From c70f20cbe903a0d8c1a6b0f391d2b1c32e3ba53e Mon Sep 17 00:00:00 2001
From: Manuel Spuhler <manuel.spuhler@chuv.ch>
Date: Wed, 12 Jun 2019 18:22:30 +0200
Subject: [PATCH] Workflow gateway methods
---
docker/config/application.tmpl | 5 +-
.../eu/hbp/mip/controllers/ExperimentApi.java | 189 ++++++++++++------
.../eu/hbp/mip/controllers/MethodsApi.java | 27 +++
src/main/java/eu/hbp/mip/utils/HTTPUtil.java | 72 ++-----
4 files changed, 172 insertions(+), 121 deletions(-)
diff --git a/docker/config/application.tmpl b/docker/config/application.tmpl
index 5f9ea27f9..b4c1909d5 100644
--- a/docker/config/application.tmpl
+++ b/docker/config/application.tmpl
@@ -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
diff --git a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java b/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
index 1f36e8710..2c6260608 100644
--- a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
@@ -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);
diff --git a/src/main/java/eu/hbp/mip/controllers/MethodsApi.java b/src/main/java/eu/hbp/mip/controllers/MethodsApi.java
index 21d3b9f2f..5eaf651b7 100644
--- a/src/main/java/eu/hbp/mip/controllers/MethodsApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/MethodsApi.java
@@ -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());
+ }
+
+ }
+
}
diff --git a/src/main/java/eu/hbp/mip/utils/HTTPUtil.java b/src/main/java/eu/hbp/mip/utils/HTTPUtil.java
index e3c1de511..5c5043463 100644
--- a/src/main/java/eu/hbp/mip/utils/HTTPUtil.java
+++ b/src/main/java/eu/hbp/mip/utils/HTTPUtil.java
@@ -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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