Examples with ProjectAnalysisSubmissionJoin ca.corefacility.bioinformatics.irida.model.workflow.submission.ProjectAnalysisSubmissionJoin used on opensource projects

Example 11 with ProjectAnalysisSubmissionJoin

use of ca.corefacility.bioinformatics.irida.model.workflow.submission.ProjectAnalysisSubmissionJoin in project irida by phac-nml.

the class ReadAnalysisSubmissionPermission method customPermissionAllowed.

/**
 * {@inheritDoc}
 */
@Override
protected boolean customPermissionAllowed(Authentication authentication, AnalysisSubmission analysisSubmission) {
    logger.trace("Testing permission for [" + authentication + "] on analysis submission [" + analysisSubmission + "]");
    User u = userRepository.loadUserByUsername(authentication.getName());
    if (analysisSubmission.getSubmitter().equals(u)) {
        logger.trace("Permission GRANTED for [" + authentication + "] on analysis submission [" + analysisSubmission + "]");
        return true;
    }
    /*
		 * If the user isn't set it might be shared to a project they have
		 * access to. Check the shared projects.
		 */
    List<ProjectAnalysisSubmissionJoin> projectsForSubmission = pasRepository.getProjectsForSubmission(analysisSubmission);
    boolean canReadProject = projectsForSubmission.stream().anyMatch(p -> readProjectPermission.customPermissionAllowed(authentication, p.getSubject()));
    if (canReadProject) {
        logger.trace("Permission GRANTED for [" + authentication + "] on analysis submission [" + analysisSubmission + "]");
        return true;
    }
    /*
		 * If the user isn't set it might be an automated submission. Check if
		 * this analysis is the auto assembly or sistr for a file and if they
		 * can read the file
		 */
    Set<SequencingObject> pairedInputFiles = sequencingObjectRepository.findSequencingObjectsForAnalysisSubmission(analysisSubmission);
    boolean anyMatch = pairedInputFiles.stream().filter(o -> {
        AnalysisSubmission a = o.getAutomatedAssembly();
        AnalysisSubmission s = o.getSistrTyping();
        // check auto assembly
        boolean allowed = false;
        if (a != null) {
            allowed = a.equals(analysisSubmission);
        }
        // if not check sistr
        if (!allowed && s != null) {
            allowed = s.equals(analysisSubmission);
        }
        return allowed;
    }).anyMatch(p -> seqObjectPermission.customPermissionAllowed(authentication, p));
    if (anyMatch) {
        logger.trace("Permission GRANTED for [" + authentication + "] on analysis submission [" + analysisSubmission + "]");
        return true;
    }
    logger.trace("Permission DENIED for [" + authentication + "] on analysis submission [" + analysisSubmission + "]");
    return false;
}