Fixing genes' orders in network sheet for ppi and grn

[ntran18]

No description provided.

[dondi]

Looks good, just needs a quick readability tweak

[dondi]

Solely for code readability, let’s define constants which assign a name to what the 0 and 1 IDs mean; something like:

Suggested change

	const sortGenes = function (genes, idToSort) {
	const GRN_STANDARD_NAME_ID = 1;
	const PPI_STANDARD_NAME_ID = 0;
	const sortGenes = function (genes, idToSort) {

[dondi]

That way, over here, we have named constants rather than hardcoded numbers:

Suggested change

	grnState.customWorkbook.genes = sortGenes(grnState.customWorkbook.genes, 1);
	grnState.customWorkbook.genes = sortGenes(grnState.customWorkbook.genes, GRN_STANDARD_NAME_ID);

[coveralls]

coverage: 80.379%. remained the same
when pulling e558f11 on maika-1191
into a7518fc on beta.

[dondi]

LGTM—thanks for making the revisions!

[dondi]

@ntran18 can we try something? I have been re-reviewing this PR to see why sorting behavior does not seem to be consistent with what you’re seeing locally, and I have now spotted something that I did not see before

In this version of the code, the sort operation is being done in line 213 above, and this is then converted into an object via Object.fromEntries. Then, Object.keys is used to produce the list which is ultimately sent to the workbook

Here is the wrinkle: Object attributes (the keys here) are not guaranteed to preserve their order. So, even if the object is built from sorted entries, later accesses of the object‘s keys are not guaranteed to retain that order

…which leads me back to the thing I’d like to try: can we move the sorting operation to the very end? I think that means doing the sort on these lines, once the final arrays are created

i.e., do the sort on genes and displayGenes after their contents are finalized

Let’s try that and see if it changes the results. Let me know if you need further elaboration. Thanks!

[dondi]

P.S. Note the specific phrasing here: order preservation of Object.keys is not “guaranteed.” That means the order might be preserved but it is not guaranteed to be that way. This would explain why you can see it work in your local copy, but the behavior may be different for others

[ntran18]

I agree that Object.keys doesn't preserve order. I think it's best if we can switch Object.keys to an array. I will create a new PR for this proposed change.