gpml2pvjson/esnext/GraphIdManager.js

convert GPML (XML) to pvjson (json)

import "source-map-support/register";
// TODO should I get rid of the lib above for production browser build?
/* pvjson: "id" is a required property.
 * GPML2013a: GraphId is sometimes optional, e.g., for Groups or Anchors.
 * GPML2017: supposed to make GraphId required.
 *
 * When converting GPML2013a, we fill in any missing GraphIds so that any
 * element that MAY have a GraphId DOES have one.
 * If the GraphId is already specified, we don't change it.
 * If it is not specified, we want to generate one with these properties:
 *   1) Stability/Purity: you can convert the same GPML file any number of times
 *      and always get the same pvjson output.
 *   2) Uniqueness: don't clobber an existing GraphId in the pathway.
 *
 *   The PathVisio algorithm for GraphId generation is basically:
 *
 *   GraphId = RandomValue + IncrementingValue
 *
 *   where IncrementingValue is generated by starting with a hex value of
 *   "0xa00" for the first GraphId and incrementing that value for each
 *   subsequent GraphId:
 *   https://github.com/PathVisio/pathvisio/blob/3cb194f120de550ef2e102877965bed3c54a6a75/modules/org.pathvisio.core/src/org/pathvisio/core/biopax/BiopaxElement.java#L245
 *
 *   We want a stable output, so instead of using a random value, we use the
 *   namespace "pvjsgeneratedid", and since that's a string, we must append
 *   the IncrementingValue instead of adding it:
 *
 *   GraphId = "pvjsgeneratedid" + IncrementingValue
 */
export class GraphIdManager {
    constructor() {
        this.namespace = "pvjsgeneratedid";
        this.incrementingValueAsInt = parseInt("0xa00", 16);
    }
    generateAndRecord() {
        this.incrementingValueAsInt += 1;
        // NOTE: the namespace is not part of incrementingValueAsInt
        return this.namespace + this.incrementingValueAsInt.toString(16);
    }
    recordExisting(graphIdAsHex) {
        const { incrementingValueAsInt } = this;
        const graphIdAsInt = parseInt(graphIdAsHex, 16);
        // NOTE: this graphIdAsInt does not refer to exactly the same thing as PathVisio's
        // IncrementingValue, because it's the sum of RandomValue and IncrementingValue.
        if (graphIdAsInt > incrementingValueAsInt) {
            this.incrementingValueAsInt = graphIdAsInt;
        }
    }
}
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