RC3 - 1.0.0-final catalog permission migration. This will need first https://gist.github.com/pfurio/f7cd90af08e0073699f0beeeef1958ba

permissionMigration.js

migrateCollection("metadata", {}, {config: 1, acl: 1}, function (bulk, doc) {
    var id = doc._id;
 
    var permissions = ["VIEW_FILE_HEADERS", "VIEW_FILE_CONTENTS", "VIEW_FILES", "WRITE_FILES", "VIEW_JOBS", "WRITE_JOBS"];
    doc.acl[0].permissions = permissions;
    doc.config.acl[0].permissions = permissions;
 
    bulk.find({_id: id}).update({$set: {"acl": doc.acl, "config.acl": doc.config.acl}});
});
 
 
migrateCollection("study", {acl:{$exists:true, $ne: []}}, {acl:1}, function (bulk, doc) {
    var ref = doc.reference;
    var id = doc._id;
 
    var modified = false;
    for (var i in doc.acl) {
        var acl = doc.acl[i];
        var permissions = [];
 
        var writeVariable = false;
        var writeFiles = false;
        var writeJobs = false;
        var writeSamples = false;
        var writeSampleAnnotations = false;
        var writeIndividuals = false;
        var writeIndividualAnnotations = false;
        var writeCohort = false;
        var writeCohortAnnotations = false;
        var writeDatasets = false;
        var writePanels = false;
 
        for (var j in acl.permissions) {
            var permission = acl.permissions[j];
 
            switch(permission) {
                case "CREATE_VARIABLE_SET":
                case "UPDATE_VARIABLE_SET":
                    modified = true;
                    writeVariable = true;
                    break;
                case "CREATE_FILES":
                case "UPDATE_FILES":
                    modified = true;
                    writeFiles = true;
                    break;
                case "CREATE_JOBS":
                case "UPDATE_JOBS":
                    modified = true;
                    writeJobs = true;
                    break;
                case "CREATE_SAMPLES":
                case "UPDATE_SAMPLES":
                    modified = true;
                    writeSamples = true;
                    break;
                case "CREATE_SAMPLE_ANNOTATIONS":
                case "UPDATE_SAMPLE_ANNOTATIONS":
                    modified = true;
                    writeSampleAnnotations = true;
                    break;
                case "CREATE_INDIVIDUALS":
                case "UPDATE_INDIVIDUALS":
                    modified = true;
                    writeIndividuals = true;
                    break;
                case "CREATE_INDIVIDUAL_ANNOTATIONS":
                case "UPDATE_INDIVIDUAL_ANNOTATIONS":
                    modified = true;
                    writeIndividualAnnotations = true;
                    break;
                case "CREATE_COHORTS":
                case "UPDATE_COHORTS":
                    modified = true;
                    writeCohort = true;
                    break;
                case "CREATE_COHORT_ANNOTATIONS":
                case "UPDATE_COHORT_ANNOTATIONS":
                    modified = true;
                    writeCohortAnnotations = true;
                    break;
                case "CREATE_DATASETS":
                case "UPDATE_DATASETS":
                    modified = true;
                    writeDatasets = true;
                    break;
                case "CREATE_PANELS":
                case "UPDATE_PANELS":
                    modified = true;
                    writePanels = true;
                    break;
                default:
                    permissions.push(permission);
                    break;
            }
        }
 
        if (writeVariable) {
            permissions.push("WRITE_VARIABLE_SET");
        }
        if (writeFiles) {
            permissions.push("WRITE_FILES");
        }
        if (writeJobs) {
            permissions.push("WRITE_JOBS");
        }
        if (writeSamples) {
            permissions.push("WRITE_SAMPLES");
        }
        if (writeSampleAnnotations) {
            permissions.push("WRITE_SAMPLE_ANNOTATIONS");
        }
        if (writeIndividuals) {
            permissions.push("WRITE_INDIVIDUALS");
        }
        if (writeIndividualAnnotations) {
            permissions.push("WRITE_INDIVIDUAL_ANNOTATIONS");
        }
        if (writeCohort) {
            permissions.push("WRITE_COHORTS");
        }
        if (writeCohortAnnotations) {
            permissions.push("WRITE_COHORT_ANNOTATIONS");
        }
        if (writeDatasets) {
            permissions.push("WRITE_DATASETS");
        }
        if (writePanels) {
            permissions.push("WRITE_PANELS");
        }
 
        doc.acl[i].permissions = permissions;
    }
 
    if (modified) {
        print("Updating permissions from study: _id : '" + id + "'");
        bulk.find({_id: id}).update({$set: {"acl": doc.acl}});
    }
});