hubmapconsortium/ccf-asct-reporter

How to handle 'skips' in AS/x chains?

Closed this issue · 2 comments

Some tables have rows that have blanks in the AS that causes crashes. The authors should correct this mistake. We need to come to a consensus on what we can/should do to help with this. We could show an informative message when detected and not show the table or we could skip the blank AS's assuming they just didn't move the descendant AS to the left, but also include a warning noting this.

Hi Bruce, I'm getting an unexpected empty object at the end of one of the anatomical structure lists in the Knee table. Both versions have the same problem. I've checked the table, and after Transitional Zone, it begins the CL list. Could you check this, please?
"anatomical_structures": [
{
"name": "knee",
"id": "UBERON:0001465",
"rdfs_label": "knee"
},
{
"name": "knee joint",
"id": "UBERON:0001485",
"rdfs_label": "knee joint",
"notes": "Stifle joint in mammals"
},
{
"name": "Distal Femur",
"id": "UBERON:0009980",
"rdfs_label": "condyle of femur"
},
{
"name": "Transitional Zone",
"id": "",
"rdfs_label": ""
},
{}
],

[Bruce]: Ah, I see it, row 41 and 43 of v1.0 (probably same for DRAFT) have nothing in it for AS/5, but does for AS/6. Which is a no-no. The asctb-api should also deal with this in a consistent way (probably returning an error object that states this problem)

Here is an example of how it worked previously, even though wrongly. #284

This is currently handled by skipping the blank AS and assumes the table author just skipped those columns for whatever reason. Works and doesn't break anything, but could result in wrong results if they intended for the blanks to be filled with the row from above. It looks like they intend it to be just skipped like we're doing now.