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Commit 307a98eb authored by Piotr Gawron's avatar Piotr Gawron
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documentation for get chemicals API calls

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rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImpl.java
View file @ 307a98eb
......@@ -140,14 +140,7 @@ public class ChemicalRestImpl extends BaseRestImpl {
protected Set<String> createChemicalColumnSet(String columns) {
Set<String> columnsSet = new LinkedHashSet<>();
if (columns.equals("")) {
columnsSet.add("name");
columnsSet.add("references");
columnsSet.add("description");
columnsSet.add("synonyms");
columnsSet.add("id");
columnsSet.add("directEvidenceReferences");
columnsSet.add("directEvidence");
columnsSet.add("targets");
columnsSet.addAll(getAvailableChemicalColumns());
} else {
columnsSet.addAll(Arrays.asList(columns.split(",")));
}
......@@ -210,4 +203,17 @@ public class ChemicalRestImpl extends BaseRestImpl {
}
return chemicalParser.getSuggestedQueryList(project, project.getDisease());
}
public List<String> getAvailableChemicalColumns() {
List<String> result = new ArrayList<>();
result.add("name");
result.add("references");
result.add("description");
result.add("synonyms");
result.add("id");
result.add("directEvidenceReferences");
result.add("directEvidence");
result.add("targets");
return result;
}
}
web/src/main/asciidoc/projects/project_chemicals.adoc 0 → 100644
View file @ 307a98eb
= Rest API Documentation - Project chemicals
Piotr Gawron
v{project-version} {build-time}
:toc: left
:sectnums:
== Get chemical
Returns chemicals data with project related connections.
=== CURL sample
include::{snippets}/projects/project_chemicals/search_by_query/curl-request.adoc[]
=== Path Parameters
include::{snippets}/projects/project_chemicals/search_by_query/path-parameters.adoc[]
=== Response Fields
include::{snippets}/projects/project_chemicals/search_by_query/response-fields.adoc[]
=== Sample Response
include::{snippets}/projects/project_chemicals/search_by_query/response-body.adoc[]
== Get suggested chemical queries
Get list of suggested chemical queries in the context of the project.
=== CURL sample
include::{snippets}/projects/project_chemicals/suggested_query_list/curl-request.adoc[]
=== Path Parameters
include::{snippets}/projects/project_chemicals/suggested_query_list/path-parameters.adoc[]
=== Response Fields
include::{snippets}/projects/project_chemicals/suggested_query_list/response-fields.adoc[]
=== Sample Response
include::{snippets}/projects/project_chemicals/suggested_query_list/response-body.adoc[]
web/src/test/java/lcsb/mapviewer/web/ChemicalControllerIntegrationTest.java
View file @ 307a98eb
package lcsb.mapviewer.web;
import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get;
import static org.junit.Assert.assertTrue;
import static org.junit.Assume.assumeTrue;
import static org.springframework.restdocs.mockmvc.MockMvcRestDocumentation.document;
import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.get;
import static org.springframework.restdocs.payload.PayloadDocumentation.*;
import static org.springframework.restdocs.request.RequestDocumentation.*;
import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.junit.Before;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.mock.web.MockHttpSession;
import org.springframework.restdocs.payload.ResponseFieldsSnippet;
import org.springframework.restdocs.request.RequestParametersSnippet;
import org.springframework.test.annotation.Rollback;
import org.springframework.test.context.ActiveProfiles;
import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
import org.springframework.test.web.servlet.RequestBuilder;
import org.springframework.transaction.annotation.Transactional;
import com.google.gson.JsonParser;
import lcsb.mapviewer.api.projects.chemicals.ChemicalRestImpl;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.services.interfaces.IProjectService;
@RunWith(SpringJUnit4ClassRunner.class)
@Transactional
@Rollback
@ActiveProfiles("ctdTestProfile")
public class ChemicalControllerIntegrationTest extends ControllerIntegrationTest {
Logger logger = LogManager.getLogger();
private static String TEST_PROJECT = "TEST_PROJECT";
private static String TEST_PROJECT2 = "TEST_PROJECT2";
@SuppressWarnings("unused")
private Logger logger = LogManager.getLogger();
@Autowired
private ChemicalRestImpl chemicalRestImpl;
@Autowired
private IProjectService projectService;
@Before
public void setup() {
assumeTrue("DAPI credentials are not provided", isDapiConfigurationAvailable());
createProject(TEST_PROJECT);
}
@Test
public void testSearchChemicalsInProjectUrl() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
RequestBuilder request = get("/projects/{projectId}/chemicals:search", BUILT_IN_PROJECT)
RequestBuilder request = get("/projects/{projectId}/chemicals:search?query=stilbene oxide", TEST_PROJECT)
.session(session);
mockMvc.perform(request)
.andDo(document("projects/project_chemicals/search_by_query",
pathParameters(parameterWithName("projectId").description("project identifier")),
getChemicalFilter(),
listOfChemicalsFields()))
.andExpect(status().is2xxSuccessful());
}
@Test
public void testGetSuggestedList() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
MiriamData bloodLossDisease = new MiriamData(MiriamType.MESH_2012, "D016063");
Project project = createEmptyProject(TEST_PROJECT2);
project.setDisease(bloodLossDisease);
projectService.updateProject(project);
RequestBuilder request = get("/projects/{projectId}/chemicals/suggestedQueryList", TEST_PROJECT2)
.session(session);
String content = mockMvc.perform(request)
.andDo(document("projects/project_chemicals/suggested_query_list",
pathParameters(parameterWithName("projectId").description("project identifier")),
responseFields(
fieldWithPath("[]")
.description("list of suggested chemical queries")
.type("Array<String>"))))
.andExpect(status().is2xxSuccessful())
.andReturn().getResponse().getContentAsString();
int elements = new JsonParser()
.parse(content)
.getAsJsonArray().size();
assertTrue(elements > 0);
}
private RequestParametersSnippet getChemicalFilter() {
return requestParameters(
parameterWithName("columns")
.description("set of columns (all by default). Available options: "
+ StringUtils.join(chemicalRestImpl.getAvailableChemicalColumns(), ", "))
.optional(),
parameterWithName("query")
.description("name of chemical that we are searching for")
.optional(),
parameterWithName("target")
.description("target element that we are searching for in format TYPE:ID")
.optional());
}
private ResponseFieldsSnippet listOfChemicalsFields() {
return responseFields(
subsectionWithPath("[].id")
.description("identifier of the chemical")
.type("Object"),
fieldWithPath("[].name")
.description("name")
.type("string"),
fieldWithPath("[].description")
.description("description")
.type("string"),
fieldWithPath("[].synonyms")
.description("list of synonyms")
.type("Array<String>"),
subsectionWithPath("[].references")
.description("list of references")
.type("Array<Reference>"),
fieldWithPath("[].targets")
.description("list of targets")
.type("Array<Target>"),
fieldWithPath("[].targets[].name")
.description("target name")
.type("string"),
subsectionWithPath("[].targets[].references")
.description("list of target references")
.type("Array<Reference>"),
subsectionWithPath("[].targets[].targetElements")
.description("list of elements on the map associated with this target")
.type("Array<Object>"),
subsectionWithPath("[].targets[].targetParticipants")
.description("list of identifiers associated with this target")
.type("Array<Object>"),
fieldWithPath("[].directEvidence")
.description("direct evidence")
.type("string"),
subsectionWithPath("[].directEvidenceReferences")
.description("list of references")
.type("Array<Reference>"));
}
@Test
public void testSearchChemicalsInAsteriskProjectId() throws Exception {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
......
web/src/test/java/lcsb/mapviewer/web/ControllerIntegrationTest.java
View file @ 307a98eb
......@@ -45,8 +45,7 @@ import lcsb.mapviewer.model.map.layout.Layout;
import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.reaction.*;
import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.*;
import lcsb.mapviewer.model.security.PrivilegeType;
import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.persist.DbUtils;
......@@ -107,6 +106,9 @@ abstract public class ControllerIntegrationTest {
private ExecutorService executorService;
private String dapiLogin;
private String dapiPassword;
@PostConstruct
public void construct() {
mockMvc = MockMvcBuilders.webAppContextSetup(context)
......@@ -156,6 +158,13 @@ abstract public class ControllerIntegrationTest {
public final void _setUp() throws Exception {
MinervaLoggerAppender.unregisterLogEventStorage(appender);
appender = MinervaLoggerAppender.createAppender();
dapiLogin = System.getenv("DAPI_TEST_LOGIN");
dapiPassword = System.getenv("DAPI_TEST_PASSWORD");
}
protected boolean isDapiConfigurationAvailable() {
return dapiLogin != null && dapiPassword != null;
}
@After
......@@ -264,6 +273,7 @@ abstract public class ControllerIntegrationTest {
reaction.addMiriamData(new MiriamData(MiriamType.PUBMED, "28725475"));
map.addReaction(reaction);
Element element = new GenericProtein("p1");
element.setName("GSTA4");
element.setWidth(100.0);
element.setHeight(20.0);
element.setX(10);
......@@ -271,11 +281,20 @@ abstract public class ControllerIntegrationTest {
element.setZ(2);
map.addElement(element);
Reactant reactant = new Reactant(element);
Element element2 = new SimpleMolecule("s2");
element2.setName("water");
element2.setWidth(100.0);
element2.setHeight(20.0);
element2.setX(10);
element2.setX(20);
element2.setZ(2);
map.addElement(element2);
Reactant reactant = new Reactant(element2);
reactant.setLine(new PolylineData(new Point2D.Double(10, 0), new Point2D.Double(0, 0)));
reaction.addReactant(reactant);
Product product = new Product(element);
Product product = new Product(element2);
product.setLine(new PolylineData(new Point2D.Double(10, 0), new Point2D.Double(20, 0)));
reaction.addProduct(product);
......@@ -284,6 +303,37 @@ abstract public class ControllerIntegrationTest {
return project;
}
protected Project createEmptyProject(String projectId) {
Project project = new Project(projectId);
project.setOwner(userService.getUserByLogin(BUILT_IN_TEST_ADMIN_LOGIN));
project.setDirectory("289b78b436176091ad900020c933c544");
project.setName("Test Disease");
try {
project.setInputData(createFile(Files.readAllBytes(Paths.get("./src/test/resources/generic.xml")),
userService.getUserByLogin(BUILT_IN_TEST_ADMIN_LOGIN)));
} catch (IOException e) {
e.printStackTrace();
}
ModelData map = new ModelData();
map.setName("map_name");
map.setTileSize(256);
map.setWidth(100);
map.setHeight(100);
Element element = new GenericProtein("p1");
element.setName("PTI");
element.setWidth(100.0);
element.setHeight(20.0);
element.setX(10);
element.setX(20);
element.setZ(2);
map.addElement(element);
project.addModel(map);
projectDao.add(project);
return project;
}
protected UploadedFileEntry createFile(String content, User user) {
return createFile(content.getBytes(), user);
}
......
web/src/test/java/lcsb/mapviewer/web/CtdDapiConfiguration.java 0 → 100644
View file @ 307a98eb
package lcsb.mapviewer.web;
import org.mockito.Mockito;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.*;
import lcsb.mapviewer.annotation.services.dapi.*;
@Profile("ctdTestProfile")
@Configuration
public class CtdDapiConfiguration {
@Autowired
private DapiConnector dapiConnector;
private String dapiLogin;
private String dapiPassword;
public CtdDapiConfiguration() {
dapiLogin = System.getenv("DAPI_TEST_LOGIN");
dapiPassword = System.getenv("DAPI_TEST_PASSWORD");
}
@Bean
@Primary
public DapiConnector dapiConnector() throws DapiConnectionException {
DapiConnectorImpl mock = (DapiConnectorImpl) Mockito.spy(dapiConnector);
Mockito.doReturn(true).when(mock).isValidConnection();
Mockito.doReturn(dapiLogin).when(mock).getDapiLogin();
Mockito.doReturn(dapiPassword).when(mock).getDapiPassword();
return mock;
}
}
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