#1694

Committed 30 Sep 2024 10:51AM UTC coverage: 70.306% (-0.5%) from 70.811%

Build # #1694

Build Type

push

github

Committed by

mr-c

Commit Message

detect non-Workflow CWL documents and give a better error message

Run Details

2 of 19 new or added lines in 4 files covered. (10.53%)

106 existing lines in 4 files now uncovered.

1700 of 2418 relevant lines covered (70.31%)

0.7 hits per line

Source File
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77.56

/src/main/java/org/commonwl/view/workflow/WorkflowController.java

/*
 * Licensed to the Apache Software Foundation (ASF) under one
 * or more contributor license agreements.  See the NOTICE file
 * distributed with this work for additional information
 * regarding copyright ownership.  The ASF licenses this file
 * to you under the Apache License, Version 2.0 (the
 * "License"); you may not use this file except in compliance
 * with the License.  You may obtain a copy of the License at
 *
 *   http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing,
 * software distributed under the License is distributed on an
 * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
 * KIND, either express or implied.  See the License for the
 * specific language governing permissions and limitations
 * under the License.
 */

package org.commonwl.view.workflow;

import jakarta.servlet.http.HttpServletRequest;
import jakarta.servlet.http.HttpServletResponse;
import jakarta.validation.Valid;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.nio.file.Path;
import java.security.NoSuchAlgorithmException;
import java.util.List;
import org.apache.commons.lang.StringUtils;
import org.commonwl.view.WebConfig;
import org.commonwl.view.cwl.CWLNotAWorkflowException;
import org.commonwl.view.cwl.CWLService;
import org.commonwl.view.cwl.CWLToolStatus;
import org.commonwl.view.cwl.CWLValidationException;
import org.commonwl.view.git.GitDetails;
import org.commonwl.view.graphviz.GraphVizService;
import org.eclipse.jgit.api.errors.GitAPIException;
import org.eclipse.jgit.api.errors.TransportException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.core.io.FileSystemResource;
import org.springframework.core.io.InputStreamResource;
import org.springframework.core.io.PathResource;
import org.springframework.core.io.Resource;
import org.springframework.data.domain.Pageable;
import org.springframework.data.web.PageableDefault;
import org.springframework.stereotype.Controller;
import org.springframework.ui.Model;
import org.springframework.validation.BeanPropertyBindingResult;
import org.springframework.validation.BindingResult;
import org.springframework.web.bind.annotation.*;
import org.springframework.web.servlet.HandlerMapping;
import org.springframework.web.servlet.ModelAndView;
import org.springframework.web.servlet.mvc.support.RedirectAttributes;

@Controller
public class WorkflowController {

  private final Logger logger = LoggerFactory.getLogger(this.getClass());

  private final WorkflowFormValidator workflowFormValidator;
  private final WorkflowService workflowService;
  private final CWLService cwlService;
  private final GraphVizService graphVizService;

  /**
   * Autowired constructor to initialise objects used by the controller.
   *
   * @param workflowFormValidator Validator to validate the workflow form
   * @param workflowService Builds new Workflow objects
   * @param graphVizService Generates and stores images
   */
  @Autowired
  public WorkflowController(
      WorkflowFormValidator workflowFormValidator,
      WorkflowService workflowService,
      GraphVizService graphVizService,
      CWLService cwlService) {
    this.workflowFormValidator = workflowFormValidator;
    this.workflowService = workflowService;
    this.graphVizService = graphVizService;
    this.cwlService = cwlService;
  }

  /**
   * List all the workflows in the database, paginated
   *
   * @param model The model for the page
   * @param pageable Pagination for the list of workflows
   * @return The workflows view
   */
  @GetMapping(value = "/workflows")
  public String listWorkflows(Model model, @PageableDefault(size = 10) Pageable pageable) {
    model.addAttribute("workflows", workflowService.getPageOfWorkflows(pageable));
    model.addAttribute("pages", pageable);
    return "workflows";
  }

  /**
   * Search all the workflows in the database, paginated
   *
   * @param model The model for the page
   * @param pageable Pagination for the list of workflows
   * @return The workflows view
   */
  @GetMapping(value = "/workflows", params = "search")
  public String searchWorkflows(
      Model model,
      @PageableDefault(size = 10) Pageable pageable,
      @RequestParam(value = "search") String search) {
    model.addAttribute("workflows", workflowService.searchPageOfWorkflows(search, pageable));
    model.addAttribute("pages", pageable);
    model.addAttribute("search", search);
    return "workflows";
  }

  /**
   * Create a new workflow from the given URL in the form
   *
   * @param workflowForm The data submitted from the form
   * @param bindingResult Spring MVC Binding Result object
   * @return The workflow view with new workflow as a model
   */
  @PostMapping("/workflows")
  public ModelAndView createWorkflow(
      @Valid WorkflowForm workflowForm, BindingResult bindingResult) {

    // Run validator which checks the git URL is valid
    GitDetails gitInfo = workflowFormValidator.validateAndParse(workflowForm, bindingResult);

    if (bindingResult.hasErrors() || gitInfo == null) {
      // Go back to index if there are validation errors
      return new ModelAndView("index");
    } else {
      // Get workflow or create if does not exist
      Workflow workflow = workflowService.getWorkflow(gitInfo);
      if (workflow == null) {
        try {
          if (gitInfo.getPath().endsWith(".cwl")) {
            QueuedWorkflow result = workflowService.createQueuedWorkflow(gitInfo);
            if (result.getWorkflowList() == null) {
              workflow = result.getTempRepresentation();
            } else {
              if (result.getWorkflowList().size() == 1) {
                gitInfo.setPackedId(result.getWorkflowList().get(0).getFileName());
              }
              return new ModelAndView("redirect:" + gitInfo.getInternalUrl());
            }
          } else {
            return new ModelAndView("redirect:" + gitInfo.getInternalUrl());
          }
        } catch (TransportException ex) {
          logger.warn("git.sshError " + workflowForm, ex);
          bindingResult.rejectValue("url", "git.sshError");
          return new ModelAndView("index");
        } catch (GitAPIException ex) {
          logger.error("git.retrievalError " + workflowForm, ex);
          bindingResult.rejectValue("url", "git.retrievalError");
          return new ModelAndView("index");
        } catch (WorkflowNotFoundException ex) {
          logger.warn("git.notFound " + workflowForm, ex);
          bindingResult.rejectValue("url", "git.notFound");
          return new ModelAndView("index");
        } catch (CWLNotAWorkflowException ex) {
          logger.warn("cwl.notAWorkflow " + workflowForm, ex);
          bindingResult.rejectValue("url", "cwl.notAWorkflow");
          return new ModelAndView("index");
        } catch (Exception ex) {
          logger.warn("url.parsingError " + workflowForm, ex);
          bindingResult.rejectValue("url", "url.parsingError");
          return new ModelAndView("index");
        }
      }
      gitInfo = workflow.getRetrievedFrom();
      // Redirect to the workflow
      return new ModelAndView("redirect:" + gitInfo.getInternalUrl());
    }
  }

  /**
   * Display a page for a particular workflow from github.com or gitlab.com format URL
   *
   * @param domain The domain of the hosting site, github.com or gitlab.com
   * @param owner The owner of the repository
   * @param repoName The name of the repository
   * @param branch The branch of repository
   * @return The workflow view with the workflow as a model
   */
  @GetMapping(
      value = {
        "/workflows/{domain}.com/{owner}/{repoName}/tree/{branch}/**",
        "/workflows/{domain}.com/{owner}/{repoName}/blob/{branch}/**"
      })
  public ModelAndView getWorkflow(
      @PathVariable("domain") String domain,
      @PathVariable("owner") String owner,
      @PathVariable("repoName") String repoName,
      @PathVariable("branch") String branch,
      HttpServletRequest request,
      RedirectAttributes redirectAttrs) {
    // The wildcard end of the URL is the path
    String path =
        (String) request.getAttribute(HandlerMapping.PATH_WITHIN_HANDLER_MAPPING_ATTRIBUTE);
    path = extractPath(path, 7);

    // Construct a GitDetails object to search for in the database
    GitDetails gitDetails = getGitDetails(domain, owner, repoName, branch, path);

    // Get workflow
    return getWorkflow(gitDetails, redirectAttrs);
  }

  /**
   * Display page for a workflow from a generic Git URL
   *
   * @param branch The branch of the repository
   * @return The workflow view with the workflow as a model
   */
  @GetMapping(value = "/workflows/*/*.git/{branch}/**")
  public ModelAndView getWorkflowGeneric(
      @Value("${applicationURL}") String applicationURL,
      @PathVariable("branch") String branch,
      HttpServletRequest request,
      RedirectAttributes redirectAttrs) {
    String path =
        (String) request.getAttribute(HandlerMapping.PATH_WITHIN_HANDLER_MAPPING_ATTRIBUTE);
    GitDetails gitDetails = getGitDetails(11, path, branch);
    return getWorkflow(gitDetails, redirectAttrs);
  }

  /**
   * Download the Research Object Bundle for a particular workflow
   *
   * @param domain The domain of the hosting site, github.com or gitlab.com
   * @param owner The owner of the repository
   * @param repoName The name of the repository
   * @param branch The branch of repository
   */
  @GetMapping(
      value = {
        "/robundle/{domain}.com/{owner}/{repoName}/tree/{branch}/**",
        "/robundle/{domain}.com/{owner}/{repoName}/blob/{branch}/**"
      },
      produces = {"application/vnd.wf4ever.robundle+zip", "application/zip"})
  @ResponseBody
  public Resource getROBundle(
      @PathVariable("domain") String domain,
      @PathVariable("owner") String owner,
      @PathVariable("repoName") String repoName,
      @PathVariable("branch") String branch,
      HttpServletRequest request,
      HttpServletResponse response) {
    String path =
        (String) request.getAttribute(HandlerMapping.PATH_WITHIN_HANDLER_MAPPING_ATTRIBUTE);
    path = extractPath(path, 7);
    GitDetails gitDetails = getGitDetails(domain, owner, repoName, branch, path);
    File bundleDownload = workflowService.getROBundle(gitDetails);
    response.setHeader("Content-Disposition", "attachment; filename=bundle.zip;");
    return new FileSystemResource(bundleDownload);
  }

  /**
   * Download the Research Object Bundle for a particular workflow
   *
   * @param branch The branch of repository
   */
  @GetMapping(
      value = "/robundle/*/*/*.git/{branch}/**",
      produces = "application/vnd.wf4ever.robundle+zip")
  @ResponseBody
  public Resource getROBundleGeneric(
      @PathVariable("branch") String branch,
      HttpServletRequest request,
      HttpServletResponse response) {
    String path =
        (String) request.getAttribute(HandlerMapping.PATH_WITHIN_HANDLER_MAPPING_ATTRIBUTE);
    GitDetails gitDetails = getGitDetails(10, path, branch);
    File bundleDownload = workflowService.getROBundle(gitDetails);
    response.setHeader("Content-Disposition", "attachment; filename=bundle.zip;");
    return new FileSystemResource(bundleDownload);
  }

  /**
   * Download a generated graph for a workflow in SVG format
   *
   * @param domain The domain of the hosting site, github.com or gitlab.com
   * @param owner The owner of the repository
   * @param repoName The name of the repository
   * @param branch The branch of repository
   */
  @GetMapping(
      value = {
        "/graph/svg/{domain}.com/{owner}/{repoName}/tree/{branch}/**",
        "/graph/svg/{domain}.com/{owner}/{repoName}/blob/{branch}/**"
      },
      produces = "image/svg+xml")
  @ResponseBody
  public Resource downloadGraphSvg(
      @PathVariable("domain") String domain,
      @PathVariable("owner") String owner,
      @PathVariable("repoName") String repoName,
      @PathVariable("branch") String branch,
      HttpServletRequest request,
      HttpServletResponse response)
      throws IOException {
    String path =
        (String) request.getAttribute(HandlerMapping.PATH_WITHIN_HANDLER_MAPPING_ATTRIBUTE);
    path = extractPath(path, 8);
    GitDetails gitDetails = getGitDetails(domain, owner, repoName, branch, path);
    response.setHeader("Content-Disposition", "inline; filename=\"graph.svg\"");
    return workflowService.getWorkflowGraph("svg", gitDetails);
  }

  /**
   * Download a generated graph for a workflow in SVG format
   *
   * @param branch The branch of repository
   */
  @GetMapping(value = "/graph/svg/*/*/*.git/{branch}/**", produces = "image/svg+xml")
  @ResponseBody
  public Resource downloadGraphSvgGeneric(
      @PathVariable("branch") String branch,
      HttpServletRequest request,
      HttpServletResponse response)
      throws IOException {
    String path =
        (String) request.getAttribute(HandlerMapping.PATH_WITHIN_HANDLER_MAPPING_ATTRIBUTE);
    GitDetails gitDetails = getGitDetails(11, path, branch);
    response.setHeader("Content-Disposition", "inline; filename=\"graph.svg\"");
    return workflowService.getWorkflowGraph("svg", gitDetails);
  }

  /**
   * Download a generated graph for a workflow in PNG format
   *
   * @param domain The domain of the hosting site, github.com or gitlab.com
   * @param owner The owner of the repository
   * @param repoName The name of the repository
   * @param branch The branch of repository
   */
  @GetMapping(
      value = {
        "/graph/png/{domain}.com/{owner}/{repoName}/tree/{branch}/**",
        "/graph/png/{domain}.com/{owner}/{repoName}/blob/{branch}/**"
      },
      produces = "image/png")
  @ResponseBody
  public Resource downloadGraphPng(
      @PathVariable("domain") String domain,
      @PathVariable("owner") String owner,
      @PathVariable("repoName") String repoName,
      @PathVariable("branch") String branch,
      HttpServletRequest request,
      HttpServletResponse response)
      throws IOException {
    String path =
        (String) request.getAttribute(HandlerMapping.PATH_WITHIN_HANDLER_MAPPING_ATTRIBUTE);
    path = extractPath(path, 8);
    GitDetails gitDetails = getGitDetails(domain, owner, repoName, branch, path);
    response.setHeader("Content-Disposition", "inline; filename=\"graph.png\"");
    return workflowService.getWorkflowGraph("png", gitDetails);
  }

  /**
   * Download a generated graph for a workflow in PNG format
   *
   * @param branch The branch of repository
   */
  @GetMapping(value = "/graph/png/*/*/*.git/{branch}/**", produces = "image/png")
  @ResponseBody
  public Resource downloadGraphPngGeneric(
      @PathVariable("branch") String branch,
      HttpServletRequest request,
      HttpServletResponse response)
      throws IOException {
    String path =
        (String) request.getAttribute(HandlerMapping.PATH_WITHIN_HANDLER_MAPPING_ATTRIBUTE);
    GitDetails gitDetails = getGitDetails(11, path, branch);
    response.setHeader("Content-Disposition", "inline; filename=\"graph.png\"");
    return workflowService.getWorkflowGraph("png", gitDetails);
  }

  /**
   * Download a generated graph for a workflow in XDOT format
   *
   * @param domain The domain of the hosting site, github.com or gitlab.com
   * @param owner The owner of the repository
   * @param repoName The name of the repository
   * @param branch The branch of repository
   */
  @GetMapping(
      value = {
        "/graph/xdot/{domain}.com/{owner}/{repoName}/tree/{branch}/**",
        "/graph/xdot/{domain}.com/{owner}/{repoName}/blob/{branch}/**"
      },
      produces = "text/vnd.graphviz")
  @ResponseBody
  public Resource downloadGraphDot(
      @PathVariable("domain") String domain,
      @PathVariable("owner") String owner,
      @PathVariable("repoName") String repoName,
      @PathVariable("branch") String branch,
      HttpServletRequest request,
      HttpServletResponse response)
      throws IOException {
    String path =
        (String) request.getAttribute(HandlerMapping.PATH_WITHIN_HANDLER_MAPPING_ATTRIBUTE);
    path = extractPath(path, 8);
    GitDetails gitDetails = getGitDetails(domain, owner, repoName, branch, path);
    response.setHeader("Content-Disposition", "inline; filename=\"graph.dot\"");
    return workflowService.getWorkflowGraph("xdot", gitDetails);
  }

  /**
   * Download a generated graph for a workflow in XDOT format
   *
   * @param branch The branch of repository
   */
  @GetMapping(value = "/graph/xdot/*/*/*.git/{branch}/**", produces = "text/vnd.graphviz")
  @ResponseBody
  public Resource downloadGraphDotGeneric(
      @PathVariable("branch") String branch,
      HttpServletRequest request,
      HttpServletResponse response)
      throws IOException {
    String path =
        (String) request.getAttribute(HandlerMapping.PATH_WITHIN_HANDLER_MAPPING_ATTRIBUTE);
    GitDetails gitDetails = getGitDetails(12, path, branch);
    response.setHeader("Content-Disposition", "inline; filename=\"graph.dot\"");
    return workflowService.getWorkflowGraph("xdot", gitDetails);
  }

  /**
   * Get a temporary graph for a pending workflow
   *
   * @param queueID The ID in the queue
   * @return The visualisation image
   */
  @GetMapping(
      value = {"/queue/{queueID}/tempgraph.png"},
      produces = "image/png")
  @ResponseBody
  public PathResource getTempGraphAsPng(
      @PathVariable("queueID") String queueID, HttpServletResponse response) throws IOException {
    QueuedWorkflow queued = workflowService.getQueuedWorkflow(queueID);
    if (queued == null) {
      throw new WorkflowNotFoundException();
    }
    Path out =
        graphVizService.getGraphPath(
            queued.getId() + ".png", queued.getTempRepresentation().getVisualisationDot(), "png");
    response.setHeader("Content-Disposition", "inline; filename=\"graph.png\"");
    return new PathResource(out);
  }

  /**
   * Take a CWL workflow from the POST body and generate a PNG graph for it.
   *
   * @param in The workflow CWL
   */
  @PostMapping(
      value = "/graph/png",
      produces = "image/png",
      consumes = {"text/yaml", "text/x-yaml", "text/plain", "application/octet-stream"})
  @ResponseBody
  public Resource downloadGraphPngFromFile(InputStream in, HttpServletResponse response)
      throws IOException, NoSuchAlgorithmException {
    response.setHeader("Content-Disposition", "inline; filename=\"graph.png\"");
    return getGraphFromInputStream(in, "png");
  }

  /**
   * Take a CWL workflow from the POST body and generate a SVG graph for it.
   *
   * @param in The workflow CWL as YAML text
   */
  @PostMapping(
      value = "/graph/svg",
      produces = "image/svg+xml",
      consumes = {"text/yaml", "text/x-yaml", "text/plain", "application/octet-stream"})
  @ResponseBody
  public Resource downloadGraphSvgFromFile(InputStream in, HttpServletResponse response)
      throws IOException, NoSuchAlgorithmException {
    response.setHeader("Content-Disposition", "inline; filename=\"graph.svg\"");
    return getGraphFromInputStream(in, "svg");
  }

  /**
   * Extract the path from the end of a full request string
   *
   * @param path The full request string path
   * @param startSlashNum The ordinal slash index of the start of the path
   * @return The path from the end
   */
  public static String extractPath(String path, int startSlashNum) {
    int pathStartIndex = StringUtils.ordinalIndexOf(path, "/", startSlashNum);
    if (pathStartIndex > -1 && pathStartIndex < path.length() - 1) {
      return path.substring(pathStartIndex + 1).replaceAll("\\/$", "");
    } else {
      return "/";
    }
  }

  /**
   * Constructs a GitDetails object for github.com/gitlab.com details
   *
   * @param domain The domain name ("github" or "gitlab", without .com)
   * @param owner The owner of the repository
   * @param repoName The name of the repository
   * @param branch The branch of the repository
   * @param path The path within the repository
   * @return A constructed GitDetails object
   */
  public static GitDetails getGitDetails(
      String domain, String owner, String repoName, String branch, String path) {
    String repoUrl;
    switch (domain) {
      case "github":
        repoUrl = "https://github.com/" + owner + "/" + repoName + ".git";
        break;
      case "gitlab":
        repoUrl = "https://gitlab.com/" + owner + "/" + repoName + ".git";
        break;
      default:
        throw new WorkflowNotFoundException();
    }
    String[] pathSplit = path.split("#");
    GitDetails details = new GitDetails(repoUrl, branch, path);
    if (pathSplit.length > 1) {
      details.setPath(pathSplit[pathSplit.length - 2]);
      details.setPackedId(pathSplit[pathSplit.length - 1]);
    }
    return details;
  }

  /**
   * Constructs a GitDetails object for a generic path
   *
   * @param startIndex The start of the repository URL
   * @param path The entire URL path
   * @param branch The branch of the repository
   * @return A constructed GitDetails object
   */
  public static GitDetails getGitDetails(int startIndex, String path, String branch) {
    // The repository URL is the part after startIndex and up to and including .git
    String repoUrl = path.substring(startIndex);
    int extensionIndex = repoUrl.indexOf(".git");
    if (extensionIndex == -1) {
      throw new WorkflowNotFoundException();
    }
    repoUrl = "https://" + repoUrl.substring(0, extensionIndex + 4);

    // The path is after the branch
    int slashAfterBranch = path.indexOf("/", path.indexOf(branch));
    if (slashAfterBranch == -1 || slashAfterBranch == path.length()) {
      throw new WorkflowNotFoundException();
    }
    path = path.substring(slashAfterBranch + 1);

    // Construct GitDetails object for this workflow
    return new GitDetails(repoUrl, branch, path);
  }

  /**
   * Get a workflow from Git Details, creating if it does not exist
   *
   * @param gitDetails The details of the Git repository
   * @param redirectAttrs Error attributes for redirect
   * @return The model and view to be returned by the controller
   */
  private ModelAndView getWorkflow(GitDetails gitDetails, RedirectAttributes redirectAttrs) {
    // Get workflow
    QueuedWorkflow queued = null;
    Workflow workflowModel = workflowService.getWorkflow(gitDetails);
    if (workflowModel == null) {
      // Check if already queued
      queued = workflowService.getQueuedWorkflow(gitDetails);
      if (queued == null) {
        // Validation
        String packedPart =
            (gitDetails.getPackedId() == null) ? "" : "#" + gitDetails.getPackedId();
        WorkflowForm workflowForm =
            new WorkflowForm(
                gitDetails.getRepoUrl(), gitDetails.getBranch(), gitDetails.getPath() + packedPart);
        BeanPropertyBindingResult errors = new BeanPropertyBindingResult(workflowForm, "errors");
        workflowFormValidator.validateAndParse(workflowForm, errors);
        if (!errors.hasErrors()) {
          try {
            if (gitDetails.getPath().endsWith(".cwl")) {
              queued = workflowService.createQueuedWorkflow(gitDetails);
              if (queued.getWorkflowList() != null) {
                // Packed workflow listing
                if (queued.getWorkflowList().size() == 1) {
                  gitDetails.setPackedId(queued.getWorkflowList().get(0).getFileName());
                  return new ModelAndView("redirect:" + gitDetails.getInternalUrl());
                }
                return new ModelAndView(
                        "selectworkflow", "workflowOverviews", queued.getWorkflowList())
                    .addObject("gitDetails", gitDetails);
              }
            } else {
              List<WorkflowOverview> workflowOverviews =
                  workflowService.getWorkflowsFromDirectory(gitDetails);
              if (workflowOverviews.size() > 1) {
                return new ModelAndView("selectworkflow", "workflowOverviews", workflowOverviews)
                    .addObject("gitDetails", gitDetails);
              } else if (workflowOverviews.size() == 1) {
                return new ModelAndView(
                    "redirect:"
                        + gitDetails.getInternalUrl()
                        + workflowOverviews.get(0).getFileName());
              } else {
                errors.rejectValue(
                    "url",
                    "url.noWorkflowsInDirectory",
                    "No workflow files were found in the given directory");
              }
            }
          } catch (TransportException ex) {
            logger.warn("git.sshError " + workflowForm, ex);
            errors.rejectValue(
                "url",
                "git.sshError",
                "SSH URLs are not supported, please provide a HTTPS URL for the repository or submodules");
          } catch (GitAPIException ex) {
            logger.error("git.retrievalError " + workflowForm, ex);
            errors.rejectValue(
                "url",
                "git.retrievalError",
                "The workflow could not be retrieved from the Git repository using the details given");
          } catch (WorkflowNotFoundException ex) {
            logger.warn("git.notFound " + workflowForm, ex);
            errors.rejectValue(
                "url", "git.notFound", "The workflow could not be found within the repository.");
          } catch (CWLValidationException ex) {
            logger.warn("cwl.invalid " + workflowForm, ex);
            errors.rejectValue(
                "url", "cwl.invalid", "The workflow had a parsing error: " + ex.getMessage());
          } catch (IOException ex) {
            logger.warn("url.parsingError " + workflowForm, ex);
            errors.rejectValue(
                "url", "url.parsingError", "The workflow could not be parsed from the given URL");
          }
        }
        // Redirect to main page with errors if they occurred
        if (errors.hasErrors()) {
          redirectAttrs.addFlashAttribute("errors", errors);
          return new ModelAndView("redirect:/?url=" + gitDetails.getUrl());
        }
      }
    }

    // Display this model along with the view
    if (queued != null) {
      // Retry creation if there has been an error in cwltool parsing
      if (queued.getCwltoolStatus() == CWLToolStatus.ERROR) {
        workflowService.retryCwltool(queued);
      }
      return new ModelAndView("loading", "queued", queued);
    } else {
      return new ModelAndView("workflow", "workflow", workflowModel)
          .addObject("lineSeparator", System.getProperty("line.separator"))
          .addObject("formats", WebConfig.Format.values());
    }
  }

  private Resource getGraphFromInputStream(InputStream in, String format)
      throws IOException, WorkflowNotFoundException, CWLValidationException {
    Workflow workflow =
        cwlService.parseWorkflowNative(in, null, "workflow"); // first workflow will do
    InputStream out = graphVizService.getGraphStream(workflow.getVisualisationDot(), format);
    return new InputStreamResource(out);
  }
}

common-workflow-language / cwlviewer / #1694

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Source File
Press 'n' to go to next uncovered line, 'b' for previous