
- // layout.setDirectory(row.getDirectory());
- layout.setTitle(row.getName());
- layout.setDescription(row.getDescription());
- }
- }
- if (!exists) {
- toRemove.add(layout);
- }
- }
- model.getLayouts().removeAll(toRemove);
-
- MiriamData disease = null;
- if (selectedProject.getNewDiseaseName() != null) {
- disease = new MiriamData(MiriamType.MESH_2012, selectedProject.getNewDiseaseName());
- }
-
- try {
- if (meshParser.isValidMeshId(disease)) {
- model.getProject().setDisease(disease);
- } else {
- model.getProject().setDisease(null);
- selectedProject.setNewDiseaseName(null);
- }
- } catch (AnnotatorException e) {
- logger.warn("Problem with accessing mesh db");
- }
-
- if (model.getProject() != null) {
- MiriamData organism = null;
- if (selectedProject.getNewOrganismName() != null && !selectedProject.getNewOrganismName().isEmpty()) {
- organism = new MiriamData(MiriamType.TAXONOMY, selectedProject.getNewOrganismName());
- }
-
- try {
- if (taxonomyBackend.getNameForTaxonomy(organism) != null) {
- model.getProject().setOrganism(organism);
- } else {
- model.getProject().setOrganism(null);
- }
- } catch (TaxonomySearchException e) {
- logger.error("Problem with accessing taxonomy db", e);
- model.getProject().setOrganism(null);
- }
- }
-
- }
-
@Override
public void removeModelFromCache(Model model) {
models.remove(model.getProject().getProjectId());
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
index a6713e8be40dbf351ce845634fe18fc958ca44f8..7480e12f91a3308d83bb71813ea2309284ecddbc 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
@@ -33,7 +33,6 @@ import lcsb.mapviewer.annotation.services.MeSHParser;
import lcsb.mapviewer.annotation.services.ModelAnnotator;
import lcsb.mapviewer.annotation.services.ProblematicAnnotation;
import lcsb.mapviewer.annotation.services.TaxonomyBackend;
-import lcsb.mapviewer.annotation.services.TaxonomySearchException;
import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
import lcsb.mapviewer.annotation.services.annotators.ElementAnnotator;
import lcsb.mapviewer.commands.ClearColorModelCommand;
@@ -106,8 +105,6 @@ import lcsb.mapviewer.services.utils.CreateProjectParams;
import lcsb.mapviewer.services.utils.EmailSender;
import lcsb.mapviewer.services.utils.InvalidDataMiningInputFile;
import lcsb.mapviewer.services.utils.data.BuildInLayout;
-import lcsb.mapviewer.services.view.ProjectView;
-import lcsb.mapviewer.services.view.ProjectViewFactory;
/**
* Implementation of the project service. It allows to manage and access project
@@ -240,12 +237,6 @@ public class ProjectService implements IProjectService {
@Autowired
private DbUtils dbUtils;
- /**
- * Factory object for {@link ProjectView} elements.
- */
- @Autowired
- private ProjectViewFactory projectViewFactory;
-
/**
* Access point and parser for the online ctd database.
*/
@@ -300,70 +291,6 @@ public class ProjectService implements IProjectService {
return result;
}
- @Override
- public List<ProjectView> getAllProjectViews(String token) throws SecurityException {
- List<ProjectView> result = new ArrayList<>();
- List<Project> projects = getAllProjects(token);
- for (Project project : projects) {
- result.add(projectViewFactory.create(project));
- }
- return result;
- }
-
- @Override
- public void updateProject(ProjectView selectedProject) {
- Project project = projectDao.getById(selectedProject.getIdObject());
- project.setProjectId(selectedProject.getProjectId());
- project.setName(selectedProject.getProjectName());
- project.setVersion(selectedProject.getVersion());
- project.setNotifyEmail(selectedProject.getNotifyEmail());
- MiriamData disease = null;
- MiriamData organism = null;
- if (selectedProject.getNewDiseaseName() != null && !selectedProject.getNewDiseaseName().isEmpty()) {
- disease = new MiriamData(MiriamType.MESH_2012, selectedProject.getNewDiseaseName());
- }
- if (selectedProject.getNewOrganismName() != null && !selectedProject.getNewOrganismName().isEmpty()) {
- organism = new MiriamData(MiriamType.TAXONOMY, selectedProject.getNewOrganismName());
- }
- try {
- if (meshParser.isValidMeshId(disease)) {
- project.setDisease(disease);
- } else {
- project.setDisease(null);
- selectedProject.setNewDiseaseName(null);
- }
- } catch (AnnotatorException e) {
- logger.error("Problem with accessing mesh", e);
- project.setDisease(null);
- selectedProject.setNewDiseaseName(null);
- }
- try {
- if (taxonomyBackend.getNameForTaxonomy(organism) != null) {
- project.setOrganism(organism);
- } else {
- project.setOrganism(null);
- selectedProject.setNewOrganismName(null);
- }
- } catch (TaxonomySearchException e) {
- logger.error("Problem with accessing taxonomy db", e);
- project.setOrganism(null);
- selectedProject.setNewOrganismName(null);
- }
- for (ModelData model : project.getModels()) {
- if (model.getId().equals(selectedProject.getModelId())) {
- modelService.updateModel(model, selectedProject);
- }
- }
- projectDao.update(project);
- }
-
- @Override
- public void removeProject(ProjectView selectedProject, String homeDir, boolean async, String token)
- throws SecurityException {
- Project project = projectDao.getById(selectedProject.getIdObject());
- removeProject(project, homeDir, async, token);
- }
-
/**
* Removes all types of privileges from every user to the project given in the
* parameter.
@@ -379,12 +306,6 @@ public class ProjectService implements IProjectService {
}
}
- @Override
- public ProjectView getProjectViewByProjectId(String name, String token) throws SecurityException {
- Project project = getProjectByProjectId(name, token);
- return projectViewFactory.create(project);
- }
-
@Override
public void removeProject(final Project p, final String dir, final boolean async, String token)
throws SecurityException {
@@ -538,18 +459,6 @@ public class ProjectService implements IProjectService {
}
- @Override
- public ProjectView getProjectViewById(Integer id, String token) throws SecurityException {
- Project project = projectDao.getById(id);
- if (userService.userHasPrivilege(token, PrivilegeType.VIEW_PROJECT, project)) {
- return projectViewFactory.create(project);
- } else if (userService.userHasPrivilege(token, PrivilegeType.ADD_MAP)) {
- return projectViewFactory.create(project);
- } else {
- throw new UserAccessException("User cannot access project");
- }
- }
-
/**
* This methods add privileges for the users listed in params to the project.
*
@@ -1277,11 +1186,6 @@ public class ProjectService implements IProjectService {
this.dataMiningService = dataMiningService;
}
- @Override
- public ProjectView createEmpty() {
- return projectViewFactory.create(null);
- }
-
/**
* Analyzes annotation of the model and put information about invalid
* annotations into the {@link Model#creationWarnings} field.
@@ -1559,30 +1463,6 @@ public class ProjectService implements IProjectService {
}
- @Override
- public byte[] getInputDataForProject(ProjectView projectView) {
- return getInputDataForProject(projectView.getIdObject());
- }
-
- /**
- * Returns byte array containing data from original input file that was used to
- * create this project.
- *
- * @param projectId
- * identifier of project for which we want to retrieve original file
- * data
- * @return original data file for given layout, if such file is not stored in
- * database (compatibility reasons) then null is returned
- */
- private byte[] getInputDataForProject(int projectId) {
- Project project = projectDao.getById(projectId);
- if (project == null || project.getInputData() == null) {
- return null;
- } else {
- return project.getInputData().getFileContent();
- }
- }
-
/**
* Method that handles exception reporting during creation of a project.
*
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/IModelService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/IModelService.java
index 57495869e7ca7959078d9ee7cc9ba1d7148c1ab4..b7ad235241bf8dc8bc86681091e0b4f0d4273bd0 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IModelService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IModelService.java
@@ -11,7 +11,6 @@ import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.search.data.LightAliasView;
import lcsb.mapviewer.services.search.data.LightReactionView;
import lcsb.mapviewer.services.view.ModelView;
-import lcsb.mapviewer.services.view.ProjectView;
/**
* Service that manages models (maps).
@@ -28,7 +27,7 @@ public interface IModelService {
* @param projectId
* {@link lcsb.mapviewer.model.Project#projectId project identifier}
* @return the newest model for the project
- * @throws SecurityException
+ * @throws SecurityException
*/
Model getLastModelByProjectId(String projectId, String token) throws SecurityException;
@@ -42,16 +41,6 @@ public interface IModelService {
*/
void cacheAllPubmedIds(Model model, IProgressUpdater updater);
- /**
- * Updates information in the model with the one taken from selectedProject.
- *
- * @param model
- * model to update
- * @param selectedProject
- * source of data that should be used in the update
- */
- void updateModel(ModelData model, ProjectView selectedProject);
-
/**
* Removes model from application cache.
*
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/IProjectService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/IProjectService.java
index aaf3bbf5d8a6a7a3a0e14a322ab9fe79a526c020..d3a236cfb7fe828b643bc1689cb1c2bb4328d6eb 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IProjectService.java
@@ -11,7 +11,6 @@ import lcsb.mapviewer.model.user.UserAnnotatorsParam;
import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.UserAccessException;
import lcsb.mapviewer.services.utils.CreateProjectParams;
-import lcsb.mapviewer.services.view.ProjectView;
/**
* Service that manages projects.
@@ -28,7 +27,7 @@ public interface IProjectService {
* {@link Project#projectId project identifier}
* @return project with an identifier given as parameter. Null if such project
* doesn't exist.
- * @throws SecurityException
+ * @throws SecurityException
*/
Project getProjectByProjectId(String projectId, String token) throws UserAccessException, SecurityException;
@@ -46,39 +45,9 @@ public interface IProjectService {
* Returns list of all projects.
*
* @return list of all projects.
- * @throws SecurityException
- */
- List<Project> getAllProjects(String token) throws SecurityException;
-
- /**
- * Returns a list of Project views for all projects.
- *
- * @return list of Project views for all projects
- * @throws SecurityException
- */
- List<ProjectView> getAllProjectViews(String token) throws SecurityException;
-
- /**
- * Updates project.
- *
- * @param projectView
- * project view with the data to update
- */
- void updateProject(ProjectView projectView);
-
- /**
- * Removes project from the system.
- *
- * @param homeDir
- * directory where the system is deployed
- *
- * @param projectView
- * information about project to remove
- * @param async
- * should the operation be done asynchronously
* @throws SecurityException
*/
- void removeProject(ProjectView projectView, String homeDir, boolean async, String token) throws SecurityException;
+ List<Project> getAllProjects(String token) throws SecurityException;
/**
* Removes project from the system.
@@ -93,17 +62,6 @@ public interface IProjectService {
*/
void removeProject(Project project, String homeDir, boolean async, String token) throws SecurityException;
- /**
- * Gets view of the project by the {@link Project#projectId project identifier}.
- *
- * @param projectId
- * {@link Project#projectId project identifier}
- * @return view of the project
- * @throws UserAccessException
- * @throws SecurityException
- */
- ProjectView getProjectViewByProjectId(String projectId, String token) throws UserAccessException, SecurityException;
-
/**
* Adds project to the system.
*
@@ -112,17 +70,6 @@ public interface IProjectService {
*/
void addProject(Project project);
- /**
- * Return the view of the project identified by database identifier.
- *
- * @param id
- * database identifier of the project
- * @return project view
- * @throws UserAccessException
- * @throws SecurityException
- */
- ProjectView getProjectViewById(Integer id, String token) throws UserAccessException, SecurityException;
-
/**
* Creates project using give parameters. See {@link CreateProjectParams}.
*
@@ -132,13 +79,6 @@ public interface IProjectService {
*/
void createProject(CreateProjectParams params) throws SecurityException;
- /**
- * Creates empty {@link ProjectView}.
- *
- * @return empty {@link ProjectView}
- */
- ProjectView createEmpty();
-
/**
* Creates {@link TreeNode} that contains information about all classes that can
* be annotated and associate set of
@@ -157,7 +97,7 @@ public interface IProjectService {
* given user and default params used when creating project.
*
* @param user
- * user for which we updte information
+ * user for which we update information
* @param sbgnFormat
* new
* {@link lcsb.mapviewer.model.user.UserAnnotationSchema#sbgnFormat}
@@ -181,18 +121,6 @@ public interface IProjectService {
*/
void updateProject(Project project);
- /**
- * Returns content of the file that was used to create project given in the
- * parameter.
- *
- * @param projectView
- * view of the {@link Project} for which we are looking for an original
- * source file
- * @return content of the file that was used to create project given in the
- * parameter
- */
- byte[] getInputDataForProject(ProjectView projectView);
-
UserAnnotationSchema prepareUserAnnotationSchema(User user);
/**
diff --git a/service/src/main/java/lcsb/mapviewer/services/view/ProjectView.java b/service/src/main/java/lcsb/mapviewer/services/view/ProjectView.java
deleted file mode 100644
index 6e1ed975ea37398c6e56a39020d759674f3932f2..0000000000000000000000000000000000000000
--- a/service/src/main/java/lcsb/mapviewer/services/view/ProjectView.java
+++ /dev/null
@@ -1,527 +0,0 @@
-package lcsb.mapviewer.services.view;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
-
-import lcsb.mapviewer.common.comparator.IntegerComparator;
-import lcsb.mapviewer.model.Project;
-
-/**
- * This class is a client view that represents {@link Project} class. Right now
- * this class highly entangles {@link Project} and
- * {@link lcsb.mapviewer.model.map.model.db.model.map.Model Model}. In the
- * future it should separate it.
- *
- * @author Piotr Gawron
- *
- */
-public class ProjectView extends AbstractView<Project> implements Comparable<ProjectView>, Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Identifier of the model that is represented in this project view (this must
- * be refactorized in the future).
- */
- private Integer modelId;
-
- /**
- * List of layouts in the model (identified by {@link #modelId}).
- */
- private List<LayoutView> layouts = new ArrayList<LayoutView>();
-
- /**
- * {@link Project#projectId Identifier} of the project.
- */
- private String projectId;
-
- /**
- * {@link Project#name Name} of the project.
- */
- private String projectName;
-
- /**
- * {@link Project#name newDiseaseName} of the project.
- */
- private String newDiseaseName;
-
- /**
- * {@link Project#organism newOrganismName} of the project.
- */
- private String newOrganismName;
-
- /**
- * {@link Project#disease Disease} of the project.
- */
- private AnnotationView projectDiseaseLink;
-
- /**
- * {@link Project#disease Disease name} of the project.
- */
- private String diseaseName = "N/A";
-
- /**
- * {@link Project#organism Organism} of the project.
- */
- private AnnotationView organismLink;
-
- /**
- * Email used for notification obut the events connected to this project.
- */
- private String notifyEmail;
-
- /**
- * Status of the project processing.
- */
- private String status;
-
- /**
- * Errors that appeard in the project.
- */
- private String errors;
-
- /**
- * Progress of the project processng (value between 0..100).
- */
- private Integer progress;
-
- /**
- * Short list of warnings that appeard during model creation.
- */
- private String warningsPreview;
-
- /**
- * List of warnings that appeard during model creation.
- */
- private List<String> warnings;
-
- /**
- * Description of the model.
- */
- private String description;
- /**
- * Version of the model.
- */
- private String version;
-
- /**
- * "true" if input file from which project was created is available, "false"
- * otherwise.
- */
- private String inputDataAvailable;
-
- /**
- * List of data mining sets used to gernerate suggested connections.
- */
- private List<DataMiningSetView> dataMiningSets = new ArrayList<DataMiningSetView>();
-
- /**
- * Default constructor.
- *
- * @param project
- * {@link Project} for which this view is created
- */
- protected ProjectView(Project project) {
- super(project);
- }
-
- /**
- * Default constructor. Should be used only for deserialization.
- */
- protected ProjectView() {
- }
-
- /**
- * Constructor that creates copy of the {@link ProjectView}.
- *
- * @param row
- * original object
- */
- public ProjectView(ProjectView row) {
- super(null);
- setIdObject(row.getIdObject());
- modelId = row.getModelId();
- layouts.addAll(row.getLayouts());
- projectId = row.getProjectId();
- projectName = row.getProjectName();
- newDiseaseName = row.getNewDiseaseName();
- newOrganismName = row.getNewOrganismName();
- projectDiseaseLink = row.getProjectDiseaseLink();
- organismLink = row.getOrganismLink();
- notifyEmail = row.getNotifyEmail();
- status = row.getStatus();
- progress = row.getProgress();
- description = row.getDescription();
- version = row.getVersion();
- errors = row.getErrors();
- warningsPreview = row.getWarningsPreview();
- warnings = row.getWarnings();
- for (DataMiningSetView view : row.getDataMiningSets()) {
- dataMiningSets.add(new DataMiningSetView(view));
- }
- inputDataAvailable = row.getInputDataAvailable();
- }
-
- @Override
- public int compareTo(ProjectView o) {
- if (o == null) {
- new IntegerComparator().compare(getIdObject(), null);
- }
- return new IntegerComparator().compare(getIdObject(), o.getIdObject());
- }
-
- /**
- * @return the modelId
- * @see #modelId
- */
- public Integer getModelId() {
- return modelId;
- }
-
- /**
- * @param modelId
- * the modelId to set
- * @see #modelId
- */
- public void setModelId(Integer modelId) {
- this.modelId = modelId;
- }
-
- /**
- * @return the layouts
- * @see #layouts
- */
- public List<LayoutView> getLayouts() {
- return layouts;
- }
-
- /**
- * @param layouts
- * the layouts to set
- * @see #layouts
- */
- public void setLayouts(List<LayoutView> layouts) {
- this.layouts = layouts;
- }
-
- /**
- * @return the name
- * @see #projectId
- */
- public String getProjectId() {
- return projectId;
- }
-
- /**
- * @param projectId
- * project identifier
- * @see #projectId
- */
- public void setProjectId(String projectId) {
- this.projectId = projectId;
- }
-
- /**
- * @return the notifyEmail
- * @see #notifyEmail
- */
- public String getNotifyEmail() {
- return notifyEmail;
- }
-
- /**
- * @param notifyEmail
- * the notifyEmail to set
- * @see #notifyEmail
- */
- public void setNotifyEmail(String notifyEmail) {
- this.notifyEmail = notifyEmail;
- }
-
- /**
- * @return the status
- * @see #status
- */
- public String getStatus() {
- return status;
- }
-
- /**
- * @param status
- * the status to set
- * @see #status
- */
- public void setStatus(String status) {
- this.status = status;
- }
-
- /**
- * @return the progress
- * @see #progress
- */
- public Integer getProgress() {
- return progress;
- }
-
- /**
- * @param progress
- * the progress to set
- * @see #progress
- */
- public void setProgress(Integer progress) {
- this.progress = progress;
- }
-
- /**
- * @return the description
- * @see #description
- */
- public String getDescription() {
- return description;
- }
-
- /**
- * @param description
- * the description to set
- * @see #description
- */
- public void setDescription(String description) {
- this.description = description;
- }
-
- /**
- * @return the version
- * @see #version
- */
- public String getVersion() {
- return version;
- }
-
- /**
- * @param version
- * the version to set
- * @see #version
- */
- public void setVersion(String version) {
- this.version = version;
- }
-
- /**
- * Adds layout to the view.
- *
- * @param row
- * layout to add
- */
- public void addLayout(LayoutView row) {
- layouts.add(row);
- }
-
- /**
- * @return the warnings
- * @see #warnings
- */
- public List<String> getWarnings() {
- return warnings;
- }
-
- /**
- * @param warnings
- * the warnings to set
- * @see #warnings
- */
- public void setWarnings(List<String> warnings) {
- this.warnings = warnings;
- }
-
- /**
- * @return the errors
- * @see #errors
- */
- public String getErrors() {
- return errors;
- }
-
- /**
- * @param errors
- * the errors to set
- * @see #errors
- */
- public void setErrors(String errors) {
- this.errors = errors;
- }
-
- /**
- * @return the dataMiningSets
- * @see #dataMiningSets
- */
- public List<DataMiningSetView> getDataMiningSets() {
- return dataMiningSets;
- }
-
- /**
- * @param dataMiningSets
- * the dataMiningSets to set
- * @see #dataMiningSets
- */
- public void setDataMiningSets(List<DataMiningSetView> dataMiningSets) {
- this.dataMiningSets = dataMiningSets;
- }
-
- /**
- * Adds {@link DataMiningSetView} to {@link #dataMiningSets}.
- *
- * @param dataMiningSetView
- * object to add
- */
- public void addDataMiningSet(DataMiningSetView dataMiningSetView) {
- dataMiningSets.add(dataMiningSetView);
- }
-
- /**
- * @return the projectName
- * @see #projectName
- */
- public String getProjectName() {
- return projectName;
- }
-
- /**
- * @param projectName
- * the projectName to set
- * @see #projectName
- */
- public void setProjectName(String projectName) {
- this.projectName = projectName;
- }
-
- /**
- * @return project disease link
- */
- public AnnotationView getProjectDiseaseLink() {
- return projectDiseaseLink;
- }
-
- /**
- * @param projectDiseaseLink
- * the link for the disease.
- */
- public void setProjectDiseaseLink(AnnotationView projectDiseaseLink) {
- this.projectDiseaseLink = projectDiseaseLink;
- }
-
- /**
- * @return this is used to update or add different disease association.
- */
- public String getNewDiseaseName() {
- return newDiseaseName;
- }
-
- /**
- * @param newDiseaseName
- * this is used to update or add different disease association.
- */
- public void setNewDiseaseName(String newDiseaseName) {
- this.newDiseaseName = newDiseaseName;
- }
-
- /**
- * @return the diseaseName
- * @see #diseaseName
- */
- public String getDiseaseName() {
- return diseaseName;
- }
-
- /**
- * @param diseaseName
- * the diseaseName to set
- * @see #diseaseName
- */
- public void setDiseaseName(String diseaseName) {
- this.diseaseName = diseaseName;
- }
-
- /**
- * @return the inputDataAvailable
- * @see #inputDataAvailable
- */
- public String getInputDataAvailable() {
- return inputDataAvailable;
- }
-
- /**
- * @param inputDataAvailable
- * the inputDataAvailable to set
- * @see #inputDataAvailable
- */
- public void setInputDataAvailable(String inputDataAvailable) {
- this.inputDataAvailable = inputDataAvailable;
- }
-
- /**
- * @param value
- * the inputDataAvailable to set
- * @see #inputDataAvailable
- */
- public void setInputDataAvailable(boolean value) {
- if (value) {
- this.inputDataAvailable = "true";
- } else {
- this.inputDataAvailable = "false";
- }
-
- }
-
- /**
- * @return the organismLink
- * @see #organismLink
- */
- public AnnotationView getOrganismLink() {
- return organismLink;
- }
-
- /**
- * @param organismLink the organismLink to set
- * @see #organismLink
- */
- public void setOrganismLink(AnnotationView organismLink) {
- this.organismLink = organismLink;
- }
-
- /**
- * @return the newOrganismName
- * @see #newOrganismName
- */
- public String getNewOrganismName() {
- return newOrganismName;
- }
-
- /**
- * @param newOrganismName the newOrganismName to set
- * @see #newOrganismName
- */
- public void setNewOrganismName(String newOrganismName) {
- this.newOrganismName = newOrganismName;
- }
-
- /**
- * @return the warningsPreview
- * @see #warningsPreview
- */
- public String getWarningsPreview() {
- return warningsPreview;
- }
-
- /**
- * @param warningsPreview the warningsPreview to set
- * @see #warningsPreview
- */
- public void setWarningsPreview(String warningsPreview) {
- this.warningsPreview = warningsPreview;
- }
-
-}
diff --git a/service/src/main/java/lcsb/mapviewer/services/view/ProjectViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/view/ProjectViewFactory.java
deleted file mode 100644
index 45af2c1ff6ed3987c486ab653b79e11a410c7ce6..0000000000000000000000000000000000000000
--- a/service/src/main/java/lcsb/mapviewer/services/view/ProjectViewFactory.java
+++ /dev/null
@@ -1,119 +0,0 @@
-package lcsb.mapviewer.services.view;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import com.google.gson.Gson;
-
-import lcsb.mapviewer.annotation.data.MeSH;
-import lcsb.mapviewer.annotation.services.MeSHParser;
-import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.graph.DataMiningSet;
-import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.model.ModelData;
-
-/**
- * Factory class for {@link ProjectView} class.
- *
- * @author Piotr Gawron
- *
- */
-public class ProjectViewFactory extends AbstractViewFactory<Project, ProjectView> {
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ProjectViewFactory.class);
-
- /**
- * Factory object for {@link LayoutView} elements.
- */
- @Autowired
- private LayoutViewFactory layoutViewFactory;
-
- /**
- * Factory object used for creation of {@link AnnotationView} elements.
- */
- @Autowired
- private AnnotationViewFactory annotationViewFactory;
-
- /**
- * Access object for information about mesh terms.
- */
- @Autowired
- private MeSHParser meSHParser;
-
- @Override
- public ProjectView create(Project project) {
- ProjectView result = new ProjectView(project);
- if (project == null) {
- return result;
- }
- result.setIdObject(project.getId());
- result.setErrors(project.getErrors());
- result.setProjectId(project.getProjectId());
- result.setProjectName(project.getName());
- result.setNotifyEmail(project.getNotifyEmail());
- if (project.getDisease() != null) {
- result.setProjectDiseaseLink(annotationViewFactory.create(project.getDisease()));
- result.setNewDiseaseName(project.getDisease().getResource());
- MeSH mesh;
- try {
- mesh = meSHParser.getMeSH(project.getDisease());
- if (mesh != null) {
- result.setDiseaseName(mesh.getName());
- }
- } catch (AnnotatorException e) {
- logger.error("Problem with getting info about mesh entry: ", e);
- }
- }
-
- if (project.getOrganism() != null) {
- result.setOrganismLink(annotationViewFactory.create(project.getOrganism()));
- result.setNewOrganismName(project.getOrganism().getResource());
- }
- result.setStatus(project.getStatus().toString());
- result.setProgress(Integer.valueOf((int) project.getProgress()));
- result.setInputDataAvailable(project.getInputData() != null);
-
- int warnCount = 0;
- String warnPreview = "";
- for (String w : project.getWarnings()) {
- if (!"".equals(w)) {
- if (warnCount <= 2) {
- warnPreview += w + "\n";
- }
- warnCount++;
- }
- }
- result.setWarningsPreview(warnPreview);
- result.setWarnings(project.getWarnings());
- result.setVersion(project.getVersion());
-
- for (ModelData model : project.getModels()) {
- result.setModelId(model.getId());
- result.setDescription(model.getNotes());
- result.getLayouts().clear();
- for (Layout layout : model.getLayouts()) {
- LayoutView layoutRow = layoutViewFactory.create(layout);
- result.addLayout(layoutRow);
- }
- for (DataMiningSet dms : model.getDataMiningSets()) {
- result.addDataMiningSet(new DataMiningSetView(dms));
- }
- }
- return result;
- }
-
- @Override
- public String createGson(ProjectView object) {
- return new Gson().toJson(object);
- }
-
- @Override
- public Project viewToObject(ProjectView view) {
- throw new NotImplementedException();
- }
-}
diff --git a/service/src/main/resources/applicationContext-service.xml b/service/src/main/resources/applicationContext-service.xml
index 60ec25e5948ca31698356a57255cffa06f6c6769..ec3ec8712ac02f1c945688271fe435ddb9ed8953 100644
--- a/service/src/main/resources/applicationContext-service.xml
+++ b/service/src/main/resources/applicationContext-service.xml
@@ -56,7 +56,6 @@
<bean id="OverviewImageViewFactory" class="lcsb.mapviewer.services.view.OverviewImageViewFactory"/>
<bean id="OverviewLinkViewFactory" class="lcsb.mapviewer.services.view.OverviewLinkViewFactory"/>
<bean id="PrivilegeViewFactory" class="lcsb.mapviewer.services.view.PrivilegeViewFactory"/>
- <bean id="ProjectViewFactory" class="lcsb.mapviewer.services.view.ProjectViewFactory"/>
<bean id="ReferenceGenomeViewFactory" class="lcsb.mapviewer.services.view.ReferenceGenomeViewFactory"/>
<bean id="ReferenceGenomeGeneMappingViewFactory" class="lcsb.mapviewer.services.view.ReferenceGenomeGeneMappingViewFactory"/>
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/ModelServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/ModelServiceTest.java
index 11cc1b98006d3ffbf892157e35d3f2b6fef8575d..48edf8414c4f3f97df236f1d36ae76c115d4ca5d 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/ModelServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/ModelServiceTest.java
@@ -1,10 +1,8 @@
package lcsb.mapviewer.services.impl;
import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
import static org.junit.Assert.fail;
-import java.io.File;
import java.util.ArrayList;
import java.util.List;
@@ -18,16 +16,11 @@ import org.springframework.test.annotation.Rollback;
import lcsb.mapviewer.annotation.services.PubmedParser;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.graphics.MapGenerator;
-import lcsb.mapviewer.converter.graphics.MapGenerator.MapGeneratorParams;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.layout.Layout;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.ServiceTestFunctions;
import lcsb.mapviewer.services.interfaces.IModelService;
import lcsb.mapviewer.services.search.data.LightAliasView;
-import lcsb.mapviewer.services.view.ProjectView;
@Rollback(true)
public class ModelServiceTest extends ServiceTestFunctions {
@@ -46,39 +39,6 @@ public class ModelServiceTest extends ServiceTestFunctions {
public void tearDown() throws Exception {
}
- @Test
- public void testRemoveModel() throws Exception {
- try {
- String directory = "test_directory";
- String projectId = "Some_id";
- Project project = new Project();
- project.setProjectId(projectId);
- projectDao.add(project);
-
- Model model = getModelForFile("testFiles/sample.xml", false);
- model.addLayout(new Layout("test", directory, false));
-
- project.addModel(model);
- projectDao.update(project);
-
- MapGenerator generator = new MapGenerator();
- MapGeneratorParams params = generator.new MapGeneratorParams().model(model).directory(directory);
- generator.generateMapImages(params);
-
- String adminToken = userService.login("admin", "admin");
- ProjectView row = projectService.getProjectViewByProjectId(project.getProjectId(), adminToken);
- projectService.removeProject(row, null, false, adminToken);
-
- File file = new File(directory);
- assertFalse(file.exists());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
@Test
public void testGetAliasByIds() throws Exception {
try {
@@ -138,28 +98,4 @@ public class ModelServiceTest extends ServiceTestFunctions {
}
- @Test
- public void testAddModel() throws Exception {
- try {
- String projectId = "Some_id";
- Project project = new Project();
- project.setProjectId(projectId);
- projectDao.add(project);
-
- Model model = getModelForFile("testFiles/db_problem_model.xml", false);
-
- project.addModel(model);
- projectDao.update(project);
-
- String adminToken = userService.login("admin", "admin");
- ProjectView row = projectService.getProjectViewByProjectId(project.getProjectId(), adminToken);
- projectService.removeProject(row, null, false, adminToken);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
}
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
index de1196579ef6b56fe915a0cab70fa3b7d88b069a..a2df3103ff7b7ddb87c133e239c1777945e42e6f 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
@@ -43,9 +43,7 @@ import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
import lcsb.mapviewer.model.map.model.SubmodelType;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.user.ObjectPrivilege;
import lcsb.mapviewer.model.user.PrivilegeType;
-import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.model.user.UserAnnotationSchema;
import lcsb.mapviewer.model.user.UserClassAnnotators;
import lcsb.mapviewer.model.user.UserClassValidAnnotations;
@@ -56,7 +54,6 @@ import lcsb.mapviewer.services.overlay.AnnotatedObjectTreeRow;
import lcsb.mapviewer.services.utils.CreateProjectParams;
import lcsb.mapviewer.services.utils.data.BuildInLayout;
import lcsb.mapviewer.services.view.ConfigurationView;
-import lcsb.mapviewer.services.view.ProjectView;
@Rollback(true)
public class ProjectServiceTest extends ServiceTestFunctions {
@@ -128,100 +125,6 @@ public class ProjectServiceTest extends ServiceTestFunctions {
}
}
- @Test
- public void testRemove() throws Exception {
-
- try {
- String project_id = "Some_id";
- Project project = new Project();
- project.setProjectId(project_id);
- projectDao.add(project);
-
- List<ProjectView> projects2 = projectService.getAllProjectViews(adminToken);
- ProjectView row = null;
- for (ProjectView projectRow : projects2) {
- if (projectRow.getIdObject() == project.getId()) {
- row = projectRow;
- }
- }
- assertNotNull(row);
-
- User user = new User();
- user.setLogin("x");
- userDao.add(user);
- userDao.evict(user);
-
- int userId = user.getId();
-
- user = userService.getUserById(userId);
-
- userDao.evict(user);
-
- userService.setUserPrivilege(user, new ObjectPrivilege(project, 1, PrivilegeType.VIEW_PROJECT, user));
-
- user = userService.getUserById(userId);
- int newAmount = user.getPrivileges().size();
-
- userDao.evict(user);
-
- projectService.removeProject(row, tmpResultDir, false, adminToken);
-
- user = userService.getUserById(userId);
-
- assertEquals("After removing project number of privileges didn't drop down", newAmount - 1,
- user.getPrivileges().size());
-
- userDao.delete(user);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRemoveUserAfterRemoveProject() throws Exception {
-
- try {
- String projectId = "Some_id";
- Project project = new Project();
- project.setProjectId(projectId);
- projectDao.add(project);
-
- List<ProjectView> projects2 = projectService.getAllProjectViews(adminToken);
- ProjectView row = null;
- for (ProjectView projectRow : projects2) {
- if (projectRow.getIdObject() == project.getId()) {
- row = projectRow;
- }
- }
- assertNotNull(row);
-
- User user = new User();
- user.setLogin("x");
- userDao.add(user);
- userDao.evict(user);
-
- int userId = user.getId();
-
- userService.setUserPrivilege(user, new ObjectPrivilege(project, 1, PrivilegeType.VIEW_PROJECT, user));
-
- user = userService.getUserById(userId);
-
- long counter = logDao.getCount();
- projectService.removeProject(row, tmpResultDir, false, adminToken);
- long counter2 = logDao.getCount();
- assertTrue("Logs didn't appear after removing project", counter < counter2);
-
- user = userService.getUserById(userId);
- userDao.delete(user);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
@Test
public void testUpdater() throws Exception {
try {
diff --git a/service/src/test/java/lcsb/mapviewer/services/view/AllViewTests.java b/service/src/test/java/lcsb/mapviewer/services/view/AllViewTests.java
index 476938b1524e2b45bdb3e28cddc22d9f3bf50d86..be2f29b80a9c1fc059038d4bed018bb4a143d32f 100644
--- a/service/src/test/java/lcsb/mapviewer/services/view/AllViewTests.java
+++ b/service/src/test/java/lcsb/mapviewer/services/view/AllViewTests.java
@@ -25,8 +25,6 @@ import org.junit.runners.Suite.SuiteClasses;
OverviewLinkViewTest.class, //
PrivilegeViewFactoryTest.class, //
PrivilegeViewTest.class, //
- ProjectViewFactoryTest.class, //
- ProjectViewTest.class, //
ReferenceGenomeViewFactoryTest.class, //
ReferenceGenomeGeneMappingViewFactoryTest.class, //
})
diff --git a/service/src/test/java/lcsb/mapviewer/services/view/ProjectViewFactoryTest.java b/service/src/test/java/lcsb/mapviewer/services/view/ProjectViewFactoryTest.java
deleted file mode 100644
index 6a7665d94aabd0e1eb97703d2f9835a90705c36d..0000000000000000000000000000000000000000
--- a/service/src/test/java/lcsb/mapviewer/services/view/ProjectViewFactoryTest.java
+++ /dev/null
@@ -1,46 +0,0 @@
-package lcsb.mapviewer.services.view;
-
-import static org.junit.Assert.*;
-import lcsb.mapviewer.services.ServiceTestFunctions;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-
-public class ProjectViewFactoryTest extends ServiceTestFunctions{
-
- @Autowired
- ProjectViewFactory projectViewFactory;
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testCreateEmpty() throws Exception {
- try {
- Object object = projectViewFactory.create(null);
- assertNotNull(object);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCreateGson() throws Exception {
- try {
- ProjectView object = projectViewFactory.create(null);
- assertNotNull(projectViewFactory.createGson(object));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
diff --git a/service/src/test/java/lcsb/mapviewer/services/view/ProjectViewTest.java b/service/src/test/java/lcsb/mapviewer/services/view/ProjectViewTest.java
deleted file mode 100644
index 6af4866b3afc03fc07e0ca53d8ab2d61d7c8eaf9..0000000000000000000000000000000000000000
--- a/service/src/test/java/lcsb/mapviewer/services/view/ProjectViewTest.java
+++ /dev/null
@@ -1,27 +0,0 @@
-package lcsb.mapviewer.services.view;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ProjectViewTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new ProjectView());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}