Manage empty lines (+ tests)

DESCRIPTION

@@ -9,8 +9,12 @@ License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.0
 URL: https://github.com/bransonf/hl7r
 BugReports: https://github.com/bransonf/hl7r/issues
 Imports:
     dplyr
+Suggests: 
+    testthat (>= 3.0.0),
+    withr
+Config/testthat/edition: 3

R/parsehl7.R

@@ -59,6 +59,7 @@ parsehl7 <- function(feed, file){
   for (line_n in seq_along(feed)){
     # Get String
     line <- feed[line_n]
+    if (line == "") next
 
     # Increment on New Message
     if(grepl('^MSH', line)){

tests/testthat.R

@@ -0,0 +1,12 @@
+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/tests.html
+# * https://testthat.r-lib.org/reference/test_package.html#special-files
+
+library(testthat)
+library(hl7r)
+
+test_check("hl7r")

tests/testthat/test-hl7df.R

@@ -0,0 +1,28 @@
+test_that("hl7df works", {
+  # setup
+  sample_txt <- c(
+    "MSH|^~`&|ECG REPORTING|ROCHESTER|ERIS|ROCHESTER|20110621050440||ORU^R01|20110621050440|P|2.1",
+    "PID|||999999999||TEST^PATIENT||18450101|F",
+    "OBR|||211088491|0^ADULT^ROCHECG|||20110620170631|||||||||M999999^^^^^^^RACFID||||||20110621060232||EC|F|||||||M999999^LASTNAME MD^FIRSTNAME^^^^^RACFID",
+    "OBX||ST|93000.2^VENTRICULAR RATE EKG/MIN^CPT4|1|52|/SEC",
+    "OBX||ST|93000.4^PR INTERVAL(MSEC)^CPT4|2|208|MSEC",
+    "OBX||ST|93000.5^QRS - INTERVAL(MSEC)^CPT4|3|88|MSEC",
+    "OBX||ST|93000.6^QT - INTERVAL(MSEC)^CPT4|4|466|MSEC",
+    "OBX||ST|93000&PTL^PHYSICAL TEST LOCATION^CPT4|5|STMA",
+    "OBX||ST|93000&PTR^PHYSICAL TEST ROOM^CPT4|6|04254",
+    "OBX||CE|93000.17^^CPT4|7|21&101^Sinus bradycardia`T`with 1st degree A-V block^MEIECG",
+    "OBX||CE|93000.17^^CPT4|8|1687^Otherwise normal ECG^MEIECG",
+    "OBX||CE|93000&CMP^^CPT4|9|1301^When compared with ECG of^MEIECG",
+    "OBX||TS|93000&CMD^EKG COMPARISON DATE^CPT4|10|201106171659",
+    "OBX||CE|93000&CMP^^CPT4|11|1305^No significant change was found^MEIECG",
+    "OBX||TX|93000.48^EKG COMMENT^CPT4|12|9917^LASTNAME MD^FIRSTNAME"
+  )
+
+  # eval
+  parsed <- parsehl7(sample_txt)
+  df <- hl7df(parsed)
+
+  # test
+  expect_s3_class(df, "data.frame")
+  expect_length(df, 133)
+})

tests/testthat/test-parsehl7.R

@@ -0,0 +1,117 @@
+test_that("parsehl7 works", {
+  # setup
+  sample_txt <- c(
+    "MSH|^~`&|ECG REPORTING|ROCHESTER|ERIS|ROCHESTER|20110621050440||ORU^R01|20110621050440|P|2.1",
+    "PID|||999999999||TEST^PATIENT||18450101|F",
+    "OBR|||211088491|0^ADULT^ROCHECG|||20110620170631|||||||||M999999^^^^^^^RACFID||||||20110621060232||EC|F|||||||M999999^LASTNAME MD^FIRSTNAME^^^^^RACFID",
+    "OBX||ST|93000.2^VENTRICULAR RATE EKG/MIN^CPT4|1|52|/SEC",
+    "OBX||ST|93000.4^PR INTERVAL(MSEC)^CPT4|2|208|MSEC",
+    "OBX||ST|93000.5^QRS - INTERVAL(MSEC)^CPT4|3|88|MSEC",
+    "OBX||ST|93000.6^QT - INTERVAL(MSEC)^CPT4|4|466|MSEC",
+    "OBX||ST|93000&PTL^PHYSICAL TEST LOCATION^CPT4|5|STMA",
+    "OBX||ST|93000&PTR^PHYSICAL TEST ROOM^CPT4|6|04254",
+    "OBX||CE|93000.17^^CPT4|7|21&101^Sinus bradycardia`T`with 1st degree A-V block^MEIECG",
+    "OBX||CE|93000.17^^CPT4|8|1687^Otherwise normal ECG^MEIECG",
+    "OBX||CE|93000&CMP^^CPT4|9|1301^When compared with ECG of^MEIECG",
+    "OBX||TS|93000&CMD^EKG COMPARISON DATE^CPT4|10|201106171659",
+    "OBX||CE|93000&CMP^^CPT4|11|1305^No significant change was found^MEIECG",
+    "OBX||TX|93000.48^EKG COMMENT^CPT4|12|9917^LASTNAME MD^FIRSTNAME"
+  )
+
+  sample_names <- c(
+    "MSH.1", "PID.1", "OBR.1", "OBX.1", "OBX.2", "OBX.3", "OBX.4",
+    "OBX.5", "OBX.6", "OBX.7", "OBX.8", "OBX.9", "OBX.10", "OBX.11",
+    "OBX.12"
+  )
+
+  sample_file <- withr::local_file("sample_hl7")
+  writeLines(sample_txt, sample_file)
+
+  # eval
+  res_txt <- parsehl7(sample_txt)
+  res_file <- parsehl7(file = sample_file)
+
+  # test
+  expect_type(res_txt, "list")
+  expect_length(res_txt, 1L)
+
+  expect_type(res_txt[[1L]], "list")
+  expect_length(res_txt[[1L]], 15L)
+  expect_named(res_txt[[1L]], sample_names)
+
+  expect_type(res_txt[[1L]][["MSH.1"]], "list")
+  expect_length(res_txt[[1L]][["MSH.1"]], 11L)
+  expect_type(res_txt[[1L]][["MSH.1"]][[1L]], "list")
+  expect_length(res_txt[[1L]][["MSH.1"]][[1L]], 2L)
+  expect_type(res_txt[[1L]][["MSH.1"]][[1L]][[2L]], "character")
+  expect_equal(res_txt[[1L]][["MSH.1"]][[1L]][[2L]], "`&")
+
+  expect_type(res_txt[[1L]][["PID.1"]], "list")
+  expect_length(res_txt[[1L]][["PID.1"]], 8L)
+
+  expect_type(res_txt[[1L]][["OBR.1"]], "list")
+  expect_length(res_txt[[1L]][["OBR.1"]], 32L)
+
+  expect_type(res_txt[[1L]][["OBX.1"]], "list")
+  expect_length(res_txt[[1L]][["OBX.1"]], 6L)
+
+
+  expect_equal(res_txt, res_file)
+})
+
+
+
+test_that("parsehl7 manage two messages", {
+  # setup
+  sample_txt <- c(
+    "MSH|^~`&|ECG REPORTING|ROCHESTER|ERIS|ROCHESTER|20110621050440||ORU^R01|20110621050440|P|2.1",
+    "PID|||999999999||TEST^PATIENT||18450101|F",
+    "OBR|||211088491|0^ADULT^ROCHECG|||20110620170631|||||||||M999999^^^^^^^RACFID||||||20110621060232||EC|F|||||||M999999^LASTNAME MD^FIRSTNAME^^^^^RACFID",
+    "OBX||ST|93000.2^VENTRICULAR RATE EKG/MIN^CPT4|1|52|/SEC",
+    "MSH|^~`&|ECG REPORTING|ROCHESTER|ERIS|ROCHESTER|20110621050440||ORU^R01|20110621050440|P|2.1",
+    "PID|||999999999||TEST^PATIENT||18450101|F",
+    "OBR|||211088491|0^ADULT^ROCHECG|||20110620170631|||||||||M999999^^^^^^^RACFID||||||20110621060232||EC|F|||||||M999999^LASTNAME MD^FIRSTNAME^^^^^RACFID",
+    "OBX||ST|93000.2^VENTRICULAR RATE EKG/MIN^CPT4|1|52|/SEC"
+  )
+
+  # eval
+  res_txt <- parsehl7(sample_txt)
+
+  # test
+  expect_length(res_txt, 2L)
+})
+
+
+test_that("parsehl7 manage two separated messages", {
+  # setup
+  sample_txt <- c(
+    "MSH|^~`&|ECG REPORTING|ROCHESTER|ERIS|ROCHESTER|20110621050440||ORU^R01|20110621050440|P|2.1",
+    "PID|||999999999||TEST^PATIENT||18450101|F",
+    "OBR|||211088491|0^ADULT^ROCHECG|||20110620170631|||||||||M999999^^^^^^^RACFID||||||20110621060232||EC|F|||||||M999999^LASTNAME MD^FIRSTNAME^^^^^RACFID",
+    "OBX||ST|93000.2^VENTRICULAR RATE EKG/MIN^CPT4|1|52|/SEC",
+    "MSH|^~`&|ECG REPORTING|ROCHESTER|ERIS|ROCHESTER|20110621050440||ORU^R01|20110621050440|P|2.1",
+    "PID|||999999999||TEST^PATIENT||18450101|F",
+    "OBR|||211088491|0^ADULT^ROCHECG|||20110620170631|||||||||M999999^^^^^^^RACFID||||||20110621060232||EC|F|||||||M999999^LASTNAME MD^FIRSTNAME^^^^^RACFID",
+    "OBX||ST|93000.2^VENTRICULAR RATE EKG/MIN^CPT4|1|52|/SEC"
+  )
+
+  sample_txt_spaced <- c(
+    "MSH|^~`&|ECG REPORTING|ROCHESTER|ERIS|ROCHESTER|20110621050440||ORU^R01|20110621050440|P|2.1",
+    "PID|||999999999||TEST^PATIENT||18450101|F",
+    "OBR|||211088491|0^ADULT^ROCHECG|||20110620170631|||||||||M999999^^^^^^^RACFID||||||20110621060232||EC|F|||||||M999999^LASTNAME MD^FIRSTNAME^^^^^RACFID",
+    "OBX||ST|93000.2^VENTRICULAR RATE EKG/MIN^CPT4|1|52|/SEC",
+    "",
+    "MSH|^~`&|ECG REPORTING|ROCHESTER|ERIS|ROCHESTER|20110621050440||ORU^R01|20110621050440|P|2.1",
+    "PID|||999999999||TEST^PATIENT||18450101|F",
+    "OBR|||211088491|0^ADULT^ROCHECG|||20110620170631|||||||||M999999^^^^^^^RACFID||||||20110621060232||EC|F|||||||M999999^LASTNAME MD^FIRSTNAME^^^^^RACFID",
+    "OBX||ST|93000.2^VENTRICULAR RATE EKG/MIN^CPT4|1|52|/SEC"
+  )
+
+  # eval
+  res_txt <- parsehl7(sample_txt)
+  res_txt_spaced <- parsehl7(sample_txt_spaced)
+
+  # test
+  expect_length(res_txt_spaced, 2L)
+  expect_equal(res_txt_spaced, res_txt)
+})