DataQualityDashboard
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OHDSI
Data Quality Dashboard Only Displaying Some Sections
So I got the shiny app to launch. The overview section is showing up. However, the sections for metadata and results are blank. The blank sections have the title, but no data. So it looks like this:
METADATA
RESULTS
Am I missing something or is this a bug?
Most likely it is not seeing the results JSON file correctly. When you launched the app, did you use this:
DataQualityDashboard::viewDqDashboard(jsonPath = "/the/full/path/to/jsonfile.json")
This is my code. I copied and pasted the the ip address below to google chrome because it was it was really warped in its display on IE. My company uses an old version so I was not surprised.
>
> DataQualityDashboard::viewDqDashboard(jsonPath = "C:/DataQualityDashboard/CDMV5.3.1/results_CDMV5.3.1.json")
Loading required package: shiny
Listening on http://127.0.0.1:7553
Yeah, IE warps pretty much most OHDSI web apps. Chrome is highly recommended here.
In Chrome, can you hit Ctrl-Shift-I to open the web developer console, then click on the Console tab to see if there are any errors being thrown?
We are getting the same problem. Here is the error from the console.
TypeError: this.results.Metadata[0] is undefined
Our metadata table is empty. I am assuming this is causing the problem. The METADATA documentation does not completely make it clear what should go in this table:
https://github.com/OHDSI/CommonDataModel/wiki/METADATA
I am assuming at the least we need one entry to describe the CDM version. So maybe the following but I have some missing values that I would appreciate some help on:
| field | value | concept_name |
|---|---|---|
| metadata_concept_id | 1147638 | OMOP CDM Version 5.3.1 |
| metadata_type_concept_id | ? | ? |
| name | ? | ? |
| value_as_string | ? | ? |
| value_as_concept_id | ? | ? |
| metadata date | ? | ? |
| metadata_datetime | ? | ? |
We use the CDM_SOURCE table to populate the Metadata section in the app, not the metadata table (which is not used at all here).
@mgurley is that table populated in your CDM?
@alondhe No the CDM_SOURCE table is not populated. I will populate CDM_SOURCE to see if it fixes the problem.
Does this fix the results not showing up either?
On Wed, Oct 9, 2019 at 2:59 PM Michael Gurley [email protected] wrote:
@alondhe https://github.com/alondhe No the CDM_SOURCE table is not populated. I will populate CDM_SOURCE to see if it fixed the problem.
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It is not very well specified that the CDM_SOURCE table needs to be populated for all results to display. I will make a note to put this in the upcoming vignette.
Okay is there supposed to be one record in this table?
On Thu, Oct 10, 2019 at 9:27 AM clairblacketer [email protected] wrote:
It is not very well specified that the CDM_SOURCE table needs to be populated for all results to display. I will make a note to put this in the upcoming vignette.
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well. there was a big discussion if one row and one row only is expected ! I am not sure the specs say one record.
When I test "Data Quality Dashboard" with [CMS SynPUF 5% Sample] data , It occurred error like bellow.
"Data Quality Dashboard" well working in 'checkLevels is ("Table") or ("Field")', But when I run the "Data Quality Dashboard ::executeDqChecks" function this error occurred in checkLevels <- c("CONCEPT").
Before I filled "CDM_SOURCE" TABLE it is well working. But After I filled "CDM_SOURCE" TABLE [Data Quality Dashboard ::executeDqChecks] is occurred error in concept checkLevel.
can I have some advice?
Docs now specify that CDM_SOURCE table must be populated: https://ohdsi.github.io/DataQualityDashboard/#data-requirements; https://ohdsi.github.io/DataQualityDashboard/articles/DataQualityDashboard.html#note
executeDqChecks also stops running & notifies user if cdm_source table is empty: https://github.com/OHDSI/DataQualityDashboard/blob/3425ba428ecfc0fd09f1324b11ac4cf35849524b/R/executeDqChecks.R#L121
