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API endpoint for connection testing (#158)
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* basic test endpoint

* tests for test
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@RadovanTomik
RadovanTomik authored Nov 14, 2022
1 parent 61edd20 commit 79a18ff
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77 changes: 49 additions & 28 deletions src/main/java/de/samply/bbmri/negotiator/rest/Directory.java
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Expand Up @@ -26,49 +26,47 @@

package de.samply.bbmri.negotiator.rest;

import java.net.URI;
import java.net.URISyntaxException;
import java.sql.SQLException;
import java.util.HashSet;
import java.util.List;
import java.util.UUID;

import javax.faces.context.ExternalContext;
import javax.faces.context.FacesContext;
import javax.servlet.http.HttpServletRequest;
import javax.ws.rs.*;
import javax.ws.rs.core.Context;
import javax.ws.rs.core.MediaType;
import javax.ws.rs.core.Response;

import de.samply.bbmri.negotiator.Config;
import de.samply.bbmri.negotiator.ConfigFactory;
import de.samply.bbmri.negotiator.NegotiatorConfig;
import de.samply.bbmri.negotiator.ServletUtil;
import de.samply.bbmri.negotiator.config.Negotiator;
import de.samply.bbmri.negotiator.db.util.DbUtil;
import de.samply.bbmri.negotiator.jooq.Tables;
import de.samply.bbmri.negotiator.jooq.tables.records.CollectionRecord;
import de.samply.bbmri.negotiator.jooq.tables.records.JsonQueryRecord;
import de.samply.bbmri.negotiator.jooq.tables.records.ListOfDirectoriesRecord;
import de.samply.bbmri.negotiator.jooq.tables.records.QueryRecord;
import de.samply.bbmri.negotiator.rest.dto.CreateQueryResultDTO;
import de.samply.bbmri.negotiator.rest.dto.QuerySearchDTO;
import de.samply.bbmri.negotiator.rest.dto.QuerySearchDTOHelper;
import de.samply.bbmri.negotiator.util.JsonCollectionUpdateHelper;
import eu.bbmri.eric.csit.service.negotiator.util.NToken;
import eu.bbmri.eric.csit.service.negotiator.lifecycle.CollectionLifeCycleStatus;
import eu.bbmri.eric.csit.service.negotiator.lifecycle.RequestLifeCycleStatus;
import eu.bbmri.eric.csit.service.negotiator.lifecycle.util.LifeCycleRequestStatusStatus;
import eu.bbmri.eric.csit.service.negotiator.lifecycle.util.LifeCycleRequestStatusType;
import eu.bbmri.eric.csit.service.negotiator.util.NToken;
import eu.bbmri.eric.csit.service.negotiator.util.QueryJsonStringManipulator;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.jetbrains.annotations.Nullable;
import org.json.simple.JSONArray;
import org.json.simple.JSONObject;
import org.json.simple.parser.JSONParser;
import de.samply.bbmri.negotiator.rest.dto.QuerySearchDTOHelper;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;

import de.samply.bbmri.negotiator.Config;
import de.samply.bbmri.negotiator.ConfigFactory;
import de.samply.bbmri.negotiator.NegotiatorConfig;
import de.samply.bbmri.negotiator.config.Negotiator;
import de.samply.bbmri.negotiator.db.util.DbUtil;
import de.samply.bbmri.negotiator.jooq.Tables;
import de.samply.bbmri.negotiator.jooq.tables.records.JsonQueryRecord;
import de.samply.bbmri.negotiator.jooq.tables.records.QueryRecord;
import de.samply.bbmri.negotiator.rest.dto.CreateQueryResultDTO;
import javax.faces.context.ExternalContext;
import javax.faces.context.FacesContext;
import javax.servlet.http.HttpServletRequest;
import javax.ws.rs.*;
import javax.ws.rs.core.Context;
import javax.ws.rs.core.MediaType;
import javax.ws.rs.core.Response;
import java.net.URI;
import java.net.URISyntaxException;
import java.sql.SQLException;
import java.util.HashSet;
import java.util.List;
import java.util.UUID;

/**
* REST endpoints for the directory
Expand Down Expand Up @@ -133,6 +131,29 @@ public Response createQuery(String queryString, @Context HttpServletRequest requ
throw new ServerErrorException(Response.Status.INTERNAL_SERVER_ERROR);
}
}
@OPTIONS
@Path("/test")
@Consumes(MediaType.APPLICATION_JSON)
public Response testConnectionOptions(String jsonString, @Context HttpServletRequest request) {
return Response
.status(200)
.header("Access-Control-Allow-Origin", "*")
.header("Access-Control-Allow-Headers", "origin, content-type, accept, authorization")
.header("Access-Control-Allow-Credentials", "true")
.header("Access-Control-Allow-Methods", "GET, POST, PUT, DELETE, OPTIONS, HEAD")
.build();
}
@POST
@Path("/test")
@Consumes(MediaType.APPLICATION_JSON)
public Response testConnection(String jsonString, @Context HttpServletRequest request){
String apiCallId = UUID.randomUUID().toString();
logger.info(apiCallId + " API call via create_query API.");
checkAuthentication(request);
return Response
.status(200)
.build();
}

private void checkAuthentication(HttpServletRequest request) throws ForbiddenException {
Negotiator negotiator = getNegotiatorConfig();
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13 changes: 12 additions & 1 deletion src/test/java/de/samply/bbmri/negotiator/rest/DirectoryAPITest.java
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Expand Up @@ -90,9 +90,20 @@ void testCreateQuery_withToken() throws SQLException {

assertEquals(202, response.getStatus());
}
@Test
void testConnection() {
Mockito.when(negotiatorConfig.getMolgenisUsername()).thenReturn("username");
Mockito.when(negotiatorConfig.getMolgenisPassword()).thenReturn("password");
Mockito.when(request.getHeader("Authorization")).thenReturn("Basic dXNlcm5hbWU6cGFzc3dvcmQ=");
Directory directorySpy = Mockito.spy(directory);
Mockito.doReturn(negotiatorConfig).when(directorySpy).getNegotiatorConfig();
Response response = directorySpy.testConnection("msg : idk", request);
assertEquals(200, response.getStatus());
}


private String finderJson = "{\n \"query_start_timestamp\":\"2021-08-10T08:04:51.019\",\n \"access_duration\":{\n \"end_date\":\"\",\n \"start_date\":\"\"\n },\n \"query_id\":\"RQ-37d68fc0-4d67-480a-9419-2580335cabc7\",\n \"user_email\":\"anni.ahonen-bishopp@bcplatforms.com\",\n \"user_id\":\"115715892511411738289\",\n \"description\":\"my description of the cohort\",\n \"cohort\":{\n \"result\":{\n \"counts\":[\n {\n \"rquest_id\":\"RQ-CC-e7c7d4d0-2a81-4833-b5b4-ac2a0c1a3e6f\",\n \"count\":\"1030\"\n }\n ]\n },\n \"input\":{\n \"collections\":[\n {\n \"rquest_id\":\"RQ-CC-e7c7d4d0-2a81-4833-b5b4-ac2a0c1a3e6f\",\n \"external_id\":\"Graz\"\n }\n ],\n \"cohorts\":[\n {\n \"name\":\"cases\",\n \"groups\":[\n {\n \"rules\":[\n {\n \"type\":\"ALT\",\n \"varname\":\"SAMPLES\",\n \"value\":\"1\"\n }\n ],\n \"rules_oper\":\"AND\"\n }\n ],\n \"groups_oper\":\"OR\"\n }\n ],\n \"time_window\":\"2018-01-01|\"\n },\n \"application\":\"bcrquest_server\",\n \"searched_codes\":{\n \n },\n \"query_url\":\"https://rquest-dev2.bcplatforms.cloud/bcrquest/#!search-results/RQ-37d68fc0-4d67-480a-9419-2580335cabc7\"\n },\n \"request_id\":\"How many subjects with samples\",\n \"items\":[\n \n ]\n}";
private String queryJsonNoNToken = "{\n \"collections\":[\n {\n \"biobankId\":\"bbmri-eric:ID:UK_GBR-1-19\",\n \"collectionId\":\"bbmri-eric:ID:UK_GBR-1-19:collection:542\"\n }\n ],\n \"humanReadable\":\"test\",\n \"URL\":\"http://d1.ref.development.bibbox.org\"\n}";
private String queryJsonNToken = "{\n \"nToken\":\"79ad527ff0bb448783461fd35b9c21d5__search__1ec374ef3a16475aa479a2c61d11fa48\", \"collections\":[\n {\n \"biobankId\":\"bbmri-eric:ID:UK_GBR-1-19\",\n \"collectionId\":\"bbmri-eric:ID:UK_GBR-1-19:collection:542\"\n }\n ],\n \"humanReadable\":\"test\",\n \"URL\":\"http://d1.ref.development.bibbox.org\"\n}";
private String recordJsonWithMultipleQueries = "{\"searchQueries\":[{\"humanReadable\":\"test\", \"URL\":\"http://d1.ref.development.bibbox.org\", \"token\":\"1ec374ef3a16475aa479a2c61d11fa48\", \"collections\":[ {\"biobankId\":\"bbmri-eric:ID:UK_GBR-1-19\",\"collectionId\":\"bbmri-eric:ID:UK_GBR-1-19:collection:542\"}]}, {\"humanReadable\":\"test2\", \"URL\":\"http://d1.ref.development.bibbox.org\", \"token\":\"2ec374ef3a16475aa479a2c61d11fa48\", \"collections\":[ {\"biobankId\":\"bbmri-eric:ID:UK_GBR-1-20\",\"collectionId\":\"bbmri-eric:ID:UK_GBR-1-20:collection:543\"}]} ]}";
}
}

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