@Override public Collection<Project> listAllProjectsByShortname() throws IOException { List<Project> sortedProjects = (ArrayList<Project>) projectStore.listAll(); /** * Uses String.compareTo to alphabetically sort Projects by shortname */ sortedProjects.sort((Project p1, Project p2) -> p1.getShortName().compareTo(p2.getShortName())); return authorizationManager.filterUnreadable(sortedProjects); }
private String generateIdentityAlias(SampleIdentity identity) throws IOException { if (identity.getProject().getShortName() == null) { throw new NullPointerException("Project shortname required to generate Identity alias"); } String internalName = identity.getProject().getShortName() + "_"; String number = sampleNumberPerProjectService.nextNumber(identity.getProject(), internalName); internalName += number; return internalName; }
@Override public String getDeleteDescription() { Project p = getProject(); return (p.getShortName() == null ? p.getAlias() : p.getShortName()) + " " + getName() + " (" + getAlias() + ")"; }
@Override public String getDeleteDescription() { Project p = getParentProject(); return (p.getShortName() == null ? p.getAlias() : p.getShortName()) + " - " + getAlias() + (getAlias().equals(getDescription()) ? "" : " (" + getDescription() + ")"); }
public static ProjectDto asDto(@Nonnull Project from) { ProjectDto dto = new ProjectDto(); dto.setId(from.getId()); dto.setName(from.getName()); dto.setAlias(from.getAlias()); dto.setShortName(from.getShortName()); dto.setDescription(from.getDescription()); dto.setProgress(from.getProgress().getKey()); if (from.getReferenceGenome() != null) { dto.setDefaultSciName(from.getReferenceGenome().getDefaultSciName()); } return dto; }
@Override public long saveProject(Project project) throws IOException { ValidationResult shortNameValidation = namingScheme.validateProjectShortName(project.getShortName()); if (!shortNameValidation.isValid()) { throw new IOException("Cannot save project - invalid shortName: " + shortNameValidation.getMessage()); original.setDefaultTargetedSequencing(null); original.setShortName(project.getShortName()); updateSecurityProfile(original.getSecurityProfile(), project.getSecurityProfile()); project = original;
if (isUniqueExternalNameWithinProjectRequired() && isExternalNameDuplicatedInProject(sample)) { throw new IllegalArgumentException("Sample with external name '" + ((SampleIdentity) sample).getExternalName() + "' already exists in project " + sample.getProject().getShortName());
v.setProjectId(proj.getId()); v.setProjectName(proj.getName()); v.setProjectShortName(proj.getShortName());