Closed johnbradley closed 8 months ago
When running the tests locally the following 500 errors occur:
══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-semsim.R:66:3'): Resnik similarity ───────────────────────────── <http_500/error/condition> Error in `get_csv_data(pkb_api("/similarity/frequency"), query = query, header = FALSE, row.names = 1, check.names = FALSE)`: (500) Internal Server Error: There was an internal server error. Backtrace: ▆ 1. └─rphenoscape::resnik_similarity(...) at test-semsim.R:66:3 2. ├─base::do.call(wt, wt_args) 3. └─rphenoscape (local) `<fn>`(as = "phenotype", corpus = "taxon-variation", x = `<chr>`) 4. └─rphenoscape:::get_csv_data(...) 5. └─rphenoscape:::stop_for_pk_status(res) ── Error ('test-semsim.R:135:3'): profile similarity with Resnik ─────────────── <http_500/error/condition> Error in `get_csv_data(pkb_api("/similarity/frequency"), query = query, header = FALSE, row.names = 1, check.names = FALSE)`: (500) Internal Server Error: There was an internal server error. Backtrace: ▆ 1. └─rphenoscape::term_freqs(...) at test-semsim.R:135:3 2. └─rphenoscape:::get_csv_data(...) 3. └─rphenoscape:::stop_for_pk_status(res) [ FAIL 2 | WARN 0 | SKIP 0 | PASS 640 ]
One of the errors can be also seen by running the following code:
phens <- get_phenotypes("basihyal bone", taxon = "Cyprinidae") subs.mat <- subsumer_matrix(phens$id, .colnames = "label", .labels = phens$label, preserveOrder = TRUE) > sm.ic <- resnik_similarity(subs.mat, wt_args = list(as = "phenotype", corpus = "taxon-variation")) Error in get_csv_data(pkb_api("/similarity/frequency"), query = query, : (500) Internal Server Error: There was an internal server error.
This error does not occur during the CircleCI tests because of the skip_on_cran() function.
skip_on_cran()
@balhoff fixed this by increasing Qlever resources in the phenoscape KB API service.
When running the tests locally the following 500 errors occur:
One of the errors can be also seen by running the following code:
This error does not occur during the CircleCI tests because of the
skip_on_cran()
function.