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Commit c70f20cb authored by Manuel Spuhler's avatar Manuel Spuhler
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Workflow gateway methods

parent 5281c187
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docker/config/application.tmpl
+ 4
− 1
View file @ c70f20cb
......@@ -89,4 +89,7 @@ endpoints:
services:
exareme:
miningExaremeUrl: {{ default .Env.EXAREME_URL "http://localhost:9090" }}/mining/query
algorithmsUrl: {{ default .Env.EXAREME_URL "http://localhost:9090" }}/mining/algorithms.json
\ No newline at end of file
algorithmsUrl: {{ default .Env.EXAREME_URL "http://localhost:9090" }}/mining/algorithms.json
workflows:
workflowUrl: {{ default .Env.WORKFLOW_URL "http://localhost:9090" }}
workflowAuthorization: {{ default .Env.WORKFLOW_AUTHORIZATION "-" }}
\ No newline at end of file
src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
+ 123
− 66
View file @ c70f20cb
......@@ -2,6 +2,7 @@ package eu.hbp.mip.controllers;
import akka.dispatch.OnSuccess;
import ch.chuv.lren.mip.portal.WokenConversions;
import com.google.gson.*;
import com.google.common.collect.Lists;
import com.google.gson.Gson;
import com.google.gson.GsonBuilder;
......@@ -46,6 +47,12 @@ public class ExperimentApi extends WokenClientController {
@Value("#{'${services.exareme.miningExaremeUrl:http://localhost:9090/mining/query}'}")
public String miningExaremeQueryUrl;
@Value("#{'${services.workflows.workflowUrl}'}")
private String workflowUrl;
@Value("#{'${services.workflows.workflowAuthorization}'}")
private String workflowAuthorization;
@Autowired
private UserInfo userInfo;
......@@ -75,7 +82,34 @@ public class ExperimentApi extends WokenClientController {
String algoCode = expQuery.getAlgorithms().get(0).getCode();
List<AlgorithmParam> params = expQuery.getAlgorithms().get(0).getParameters();
sendExaremeExperiment(experiment, algoCode, params);
new Thread(() -> {
List<HashMap<String, String>> queryList = new ArrayList<HashMap<String, String>>();
if (params != null) {
for (AlgorithmParam p : params) {
queryList.add(makeObject(p.getName(), p.getValue()));
}
}
String query = gson.toJson(queryList);
String url = miningExaremeQueryUrl + "/" + algoCode;
// Results are stored in the experiment object
try {
StringBuilder results = new StringBuilder();
int code = HTTPUtil.sendPost(url, query, results);
experiment.setResult("[" + results.toString() + "]");
experiment.setHasError(code >= 400);
experiment.setHasServerError(code >= 500);
} catch (IOException e) {
LOGGER.trace("Invalid UUID", e);
LOGGER.warn("Exareme experiment failed to run properly !");
experiment.setHasError(true);
experiment.setHasServerError(true);
experiment.setResult(e.getMessage());
}
finishExperiment(experiment);
}).start();
return new ResponseEntity<>(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
}
......@@ -89,7 +123,37 @@ public class ExperimentApi extends WokenClientController {
String algoCode = expQuery.getAlgorithms().get(0).getCode();
List<AlgorithmParam> params = expQuery.getAlgorithms().get(0).getParameters();
sendWorkflow(experiment, algoCode, params);
new Thread(() -> {
HashMap<String, String> queryMap = new HashMap<String, String>();
if (params != null) {
for (AlgorithmParam p : params) {
queryMap.put(p.getName(), p.getValue());
}
}
String query = gson.toJson(queryMap);
LOGGER.info("****************************** query");
LOGGER.info(query);
String url = workflowUrl + "/runWorkflow/" + algoCode;
// Results are stored in the experiment object
try {
StringBuilder results = new StringBuilder();
int code = HTTPUtil.sendAuthorizedHTTP(url, query, results, "POST", workflowAuthorization);
experiment.setResult("[" + results.toString() + "]");
LOGGER.info("****************************** results");
LOGGER.info(results.toString());
experiment.setHasError(code >= 400);
experiment.setHasServerError(code >= 500);
} catch (IOException e) {
LOGGER.trace("Invalid UUID", e);
LOGGER.warn("Workflow failed to run properly !");
experiment.setHasError(true);
experiment.setHasServerError(true);
experiment.setResult(e.getMessage());
}
finishExperiment(experiment);
}).start();
return new ResponseEntity<>(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
}
......@@ -119,6 +183,62 @@ public class ExperimentApi extends WokenClientController {
return new ResponseEntity<>(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
}
@ApiOperation(value = "get workflow status", response = String.class)
@RequestMapping(value = "/workflow/status/{historyId}", method = RequestMethod.GET)
public ResponseEntity<String> getWorkflowStatus(
@ApiParam(value = "historyId", required = true) @PathVariable("historyId") String historyId) {
LOGGER.info("Get a workflow status");
String url = workflowUrl + "/getWorkflowStatus/" + historyId;
try {
StringBuilder response = new StringBuilder();
HTTPUtil.sendAuthorizedHTTP(url, "", response, "GET", workflowAuthorization);
JsonElement element = new JsonParser().parse(response.toString());
return ResponseEntity.ok(gson.toJson(element));
} catch (IOException e) {
return ResponseEntity.status(500).body(e.getMessage());
}
}
// TODO: factorize workflow results
@ApiOperation(value = "get workflow results", response = String.class)
@RequestMapping(value = "/workflow/results/{historyId}", method = RequestMethod.GET)
public ResponseEntity<String> getWorkflowResults(
@ApiParam(value = "historyId", required = true) @PathVariable("historyId") String historyId) {
LOGGER.info("Get a workflow results");
String url = workflowUrl + "/getWorkflowResults/" + historyId;
try {
StringBuilder response = new StringBuilder();
HTTPUtil.sendAuthorizedHTTP(url, "", response, "GET", workflowAuthorization);
JsonElement element = new JsonParser().parse(response.toString());
return ResponseEntity.ok(gson.toJson(element));
} catch (IOException e) {
return ResponseEntity.status(500).body(e.getMessage());
}
}
@ApiOperation(value = "get workflow result body", response = String.class)
@RequestMapping(value = "/workflow/resultsbody/{historyId}/content/{resultId}", method = RequestMethod.GET)
public ResponseEntity<String> getWorkflowResultBody(
@ApiParam(value = "historyId", required = true) @PathVariable("historyId") String historyId,
@ApiParam(value = "resultId", required = true) @PathVariable("resultId") String resultId) {
LOGGER.info("Get a workflow result content");
String url = workflowUrl + "/getWorkflowResultsBody/" + historyId + "/contents/" + resultId;
try {
StringBuilder response = new StringBuilder();
HTTPUtil.sendAuthorizedHTTP(url, "", response, "GET", workflowAuthorization);
JsonElement element = new JsonParser().parse(response.toString());
return ResponseEntity.ok(gson.toJson(element));
} catch (IOException e) {
return ResponseEntity.status(500).body(e.getMessage());
}
}
@ApiOperation(value = "Mark an experiment as viewed", response = Experiment.class)
@RequestMapping(value = "/{uuid}/markAsViewed", method = RequestMethod.GET)
public ResponseEntity<String> markExperimentAsViewed(
......@@ -279,69 +399,6 @@ public class ExperimentApi extends WokenClientController {
}, ec);
}
private void sendExaremeExperiment(Experiment experiment, String algoCode, List<AlgorithmParam> params) {
// this runs in the background. For future optimization: use a thread pool
new Thread(() -> {
List<HashMap<String, String>> queryList = new ArrayList<HashMap<String, String>>();
if (params != null) {
for (AlgorithmParam p : params) {
queryList.add(makeObject(p.getName(), p.getValue()));
}
}
String query = gson.toJson(queryList);
String url = miningExaremeQueryUrl + "/" + algoCode;
// Results are stored in the experiment object
try {
StringBuilder results = new StringBuilder();
int code = HTTPUtil.sendPost(url, query, results);
experiment.setResult("[" + results.toString() + "]");
experiment.setHasError(code >= 400);
experiment.setHasServerError(code >= 500);
} catch (IOException e) {
LOGGER.trace("Invalid UUID", e);
LOGGER.warn("Exareme experiment failed to run properly !");
experiment.setHasError(true);
experiment.setHasServerError(true);
experiment.setResult(e.getMessage());
}
finishExperiment(experiment);
}).start();
}
private void sendWorkflow(Experiment experiment, String algoCode, List<AlgorithmParam> params) {
// this runs in the background. For future optimization: use a thread pool
new Thread(() -> {
HashMap<String, String> queryMap = new HashMap<String, String>();
if (params != null) {
for (AlgorithmParam p : params) {
queryMap.put(p.getName(), p.getValue());
}
}
String query = gson.toJson(queryMap);
String url = "http://88.197.53.36:8080/Gateway_API-1.0.0-SNAPSHOT/api/runWorkflow/3f5830403180d620";
// Results are stored in the experiment object
try {
StringBuilder results = new StringBuilder();
int code = HTTPUtil.sendWorkflowHTTP(url, query, results);
experiment.setResult("[" + results.toString() + "]");
experiment.setHasError(code >= 400);
experiment.setHasServerError(code >= 500);
} catch (IOException e) {
LOGGER.trace("Invalid UUID", e);
LOGGER.warn("Exareme experiment failed to run properly !");
experiment.setHasError(true);
experiment.setHasServerError(true);
experiment.setResult(e.getMessage());
}
finishExperiment(experiment);
}).start();
}
private void finishExperiment(Experiment experiment) {
experiment.setFinished(new Date());
experimentRepository.save(experiment);
......@@ -350,7 +407,7 @@ public class ExperimentApi extends WokenClientController {
}
private HashMap<String, String> makeObject(String name, String value) {
HashMap<String, String> o = new HashMap<String, String>();
HashMap<String, String> o = new HashMap<String, String>();
o.put("name", name);
o.put("value", value);
......
src/main/java/eu/hbp/mip/controllers/MethodsApi.java
+ 27
− 0
View file @ c70f20cb
......@@ -30,6 +30,12 @@ public class MethodsApi extends WokenClientController {
@Value("#{'${services.exareme.algorithmsUrl:http://localhost:9090/mining/algorithms.json}'}")
private String exaremeAlgorithmsUrl;
@Value("#{'${services.workflows.workflowUrl}'}")
private String workflowUrl;
@Value("#{'${services.workflows.workflowAuthorization}'}")
private String workflowAuthorization;
@ApiOperation(value = "List available methods and validations", response = String.class)
@Cacheable(value = "methods", unless = "#result.getStatusCode().value()!=200")
@RequestMapping(method = RequestMethod.GET)
......@@ -62,4 +68,25 @@ public class MethodsApi extends WokenClientController {
}
@ApiOperation(value = "List Galaxy workflows", response = String.class)
@RequestMapping(value = "/workflows", method = RequestMethod.GET)
public ResponseEntity<Object> getWorkflows() {
LOGGER.info("List Galaxy workflows");
try {
StringBuilder response = new StringBuilder();
HTTPUtil.sendAuthorizedHTTP(workflowUrl + "/getAllWorkflowWithDetails", "", response, "GET", workflowAuthorization);
LOGGER.info("************************************************* workflows");
LOGGER.info(workflowUrl + "/getAllWorkflowWithDetails");
LOGGER.info(workflowAuthorization);
LOGGER.info(response.toString());
JsonElement element = new JsonParser().parse(response.toString());
return ResponseEntity.ok(gson.toJson(element));
} catch (IOException e) {
return ResponseEntity.status(500).body(e.getMessage());
}
}
}
src/main/java/eu/hbp/mip/utils/HTTPUtil.java
+ 18
− 54
View file @ c70f20cb
......@@ -13,29 +13,37 @@ import java.nio.charset.StandardCharsets;
*/
public class HTTPUtil {
private HTTPUtil()
{
private HTTPUtil() {
/* Hide implicit public constructor */
throw new IllegalAccessError("HTTPUtil class");
}
public static int sendGet(String url, StringBuilder resp) throws IOException {
return sendHTTP(url, "", resp, "GET");
return sendHTTP(url, "", resp, "GET", null);
}
public static int sendPost(String url, String query, StringBuilder resp) throws IOException {
return sendHTTP(url, query, resp, "POST");
return sendHTTP(url, query, resp, "POST", null);
}
private static int sendHTTP(String url, String query, StringBuilder resp, String httpVerb) throws IOException {
public static int sendAuthorizedHTTP(String url, String query, StringBuilder resp, String httpVerb,
String authorization) throws IOException {
return sendHTTP(url, query, resp, httpVerb, authorization);
}
private static int sendHTTP(String url, String query, StringBuilder resp, String httpVerb, String authorization)
throws IOException {
URL obj = new URL(url);
HttpURLConnection con = (HttpURLConnection) obj.openConnection();
if(!"GET".equals(httpVerb)) {
if (authorization != null) {
con.setRequestProperty("Authorization", authorization);
}
if (!"GET".equals(httpVerb)) {
con.setRequestMethod(httpVerb);
if(query != null && query.length() > 0)
{
if (query != null && query.length() > 0) {
con.addRequestProperty("Content-Type", "application/json");
con.setRequestProperty("Content-Length", Integer.toString(query.length()));
......@@ -50,53 +58,9 @@ public class HTTPUtil {
int respCode = con.getResponseCode();
BufferedReader in;
if(respCode == 200) {
if (respCode == 200) {
in = new BufferedReader(new InputStreamReader(con.getInputStream()));
}
else
{
in = new BufferedReader(new InputStreamReader(con.getErrorStream()));
}
String inputLine;
StringBuilder response = new StringBuilder();
while ((inputLine = in.readLine()) != null) {
response.append(inputLine);
}
in.close();
resp.append(response.toString());
return respCode;
}
/* FIXME: Authorization */
public static int sendWorkflowHTTP(String url, String query, StringBuilder resp) throws IOException {
URL obj = new URL(url);
HttpURLConnection con = (HttpURLConnection) obj.openConnection();
con.setRequestMethod("POST");
if(query != null && query.length() > 0)
{
con.addRequestProperty("Content-Type", "application/json");
con.setRequestProperty("Content-Length", Integer.toString(query.length()));
con.setDoOutput(true);
DataOutputStream wr = new DataOutputStream(con.getOutputStream());
wr.write(query.getBytes(StandardCharsets.UTF_8));
wr.flush();
wr.close();
}
int respCode = con.getResponseCode();
BufferedReader in;
if(respCode == 200) {
in = new BufferedReader(new InputStreamReader(con.getInputStream()));
}
else
{
} else {
in = new BufferedReader(new InputStreamReader(con.getErrorStream()));
}
String inputLine;
......
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