Argument "cohort" not working in functions

[heimannch]

@andrewelamb, adding the argument cohort to a query makes it return no results. Example below:

Before:

#getting ICI data
#datasets that we have in the iAtlas database
ici_datasets <- iatlasGraphQLClient::query_datasets(types = "ici")

#immune features of all samples in the ici datasets
features_df <- iatlasGraphQLClient::query_features(cohorts = ici_datasets$name)
head(features_df)

name	display	class	order	unit	method_tag
B_cells_Aggregate2	B Cells	Immune Cell Proportion - Common Lymphoid and Myeloid Cell Derivative Class	3	Fraction	CIBERSORT
B_cells_Aggregate3	B Cells	Immune Cell Proportion - Differentiated Lymphoid and Myeloid Cell Derivative Class	4	Fraction	CIBERSORT
B_cells_memory	B Cells Memory	Immune Cell Proportion - Original	9	Fraction	CIBERSORT
B_cells_naive	B Cells Naive	Immune Cell Proportion - Original	8	Fraction	CIBERSORT
BIOCARTA_CTLA4_V_Bindea_Th1_Cells	CTLA4 vs Th1	Predictor of Response to Immune Checkpoint Treatment	NA	Fraction	NA
Cytolytic_Score	Cytolytic Score	Predictor of Response to Immune Checkpoint Treatment	NA	Score	NA

Now:

#getting ICI data
ici_datasets <- iatlasGraphQLClient::query_datasets(types = "ici")

features_df <- iatlasGraphQLClient::query_features(cohorts = ici_datasets$name)

# now, this query returns nothing:
head(features_df)
# A tibble: 0 × 6
# ℹ 6 variables: name <chr>, display <chr>, class <chr>, order <int>, unit <chr>, method_tag <chr>

This was observed for the following queries:

iatlasGraphQLClient::query_features()
iatlasGraphQLClient::query_tags()
iatlasGraphQLClient::query_genes()

I am using iatlasGraphQLClient_0.2.4 and the live database.

This is only affecting a few notebooks, the web app is working fine - so this is not an urgent issue.

[heimannch]

Update: I decided to be more explicit in setting the database version used, and with that I noticed that this issue only happens in the current staging database.

.GlobalEnv$API_URL <- "https://api.cri-iatlas.org/api"
# queries work fine!

.GlobalEnv$API_URL <- "https://api-staging.cri-iatlas.org/api"
# issue happens