Metadata & Attributes

Properties as h5 metadata attributes

Attributes can be attached to Groups by flush after the properties are added to javascript group instance. Prototype properties also get flushed. Because javascript has the ability to have property names with spaces via [ ‘’ ] these readily map to h5’s similar nature.

var groupTargets=file.createGroup('pmcservices/sodium-icosanoate');
groupTargets['Computed Heat of Formation' ] = -221.78436098572274;
groupTargets['Computed Ionization Potential' ] = 9.57689311885752;
groupTargets['Computed Total Energy' ] = -3573.674399276322;
groupTargets.Status = 256;
groupTargets.Information = "\"There are no solutions; there are only trade-offs.\" -- Thomas Sowell";
groupTargets.flush();

Types are allowed to change to match the javascript side. If an attribute is already there it will get updated by h5’s existence check, removed and then added back. When opening an h5 the group’s attributes can be refreshed to the javascript in a reverse manner

var groupTarget = file.openGroup('pmcservices/sodium-icosanoate');
groupTarget.refresh();
console.dir(groupTarget.['Computed Heat Of Formation']);
console.dir(groupTarget.Information);

For the attributes on datasets a representative object can be obtained from Group.prototype.getDatasetAttributes with the attributes on as properties. Since h5 attributes can be arrays they are returned in javascript Arrays. So need to check the constructor for Array.

var group = file.openGroup('pmc/refinement');
var attrs = group.getDatasetAttributes("Data");
var attrText = '';
Object.getOwnPropertyNames(attrs).forEach(function(val, idx, array) {
  if (val !=  'id') {
    if (attrs[val].constructor.name === Array) {
      attrText += val + ' :  ';
      for (var mIndex = 0; mIndex < attrs[val].Length(); mIndex++) {
        attrText += attrs[val][mIndex];
        if (mIndex < attrs[val].Length() - 1) {
          attrText += ',';
        }
      }
    }
    else{
      attrText += val + ' :  ' + attrs[val] + '\n';
    }
  }
});

If attribute names conflict with this API you can read the attributes separately using destructuring assignment:

    var group, attrs;
    [group, attrs]= file.openGroup('pmc/refinement', {separate_attributes: true});

If you want to delete an attribute on the file or a group

group.deleteAttribute("unitCell");

or

delete group.unitCell;

both will delete from the h5 without any further steps.