Species filter is getting ignored in the metadata search

[ke4]

The Species filter in the metadata search is getting ignored.

Steps to reproduce:

1. Go to the metadata search in Single Cell Expression Atlas
2. Type a search term into the Search term box. For example: liver
3. Click on the Search button
4. On the appearing cell type wheel page select a Species from the dropdown, for example: Mus musculus

Expected result:
The cell type wheel only shows the result for the selected species.

Actual result:
The cell type wheel shows the result for all the species.

The above description was a bit confusing:

So, I'm adding here detailed requirements after our meeting

Use cases:

• 1. Gene search

• Go to SCXA Home

• Enter a gene ID/Symbol as a search term(pick only from gene Symbol category) and species drop-down -> any/choose species and click search

• Now expected and actual are the same as we will be on the "gene-search-results" page

  Endpoint: json/search

• 2. Metadata search

  • Go to SCXA Home
  • Enter the organism part as a search term (pick only from the metadata category from the popup suggestions for the organism part). Example: liver
  • Choose a species or default to 'any'
  • Click on 'search' button

Now expected and actual is the "cell-type-wheel-experiment-heatmap" page with the cell-type wheel data

Bug

• 3. Metadata search

  • Go to SCXA Home
  • Enter the organism part as a search term (pick only from the metadata category from the popup suggestions for the organism part). Example: liver
  • Choose a species mus musculus
  • Click on 'search' button

  Expected is: cell type wheel should refresh only species mus musculus data + search term(liver)
  Actual is: Cell type wheel data still contains multiple species data

Bug fix - The Cell type wheel should refresh based on the user search term input and species drop-down value(Input) after pressing the 'search' button

Expected and actual - Wheel data should be user-selected species data with the mentioned organism part

Note: Follow the metadata rule as I mentioned in the point 2

Endpoint navigation in the backend for points 2 and 3 is the same as I provided here:

Endpoint1- json/search -> redirects to Endpoint2
Endpoint2- /search/metadata/{term} ->Produce HTML response
Endpoint3- /json/cell-type-wheel/{searchTerm} -> Json payload

[upendrakumbham]

During my investigation, I found that we are supporting from the backend - but we are not passing species param from the frontend I believe as per the code:

@GetMapping(value = "/json/cell-type-wheel/{searchTerm}",
                produces = MediaType.APPLICATION_JSON_UTF8_VALUE)
    public String jsonCellTypeWheel(@PathVariable String searchTerm,
                                    @RequestParam(name = "species", defaultValue = "") String species) {
        return GSON.toJson(
                highchartsSunburstAdapter
                        .getCellTypeWheelSunburst(searchTerm, cellTypeWheelService.search(searchTerm, species)));
    }

[upendrakumbham]

In the Atlas components repo - file name - CellTypeWheelExperimentHeatmap.js

 <CellTypeWheelFetchLoader
              host={props.host}
              resource={URI(props.searchTerm, props.cellTypeWheelResource).toString()}
              fulfilledPayloadProvider={cellTypeWheelData => ({ data: cellTypeWheelData })}
              searchTerm={props.searchTerm}
              onCellTypeWheelClick={onCellTypeWheelClick}
            />

I believe we need to pass species here from the dropdown when user chooses a species along with search term

[lingyun1010]

Bugs we observed for now related to cell type wheel gene expression page:

1. From home page to cell type wheel page, species is not passed by routing/URL.

2. In the cell type wheel page

   Search boxes

   • species box is not always working: it is not working when you change the species alone but is working when you change the species and then followed by search term changes
   • search term box is not always working: when you select from user free typing section, for example liver, no cell type data responded; when you select from metadata section, search button is not trigerring any requests.

   Cell type wheel

   • it doesn't take species parameter from the search box
   • when there are a lot of data loaded, for example, homo sapiens, it doesn't display by giving info like no data to display
   • when the search term is species like homo sapiens , the cell type wheel is not working by clicking to show the marker gene heatmap view.

3. Endpoint issue

• Species parameter is not working under this json endpoint, as we can see these are the same response:
  With species
  Without species

[ke4]

Based on the previous comment by @lingyun1010 I created the following separate tickets:

• Species parameter is not passed from homepage
• Search button not working after an initial metadata search

and we already had this ticket:

• Wrong message when cell type wheel got too much data to display

I won't delete the above comment, just to have it if we need it, but that comment does not belong to this current ticket.

[ke4]

We need another PR for single cell repo where we are using the latest components from atlas-components repo.
Thanks