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Commit 93a12b0f authored by Piotr Gawron's avatar Piotr Gawron
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provide inof about modifier type

parent d81a0f64
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CHANGELOG
View file @ 93a12b0f
minerva (16.1.0~alpha.0) stable; urgency=medium
* Small improvement: API provides information about modifier type (#1085)
* Bug fix: api endpoints were exposed without 'api' prefix
* Bug fix: anonymous user could upload file using API
* Bug fix: when passing JSON in patch/post methods contentType was not
......
model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionNode.java
View file @ 93a12b0f
package lcsb.mapviewer.model.map.reaction;
import javax.persistence.*;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
import javax.persistence.ManyToOne;
import com.fasterxml.jackson.databind.annotation.JsonSerialize;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.modelutils.map.ElementUtils;
import lcsb.mapviewer.modelutils.serializer.model.map.reaction.ReactionNodeSerializer;
/**
* One of two known types of nodes in the {@link Reaction}. It defines input or
......@@ -22,6 +27,7 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
*/
@Entity
@DiscriminatorValue("GENERIC_REACTION_NODE")
@JsonSerialize(using = ReactionNodeSerializer.class)
public abstract class ReactionNode extends AbstractNode {
/**
......
model/src/main/java/lcsb/mapviewer/modelutils/serializer/model/map/reaction/ReactionNodeSerializer.java 0 → 100644
View file @ 93a12b0f
package lcsb.mapviewer.modelutils.serializer.model.map.reaction;
import java.io.IOException;
import com.fasterxml.jackson.core.JsonGenerator;
import com.fasterxml.jackson.databind.JsonSerializer;
import com.fasterxml.jackson.databind.SerializerProvider;
import lcsb.mapviewer.model.map.reaction.ReactionNode;
public class ReactionNodeSerializer extends JsonSerializer<ReactionNode> {
@Override
public void serialize(final ReactionNode node, final JsonGenerator gen,
final SerializerProvider serializers)
throws IOException {
gen.writeStartObject();
gen.writeNumberField("aliasId", node.getElement().getId());
gen.writeObjectField("stoichiometry", node.getStoichiometry());
gen.writeStringField("type", node.getClass().getSimpleName());
gen.writeEndObject();
}
}
\ No newline at end of file
rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsController.java
View file @ 93a12b0f
......@@ -36,7 +36,6 @@ import lcsb.mapviewer.model.map.reaction.NodeOperator;
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.reaction.ReactionNode;
import lcsb.mapviewer.modelutils.serializer.MathMLSerializer;
import lcsb.mapviewer.services.QueryException;
import lcsb.mapviewer.services.interfaces.IReactionService;
......@@ -113,27 +112,15 @@ public class ReactionsController extends BaseController {
value = pt.getPointOnLine(centerLine.getP1(), centerLine.getP2(), 0.5);
break;
case "products": {
List<Map<String, Object>> ids = new ArrayList<>();
for (Product product : reaction.getProducts()) {
ids.add(createReactionNode(product));
}
value = ids;
value = reaction.getProducts();
break;
}
case "reactants": {
List<Map<String, Object>> ids = new ArrayList<>();
for (Reactant reactant : reaction.getReactants()) {
ids.add(createReactionNode(reactant));
}
value = ids;
value = reaction.getReactants();
break;
}
case "modifiers": {
List<Map<String, Object>> ids = new ArrayList<>();
for (Modifier modifier : reaction.getModifiers()) {
ids.add(createReactionNode(modifier));
}
value = ids;
value = reaction.getModifiers();
break;
}
case "type":
......@@ -233,13 +220,6 @@ public class ReactionsController extends BaseController {
return result;
}
private Map<String, Object> createReactionNode(ReactionNode node) {
Map<String, Object> result = new TreeMap<>();
result.put("aliasId", node.getElement().getId());
result.put("stoichiometry", node.getStoichiometry());
return result;
}
private Map<String, Object> kineticsToMap(SbmlKinetics kinetics) {
if (kinetics == null) {
return null;
......
service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
View file @ 93a12b0f
......@@ -1382,4 +1382,9 @@ public class ProjectService implements IProjectService {
return new ArrayList<>();
}
}
@Override
public void add(Project project) {
projectDao.add(project);
}
}
service/src/main/java/lcsb/mapviewer/services/interfaces/IProjectService.java
View file @ 93a12b0f
......@@ -124,4 +124,6 @@ public interface IProjectService {
UploadedFileEntry getFileByProjectId(String projectId);
List<ProjectBackground> getBackgrounds(String projectId, boolean initializeLazy);
void add(Project project);
}
web/src/test/java/lcsb/mapviewer/web/ControllerIntegrationTest.java
View file @ 93a12b0f
......@@ -107,6 +107,7 @@ import lcsb.mapviewer.persist.dao.map.ModelDao;
import lcsb.mapviewer.persist.dao.user.ResetPasswordTokenDao;
import lcsb.mapviewer.persist.dao.user.UserDao;
import lcsb.mapviewer.services.interfaces.IDataOverlayService;
import lcsb.mapviewer.services.interfaces.IFileService;
import lcsb.mapviewer.services.interfaces.IProjectService;
import lcsb.mapviewer.services.interfaces.IUserService;
import lcsb.mapviewer.web.config.SpringWebConfig;
......@@ -161,6 +162,9 @@ abstract public class ControllerIntegrationTest {
@Autowired
private UploadedFileEntryDao fileDao;
@Autowired
private IFileService fileService;
@Autowired
private DataOverlayDao dataOverlayDao;
......@@ -444,7 +448,7 @@ abstract public class ControllerIntegrationTest {
background.setCreator(userService.getUserByLogin(BUILT_IN_TEST_ADMIN_LOGIN));
project.addProjectBackground(background);
projectDao.add(project);
projectService.add(project);
return project;
}
......@@ -516,7 +520,7 @@ abstract public class ControllerIntegrationTest {
file.setOriginalFileName("test_file");
file.setLength(content.length);
file.setOwner(user);
fileDao.add(file);
fileService.add(file);
return file;
}
......
web/src/test/java/lcsb/mapviewer/web/MapControllerIntegrationTest.java
View file @ 93a12b0f
......@@ -16,6 +16,8 @@ import static org.springframework.restdocs.request.RequestDocumentation.pathPara
import static org.springframework.restdocs.request.RequestDocumentation.requestParameters;
import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Map;
import java.util.function.Supplier;
......@@ -30,6 +32,8 @@ import org.junit.runner.RunWith;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.MediaType;
import org.springframework.mock.web.MockHttpSession;
import org.springframework.restdocs.payload.FieldDescriptor;
import org.springframework.restdocs.payload.JsonFieldType;
import org.springframework.restdocs.payload.ResponseFieldsSnippet;
import org.springframework.restdocs.request.PathParametersSnippet;
import org.springframework.restdocs.request.RequestParametersSnippet;
......@@ -229,62 +233,85 @@ public class MapControllerIntegrationTest extends ControllerIntegrationTest {
}
private ResponseFieldsSnippet listOfReactionResponseFields() {
return responseFields(
List<FieldDescriptor> fields = new ArrayList<>(Arrays.asList(
fieldWithPath("[].id")
.description("unique element identifier")
.type("number")
.type(JsonFieldType.NUMBER)
.optional(),
fieldWithPath("[].reactionId")
.description("reaction identifier taken from source file")
.type("string")
.type(JsonFieldType.STRING)
.optional(),
fieldWithPath("[].modelId")
.description("map identifier")
.type("number")
.type(JsonFieldType.NUMBER)
.optional(),
fieldWithPath("[].type")
.description("reaction type")
.type("string")
.type(JsonFieldType.STRING)
.optional(),
subsectionWithPath("[].centerPoint")
.description("center point")
.type("point")
.type(JsonFieldType.OBJECT)
.optional(),
subsectionWithPath("[].lines")
.description("list of lines used to draw reaction")
.type("array<line>")
.type(JsonFieldType.ARRAY)
.optional(),
fieldWithPath("[].hierarchyVisibilityLevel")
.description("at what zoom level this element becomes visible in hierarchical view")
.type("string")
.type(JsonFieldType.STRING)
.optional(),
subsectionWithPath("[].references")
.description("list of references")
.type("array<Reference>")
.type(JsonFieldType.ARRAY)
.optional(),
subsectionWithPath("[].modifiers")
fieldWithPath("[].modifiers")
.description("list of modifiers")
.type("array<object>")
.type(JsonFieldType.ARRAY)
.optional(),
subsectionWithPath("[].reactants")
fieldWithPath("[].reactants")
.description("list of reactants")
.type("array<object>")
.type(JsonFieldType.ARRAY)
.optional(),
subsectionWithPath("[].products")
fieldWithPath("[].products")
.description("list of products")
.type("array<object>")
.type(JsonFieldType.ARRAY)
.optional(),
fieldWithPath("[].notes")
.description("notes and description")
.type("string")
.type(JsonFieldType.STRING)
.optional(),
fieldWithPath("[].kineticLaw")
.description("SBML kinetics law")
.type("object")
.type(JsonFieldType.OBJECT)
.optional(),
subsectionWithPath("[].other")
.description("list of oher properties")
.type("object")
.type(JsonFieldType.OBJECT)
.optional()));
fields.addAll(reactionNodeFields("[].reactants[]"));
fields.addAll(reactionNodeFields("[].products[]"));
fields.addAll(reactionNodeFields("[].modifiers[]"));
return responseFields(fields);
}
private List<FieldDescriptor> reactionNodeFields(String prefix) {
if (!prefix.endsWith(".") && !prefix.isEmpty()) {
prefix = prefix + ".";
}
return Arrays.asList(
fieldWithPath(prefix + "aliasId")
.description("element identifier")
.type(JsonFieldType.NUMBER)
.optional(),
fieldWithPath(prefix + "type")
.description("type")
.type(JsonFieldType.STRING)
.optional(),
fieldWithPath(prefix + "stoichiometry")
.description("element stoichiometry")
.type(JsonFieldType.STRING)
.optional());
}
......
web/src/test/java/lcsb/mapviewer/web/ReactionControllerIntegrationTest.java
View file @ 93a12b0f
......@@ -6,10 +6,11 @@ import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.junit.*;
import org.junit.After;
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.mock.web.MockHttpSession;
import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
import org.springframework.test.web.servlet.RequestBuilder;
......@@ -36,10 +37,8 @@ public class ReactionControllerIntegrationTest extends ControllerIntegrationTest
@Before
public void setup() {
callInSeparateThreadNoReturn(() -> {
project = createProject(TEST_PROJECT);
anonymous = userService.getUserByLogin(Configuration.ANONYMOUS_LOGIN);
});
project = createProject(TEST_PROJECT);
anonymous = userService.getUserByLogin(Configuration.ANONYMOUS_LOGIN);
}
@After
......@@ -51,8 +50,7 @@ public class ReactionControllerIntegrationTest extends ControllerIntegrationTest
public void testGetAllReactions() throws Exception {
userService.grantUserPrivilege(anonymous, PrivilegeType.READ_PROJECT, project.getProjectId());
RequestBuilder request = get("/api/projects/" + TEST_PROJECT + "/models/*/bioEntities/reactions/")
.contentType(MediaType.APPLICATION_FORM_URLENCODED);
RequestBuilder request = get("/api/projects/{projectId}/models/*/bioEntities/reactions/", TEST_PROJECT);
String response = mockMvc.perform(request)
.andExpect(status().is2xxSuccessful())
......@@ -70,7 +68,6 @@ public class ReactionControllerIntegrationTest extends ControllerIntegrationTest
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
RequestBuilder request = get("/api/projects/*/models/*/bioEntities/reactions/")
.contentType(MediaType.APPLICATION_FORM_URLENCODED)
.session(session);
mockMvc.perform(request)
......
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