AchillesWeb: Java script error on Observation Period tab

Megha_Maheshwari · June 1, 2017, 7:43am

Hi All,

I have exported the Achilles Result to JSON. I am facing issue with Observation Period tab as data is not getting displayed.
When I checked the console, I could see there is an JavaScript error.

Please find below the screenshot of error:

When I backtracked to code, it seems to be ok.

Any help would be greatly appreciated.

Chris_Knoll · June 1, 2017, 2:44pm

If it says ‘map is not a function’, it means that the target of the call to .map() is not an array. Can you check your JSON file and check what is being returned in the object:
AGE_BY_GENDER.CATEGORY

This should be an array.

Megha_Maheshwari · June 2, 2017, 5:51am

Hey Chris,

I check the JSON file for observation period it is an array only. Please find below screenshot of JSON.
Is there anything else that I can check ??

Chris_Knoll · June 2, 2017, 3:29pm

I can see in your screenshot that the AGE_BY_GENDER property is a single object element with 4 properties. I think this is a problem with the rjson serialization that doesn’t create arrays around single row results. The json structure you have is:

AGE_BY_GENDER: { "CATEGORY": "FEMALE", "MIN_VALUE": 4, "P10_VALUE": 22, "P25_VALUE": 34 ....}

What it should be is:

AGE_BY_GENDER: {"CATEGORY": ["FEMALE"], "MIN_VALUE": [4], "P10_VALUE": [22] ...

So, it looks like your database only has females? We’ve seen this issue in the past and there’s a ‘normalizeDataframe’
function that we call on a result property to make the elements in it arrays instead of the single-value objects.

Here’s an example where it is called:

github.com

OHDSI/AchillesWeb/blob/8750eb13ee64d3ef7e504abd5ec491779bf806b5/js/app/reports/visit_occurrence.js#L33


					$('.drilldown svg').remove();
					$('#visitDrilldownTitle').text(concept_name);
					$('#reportVisitOccurrencesDrilldown').removeClass('hidden');


					$.ajax({
						type: "GET",
						url: getUrlFromDataCollection(page_vm.datasource(), "visits", concept_id),
						success: function (data) {


							// render trellis
							trellisData = common.normalizeDataframe(data.PREVALENCE_BY_GENDER_AGE_YEAR);


							var allDeciles = ["0-9", "10-19", "20-29", "30-39", "40-49", "50-59", "60-69", "70-79", "80-89", "90-99"];
							var allSeries = ["MALE", "FEMALE"];
							var minYear = d3.min(trellisData.X_CALENDAR_YEAR),
								maxYear = d3.max(trellisData.X_CALENDAR_YEAR);


							var seriesInitializer = function (tName, sName, x, y) {
								return {
									TRELLIS_NAME: tName,
									SERIES_NAME: sName,

What we need to do is call that function on the AGE_BY_GENDER object before it renders into the plot. I can make a branch and pr on this. I’ll open up an issue on git and we can track it there.

Chris_Knoll · June 2, 2017, 3:48pm

@Megha_Maheshwari
I’ve pushed up a branch with an attempt to fix your issue. The branch is called ‘issue-64’ and you can see it here:

Would you be able to pull that branch down and confirm in your environment before I merge into master? There may be other issues uncovered by your dataset’s characteristics, and I’d prefer to capture all the issues before making a merge into master.

If you aren’t familiar with pulling and checking out the branch, I understand and I’ll merge it into master if you are unable to verify the branch.

Megha_Maheshwari · June 4, 2017, 9:55am

@Chris_Knoll
I tested the updated code (for Achilles.js). Issue with Observation Period tab is resolved. I am not familiar with pulling and checking out the branch. Could you please do that.

I am facing problem with Drug and Drug Era tab.For these two table ,export_to_JSON results in no files. When I backtracked and checked, it seems SQL queries for Drug tables export have join with vocabulary ATC and for our conversion we have used vocabulary NDC. So I just wanted to check with you whether it is expected that for conversion only ATC vocabulary will be used? Let me know if my understanding is wrong.

Chris_Knoll · June 4, 2017, 4:45pm

Do you mean that you are storing NDC concepts directly into the drug exposure table as the drug_concept_id?

Megha_Maheshwari · June 4, 2017, 5:09pm

Yes…we are not using standard concepts.
Just wanted to check on that part.

Chris_Knoll · June 5, 2017, 2:37pm

Right, not using standard concepts will not allow a rollup from a drug exposure (found in the RxNorm vocabulary) to the ingredient or ATC class.This is required for the drug exposure/drug era reports.