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[SPARK-31573][R] Apply fixed=TRUE as appropriate to regex usage in R #28367

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[SPARK-31573][R] Apply fixed=TRUE as appropriate to regex usage in R #28367

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34c7417
apply fixed=TRUE as appopriate to regex usage in R
Apr 27, 2020
8676253
linting
Apr 27, 2020
14652d1
grep should be grepl
Apr 27, 2020
cb6d263
Merge branch 'master' into r-regex-fixed
Apr 28, 2020
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2 changes: 1 addition & 1 deletion R/pkg/R/DataFrame.R
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Original file line number Diff line number Diff line change
Expand Up @@ -2614,7 +2614,7 @@ setMethod("join",
"left", "leftouter", "left_outer",
"right", "rightouter", "right_outer",
"semi", "left_semi", "leftsemi", "anti", "left_anti", "leftanti")) {
joinType <- gsub("_", "", joinType)
joinType <- gsub("_", "", joinType, fixed = TRUE)
sdf <- callJMethod(x@sdf, "join", y@sdf, joinExpr@jc, joinType)
} else {
stop(paste("joinType must be one of the following types:",
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7 changes: 4 additions & 3 deletions R/pkg/R/SQLContext.R
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Expand Up @@ -110,10 +110,11 @@ sparkR.conf <- function(key, defaultValue) {
value <- if (missing(defaultValue)) {
tryCatch(callJMethod(conf, "get", key),
error = function(e) {
if (any(grep("java.util.NoSuchElementException", as.character(e)))) {
estr <- as.character(e)
if (any(grepl("java.util.NoSuchElementException", estr, fixed = TRUE))) {
stop(paste0("Config '", key, "' is not set"))
} else {
stop(paste0("Unknown error: ", as.character(e)))
stop(paste0("Unknown error: ", estr))
}
})
} else {
Expand Down Expand Up @@ -205,7 +206,7 @@ getSchema <- function(schema, firstRow = NULL, rdd = NULL) {
# SPAKR-SQL does not support '.' in column name, so replace it with '_'
# TODO(davies): remove this once SPARK-2775 is fixed
names <- lapply(names, function(n) {
nn <- gsub("[.]", "_", n)
nn <- gsub(".", "_", n, fixed = TRUE)
if (nn != n) {
warning(paste("Use", nn, "instead of", n, "as column name"))
}
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10 changes: 5 additions & 5 deletions R/pkg/R/client.R
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Expand Up @@ -65,8 +65,8 @@ checkJavaVersion <- function() {
javaHome <- Sys.getenv("JAVA_HOME")
javaReqs <- utils::packageDescription(utils::packageName(), fields = c("SystemRequirements"))
sparkJavaVersions <- strsplit(javaReqs, "[(,)]")[[1]]
minJavaVersion <- as.numeric(strsplit(sparkJavaVersions[[2]], ">= ")[[1]][[2]])
maxJavaVersion <- as.numeric(strsplit(sparkJavaVersions[[3]], "< ")[[1]][[2]])
minJavaVersion <- as.numeric(strsplit(sparkJavaVersions[[2]], ">= ", fixed = TRUE)[[1]][[2]])
maxJavaVersion <- as.numeric(strsplit(sparkJavaVersions[[3]], "< ", fixed = TRUE)[[1]][[2]])
if (javaHome != "") {
javaBin <- file.path(javaHome, "bin", javaBin)
}
Expand All @@ -89,13 +89,13 @@ checkJavaVersion <- function() {
})
javaVersionFilter <- Filter(
function(x) {
grepl(" version", x)
grepl(" version", x, fixed = TRUE)
}, javaVersionOut)

javaVersionStr <- strsplit(javaVersionFilter[[1]], "[\"]")[[1L]][2]
javaVersionStr <- strsplit(javaVersionFilter[[1]], '"', fixed = TRUE)[[1L]][2]
# javaVersionStr is of the form 1.8.0_92/9.0.x/11.0.x.
# We are using 8, 9, 10, 11 for sparkJavaVersion.
versions <- strsplit(javaVersionStr, "[.]")[[1L]]
versions <- strsplit(javaVersionStr, ".", fixed = TRUE)[[1L]]
if ("1" == versions[1]) {
javaVersionNum <- as.integer(versions[2])
} else {
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4 changes: 2 additions & 2 deletions R/pkg/R/install.R
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Expand Up @@ -214,9 +214,9 @@ getPreferredMirror <- function(version, packageName) {
file.path("spark", version, packageName),
".tgz&as_json=1")
textLines <- readLines(jsonUrl, warn = FALSE)
rowNum <- grep("\"preferred\"", textLines)
rowNum <- grep('"preferred"', textLines, fixed = TRUE)
linePreferred <- textLines[rowNum]
matchInfo <- regexpr("\"[A-Za-z][A-Za-z0-9+-.]*://.+\"", linePreferred)
matchInfo <- regexpr('"[A-Za-z][A-Za-z0-9+-.]*://.+"', linePreferred)
if (matchInfo != -1) {
startPos <- matchInfo + 1
endPos <- matchInfo + attr(matchInfo, "match.length") - 2
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2 changes: 1 addition & 1 deletion R/pkg/R/schema.R
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Expand Up @@ -182,7 +182,7 @@ checkType <- function(type) {
# strsplit does not return the final empty string, so check if
# the final char is ","
if (substr(fieldsString, nchar(fieldsString), nchar(fieldsString)) != ",") {
fields <- strsplit(fieldsString, ",")[[1]]
fields <- strsplit(fieldsString, ",", fixed = TRUE)[[1]]
for (field in fields) {
m <- regexec("^(.+):(.+)$", field)
matchedStrings <- regmatches(field, m)
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4 changes: 2 additions & 2 deletions R/pkg/R/sparkR.R
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Expand Up @@ -435,7 +435,7 @@ sparkR.session <- function(
# Check if version number of SparkSession matches version number of SparkR package
jvmVersion <- callJMethod(sparkSession, "version")
# Remove -SNAPSHOT from jvm versions
jvmVersionStrip <- gsub("-SNAPSHOT", "", jvmVersion)
jvmVersionStrip <- gsub("-SNAPSHOT", "", jvmVersion, fixed = TRUE)
rPackageVersion <- paste0(packageVersion("SparkR"))

if (jvmVersionStrip != rPackageVersion) {
Expand Down Expand Up @@ -606,7 +606,7 @@ getClientModeSparkSubmitOpts <- function(submitOps, sparkEnvirMap) {
# process only if --option is not already specified
if (!is.null(opsValue) &&
nchar(opsValue) > 1 &&
!grepl(sparkConfToSubmitOps[[conf]], submitOps)) {
!grepl(sparkConfToSubmitOps[[conf]], submitOps, fixed = TRUE)) {
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@HyukjinKwon HyukjinKwon Apr 27, 2020

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This could actually be a bug fix too for very, very unlikely corner cases such as spark.driver.memory <> sparkAdriverXmemory

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@MichaelChirico MichaelChirico Apr 27, 2020

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yes exactly. there were a few other like this in utils.R e.g.

grep("org.apache.spark.sql.streaming.StreamingQueryException: "

# put "" around value in case it has spaces
paste0(sparkConfToSubmitOps[[conf]], " \"", opsValue, "\" ")
} else {
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16 changes: 10 additions & 6 deletions R/pkg/R/utils.R
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Expand Up @@ -818,30 +818,32 @@ captureJVMException <- function(e, method) {
}

# StreamingQueryException could wrap an IllegalArgumentException, so look for that first
if (any(grep("org.apache.spark.sql.streaming.StreamingQueryException: ", stacktrace))) {
if (any(grep("org.apache.spark.sql.streaming.StreamingQueryException: ",
stacktrace, fixed = TRUE))) {
msg <- strsplit(stacktrace, "org.apache.spark.sql.streaming.StreamingQueryException: ",
fixed = TRUE)[[1]]
# Extract "Error in ..." message.
rmsg <- msg[1]
# Extract the first message of JVM exception.
first <- strsplit(msg[2], "\r?\n\tat")[[1]][1]
stop(paste0(rmsg, "streaming query error - ", first), call. = FALSE)
} else if (any(grep("java.lang.IllegalArgumentException: ", stacktrace))) {
} else if (any(grep("java.lang.IllegalArgumentException: ", stacktrace, fixed = TRUE))) {
msg <- strsplit(stacktrace, "java.lang.IllegalArgumentException: ", fixed = TRUE)[[1]]
# Extract "Error in ..." message.
rmsg <- msg[1]
# Extract the first message of JVM exception.
first <- strsplit(msg[2], "\r?\n\tat")[[1]][1]
stop(paste0(rmsg, "illegal argument - ", first), call. = FALSE)
} else if (any(grep("org.apache.spark.sql.AnalysisException: ", stacktrace))) {
} else if (any(grep("org.apache.spark.sql.AnalysisException: ", stacktrace, fixed = TRUE))) {
msg <- strsplit(stacktrace, "org.apache.spark.sql.AnalysisException: ", fixed = TRUE)[[1]]
# Extract "Error in ..." message.
rmsg <- msg[1]
# Extract the first message of JVM exception.
first <- strsplit(msg[2], "\r?\n\tat")[[1]][1]
stop(paste0(rmsg, "analysis error - ", first), call. = FALSE)
} else
if (any(grep("org.apache.spark.sql.catalyst.analysis.NoSuchDatabaseException: ", stacktrace))) {
if (any(grep("org.apache.spark.sql.catalyst.analysis.NoSuchDatabaseException: ",
stacktrace, fixed = TRUE))) {
msg <- strsplit(stacktrace, "org.apache.spark.sql.catalyst.analysis.NoSuchDatabaseException: ",
fixed = TRUE)[[1]]
# Extract "Error in ..." message.
Expand All @@ -850,15 +852,17 @@ captureJVMException <- function(e, method) {
first <- strsplit(msg[2], "\r?\n\tat")[[1]][1]
stop(paste0(rmsg, "no such database - ", first), call. = FALSE)
} else
if (any(grep("org.apache.spark.sql.catalyst.analysis.NoSuchTableException: ", stacktrace))) {
if (any(grep("org.apache.spark.sql.catalyst.analysis.NoSuchTableException: ",
stacktrace, fixed = TRUE))) {
msg <- strsplit(stacktrace, "org.apache.spark.sql.catalyst.analysis.NoSuchTableException: ",
fixed = TRUE)[[1]]
# Extract "Error in ..." message.
rmsg <- msg[1]
# Extract the first message of JVM exception.
first <- strsplit(msg[2], "\r?\n\tat")[[1]][1]
stop(paste0(rmsg, "no such table - ", first), call. = FALSE)
} else if (any(grep("org.apache.spark.sql.catalyst.parser.ParseException: ", stacktrace))) {
} else if (any(grep("org.apache.spark.sql.catalyst.parser.ParseException: ",
stacktrace, fixed = TRUE))) {
msg <- strsplit(stacktrace, "org.apache.spark.sql.catalyst.parser.ParseException: ",
fixed = TRUE)[[1]]
# Extract "Error in ..." message.
Expand Down