Package com.eaglegenomics.simlims.core

Examples of com.eaglegenomics.simlims.core.User

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      throw new IllegalStateException("Cannot convert more or less than 4 96 well plates into a single 384 well plate");
    }
    else {
      Map<Integer, _96WellPlate> convertedPlateMap = new HashMap<Integer, _96WellPlate>();
      for (int i = 0; i < plates.size(); i++) {
        User owner = plates.get(i).getSecurityProfile().getOwner();
        _96WellPlate p = new _96WellPlate(owner);
        convertedPlateMap.put((i+1), p);
      }

      //_96WellPlates are in a 12x8 (A01-A12,B01-B12 etc) configuration
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  @RequestMapping(value = "/new/{projectId}", method = RequestMethod.GET)
  public ModelAndView newAssignedProject(@PathVariable Long projectId,
                                         ModelMap model) throws IOException {
    try {
      User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());

      StringBuilder a = new StringBuilder();
      StringBuilder b = new StringBuilder();

      for (Platform platform : requestManager.listAllPlatforms()) {
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  }

  @RequestMapping(value = "/project/{projectId}")
  public void fireGetProjectReport(@PathVariable("projectId") Long projectId, ModelMap modelMap, HttpServletResponse response) {

    User user = null;
    String format = PDF;
    try {
      user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
      Project project = projectId == AbstractProject.UNSAVED_ID ? null : requestManager.getProjectById(projectId);
      if (project != null) {
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  @RequestMapping(value = "/sample/{sampleId}")
  public void fireGetSampleReport(@PathVariable("sampleId") Long sampleId, ModelMap modelMap, HttpServletResponse response) {

    User user = null;
    String format = PDF;
    try {
      user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
      Sample sample = sampleId == AbstractSample.UNSAVED_ID ? null : requestManager.getSampleById(sampleId);
      if (sample != null) {
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    }
  }

  @RequestMapping(value = "/samples", method = RequestMethod.GET)
  public void fireGetSamplesReport(ModelMap modelMap, HttpServletResponse response) {
    User user = null;
    String format = PDF;
    try {
      user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
      try {
        if (format.equals(PDF)) {
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  }

  @RequestMapping(value = "/run/{runId}")
  public void fireGetRunReport(@PathVariable("runId") Long runId, ModelMap modelMap, HttpServletResponse response) {

    User user = null;
    String format = PDF;
    try {
      user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
      Run run = runId == AbstractRun.UNSAVED_ID ? null : requestManager.getRunById(runId);
      if (run != null) {
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  @RequestMapping(value = "/project/{id}/{hashcode}", method = RequestMethod.GET)
  protected void downloadProjectFile(@PathVariable Long id,
                                     @PathVariable Integer hashcode,
                                     HttpServletResponse response)
          throws Exception {
    User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
    Project project = requestManager.getProjectById(id);
    if (project.userCanRead(user)) {
      lookupAndRetrieveFile(Project.class, id.toString(), hashcode, response);
    }
    else {
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  @RequestMapping(value = "/plate/forms/{hashcode}", method = RequestMethod.GET)
  protected void downloadPlateExportFile(@PathVariable Integer hashcode,
                                     HttpServletResponse response)
      throws Exception {
    User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
      lookupAndRetrieveFile(Plate.class,  "forms", hashcode, response);
  }
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  @RequestMapping(value = "/submission/{id}/{hashcode}", method = RequestMethod.GET)
  protected void downloadSubmissionFile(@PathVariable Long id,
                                     @PathVariable Integer hashcode,
                                     HttpServletResponse response)
          throws Exception {
    User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
    Submission submission = requestManager.getSubmissionById(id);
    if (submission.userCanRead(user)) {
      lookupAndRetrieveFile(Submission.class, "SUB"+id, hashcode, response);
    }
    else {
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  @RequestMapping(value = "/libraryqc/{id}/{hashcode}", method = RequestMethod.GET)
  protected void downloadLibraryQcFile(@PathVariable Long id,
                                     @PathVariable Integer hashcode,
                                     HttpServletResponse response)
          throws Exception {
    User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
    Library library = requestManager.getLibraryById(id);
    if (library.userCanRead(user)) {
      lookupAndRetrieveFile(LibraryQC.class, id.toString(), hashcode, response);
    }
    else {
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Related Classes of com.eaglegenomics.simlims.core.User

  • uk.ac.bbsrc.tgac.miso.core.data.impl.UserImpl
  • uk.ac.bbsrc.tgac.miso.core.event.impl.SystemAlert
  • uk.ac.bbsrc.tgac.miso.core.event.manager.PoolAlertManager
  • uk.ac.bbsrc.tgac.miso.core.event.manager.ProjectAlertManager
  • uk.ac.bbsrc.tgac.miso.core.event.manager.RunAlertManager
  • uk.ac.bbsrc.tgac.miso.core.manager.UserAuthMisoRequestManager
  • uk.ac.bbsrc.tgac.miso.core.security.LDAPSecurityManager
  • uk.ac.bbsrc.tgac.miso.core.service.plate.Default384WellPlateConversionStrategy
  • uk.ac.bbsrc.tgac.miso.core.service.printing.factory.FileGeneratingBarcodeLabelFactory
  • uk.ac.bbsrc.tgac.miso.core.service.printing.factory.ImageRasterBarcodeLabelFactory
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