documentation for drug API calls

web/src/main/asciidoc/projects/project_drugs.adoc

+= Rest API Documentation - Project drugs
+Piotr Gawron
+v{project-version} {build-time}
+:toc: left
+:sectnums:
+
+== Get drug
+Returns drugs data with project related connections.
+
+=== CURL sample
+include::{snippets}/projects/project_drugs/search_by_query/curl-request.adoc[]
+
+=== Path Parameters
+include::{snippets}/projects/project_drugs/search_by_query/path-parameters.adoc[]
+
+=== Response Fields
+include::{snippets}/projects/project_drugs/search_by_query/response-fields.adoc[]
+
+=== Sample Response
+include::{snippets}/projects/project_drugs/search_by_query/response-body.adoc[]
+
+
+== Get suggested drug queries
+Get list of suggested drug queries in the context of the project.
+
+=== CURL sample
+include::{snippets}/projects/project_drugs/suggested_query_list/curl-request.adoc[]
+
+=== Path Parameters
+include::{snippets}/projects/project_drugs/suggested_query_list/path-parameters.adoc[]
+
+=== Response Fields
+include::{snippets}/projects/project_drugs/suggested_query_list/response-fields.adoc[]
+
+=== Sample Response
+include::{snippets}/projects/project_drugs/suggested_query_list/response-body.adoc[]
+

web/src/test/java/lcsb/mapviewer/web/ChemicalControllerIntegrationTest.java

@@ -5,11 +5,8 @@ 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.parameterWithName;
-import static org.springframework.restdocs.request.RequestDocumentation.requestParameters;
 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;
@@ -18,7 +15,6 @@ 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;
@@ -27,7 +23,6 @@ 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;
@@ -45,9 +40,6 @@ public class ChemicalControllerIntegrationTest extends ControllerIntegrationTest
   @SuppressWarnings("unused")
   private Logger logger = LogManager.getLogger();
 
-  @Autowired
-  private ChemicalRestImpl chemicalRestImpl;
-
   @Autowired
   private IProjectService projectService;
 
@@ -102,20 +94,6 @@ public class ChemicalControllerIntegrationTest extends ControllerIntegrationTest
 
   }
 
-  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")

web/src/test/java/lcsb/mapviewer/web/ControllerIntegrationTest.java

 package lcsb.mapviewer.web;
 
 import static org.springframework.restdocs.mockmvc.MockMvcRestDocumentation.documentationConfiguration;
-import static org.springframework.restdocs.request.RequestDocumentation.parameterWithName;
-import static org.springframework.restdocs.request.RequestDocumentation.pathParameters;
+import static org.springframework.restdocs.request.RequestDocumentation.*;
 import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.post;
 import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
 
@@ -19,6 +18,7 @@ import javax.annotation.PostConstruct;
 import javax.annotation.PreDestroy;
 import javax.servlet.Filter;
 
+import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.apache.logging.log4j.core.LogEvent;
@@ -28,6 +28,7 @@ import org.springframework.mock.web.MockHttpSession;
 import org.springframework.restdocs.JUnitRestDocumentation;
 import org.springframework.restdocs.operation.preprocess.Preprocessors;
 import org.springframework.restdocs.request.PathParametersSnippet;
+import org.springframework.restdocs.request.RequestParametersSnippet;
 import org.springframework.security.crypto.password.PasswordEncoder;
 import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.web.WebAppConfiguration;
@@ -36,6 +37,7 @@ import org.springframework.test.web.servlet.RequestBuilder;
 import org.springframework.test.web.servlet.setup.MockMvcBuilders;
 import org.springframework.web.context.WebApplicationContext;
 
+import lcsb.mapviewer.api.projects.chemicals.ChemicalRestImpl;
 import lcsb.mapviewer.common.MinervaLoggerAppender;
 import lcsb.mapviewer.common.UnitTestFailedWatcher;
 import lcsb.mapviewer.model.*;
@@ -113,6 +115,10 @@ abstract public class ControllerIntegrationTest {
   private String dapiLogin;
   private String dapiPassword;
 
+
+  @Autowired
+  private ChemicalRestImpl chemicalRestImpl;
+
   @PostConstruct
   public void construct() {
     mockMvc = MockMvcBuilders.webAppContextSetup(context)
@@ -532,4 +538,19 @@ abstract public class ControllerIntegrationTest {
     return getProjectPathParameters().and(parameterWithName("mapId").description("map identifier"));
   }
 
+  protected 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());
+  }
+
+
 }

web/src/test/java/lcsb/mapviewer/web/DrugControllerIntegrationTest.java

 package lcsb.mapviewer.web;
 
-import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get;
+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.test.web.servlet.result.MockMvcResultMatchers.status;
 
 import org.apache.logging.log4j.LogManager;
@@ -8,8 +10,8 @@ import org.apache.logging.log4j.Logger;
 import org.junit.Before;
 import org.junit.Test;
 import org.junit.runner.RunWith;
-import org.springframework.http.MediaType;
 import org.springframework.mock.web.MockHttpSession;
+import org.springframework.restdocs.payload.ResponseFieldsSnippet;
 import org.springframework.test.annotation.Rollback;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 import org.springframework.test.web.servlet.RequestBuilder;
@@ -20,21 +22,28 @@ import org.springframework.transaction.annotation.Transactional;
 @Rollback
 public class DrugControllerIntegrationTest extends ControllerIntegrationTest {
 
+  private static String TEST_PROJECT = "TEST_PROJECT";
+
   Logger logger = LogManager.getLogger();
 
   @Before
   public void setup() {
+    createProject(TEST_PROJECT);
   }
 
   @Test
   public void testSearchDrugsInProjectUrl() throws Exception {
     MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
 
-    RequestBuilder request = get("/projects/" + BUILT_IN_PROJECT + "/drugs:search")
+    RequestBuilder request = get("/projects/{projectId}/drugs:search?query=aspirin", TEST_PROJECT)
         .session(session);
 
     mockMvc.perform(request)
-        .andExpect(status().is2xxSuccessful());
+        .andExpect(status().is2xxSuccessful())
+        .andDo(document("projects/project_drugs/search_by_query",
+            getProjectPathParameters(),
+            getChemicalFilter(),
+            listOfDrugFields()));
   }
 
   @Test
@@ -63,10 +72,16 @@ public class DrugControllerIntegrationTest extends ControllerIntegrationTest {
   public void testGetSuggestedList() throws Exception {
     MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
 
-    RequestBuilder request = get("/projects/" + BUILT_IN_PROJECT + "/drugs/suggestedQueryList")
+    RequestBuilder request = get("/projects/{projectId}/drugs/suggestedQueryList", TEST_PROJECT)
         .session(session);
 
     mockMvc.perform(request)
+        .andDo(document("projects/project_drugs/suggested_query_list",
+            getProjectPathParameters(),
+            responseFields(
+                fieldWithPath("[]")
+                    .description("list of suggested drug queries")
+                    .type("Array<String>"))))
         .andExpect(status().is2xxSuccessful());
   }
 
@@ -81,4 +96,44 @@ public class DrugControllerIntegrationTest extends ControllerIntegrationTest {
         .andExpect(status().isNotFound());
   }
 
+  private ResponseFieldsSnippet listOfDrugFields() {
+    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>"),
+        fieldWithPath("[].brandNames")
+            .description("list of brand names")
+            .type("Array<String>"),
+        fieldWithPath("[].bloodBrainBarrier")
+            .description("does drug cross blood brain barrier")
+            .type("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>"));
+  }
+
 }