Shanoir vip back to back

shanoir-ng-datasets/src/main/java/org/shanoir/ng/vip/controller/ExecutionDataApi.java

@@ -25,13 +25,14 @@
 import jakarta.validation.constraints.NotNull;
 import org.shanoir.ng.shared.exception.EntityNotFoundException;
 import org.shanoir.ng.shared.exception.RestServiceException;
+import org.shanoir.ng.shared.exception.SecurityException;
+import org.shanoir.ng.vip.monitoring.model.ExecutionDTO;
+import org.springframework.http.HttpHeaders;
 import org.springframework.http.ResponseEntity;
-import org.springframework.web.bind.annotation.PathVariable;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestMethod;
-import org.springframework.web.bind.annotation.RequestParam;
+import org.springframework.web.bind.annotation.*;
 
 import java.io.IOException;
+import java.util.List;
 
 /**
  * @author Alae Es-saki
@@ -46,11 +47,32 @@ public interface ExecutionDataApi {
             @ApiResponse(responseCode = "403", description = "forbidden"),
             @ApiResponse(responseCode = "404", description = "No dataset found"),
             @ApiResponse(responseCode = "500", description = "unexpected error") })
-
     @RequestMapping(value = "/path/{completePath}",
             produces = { "application/json", "application/octet-stream" },
             method = RequestMethod.GET)
     ResponseEntity<?> getPath(@Parameter(name = "the complete path on which to request information. It can contain non-encoded slashes. Except for the \"exists\" action, any request on a non-existing path should return an error", required=true) @PathVariable("completePath") String completePath, @NotNull @Parameter(name = "The \"content\" action downloads the raw file. If the path points to a directory, a tarball of this directory is returned. The \"exists\" action returns a BooleanResponse object (see definition) indicating if the path exists or not. The \"properties\" action returns a Path object (see definition) with the path properties. The \"list\" action returns a DirectoryList object (see definition) with the properties of all the files of the directory (if the path is not a directory an error must be returned). The \"md5\" action is optional and returns a PathMd5 object (see definition)." ,required=true
     ) @Valid @RequestParam(value = "action", required = true) String action, @Valid @RequestParam(value = "format", required = false, defaultValue = "dcm") final String format, HttpServletResponse response) throws IOException, RestServiceException, EntityNotFoundException;
 
+    @Operation(summary = "Creates an execution inside VIP", description = "Creates the ressources and path control in shanoir before creating an execution in VIP", tags={  })
+    @ApiResponses(value = {
+            @ApiResponse(responseCode = "200", description = "Execution successfully created response."),
+            @ApiResponse(responseCode = "403", description = "forbidden"),
+            @ApiResponse(responseCode = "500", description = "unexpected error") })
+    @RequestMapping(value = "/createExecution",
+            produces = {"application/json"},
+            consumes = {"application/json"},
+            method = RequestMethod.POST)
+    ResponseEntity<?> createExecution(
+            @Parameter(name = "execution", required = true) @RequestBody final String execution) throws EntityNotFoundException, SecurityException;
+
+    @Operation(summary = "Get status for the given execution identifier", description = "Returns the status of the VIP execution that has the given identifier in parameter.", tags={  })
+    @ApiResponses(value = {
+            @ApiResponse(responseCode = "200", description = "successful response, returns the status"),
+            @ApiResponse(responseCode = "403", description = "forbidden"),
+            @ApiResponse(responseCode = "500", description = "unexpected error") })
+    @RequestMapping(value = "/execution/{identifier}",
+            produces = { "application/json", "application/octet-stream" },
+            method = RequestMethod.GET)
+    ResponseEntity<String> getexecutionStatus(@Parameter(name = "The execution identifier", required=true) @PathVariable("identifier") String identifier) throws IOException, RestServiceException, EntityNotFoundException, SecurityException;
+
 }

shanoir-ng-datasets/src/main/java/org/shanoir/ng/vip/controller/ExecutionDataApiController.java

@@ -15,26 +15,52 @@
 
 package org.shanoir.ng.vip.controller;
 
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import io.swagger.v3.oas.annotations.Parameter;
 import jakarta.servlet.http.HttpServletResponse;
 import jakarta.validation.Valid;
 import jakarta.validation.constraints.NotNull;
+import jakarta.ws.rs.core.Response;
+import org.apache.xmlbeans.impl.jam.JParameter;
+import org.hibernate.jpa.internal.util.LockOptionsHelper;
+import org.keycloak.representations.AccessTokenResponse;
 import org.shanoir.ng.dataset.model.Dataset;
+import org.shanoir.ng.dataset.security.DatasetSecurityService;
 import org.shanoir.ng.dataset.service.DatasetDownloaderServiceImpl;
+import org.shanoir.ng.dataset.service.DatasetService;
+import org.shanoir.ng.processing.dto.ParameterResourcesDTO;
+import org.shanoir.ng.processing.model.DatasetProcessingType;
+import org.shanoir.ng.shared.exception.ErrorModel;
+import org.shanoir.ng.shared.exception.SecurityException;
+import org.shanoir.ng.shared.security.KeycloakServiceAccountUtils;
+import org.shanoir.ng.utils.KeycloakUtil;
+import org.shanoir.ng.vip.dto.ExecutionMonitoringDTO;
+import org.shanoir.ng.vip.monitoring.model.*;
+import org.shanoir.ng.vip.monitoring.schedule.ExecutionStatusMonitorService;
+import org.shanoir.ng.vip.monitoring.service.ExecutionMonitoringService;
 import org.shanoir.ng.vip.resource.ProcessingResourceService;
 import org.shanoir.ng.shared.exception.EntityNotFoundException;
 import org.shanoir.ng.shared.exception.RestServiceException;
+import org.shanoir.ng.vip.resulthandler.ResultHandlerException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.HttpStatus;
-import org.springframework.http.ResponseEntity;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.http.*;
 import org.springframework.stereotype.Controller;
 import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestBody;
+import org.springframework.web.bind.annotation.RequestHeader;
 import org.springframework.web.bind.annotation.RequestParam;
+import org.springframework.web.client.HttpStatusCodeException;
+import org.springframework.web.client.RestClientException;
+import org.springframework.web.client.RestTemplate;
 
 import java.io.IOException;
-import java.util.List;
+import java.sql.Array;
+import java.time.LocalDate;
+import java.util.*;
 
 @Controller
 public class ExecutionDataApiController implements ExecutionDataApi {
@@ -49,6 +75,27 @@ public class ExecutionDataApiController implements ExecutionDataApi {
     @Autowired
     private ProcessingResourceService processingResourceService;
 
+    @Autowired
+    private DatasetService datasetService;
+
+    @Autowired
+    private DatasetSecurityService datasetSecurityService;
+
+    @Autowired
+    private RestTemplate restTemplate;
+
+    @Autowired
+    private KeycloakServiceAccountUtils keycloakServiceAccountUtils;
+
+    @Autowired
+    private ExecutionMonitoringService executionMonitoringService;
+
+    @Autowired
+    private ExecutionStatusMonitorService executionStatusMonitorService;
+
+    @Value("${vip.uri}")
+    private String VIP_URI;
+
     @Override
     public ResponseEntity<?> getPath(
             @Parameter(name = "the complete path on which to request information. It can contain non-encoded slashes. Except for the \"exists\" action, any request on a non-existing path should return an error",
@@ -84,4 +131,123 @@ public ResponseEntity<?> getPath(
 
     }
 
+    @Override
+    public ResponseEntity<ExecutionDTO> createExecution(
+            @Parameter(name = "execution", required = true) @RequestBody final String executionAsString) throws EntityNotFoundException, SecurityException {
+
+        String authenticationToken = KeycloakUtil.getToken();
+
+        // 1: Get dataset IDS and check rights
+        List<Long> datasetsIds = new ArrayList<>();
+        ObjectMapper mapper = new ObjectMapper();
+        ExecutionDTO execution = null;
+        try {
+            execution = mapper.readValue(executionAsString, ExecutionDTO.class);
+        } catch (JsonProcessingException e) {
+            LOG.error("Could not parse execution DTO from input, please respect the expected structure.", e);
+            return new ResponseEntity<>(HttpStatus.BAD_REQUEST);
+        }
+        String clientId = execution.getClient();
+
+        for (ParameterResourcesDTO param : execution.getParametersRessources()) {
+            datasetsIds.addAll(param.getDatasetIds());
+        }
+
+        if (!this.datasetSecurityService.hasRightOnEveryDataset(datasetsIds, "CAN_IMPORT")) {
+            LOG.error("Import right is mandatory for every study we are updating");
+            return new ResponseEntity<>(HttpStatus.UNAUTHORIZED);
+        };
+
+        List<Dataset> inputDatasets = this.datasetService.findByIdIn(datasetsIds);
+
+        // 2: Create monitoring on shanoir
+        ExecutionMonitoring executionMonitoring = createExecutionMonitoring(execution, inputDatasets);
+
+        // Save monitoring in db.
+        final ExecutionMonitoring createdMonitoring = executionMonitoringService.create(executionMonitoring);
+
+        List<ParameterResourcesDTO> parametersDatasets = executionMonitoringService.createProcessingResources(createdMonitoring, execution.getParametersRessources());
+
+        // 3: create Execution on VIP
+        // init headers with the active access token
+
+        execution.setResultsLocation("shanoir:/" + createdMonitoring.getResultsLocation() + "?token=" + authenticationToken + "&refreshToken=" + execution.getRefreshToken() + "&clientId=" + clientId + "&md5=none&type=File");
+
+        String exportFormat = execution.getExportFormat();
+        String extension = ".nii.gz";
+        if ("dcm".equals(execution.getExportFormat())) {
+            extension = ".zip";
+        }
+
+        Map<String, List<String>> parametersDatasetsInputValues = new HashMap<>();
+        for (ParameterResourcesDTO parameterResourcesDTO : parametersDatasets) {
+            parametersDatasetsInputValues.put(parameterResourcesDTO.getParameter(), new ArrayList<>());
+
+            for (String ressourceId : parameterResourcesDTO.getResourceIds()) {
+                String entityName = "resource_id+" + ressourceId + "+" + parameterResourcesDTO.getGroupBy().name().toLowerCase() + extension;
+                String inputValue = "shanoir:/" + entityName + "?format=" + exportFormat + "&datasetId=" + ressourceId
+                 + "&token=" + authenticationToken + "&refreshToken=" + execution.getRefreshToken() + "&clientId=" + clientId + "&md5=none&type=File";
+                parametersDatasetsInputValues.get(parameterResourcesDTO.getParameter()).add(inputValue);
+            }
+        }
+        execution.setInputValues(parametersDatasetsInputValues);
+
+        try {
+            LOG.error(mapper.writeValueAsString(execution));
+        }  catch (JsonProcessingException e) {
+            LOG.error("Could not parse execution DTO from VIP response, please contact an administrator", e);
+            return new ResponseEntity<>(HttpStatus.INTERNAL_SERVER_ERROR);
+        }
+
+        HttpHeaders headers = KeycloakUtil.getKeycloakHeader();
+        HttpEntity<ExecutionDTO> entity = new HttpEntity<>(execution, headers);
+
+        ResponseEntity<ExecutionDTO> execResult = this.restTemplate.exchange(VIP_URI, HttpMethod.POST, entity, ExecutionDTO.class);
+
+        ExecutionDTO execCreated = execResult.getBody();
+
+        executionMonitoring.setIdentifier(execCreated.getIdentifier());
+        executionMonitoring.setStatus(execCreated.getStatus());
+        executionMonitoring.setStartDate(execCreated.getStartDate());
+
+        executionMonitoring = this.executionMonitoringService.update(executionMonitoring);
+        this.executionStatusMonitorService.startMonitoringJob(executionMonitoring.getIdentifier());
+
+        return new ResponseEntity<>(execCreated, HttpStatus.OK);
+    }
+
+    private ExecutionMonitoring createExecutionMonitoring(ExecutionDTO execution, List<Dataset> inputDatasets) {
+        ExecutionMonitoring executionMonitoring = new ExecutionMonitoring();
+        executionMonitoring.setName(execution.getName());
+        executionMonitoring.setPipelineIdentifier(execution.getPipelineIdentifier());
+        executionMonitoring.setResultsLocation(KeycloakUtil.getTokenUserId() + "/" + LocalDate.now());
+        executionMonitoring.setTimeout(20);
+        executionMonitoring.setStudyId(Long.valueOf(execution.getStudyIdentifier()));
+        executionMonitoring.setStatus(ExecutionStatus.RUNNING);
+        executionMonitoring.setComment(execution.getName());
+        executionMonitoring.setDatasetProcessingType(DatasetProcessingType.valueOf(execution.getProcessingType()));
+        executionMonitoring.setOutputProcessing(execution.getOutputProcessing());
+        executionMonitoring.setInputDatasets(inputDatasets);
+        return executionMonitoring;
+    }
+
+    @Override
+    public ResponseEntity<String> getexecutionStatus(@Parameter(name = "The execution identifier", required=true) @PathVariable("identifier") String identifier) throws IOException, RestServiceException, EntityNotFoundException, SecurityException {
+
+        AccessTokenResponse accessTokenResponse = keycloakServiceAccountUtils.getServiceAccountAccessToken();
+        HttpHeaders headers = new HttpHeaders();
+        headers.set("Authorization", "Bearer " + accessTokenResponse.getToken());
+        HttpEntity<String> entity = new HttpEntity<>(headers);
+
+        Execution execution;
+        try {
+            String uri = VIP_URI + identifier + "/summary";
+            ResponseEntity<Execution> execResult = this.restTemplate.exchange(uri, HttpMethod.GET, entity, Execution.class);
+            execution = execResult.getBody();
+        } catch (HttpStatusCodeException e) {
+            // in case of an error with response payload
+            return new ResponseEntity<>(HttpStatus.NO_CONTENT);
+        }
+        return new ResponseEntity<>(execution.getStatus().getRestLabel(), HttpStatus.OK);
+    }
 }