docs: attributes and values should be in ASCII encoding

see #58

R/track.R

@@ -317,6 +317,8 @@ emr_track.attr.rm <- function(track = NULL, attr = NULL) {
 #' This function creates a track attribute and assigns 'value' to it. If the
 #' attribute already exists its value is overwritten.
 #'
+#' Note that both attributes and values sould be in ASCII encoding.
+#'
 #' @param track track name
 #' @param attr attribute name
 #' @param value value

src/EMRTrack.cpp

@@ -193,10 +193,10 @@ EMRTrack::TrackAttrs EMRTrack::load_attrs(const char *, const char *filename)
 		} else {
 			if (idx) {
 				if (name.empty() || val.empty())
-					TGLError<EMRTrack>(BAD_FORMAT, "Invalid format of attributes file %s", filename); 
+					TGLError<EMRTrack>(BAD_FORMAT, "Invalid format of attributes file %s (1)", filename); 
 
 				if (attrs.find(name) != attrs.end()) // duplicated attributes
-					TGLError<EMRTrack>(BAD_FORMAT, "Invalid format of attributes file %s", filename); 
+					TGLError<EMRTrack>(BAD_FORMAT, "Invalid format of attributes file %s (2)", filename); 
 
 				attrs[name] = val;
 				name.clear();
@@ -210,7 +210,7 @@ EMRTrack::TrackAttrs EMRTrack::load_attrs(const char *, const char *filename)
 		TGLError<EMRTrack>(FILE_ERROR, "Failed to read attributes file %s: %s", filename, strerror(errno));
 
 	if (idx) 
-		TGLError<EMRTrack>(BAD_FORMAT, "Invalid format of attributes file %s", filename); 
+		TGLError<EMRTrack>(BAD_FORMAT, "Invalid format of attributes file %s (3)", filename); 
     return attrs;
 }
 

tests/testthat/mock_tests.r

@@ -0,0 +1,81 @@
+mock <- "/net/mraid14/export/tgdata/db/tgdb/emr/mock/"
+tmp <- tempdir()
+emr_db.connect(c(mock, tmp))
+
+## 1 anemia
+
+withr::local_options(list(emr_max.data.size = 1e9))
+emr_filter.create("female", "patients.female", time.shift = c(-years(120), 0))
+emr_filter.create("male", "patients.male", time.shift = c(-years(120), 0))
+hgb_female <- emr_screen("lab.103 < 12", filter = "female", keepref = TRUE)
+hgb_male <- emr_screen("lab.103 < 14", filter = "male", keepref = TRUE)
+emr_filter.create("abnormal_hgb_female", hgb_female %>% dplyr::distinct(id, time))
+emr_filter.create("abnormal_hgb_male", hgb_male %>% dplyr::distinct(id, time))
+emr_track.create("anemia",
+    categorical = FALSE, expr = "lab.103",
+    filter = "abnormal_hgb_female | abnormal_hgb_male"
+)
+# 14.642 seconds
+a <- emr_extract("anemia", names = "v")
+
+withr::local_options(list(emr_max.data.size = 1e9))
+emr_filter.create("female", "patients.female", time.shift = c(-years(120), 0))
+emr_filter.create("male", "patients.male", time.shift = c(-years(120), 0))
+emr_filter.create("abnormal_hgb_female", src = "lab.103", val = 12, operator = "<")
+emr_filter.create("abnormal_hgb_male", src = "lab.103", val = 14, operator = "<")
+emr_track.create("anemia1",
+    categorical = FALSE, expr = "lab.103",
+    filter = "(female & abnormal_hgb_female) | (male & abnormal_hgb_male)"
+)
+# 5.504 seconds
+
+b <- emr_extract("anemia1", names = "v")
+expect_equal(a, b)
+
+## 3 abnormal hematocrit second time
+withr::local_options(list(emr_max.data.size = 1e9))
+emr_filter.create("female", "patients.female", time.shift = c(-years(120), 0))
+emr_filter.create("male", "patients.male", time.shift = c(-years(120), 0))
+hct_female_48 <- emr_screen("lab.104 > 48", filter = "female", keepref = TRUE)
+hct_male_49 <- emr_screen("lab.104 > 49", filter = "male", keepref = TRUE)
+emr_filter.create("abnormal_hct_female_past", hct_female_48 %>% dplyr::distinct(id, time), time.shift = c(-years(3), -1))
+emr_filter.create("abnormal_hct_male_past", hct_male_49 %>% dplyr::distinct(id, time), time.shift = c(-years(3), -1))
+emr_filter.create("abnormal_hct_female_current", hct_female_48 %>% dplyr::distinct(id, time))
+emr_filter.create("abnormal_hct_male_current", hct_male_49 %>% dplyr::distinct(id, time))
+emr_track.create("abnormal_hct_second_time",
+    categorical = FALSE, expr = "lab.104",
+    filter = "(abnormal_hct_female_past & abnormal_hct_female_current) | (abnormal_hct_male_past & abnormal_hct_male_current)"
+)
+# 3.339 seconds
+
+a <- emr_extract("abnormal_hct_second_time", names = "v")
+
+emr_filter.clear()
+withr::local_options(list(emr_max.data.size = 1e9))
+emr_filter.create("female", "patients.female", time.shift = c(-years(120), 0))
+emr_filter.create("male", "patients.male", time.shift = c(-years(120), 0))
+emr_filter.create("abnormal_hct_female", src = "lab.104", val = 48, operator = ">")
+emr_filter.create("abnormal_hct_male", src = "lab.104", val = 49, operator = ">")
+emr_vtrack.create("abnormal_hct_past", src = "lab.104", filter = "(female & abnormal_hct_female) | (male & abnormal_hct_male)", time.shift = c(-years(3), -1))
+emr_track.create("abnormal_hct_second_time1",
+    categorical = FALSE, expr = "lab.104",
+    filter = "abnormal_hct_past & ((female & abnormal_hct_female) | (male & abnormal_hct_male))", iterator = "lab.104"
+)
+# 2.222 seconds
+
+b <- emr_extract("abnormal_hct_second_time1", names = "v")
+expect_equal(a, b)
+
+withr::local_options(list(emr_max.data.size = 1e9))
+emr_filter.clear()
+emr_filter.create("female", "patients.female", time.shift = c(-years(120), 0))
+emr_filter.create("male", "patients.male", time.shift = c(-years(120), 0))
+emr_filter.create("abnormal_hct_female", src = "lab.104", val = 48, operator = ">")
+emr_filter.create("abnormal_hct_male", src = "lab.104", val = 49, operator = ">")
+emr_vtrack.create("num_abnormal_hct", src = "lab.104", func = "size", filter = "(female & abnormal_hct_female) | (male & abnormal_hct_male)", time.shift = c(-years(3), 0))
+emr_filter.create("abnormal_hct_twice", src = "num_abnormal_hct", val = 2, operator = ">=")
+emr_track.create("abnormal_hct_second_time2", categorical = FALSE, expr = "lab.104", filter = "abnormal_hct_twice & ((female & abnormal_hct_female) | (male & abnormal_hct_male))", iterator = "lab.104")
+# 2.347 seconds
+
+d <- emr_extract("abnormal_hct_second_time2", names = "v")
+expect_equal(a, d)