Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -20,7 +20,7 @@ Imports: | |
| stringr, | ||
| tibble | ||
| Remotes: | ||
| hillalex/porcelain@i39, | ||
| Suggests: | ||
| fs, | ||
| lintr (>= 3.1.2), | ||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,116 @@ | ||
| test_that("GET /", { | ||
| res <- target_get_root() | ||
| expect_equal(res, jsonlite::unbox("Welcome to serovizr")) | ||
|
|
||
| endpoint <- get_root() | ||
| res_endpoint <- endpoint$run() | ||
| expect_equal(res_endpoint$status_code, 200) | ||
| expect_equal(res_endpoint$content_type, "application/json") | ||
| expect_equal(res_endpoint$data, res) | ||
|
|
||
| router <- build_routes() | ||
| res_api <- router$request("GET", "/") | ||
| expect_equal(res_api$status, 200) | ||
| expect_equal(res_api$body, res_endpoint$body) | ||
| }) | ||
|
|
||
| test_that("GET /version", { | ||
| res <- target_get_version() | ||
| expect_equal(res, jsonlite::unbox(as.character(packageVersion("serovizr")))) | ||
|
|
||
| router <- build_routes() | ||
| res_api <- router$request("GET", "/version/") | ||
| expect_equal(res_api$status, 200) | ||
| body <- jsonlite::fromJSON(res_api$body) | ||
| expect_equal(unclass(res), unclass(body$data)) | ||
| }) | ||
|
|
||
| test_that("POST /dataset", { | ||
| router <- build_routes() | ||
| request <- local_POST_dataset_request(data.frame(biomarker = "ab", | ||
| value = 1, | ||
| day = 1:10), | ||
| "testdataset") | ||
| res <- router$call(request) | ||
| expect_equal(res$status, 200) | ||
| body <- jsonlite::fromJSON(res$body) | ||
| expect_equal(body$data, "testdataset") | ||
| porcelain:::porcelain_validator("ResponseSuccess", | ||
| root = schema_root, | ||
| query = NULL)(res$body) | ||
| porcelain:::porcelain_validator("UploadResult", | ||
| root = schema_root, | ||
| query = NULL)( | ||
| jsonlite::toJSON(body$data, auto_unbox = TRUE) | ||
| ) | ||
| }) | ||
|
|
||
| test_that("GET /datasets", { | ||
| local_add_dataset(data.frame(biomarker = "ab", value = 1, day = 1:10), | ||
| "testdataset") | ||
| local_add_dataset(data.frame(biomarker = "ab", value = 1, day = 1:10), | ||
| "anotherdataset") | ||
| router <- build_routes() | ||
| set.seed(1) | ||
| res <- router$request("GET", "/datasets/") | ||
| expect_equal(res$status, 200) | ||
| body <- jsonlite::fromJSON(res$body) | ||
| expect_equal(body$data, c("anotherdataset", "testdataset")) | ||
| }) | ||
|
|
||
| test_that("GET /dataset<name>", { | ||
| local_add_dataset(data.frame(biomarker = c("ab", "ba"), | ||
| value = 1, | ||
| day = 1:10, | ||
| age = "0-5", | ||
| sex = c("M", "F")), | ||
| "testdataset") | ||
| router <- build_routes() | ||
| set.seed(1) | ||
| res <- router$request("GET", "/dataset/testdataset/") | ||
| expect_equal(res$status, 200) | ||
| body <- jsonlite::fromJSON(res$body) | ||
| expect_equal(body$data$variables$name, c("age", "sex")) | ||
| expect_equal(body$data$variables$levels, list(c("0-5"), c("M", "F"))) | ||
| expect_equal(body$data$biomarkers, c("ab", "ba")) | ||
| expect_equal(body$data$xcol, "day") | ||
| }) | ||
|
|
||
| test_that("GET /dataset/<name>/trace/<biomarker>", { | ||
| dat <- data.frame(biomarker = c("ab", "ba"), | ||
| value = c(1, 1.5, 2, 3, 3.2, 4, 5, 6, 6.1, 7), | ||
| day = 1:10, | ||
| age = "0-5", | ||
| sex = c("M", "F")) | ||
| local_add_dataset(dat, | ||
| "testdataset") | ||
| suppressWarnings({ | ||
| m <- stats::loess(value ~ day, data = dat[dat["biomarker"] == "ab",], span = 0.75) | ||
| model <- list(x = 1:9, y = stats::predict(m, tibble::data_frame(day = 1:9))) | ||
| }) | ||
| router <- build_routes() | ||
| set.seed(1) | ||
| res <- router$request("GET", "/dataset/testdataset/trace/ab/") | ||
| expect_equal(res$status, 200) | ||
| expected_warnings <- list("span too small. fewer data values than degrees of freedom.", | ||
| "pseudoinverse used at 0.96", | ||
| "neighborhood radius 4.04", | ||
| "reciprocal condition number 0", | ||
| "There are other near singularities as well. 16.322") | ||
| expected <- jsonlite::toJSON(list(list(name = jsonlite::unbox("all"), | ||
| model = model, | ||
| raw = list( | ||
| x = c(1, 3, 5, 7, 9), | ||
| y = c(1, 2, 3.2, 5, 6.1)), | ||
| warnings = lapply(expected_warnings, | ||
| jsonlite::unbox)) | ||
| )) | ||
| body <- jsonlite::fromJSON(res$body) | ||
| expect_equal(body$data, jsonlite::fromJSON(expected)) | ||
| }) | ||
|
|
||
| test_that("requests without trailing slash are redirected", { | ||
| router <- build_routes() | ||
| res_api <- router$request("GET", "/version") | ||
| expect_equal(res_api$status, 307) | ||
| }) |
Oops, something went wrong.