From b806fc06bf17acd8ce461d49403c7592741297eb Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 20 Jan 2017 14:53:07 +0100
Subject: [PATCH] mirna api
---
.../mapviewer/api/mirna/MiRnaController.java | 38 +++
.../mapviewer/api/mirna/MiRnaRestImpl.java | 269 ++++++++++++++++++
.../resources/applicationContext-rest.xml | 1 +
3 files changed, 308 insertions(+)
create mode 100644 rest-api/src/main/java/lcsb/mapviewer/api/mirna/MiRnaController.java
create mode 100644 rest-api/src/main/java/lcsb/mapviewer/api/mirna/MiRnaRestImpl.java
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/mirna/MiRnaController.java b/rest-api/src/main/java/lcsb/mapviewer/api/mirna/MiRnaController.java
new file mode 100644
index 0000000000..46ec8084bf
--- /dev/null
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/mirna/MiRnaController.java
@@ -0,0 +1,38 @@
+package lcsb.mapviewer.api.mirna;
+
+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.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.api.QueryException;
+import lcsb.mapviewer.services.SecurityException;
+
+@RestController
+@RequestMapping("/miRna")
+public class MiRnaController extends BaseController {
+
+ @Autowired
+ private MiRnaRestImpl miRnaController;
+
+ @RequestMapping(value = "/getMiRnasByQuery", method = { RequestMethod.GET, RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getMiRnasByQuery(@RequestParam(value = "token") String token, @RequestParam(value = "projectId") String projectId,
+ @RequestParam(value = "columns", defaultValue = "") String columns, @RequestParam(value = "query") String query)
+ throws SecurityException, QueryException {
+ return miRnaController.getMiRnasByQuery(token, projectId, columns, query);
+ }
+
+ @RequestMapping(value = "/getMiRnasByTarget", method = { RequestMethod.GET, RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getMiRnasByTarget(@RequestParam(value = "token") String token, @RequestParam(value = "projectId") String projectId,
+ @RequestParam(value = "targetType", defaultValue = "ALIAS") String targetType, @RequestParam(value = "targetId", defaultValue = "") String targetId,
+ @RequestParam(value = "columns", defaultValue = "") String columns) throws SecurityException, QueryException {
+ return miRnaController.getMiRnasByTarget(token, projectId, targetType, targetId, columns);
+ }
+
+}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/mirna/MiRnaRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/mirna/MiRnaRestImpl.java
new file mode 100644
index 0000000000..9041e2d848
--- /dev/null
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/mirna/MiRnaRestImpl.java
@@ -0,0 +1,269 @@
+package lcsb.mapviewer.api.mirna;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Transactional;
+
+import lcsb.mapviewer.annotation.services.TaxonomyBackend;
+import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.MiriamData;
+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.ElementMatcher;
+import lcsb.mapviewer.services.search.data.ElementIdentifier.ElementIdentifierType;
+import lcsb.mapviewer.services.search.db.DbSearchCriteria;
+import lcsb.mapviewer.services.search.db.GeneRow;
+import lcsb.mapviewer.services.search.db.TargetView;
+import lcsb.mapviewer.services.search.db.mirna.IMiRNAService;
+import lcsb.mapviewer.services.search.db.mirna.MiRNAView;
+import lcsb.mapviewer.services.view.AnnotationView;
+import lcsb.mapviewer.services.view.AuthenticationToken;
+
+@Transactional(value = "txManager")
+public class MiRnaRestImpl {
+
+ Logger logger = Logger.getLogger(MiRnaRestImpl.class);
+
+ @Autowired
+ private IMiRNAService miRnaService;
+
+ @Autowired
+ private IModelService modelService;
+
+ @Autowired
+ private IUserService userService;
+
+ @Autowired
+ private ElementMatcher elementMatcher;
+
+ public List<Map<String, Object>> getMiRnasByQuery(String token, String projectId, String columns, String query) throws SecurityException, QueryException {
+ AuthenticationToken authenticationToken = userService.getToken(token);
+ Model model = modelService.getLastModelByProjectId(projectId, authenticationToken);
+ if (model == null) {
+ throw new QueryException("Project with given id doesn't exist");
+ }
+ Project project = model.getProject();
+ if (project.getDisease() == null) {
+ throw new QueryException("Project doesn't have disease associated to it");
+ }
+
+ Set<String> columnSet = createMiRnaColumnSet(columns);
+
+ List<Map<String, Object>> result = new ArrayList<>();
+
+ MiriamData organism = project.getOrganism();
+ if (organism == null) {
+ organism = TaxonomyBackend.HUMAN_TAXONOMY;
+ }
+ MiRNAView miRna = miRnaService.getByName(query, new DbSearchCriteria().model(model).organisms(organism).colorSet(0).disease(project.getDisease()));
+ if (miRna != null) {
+ List<Model> models = getModels(model);
+ result.add(prepareMiRna(miRna, columnSet, models));
+ }
+
+ return result;
+ }
+
+ private List<Model> getModels(Model model) {
+ List<Model> models = new ArrayList<>();
+ models.add(model);
+ models.addAll(model.getSubmodels());
+ return models;
+ }
+
+ /**
+ * @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;
+ }
+
+ /**
+ * @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;
+ }
+
+ private Map<String, Object> prepareMiRna(MiRNAView miRna, Set<String> columnsSet, List<Model> models) {
+ 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 = miRna.getUniqueId();
+ } else if (column.equals("name")) {
+ value = miRna.getName();
+ } else if (column.equals("targets")) {
+ value = prepareTargets(miRna.getTargetRows(), models);
+ } else {
+ value = "Unknown column";
+ }
+ result.put(string, value);
+ }
+ return result;
+ }
+
+ private List<Map<String, Object>> prepareTargets(Collection<TargetView> targets, List<Model> models) {
+ List<Map<String, Object>> result = new ArrayList<>();
+ for (TargetView target : targets) {
+ result.add(prepareTarget(target, models));
+ }
+ return result;
+ }
+
+ private Map<String, Object> prepareTarget(TargetView target, List<Model> models) {
+ Map<String, Object> result = new HashMap<>();
+ result.put("name", target.getName());
+ result.put("references", target.getReferences());
+ List<AnnotationView> participants = new ArrayList<>();
+ for (GeneRow row : target.getProteins()) {
+ participants.add(row.getAnnotation());
+ }
+ result.put("targetParticipants", participants);
+
+ List<Map<String, Object>> targetedObjects = new ArrayList<>();
+ for (Model model : models) {
+ for (AnnotatedObject object : model.getAnnotatedObjects()) {
+ if (elementMatcher.elementMatch(target, object)) {
+ Map<String, Object> elementMapping = new HashMap<>();
+
+ elementMapping.put("id", object.getId());
+ elementMapping.put("type", getType(object));
+ elementMapping.put("modelId", model.getId());
+ targetedObjects.add(elementMapping);
+ }
+ }
+ }
+
+ result.put("targetElements", targetedObjects);
+
+ return result;
+ }
+
+ private String getType(AnnotatedObject object) {
+ if (object instanceof Reaction) {
+ return ElementIdentifierType.REACTION.getJsName();
+ } else if (object instanceof Element) {
+ return ElementIdentifierType.ALIAS.getJsName();
+ } else {
+ throw new InvalidArgumentException("Unknown type of element " + object.getClass());
+ }
+ }
+
+ private Set<String> createMiRnaColumnSet(String columns) {
+ Set<String> columnsSet = new HashSet<>();
+ if (columns.equals("")) {
+ columnsSet.add("name");
+ columnsSet.add("id");
+ columnsSet.add("targets");
+ } else {
+ for (String str : columns.split(",")) {
+ columnsSet.add(str);
+ }
+ }
+ return columnsSet;
+ }
+
+ /**
+ * @return the miRnaService
+ * @see #miRnaService
+ */
+ public IMiRNAService getMiRnaService() {
+ return miRnaService;
+ }
+
+ /**
+ * @param miRnaService
+ * the miRnaService to set
+ * @see #miRnaService
+ */
+ public void setMiRnaService(IMiRNAService miRnaService) {
+ this.miRnaService = miRnaService;
+ }
+
+ public List<Map<String, Object>> getMiRnasByTarget(String token, String projectId, String targetType, String targetId, String columns)
+ throws SecurityException, QueryException {
+ AuthenticationToken authenticationToken = userService.getToken(token);
+ Model model = modelService.getLastModelByProjectId(projectId, authenticationToken);
+ if (model == null) {
+ throw new QueryException("Project with given id doesn't exist");
+ }
+ Project project = model.getProject();
+
+ if (project.getDisease() == null) {
+ throw new QueryException("Project doesn't have disease associated to it");
+ }
+
+ Integer dbId = Integer.valueOf(targetId);
+ List<Element> targets = new ArrayList<>();
+ if (targetType.equals(ElementIdentifierType.ALIAS.getJsName())) {
+ Element element = model.getElementByDbId(dbId);
+ for (Model m : model.getSubmodels()) {
+ if (element == null) {
+ element = m.getElementByDbId(dbId);
+ }
+ }
+ if (element == null) {
+ throw new QueryException("Invalid element identifier for given project");
+ }
+ targets.add(element);
+ } else {
+ throw new QueryException("Targeting for the type not implemented");
+ }
+ MiriamData organism = project.getOrganism();
+ if (organism == null) {
+ organism = TaxonomyBackend.HUMAN_TAXONOMY;
+ }
+
+ Set<String> columnSet = createMiRnaColumnSet(columns);
+
+ List<MiRNAView> miRnas = miRnaService.getForTargets(targets, new DbSearchCriteria().model(model).organisms(organism).disease(project.getDisease()));
+
+ List<Map<String, Object>> result = new ArrayList<>();
+
+ List<Model> models = getModels(model);
+
+ for (MiRNAView miRna : miRnas) {
+ result.add(prepareMiRna(miRna, columnSet, models));
+ }
+
+ return result;
+ }
+
+}
diff --git a/rest-api/src/main/resources/applicationContext-rest.xml b/rest-api/src/main/resources/applicationContext-rest.xml
index 935d23b1a9..d86f6e3c69 100644
--- a/rest-api/src/main/resources/applicationContext-rest.xml
+++ b/rest-api/src/main/resources/applicationContext-rest.xml
@@ -15,6 +15,7 @@
<bean id="ConfigurationRestImpl" class="lcsb.mapviewer.api.configuration.ConfigurationRestImpl"/>
<bean id="CommentRestImpl" class="lcsb.mapviewer.api.comment.CommentRestImpl"/>
<bean id="DrugRestImpl" class="lcsb.mapviewer.api.drug.DrugRestImpl"/>
+ <bean id="MiRnaRestImpl" class="lcsb.mapviewer.api.mirna.MiRnaRestImpl"/>
<bean id="OverlayRestImpl" class="lcsb.mapviewer.api.overlay.OverlayRestImpl"/>
<bean id="ProjectRestImpl" class="lcsb.mapviewer.api.project.ProjectRestImpl"/>
--
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