setup({
sc <- testthat_spark_connection()
text_tbl <- testthat_tbl("test_text")
# These lines should set a pipeline that will ultimately create the columns needed for testing the annotator
assembler <- nlp_document_assembler(sc, input_col = "text", output_col = "document")
sentdetect <- nlp_sentence_detector(sc, input_cols = c("document"), output_col = "sentence")
tokenizer <- nlp_tokenizer(sc, input_cols = c("sentence"), output_col = "token")
embeddings <- nlp_word_embeddings_pretrained(sc, name = "embeddings_clinical", input_cols = c("sentence", "token"),
output_col = "embeddings", remote_loc = "clinical/models")
ner_model <- nlp_ner_dl_pretrained(sc, name = "ner_radiology", input_cols = c("sentence", "token", "embeddings"),
output_col = "ner", lang = "en", remote_loc = "clinical/models")
pipeline <- ml_pipeline(assembler, sentdetect, tokenizer, embeddings, ner_model)
test_data <- ml_fit_and_transform(pipeline, text_tbl)
assign("sc", sc, envir = parent.frame())
assign("pipeline", pipeline, envir = parent.frame())
assign("test_data", test_data, envir = parent.frame())
})
teardown({
rm(sc, envir = .GlobalEnv)
rm(pipeline, envir = .GlobalEnv)
rm(test_data, envir = .GlobalEnv)
})
test_that("ner_chunker param setting", {
test_args <- list(
input_cols = c("string1", "string2"),
output_col = "string1",
regex_parsers = c("string1", "string2")
)
test_param_setting(sc, nlp_ner_chunker, test_args)
})
test_that("nlp_ner_chunker spark_connection", {
test_annotator <- nlp_ner_chunker(sc, input_cols = c("sentence","ner"), output_col = "ner_chunk")
transformed_data <- ml_transform(test_annotator, test_data)
expect_true("ner_chunk" %in% colnames(transformed_data))
expect_true(inherits(test_annotator, "nlp_ner_chunker"))
})
test_that("nlp_ner_chunker ml_pipeline", {
test_annotator <- nlp_ner_chunker(pipeline, input_cols = c("sentence","ner"), output_col = "ner_chunk")
transformed_data <- ml_fit_and_transform(test_annotator, test_data)
expect_true("ner_chunk" %in% colnames(transformed_data))
})
test_that("nlp_ner_chunker tbl_spark", {
transformed_data <- nlp_ner_chunker(test_data, input_cols = c("sentence","ner"), output_col = "ner_chunk")
expect_true("ner_chunk" %in% colnames(transformed_data))
})
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