Opencga 1.1.0 migration

opencga-1.1.0-migration.js

// Use migration script https://gist.github.com/pfurio/f7cd90af08e0073699f0beeeef1958ba

/*
Migrate NUMERIC variables to DOUBLE https://github.com/opencb/opencga/issues/545
*/

// This function receives an array of variables (not variableSet),
// and will modify NUMERIC variables to DOUBLE recursively
function modifyNumeric(variables) {
    var modified = false;

    if (typeof variables === "undefined" || variables === null || variables.length == 0) {
        return modified;
    }
    for (var i in variables) {
        var variable = variables[i];
        if (variable.type === "NUMERIC") {
            variable.type = "DOUBLE";
            modified = true;
        } else if (typeof variable.variableSet !== "undefined") {
            if (modifyNumeric(variable.variableSet)) {
                modified = true;
            }
        }
    }
    return modified;
}

migrateCollection("study", {"variableSets" : { $exists: true, $ne: [] } }, {}, function(bulk, doc) {
    var modified = false;
    var variableSets = doc.variableSets;
    for (i in variableSets) {
        modified = modifyNumeric(variableSets[i].variables);
    }

    if (modified) {
        print("Migrating variable sets from study "  + doc.alias);
        bulk.find({"_id": doc._id}).updateOne({"$set": {"variableSets": variableSets}});
    }
});

/*
Create indexes for new family collection https://github.com/opencb/opencga/issues/582
*/
db.family.createIndex({"name": 1, "_studyId": 1}, {"unique": true});
db.family.createIndex({"mother.id": 1}, {});
db.family.createIndex({"father.id": 1}, {});
db.family.createIndex({"children.id": 1}, {});
db.family.createIndex({"acl.member": 1, "_studyId": 1}, {});
db.family.createIndex({"status.name": 1, "_studyId": 1}, {});
db.family.createIndex({"annotationSets.name": 1}, {});
db.family.createIndex({"annotationSets.variableSetId": 1}, {});
db.family.createIndex({"annotationSets.annotations.name": 1, "annotationSets.annotations.value": 1}, {});