From 76e497fd5404d86d61864f826571f392d96c4431 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Thu, 8 Feb 2018 12:59:00 +0100
Subject: [PATCH] rest API for units
---
.../map/kinetics/SbmlUnitTypeFactor.java | 4 +
.../models/units/UnitsController.java | 45 +++++++++++
.../projects/models/units/UnitsRestImpl.java | 75 +++++++++++++++++++
.../resources/applicationContext-rest.xml | 1 +
4 files changed, 125 insertions(+)
create mode 100644 rest-api/src/main/java/lcsb/mapviewer/api/projects/models/units/UnitsController.java
create mode 100644 rest-api/src/main/java/lcsb/mapviewer/api/projects/models/units/UnitsRestImpl.java
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactor.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactor.java
index b718204ce9..f1d6f1975b 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactor.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactor.java
@@ -124,4 +124,8 @@ public class SbmlUnitTypeFactor implements Serializable {
return new SbmlUnitTypeFactor(this);
}
+ public int getId() {
+ return id;
+ }
+
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/units/UnitsController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/units/UnitsController.java
new file mode 100644
index 0000000000..c55f3b092c
--- /dev/null
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/units/UnitsController.java
@@ -0,0 +1,45 @@
+package lcsb.mapviewer.api.projects.models.units;
+
+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.CookieValue;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RestController;
+
+import lcsb.mapviewer.api.BaseController;
+import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.services.SecurityException;
+
+@RestController
+public class UnitsController extends BaseController {
+ @Autowired
+ private UnitsRestImpl unitController;
+
+ @RequestMapping(value = "/projects/{projectId}/models/{modelId}/units/{unitId}", method = {
+ RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> getUnit(//
+ @PathVariable(value = "projectId") String projectId, //
+ @PathVariable(value = "modelId") String modelId, //
+ @PathVariable(value = "unitId") String unitId, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws QueryException, SecurityException {
+ return unitController.getUnit(projectId, modelId, token, unitId);
+ }
+
+ @RequestMapping(value = "/projects/{projectId}/models/{modelId}/units/", method = {
+ RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getUnits(//
+ @PathVariable(value = "projectId") String projectId, //
+ @PathVariable(value = "modelId") String modelId, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws QueryException, SecurityException {
+ return unitController.getUnits(projectId, modelId, token);
+ }
+
+}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/units/UnitsRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/units/UnitsRestImpl.java
new file mode 100644
index 0000000000..887b551fbe
--- /dev/null
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/units/UnitsRestImpl.java
@@ -0,0 +1,75 @@
+package lcsb.mapviewer.api.projects.models.units;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+import org.springframework.transaction.annotation.Transactional;
+
+import lcsb.mapviewer.api.BaseRestImpl;
+import lcsb.mapviewer.api.ObjectNotFoundException;
+import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnitTypeFactor;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.services.SecurityException;
+
+@Transactional(value = "txManager")
+public class UnitsRestImpl extends BaseRestImpl {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(UnitsRestImpl.class);
+
+ public Map<String, Object> getUnit(String projectId, String modelId, String token, String unitId)
+ throws SecurityException, QueryException {
+ List<Model> models = getModels(projectId, modelId, token);
+ int id = Integer.valueOf(unitId);
+ for (Model model : models) {
+ for (SbmlUnit unit : model.getUnits()) {
+ if (unit.getId() == id) {
+ return unitToMap(unit);
+ }
+ }
+ }
+ throw new ObjectNotFoundException("Unit with given id doesn't exist");
+ }
+
+ private Map<String, Object> unitToMap(SbmlUnit unit) {
+ Map<String, Object> result = new HashMap<>();
+ result.put("id", unit.getId());
+ result.put("unitId", unit.getUnitId());
+ result.put("name", unit.getName());
+ List<Map<String, Object>> factors = new ArrayList<>();
+ for (SbmlUnitTypeFactor factor : unit.getUnitTypeFactors()) {
+ factors.add(factorToMap(factor));
+ }
+ result.put("unitTypeFactors", factors);
+ return result;
+ }
+
+ private Map<String, Object> factorToMap(SbmlUnitTypeFactor factor) {
+ Map<String, Object> result = new HashMap<>();
+ result.put("id", factor.getId());
+ result.put("exponent", factor.getExponent());
+ result.put("multiplier", factor.getMultiplier());
+ result.put("scale", factor.getScale());
+ result.put("unitType", factor.getUnitType());
+ return result;
+ }
+
+ public List<Map<String, Object>> getUnits(String projectId, String modelId, String token) throws SecurityException {
+ List<Map<String, Object>> result = new ArrayList<>();
+ List<Model> models = getModels(projectId, modelId, token);
+ for (Model model : models) {
+ for (SbmlUnit unit : model.getUnits()) {
+ result.add(unitToMap(unit));
+ }
+ }
+ return result;
+ }
+}
diff --git a/rest-api/src/main/resources/applicationContext-rest.xml b/rest-api/src/main/resources/applicationContext-rest.xml
index 8393530a34..fac20694fa 100644
--- a/rest-api/src/main/resources/applicationContext-rest.xml
+++ b/rest-api/src/main/resources/applicationContext-rest.xml
@@ -23,6 +23,7 @@
<bean id="ElementsRestImpl" class="lcsb.mapviewer.api.projects.models.bioEntities.elements.ElementsRestImpl"/>
<bean id="FunctionsRestImpl" class="lcsb.mapviewer.api.projects.models.functions.FunctionsRestImpl"/>
<bean id="ParametersRestImpl" class="lcsb.mapviewer.api.projects.models.parameters.ParametersRestImpl"/>
+ <bean id="UnitsRestImpl" class="lcsb.mapviewer.api.projects.models.units.UnitsRestImpl"/>
<bean id="DrugRestImpl" class="lcsb.mapviewer.api.projects.drugs.DrugRestImpl"/>
<bean id="MiRnaRestImpl" class="lcsb.mapviewer.api.projects.mirnas.MiRnaRestImpl"/>
<bean id="OverlayRestImpl" class="lcsb.mapviewer.api.projects.overlays.OverlayRestImpl"/>
--
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