Developer Feedback from Coding to the DCP

[DailyDreaming]

Summarizing some of my experience in attempting to use the API for the first time:

• It's unclear how to submit the filter param from the documentation.
• "format": "zarr" seems like it should be valid in a submission (see below).
• GET valid filters and fields return the exact same lists and it's unclear how these are different.
• The difference in the v0 and v1 endpoints don't seem to be explained.

To explain further, running a query, I was able to successfully submit a request, however the documentation does not seem to exist in constructing a "filter". I constructed a working query by inspecting:

matrix-service/tests/functional/test_matrix_service.py

Line 406 in e76e103

filter_={"op": "and",

It surprised me that the zarr file format is not accepted. So this is invalid:

{
  "feature": "gene",
  "fields": [
    "genes_detected"
  ],
  "filter": {"op": "and",
                     "value": [
                         {"op": "=",
                          "field": "library_preparation_protocol.library_construction_method.ontology",
                          "value": "EFO:0008931"},
                         {"op": "!=",
                          "field": "derived_organ_label",
                          "value": "decidua"}]},
  "format": "zarr"
}

But removing the "format": "zarr" allows for a successful submission. Also querying the valid formats does not return zarr (curl -X GET "https://matrix.dev.data.humancellatlas.org/v1/formats" -H "accept: application/json"), which does not seem intuitive to me.

[brianraymor]

Currently, Swagger UI supports example but currently does not support multiple examples. Here's a pointer to our multiple examples.

We also have vignettes in progress - #309

We do not expose zarr as an external format. See #289.

[DailyDreaming]

Zarr is still in the docs and should probably be removed and a mention added that loom is the actual default now.

@brianraymor The vignette looks awesome and enormously helpful. I think a number of other people at this breakout session found it to be useful as well.

[maximilianh]

Hmm... why would it support zarr? Should it support that ?

…

On Wed 19 Jun 2019 at 10:20, Lon Blauvelt ***@***.***> wrote: Running a query, I was able to successfully submit a request, however the documentation does not seem to exist in constructing a "filter". I constructed a working query by inspecting: https://github.com/HumanCellAtlas/matrix-service/blob/e76e1038cd388d6bc064ce95eea585a4923df82b/tests/functional/test_matrix_service.py#L406 It surprised me that the zarr file format is not accepted. So this is invalid: { "feature": "gene", "fields": [ "genes_detected" ], "filter": {"op": "and", "value": [ {"op": "=", "field": "library_preparation_protocol.library_construction_method.ontology", "value": "EFO:0008931"}, {"op": "!=", "field": "derived_organ_label", "value": "decidua"}]}, "format": "zarr" } But removing the "format": "zarr" allows for a successful submission. Also querying the valid formats does not return zarr (curl -X GET " https://matrix.dev.data.humancellatlas.org/v1/formats" -H "accept: application/json"), which does not seem intuitive to me. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#322?email_source=notifications&email_token=AACL4TI7GCWZ3XLOTFXD6FDP3H24RA5CNFSM4HZHSG22YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4G2LAAOA>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AACL4TLEUUEQAZVWJ4LK2NTP3H24RANCNFSM4HZHSG2Q> .

[brianraymor]

RE zarr references - the unsupported format is listed in README.md.