From 5e18be3ecac114d2d4a31ccd56271a7b6f1f0bc7 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Thu, 1 Jun 2017 15:10:10 +0200
Subject: [PATCH] new version of rest API for reactions
---
README.md | 7 +
.../java/lcsb/mapviewer/api/BaseRestImpl.java | 64 ++++++
.../api/projects/ProjectController.java | 7 -
.../api/projects/ProjectRestImpl.java | 199 ------------------
.../elements/ElementsController.java | 12 +-
.../elements/ElementsRestImpl.java | 36 +---
.../reactions/ReactionsController.java | 35 +++
.../reactions/ReactionsRestImpl.java | 198 +++++++++++++++++
.../resources/applicationContext-rest.xml | 1 +
.../services/impl/ReferenceGenomeService.java | 5 -
10 files changed, 316 insertions(+), 248 deletions(-)
create mode 100644 rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsController.java
create mode 100644 rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsRestImpl.java
diff --git a/README.md b/README.md
index 0e2c0ac693..4617a0f21d 100644
--- a/README.md
+++ b/README.md
@@ -21,5 +21,12 @@ Rest API tries to follow [API Design Guide](https://cloud.google.com/apis/design
* `columns` - set of columns. Possible values are: id, modelId, name, type, description, symbol, complexId, compartmentId, fullName, abbreviation, formula, name, synonyms, formerSymbols, references, bounds, hierarchyVisibilityLevel,
* `ids` - set of database ids
* Example: `/projects/pdmap_feb17/bioEntities/elements/?columns=id,name,type`
+* Reactions:
+ * URL: `/projects/{projectId}/bioEntities/reactions/`
+ * Method: GET
+ * Parameters:
+ * `columns` - set of columns. Possible values are:
+ * `ids` - set of database ids
+ * Example: `/projects/pdmap_feb17/bioEntities/reactions/?columns=id,name,type`
### Users
### Configuration
\ No newline at end of file
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 82a8400836..8cfea323f1 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
@@ -1,14 +1,29 @@
package lcsb.mapviewer.api;
+import java.util.ArrayList;
import java.util.HashMap;
+import java.util.List;
import java.util.Map;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Transactional;
+
import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.model.map.model.Model;
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.IUserService;
import lcsb.mapviewer.services.search.data.ElementIdentifier.ElementIdentifierType;
+@Transactional(value = "txManager")
public abstract class BaseRestImpl {
+ @Autowired
+ private IModelService modelService;
+ @Autowired
+ private IUserService userService;
+
protected Map<String, Object> okStatus() {
Map<String, Object> result = new HashMap<>();
result.put("status", "OK");
@@ -34,4 +49,53 @@ public abstract class BaseRestImpl {
return result;
};
+ protected List<Model> getModels(String projectId, String modelId, String token) throws SecurityException {
+ Model model = modelService.getLastModelByProjectId(projectId, userService.getToken(token));
+ List<Model> models = new ArrayList<>();
+
+ if (!modelId.equals("*")) {
+ for (String str : modelId.split(",")) {
+ models.add(model.getSubmodelById(Integer.valueOf(str)));
+ }
+ } else {
+ models.addAll(model.getSubmodels());
+ models.add(model);
+ }
+ return models;
+ }
+
+ /**
+ * @return the modelService
+ * @see #modelService
+ */
+ public IModelService getModelService() {
+ return modelService;
+ }
+
+ /**
+ * @param modelService
+ * the modelService to set
+ * @see #modelService
+ */
+ public void setModelService(IModelService modelService) {
+ this.modelService = modelService;
+ }
+
+ /**
+ * @return the userService
+ * @see #userService
+ */
+ public IUserService getUserService() {
+ return userService;
+ }
+
+ /**
+ * @param userService
+ * the userService to set
+ * @see #userService
+ */
+ public void setUserService(IUserService userService) {
+ this.userService = userService;
+ }
+
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectController.java
index 295e33e676..5ce7802b5d 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectController.java
@@ -41,13 +41,6 @@ public class ProjectController extends BaseController {
return projectController.getSuggestedQueryList(projectId, token);
}
- @RequestMapping(value = "/project/getReactions", method = { RequestMethod.GET, RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getReactions(@RequestParam(value = "projectId") String projectId, @RequestParam(value = "id", defaultValue = "") String id,
- @RequestParam(value = "columns", defaultValue = "") String columns, @RequestParam(value = "token") String token,
- @RequestParam(value = "participantId", defaultValue = "") String participantId) throws SecurityException {
- return projectController.getReactions(projectId, id, columns, token, participantId);
- }
-
@RequestMapping(value = "/project/getClosestElementsByCoordinates", method = { RequestMethod.GET, RequestMethod.POST },
produces = { MediaType.APPLICATION_JSON_VALUE })
public List<Map<String, Object>> getClosestElementsByCoordinates(@RequestParam(value = "projectId") String projectId,
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 55fe29eb11..882b991bf9 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
@@ -3,7 +3,6 @@ package lcsb.mapviewer.api.projects;
import java.awt.geom.Path2D;
import java.awt.geom.PathIterator;
import java.awt.geom.Point2D;
-import java.awt.geom.Rectangle2D;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
@@ -19,7 +18,6 @@ import java.util.SortedMap;
import java.util.TreeMap;
import org.apache.commons.io.IOUtils;
-import org.apache.commons.lang3.StringUtils;
import org.apache.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.annotation.Transactional;
@@ -57,12 +55,8 @@ 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.ModelSubmodelConnection;
-import lcsb.mapviewer.model.map.reaction.Modifier;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.UserAccessException;
@@ -72,7 +66,6 @@ import lcsb.mapviewer.services.interfaces.IProjectService;
import lcsb.mapviewer.services.interfaces.ISearchService;
import lcsb.mapviewer.services.interfaces.IUserService;
import lcsb.mapviewer.services.search.data.ElementIdentifier.ElementIdentifierType;
-import lcsb.mapviewer.services.search.data.LightReactionView;
import lcsb.mapviewer.services.utils.ColorSchemaReader;
import lcsb.mapviewer.services.utils.data.BuildInLayout;
import lcsb.mapviewer.services.utils.gmap.CoordinationConverter;
@@ -258,198 +251,6 @@ public class ProjectRestImpl {
return result;
};
- public List<Map<String, Object>> getReactions(String projectId, String id, String columns, String token, String participantElementId)
- throws UserAccessException, SecurityException {
- Model model = modelService.getLastModelByProjectId(projectId, userService.getToken(token));
- Set<Integer> ids = new HashSet<>();
- if (!id.equals("")) {
- for (String str : id.split(",")) {
- ids.add(Integer.valueOf(str));
- }
- }
- Set<Element> elementSet = new HashSet<>();
- if (!participantElementId.equals("")) {
- for (String str : participantElementId.split(",")) {
- elementSet.add(model.getElementByDbId(Integer.valueOf(str)));
- }
- }
- Set<String> columnsSet = createReactionColumnSet(columns);
-
- List<Map<String, Object>> result = new ArrayList<>();
-
- List<Model> models = new ArrayList<>();
- models.addAll(model.getSubmodels());
- models.add(model);
- for (Model model2 : models) {
- for (Reaction reaction : model2.getReactions()) {
- if (ids.size() == 0 || ids.contains(reaction.getId())) {
- if (elementSet.size() == 0 || reactionContainsElement(reaction, elementSet)) {
- result.add(preparedReaction(reaction, columnsSet));
- }
- }
- }
- }
-
- return result;
- }
-
- private boolean reactionContainsElement(Reaction reaction, Set<Element> elementSet) {
- for (Element element : elementSet) {
- if (reaction.containsElement(element)) {
- return true;
- }
- }
- return false;
- }
-
- private Map<String, Object> preparedReaction(Reaction reaction, Set<String> columnsSet) {
- Map<String, Object> result = new HashMap<>();
- for (String string : columnsSet) {
- String column = string.toLowerCase();
- Object value = null;
- if (column.equals("id") || column.equals("idobject")) {
- value = reaction.getId();
- } else if (column.equals("modelid")) {
- value = reaction.getModelData().getId();
- } else if (column.equals("reactionid")) {
- value = reaction.getIdReaction();
- } else if (column.equals("name")) {
- value = reaction.getName();
- } else if (column.equals("centerpoint")) {
- value = reaction.getCenterPoint();
- } else if (column.equals("products")) {
- List<Integer> ids = new ArrayList<>();
- for (Product product : reaction.getProducts()) {
- ids.add(product.getElement().getId());
- }
- value = StringUtils.join(ids, ",");
- } else if (column.equals("reactants")) {
- List<Integer> ids = new ArrayList<>();
- for (Reactant reactant : reaction.getReactants()) {
- ids.add(reactant.getElement().getId());
- }
- value = StringUtils.join(ids, ",");
- } else if (column.equals("modifiers")) {
- List<Integer> ids = new ArrayList<>();
- for (Modifier product : reaction.getModifiers()) {
- ids.add(product.getElement().getId());
- }
- value = StringUtils.join(ids, ",");
- } else if (column.equals("type")) {
- value = reaction.getStringType();
- } else if (column.equals("hierarchyvisibilitylevel")) {
- value = reaction.getVisibilityLevel();
- } else if (column.equals("lines")) {
- value = new LightReactionView(reaction).getLines();
- } else {
- value = "Unknown column";
- }
- result.put(string, value);
- }
- return result;
- }
-
- private Map<String, Object> preparedElement(Element element, Set<String> columnsSet) {
- Map<String, Object> result = new HashMap<>();
- for (String string : columnsSet) {
- String column = string.toLowerCase();
- Object value = null;
- if (column.equals("id") || column.equals("idobject")) {
- value = element.getId();
- } else if (column.equals("modelid")) {
- value = element.getModelData().getId();
- } else if (column.equals("name")) {
- value = element.getName();
- } else if (column.equals("type")) {
- value = element.getStringType();
- } else if (column.equals("symbol")) {
- value = element.getSymbol();
- } else if (column.equals("fullname")) {
- value = element.getFullName();
- } else if (column.equals("abbreviation")) {
- value = element.getAbbreviation();
- } else if (column.equals("compartmentid")) {
- if (element.getCompartment() != null) {
- value = element.getCompartment().getId();
- }
- } else if (column.equals("complexid")) {
- if (element instanceof Species) {
- if (((Species) element).getComplex() != null) {
- value = ((Species) element).getComplex().getId();
- }
- }
- } else if (column.equals("references")) {
- value = annotationViewFactory.createList(element.getMiriamData());
- } else if (column.equals("synonyms")) {
- value = element.getSynonyms();
- } else if (column.equals("formula")) {
- value = element.getFormula();
- } else if (column.equals("description")) {
- value = element.getNotes();
- } else if (column.equals("formersymbols")) {
- value = element.getFormerSymbols();
- } else if (column.equals("hierarchyvisibilitylevel")) {
- value = element.getVisibilityLevel();
- } else if (column.equals("bounds")) {
- value = new Rectangle2D.Double(element.getX(), element.getY(), element.getWidth(), element.getHeight());
- } else {
- value = "Unknown column";
- }
- result.put(string, value);
- }
- return result;
- }
-
- private Set<String> createElementColumnSet(String columns) {
- Set<String> columnsSet = new HashSet<>();
- if (columns.equals("")) {
- columnsSet.add("id");
- columnsSet.add("modelId");
- columnsSet.add("name");
- columnsSet.add("type");
- columnsSet.add("description");
- columnsSet.add("type");
- columnsSet.add("symbol");
- columnsSet.add("complexId");
- columnsSet.add("compartmentId");
- columnsSet.add("fullName");
- columnsSet.add("abbreviation");
- columnsSet.add("formula");
- columnsSet.add("name");
- columnsSet.add("synonyms");
- columnsSet.add("formerSymbols");
- columnsSet.add("references");
- columnsSet.add("bounds");
- columnsSet.add("hierarchyVisibilityLevel");
- } else {
- for (String str : columns.split(",")) {
- columnsSet.add(str);
- }
- }
- return columnsSet;
- }
-
- private Set<String> createReactionColumnSet(String columns) {
- Set<String> columnsSet = new HashSet<>();
- if (columns.equals("")) {
- columnsSet.add("id");
- columnsSet.add("reactionId");
- columnsSet.add("modelId");
- columnsSet.add("type");
- columnsSet.add("lines");
- columnsSet.add("centerPoint");
- columnsSet.add("products");
- columnsSet.add("reactants");
- columnsSet.add("modifiers");
- columnsSet.add("hierarchyVisibilityLevel");
- } else {
- for (String str : columns.split(",")) {
- columnsSet.add(str);
- }
- }
- return columnsSet;
- }
-
/**
* @return the modelService
* @see #modelService
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsController.java
index ee7b732401..d006a63c73 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsController.java
@@ -19,11 +19,15 @@ public class ElementsController extends BaseController {
@Autowired
private ElementsRestImpl projectController;
- @RequestMapping(value = "/projects/{projectId}/models/{modelId}/bioEntities/elements/", method = { RequestMethod.GET},
+ @RequestMapping(value = "/projects/{projectId}/models/{modelId}/bioEntities/elements/", method = { RequestMethod.GET },
produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getElements(@PathVariable(value = "projectId") String projectId, @PathVariable(value = "modelId") String modelId,
- @RequestParam(value = "id", defaultValue = "") String id, @RequestParam(value = "columns", defaultValue = "") String columns,
- @RequestParam(value = "token") String token) throws SecurityException {
+ public List<Map<String, Object>> getElements(//
+ @PathVariable(value = "projectId") String projectId, //
+ @PathVariable(value = "modelId") String modelId, //
+ @RequestParam(value = "id", defaultValue = "") String id, //
+ @RequestParam(value = "columns", defaultValue = "") String columns, //
+ @RequestParam(value = "token") String token//
+ ) throws SecurityException {
return projectController.getElements(projectId, id, columns, modelId, token);
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java
index d34fc6e610..6336c0e0a8 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java
@@ -12,24 +12,21 @@ import org.apache.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.annotation.Transactional;
+import lcsb.mapviewer.api.BaseRestImpl;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.UserAccessException;
import lcsb.mapviewer.services.interfaces.IModelService;
-import lcsb.mapviewer.services.interfaces.IUserService;
import lcsb.mapviewer.services.view.AnnotationViewFactory;
import lcsb.mapviewer.services.view.OverviewImageViewFactory;
@Transactional(value = "txManager")
-public class ElementsRestImpl {
+public class ElementsRestImpl extends BaseRestImpl {
Logger logger = Logger.getLogger(ElementsRestImpl.class);
- @Autowired
- private IUserService userService;
-
@Autowired
private IModelService modelService;
@@ -39,26 +36,8 @@ public class ElementsRestImpl {
@Autowired
private OverviewImageViewFactory factory;
- /**
- * @return the userService
- * @see #userService
- */
- public IUserService getUserService() {
- return userService;
- }
-
- /**
- * @param userService
- * the userService to set
- * @see #userService
- */
- public void setUserService(IUserService userService) {
- this.userService = userService;
- }
-
public List<Map<String, Object>> getElements(String projectId, String id, String columns, String modelId, String token)
throws UserAccessException, SecurityException {
- Model model = modelService.getLastModelByProjectId(projectId, userService.getToken(token));
Set<Integer> ids = new HashSet<>();
if (!id.equals("")) {
for (String str : id.split(",")) {
@@ -69,16 +48,7 @@ public class ElementsRestImpl {
List<Map<String, Object>> result = new ArrayList<>();
- List<Model> models = new ArrayList<>();
-
- if (!modelId.equals("*")) {
- for (String str : modelId.split(",")) {
- models.add(model.getSubmodelById(Integer.valueOf(str)));
- }
- } else {
- models.addAll(model.getSubmodels());
- models.add(model);
- }
+ List<Model> models = getModels(projectId, modelId, token);
for (Model model2 : models) {
for (Element element : model2.getElements()) {
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsController.java
new file mode 100644
index 0000000000..342e044466
--- /dev/null
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsController.java
@@ -0,0 +1,35 @@
+package lcsb.mapviewer.api.projects.models.bioEntities.reactions;
+
+import java.util.List;
+import java.util.Map;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.MediaType;
+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.RequestParam;
+import org.springframework.web.bind.annotation.RestController;
+
+import lcsb.mapviewer.api.BaseController;
+import lcsb.mapviewer.services.SecurityException;
+
+@RestController
+public class ReactionsController extends BaseController {
+ @Autowired
+ private ReactionsRestImpl reactionController;
+
+ @RequestMapping(value = "/projects/{projectId}/models/{modelId}/bioEntities/reactions/", method = { RequestMethod.GET },
+ produces = { MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getReactions(//
+ @PathVariable(value = "projectId") String projectId, //
+ @PathVariable(value = "modelId") String modelId,
+ @RequestParam(value = "id", defaultValue = "") String id, //
+ @RequestParam(value = "columns", defaultValue = "") String columns, //
+ @RequestParam(value = "token") String token, //
+ @RequestParam(value = "participantId", defaultValue = "") String participantId//
+ ) throws SecurityException {
+ return reactionController.getReactions(projectId, id, columns, modelId, token, participantId);
+ }
+
+}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsRestImpl.java
new file mode 100644
index 0000000000..64bd74ad1f
--- /dev/null
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsRestImpl.java
@@ -0,0 +1,198 @@
+package lcsb.mapviewer.api.projects.models.bioEntities.reactions;
+
+import java.awt.geom.PathIterator;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.apache.commons.lang3.StringUtils;
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Transactional;
+
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.services.SecurityException;
+import lcsb.mapviewer.services.UserAccessException;
+import lcsb.mapviewer.services.interfaces.IModelService;
+import lcsb.mapviewer.services.interfaces.IUserService;
+import lcsb.mapviewer.services.search.data.LightReactionView;
+import lcsb.mapviewer.services.view.AnnotationViewFactory;
+
+@Transactional(value = "txManager")
+public class ReactionsRestImpl {
+
+ /**
+ * Constant defining size of the array returned by
+ * {@link PathIterator#currentSegment(double[])} method. More nformation can
+ * be found <a href=
+ * "http://docs.oracle.com/javase/7/docs/api/java/awt/geom/PathIterator.html#currentSegment(double[])"
+ * >here</a>
+ */
+ private static final int PATH_ITERATOR_SEGMENT_SIZE = 6;
+
+ Logger logger = Logger.getLogger(ReactionsRestImpl.class);
+
+ @Autowired
+ private IUserService userService;
+
+ @Autowired
+ private IModelService modelService;
+
+ @Autowired
+ AnnotationViewFactory annotationViewFactory;
+
+ /**
+ * @return the userService
+ * @see #userService
+ */
+ public IUserService getUserService() {
+ return userService;
+ }
+
+ /**
+ * @param userService
+ * the userService to set
+ * @see #userService
+ */
+ public void setUserService(IUserService userService) {
+ this.userService = userService;
+ }
+
+ public List<Map<String, Object>> getReactions(String projectId, String id, String columns, String modelId, String token, String participantElementId)
+ throws UserAccessException, SecurityException {
+ Model model = modelService.getLastModelByProjectId(projectId, userService.getToken(token));
+ Set<Integer> ids = new HashSet<>();
+ if (!id.equals("")) {
+ for (String str : id.split(",")) {
+ ids.add(Integer.valueOf(str));
+ }
+ }
+ Set<Element> elementSet = new HashSet<>();
+ if (!participantElementId.equals("")) {
+ for (String str : participantElementId.split(",")) {
+ elementSet.add(model.getElementByDbId(Integer.valueOf(str)));
+ }
+ }
+ Set<String> columnsSet = createReactionColumnSet(columns);
+
+ List<Map<String, Object>> result = new ArrayList<>();
+
+ List<Model> models = new ArrayList<>();
+ models.addAll(model.getSubmodels());
+ models.add(model);
+ for (Model model2 : models) {
+ for (Reaction reaction : model2.getReactions()) {
+ if (ids.size() == 0 || ids.contains(reaction.getId())) {
+ if (elementSet.size() == 0 || reactionContainsElement(reaction, elementSet)) {
+ result.add(preparedReaction(reaction, columnsSet));
+ }
+ }
+ }
+ }
+
+ return result;
+ }
+
+ private boolean reactionContainsElement(Reaction reaction, Set<Element> elementSet) {
+ for (Element element : elementSet) {
+ if (reaction.containsElement(element)) {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ private Map<String, Object> preparedReaction(Reaction reaction, Set<String> columnsSet) {
+ Map<String, Object> result = new HashMap<>();
+ for (String string : columnsSet) {
+ String column = string.toLowerCase();
+ Object value = null;
+ if (column.equals("id") || column.equals("idobject")) {
+ value = reaction.getId();
+ } else if (column.equals("modelid")) {
+ value = reaction.getModelData().getId();
+ } else if (column.equals("reactionid")) {
+ value = reaction.getIdReaction();
+ } else if (column.equals("name")) {
+ value = reaction.getName();
+ } else if (column.equals("centerpoint")) {
+ value = reaction.getCenterPoint();
+ } else if (column.equals("products")) {
+ List<Integer> ids = new ArrayList<>();
+ for (Product product : reaction.getProducts()) {
+ ids.add(product.getElement().getId());
+ }
+ value = StringUtils.join(ids, ",");
+ } else if (column.equals("reactants")) {
+ List<Integer> ids = new ArrayList<>();
+ for (Reactant reactant : reaction.getReactants()) {
+ ids.add(reactant.getElement().getId());
+ }
+ value = StringUtils.join(ids, ",");
+ } else if (column.equals("modifiers")) {
+ List<Integer> ids = new ArrayList<>();
+ for (Modifier product : reaction.getModifiers()) {
+ ids.add(product.getElement().getId());
+ }
+ value = StringUtils.join(ids, ",");
+ } else if (column.equals("type")) {
+ value = reaction.getStringType();
+ } else if (column.equals("hierarchyvisibilitylevel")) {
+ value = reaction.getVisibilityLevel();
+ } else if (column.equals("lines")) {
+ value = new LightReactionView(reaction).getLines();
+ } else {
+ value = "Unknown column";
+ }
+ result.put(string, value);
+ }
+ return result;
+ }
+
+ private Set<String> createReactionColumnSet(String columns) {
+ Set<String> columnsSet = new HashSet<>();
+ if (columns.equals("")) {
+ columnsSet.add("id");
+ columnsSet.add("reactionId");
+ columnsSet.add("modelId");
+ columnsSet.add("type");
+ columnsSet.add("lines");
+ columnsSet.add("centerPoint");
+ columnsSet.add("products");
+ columnsSet.add("reactants");
+ columnsSet.add("modifiers");
+ columnsSet.add("hierarchyVisibilityLevel");
+ } else {
+ for (String str : columns.split(",")) {
+ columnsSet.add(str);
+ }
+ }
+ return columnsSet;
+ }
+
+ /**
+ * @return the modelService
+ * @see #modelService
+ */
+ public IModelService getModelService() {
+ return modelService;
+ }
+
+ /**
+ * @param modelService
+ * the modelService to set
+ * @see #modelService
+ */
+ public void setModelService(IModelService modelService) {
+ this.modelService = modelService;
+ }
+
+}
diff --git a/rest-api/src/main/resources/applicationContext-rest.xml b/rest-api/src/main/resources/applicationContext-rest.xml
index 3d406d92d3..5bcd700f1b 100644
--- a/rest-api/src/main/resources/applicationContext-rest.xml
+++ b/rest-api/src/main/resources/applicationContext-rest.xml
@@ -20,6 +20,7 @@
<bean id="ProjectRestImpl" class="lcsb.mapviewer.api.projects.ProjectRestImpl"/>
<bean id="ElementsRestImpl" class="lcsb.mapviewer.api.projects.models.bioEntities.elements.ElementsRestImpl"/>
+ <bean id="ReactionsRestImpl" class="lcsb.mapviewer.api.projects.models.bioEntities.reactions.ReactionsRestImpl"/>
<bean id="ReferenceGenomeRestImpl" class="lcsb.mapviewer.api.genomics.ReferenceGenomeRestImpl"/>
<bean id="UserRestImpl" class="lcsb.mapviewer.api.controller.UserRestImpl"/>
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ReferenceGenomeService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ReferenceGenomeService.java
index c17dc5ebcd..666eda198c 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ReferenceGenomeService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ReferenceGenomeService.java
@@ -136,11 +136,6 @@ public class ReferenceGenomeService implements IReferenceGenomeService {
public ReferenceGenomeView getReferenceGenomeViewByParams(MiriamData miriamData, ReferenceGenomeType genomeType, String version) {
List<ReferenceGenome> list = referenceGenomeDao.getByType(genomeType);
for (ReferenceGenome referenceGenome : list) {
- logger.debug(referenceGenome.getOrganism());
- logger.debug(referenceGenome.getVersion());
- logger.debug("---");
- logger.debug(miriamData);
- logger.debug(version);
if (referenceGenome.getOrganism().equals(miriamData) && referenceGenome.getVersion().equals(version)) {
return factory.create(referenceGenome);
}
--
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