Replace egrep with grep -E (#3485)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>

docs/sync-doc.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 TARGET=../../nextflow-website/assets
-if egrep "^release = '.*edge|.*SNAPSHOT'$" -c conf.py >/dev/null; then
+if grep -E "^release = '.*edge|.*SNAPSHOT'$" -c conf.py >/dev/null; then
 MODE=edge
 else
 MODE=latest

docs/tracing.rst

@@ -138,7 +138,7 @@ and many other metrics. You can see an example below:
 
 .. note::
   Nextflow collects these metrics through a background process for each job in the target environment.
-  Make sure the following tools are available in the environment where tasks are executed: ``awk``, ``date``, ``grep``, ``egrep``, ``ps``, ``sed``, ``tail``, ``tee``.
+  Make sure the following tools are available in the environment where tasks are executed: ``awk``, ``date``, ``grep``, ``ps``, ``sed``, ``tail``, ``tee``.
   Moreover, some of these metrics are not reported when running on Mac OS X. See the note
   about that in the `Trace report`_ below.
 

modules/nextflow/src/main/groovy/nextflow/container/UdockerBuilder.groovy

@@ -96,7 +96,7 @@ class UdockerBuilder extends ContainerBuilder<UdockerBuilder> {
     @Override
     String getRunCommand() {
         def run = super.getRunCommand()
-        def result = "((udocker.py images | egrep -o \"^$image\\s\") || udocker.py pull \"$image\")>/dev/null\n"
+        def result = "((udocker.py images | grep -E -o \"^$image\\s\") || udocker.py pull \"$image\")>/dev/null\n"
         result += "[[ \$? != 0 ]] && echo \"Udocker failed while pulling container \\`$image\\`\" >&2 && exit 1\n"
         result += run
         return result

modules/nextflow/src/main/groovy/nextflow/executor/OarExecutor.groovy

@@ -132,7 +132,7 @@ class OarExecutor extends AbstractGridExecutor {
         // see page 21 http://oar.imag.fr/docs/2.5/OAR-Documentation.pdf
         String cmd = 'oarstat -f'
         if( queue ) cmd += ' ' + queue
-        return ['sh','-c', "$cmd | egrep '(Job_Id:|state =)' ".toString()]
+        return ['sh','-c', "$cmd | grep -E '(Job_Id:|state =)' ".toString()]
     }
 
     /*

modules/nextflow/src/main/groovy/nextflow/executor/PbsExecutor.groovy

@@ -127,7 +127,7 @@ class PbsExecutor extends AbstractGridExecutor {
     protected List<String> queueStatusCommand(Object queue) {
         String cmd = 'qstat -f -1'
         if( queue ) cmd += ' ' + queue
-        return ['bash','-c', "set -o pipefail; $cmd | { egrep '(Job Id:|job_state =)' || true; }".toString()]
+        return ['bash','-c', "set -o pipefail; $cmd | { grep -E '(Job Id:|job_state =)' || true; }".toString()]
     }
 
     static private Map DECODE_STATUS = [

modules/nextflow/src/main/groovy/nextflow/executor/PbsProExecutor.groovy

@@ -88,9 +88,9 @@ class PbsProExecutor extends PbsExecutor {
         if( queue ) {
             cmd += queue
         } else {
-            cmd += '$( qstat -B | egrep -v \'(^Server|^---)\' | awk -v ORS=\' \' \'{print \"@\"\$1}\' )'
+            cmd += '$( qstat -B | grep -E -v \'(^Server|^---)\' | awk -v ORS=\' \' \'{print \"@\"\$1}\' )'
         }
-        return ['bash','-c', "set -o pipefail; $cmd | { egrep '(Job Id:|job_state =)' || true; }".toString()]
+        return ['bash','-c', "set -o pipefail; $cmd | { grep -E '(Job Id:|job_state =)' || true; }".toString()]
     }
 
     // see https://www.pbsworks.com/pdfs/PBSRefGuide18.2.pdf

modules/nextflow/src/main/resources/nextflow/executor/command-trace.txt

@@ -24,12 +24,12 @@ nxf_tree() {
 
     pstat() {
         local x_pid=$1
-        local STATUS=$(2> /dev/null < /proc/$1/status egrep 'Vm|ctxt')
+        local STATUS=$(2> /dev/null < /proc/$1/status grep -E 'Vm|ctxt')
 
         if [ $? = 0 ]; then
         local  x_vsz=$(echo "$STATUS" | grep VmSize | awk '{print $2}' || echo -n '0')
         local  x_rss=$(echo "$STATUS" | grep VmRSS | awk '{print $2}' || echo -n '0')
-        local x_peak=$(echo "$STATUS" | egrep 'VmPeak|VmHWM' | sed 's/^.*:\s*//' | sed 's/[\sa-zA-Z]*$//' | tr '\n' ' ' || echo -n '0 0')
+        local x_peak=$(echo "$STATUS" | grep -E 'VmPeak|VmHWM' | sed 's/^.*:\s*//' | sed 's/[\sa-zA-Z]*$//' | tr '\n' ' ' || echo -n '0 0')
         local x_pmem=$(awk -v rss=$x_rss -v mem_tot=$mem_tot 'BEGIN {printf "%.0f", rss/mem_tot*100*10}' || echo -n '0')
         local vol_ctxt=$(echo "$STATUS" | grep '\bvoluntary_ctxt_switches' | awk '{print $2}' || echo -n '0')
         local inv_ctxt=$(echo "$STATUS" | grep '\bnonvoluntary_ctxt_switches' | awk '{print $2}' || echo -n '0')

modules/nextflow/src/test/groovy/nextflow/container/UdockerBuilderTest.groovy

@@ -108,7 +108,7 @@ class UdockerBuilderTest extends Specification {
         def result = builder.build().getRunCommand()
         then:
         result == '''
-            ((udocker.py images | egrep -o "^ubuntu:latest\\s") || udocker.py pull "ubuntu:latest")>/dev/null
+            ((udocker.py images | grep -E -o "^ubuntu:latest\\s") || udocker.py pull "ubuntu:latest")>/dev/null
             [[ $? != 0 ]] && echo "Udocker failed while pulling container \\`ubuntu:latest\\`" >&2 && exit 1
             udocker.py run --rm -v "$PWD":"$PWD" -w "$PWD" --bindhome $(udocker.py create "ubuntu:latest")
             '''
@@ -125,7 +125,7 @@ class UdockerBuilderTest extends Specification {
         def result = builder.build().getRunCommand('bwa --this --that')
         then:
         result == '''
-            ((udocker.py images | egrep -o "^ubuntu:latest\\s") || udocker.py pull "ubuntu:latest")>/dev/null
+            ((udocker.py images | grep -E -o "^ubuntu:latest\\s") || udocker.py pull "ubuntu:latest")>/dev/null
             [[ $? != 0 ]] && echo "Udocker failed while pulling container \\`ubuntu:latest\\`" >&2 && exit 1
             udocker.py run --rm -v "$PWD":"$PWD" -w "$PWD" --bindhome $(udocker.py create "ubuntu:latest") bwa --this --that
             '''
@@ -140,7 +140,7 @@ class UdockerBuilderTest extends Specification {
         result = builder.build().getRunCommand('bwa --this --that')
         then:
         result == '''
-            ((udocker.py images | egrep -o "^ubuntu:latest\\s") || udocker.py pull "ubuntu:latest")>/dev/null
+            ((udocker.py images | grep -E -o "^ubuntu:latest\\s") || udocker.py pull "ubuntu:latest")>/dev/null
             [[ $? != 0 ]] && echo "Udocker failed while pulling container \\`ubuntu:latest\\`" >&2 && exit 1
             udocker.py run --rm -v "$PWD":"$PWD" -w "$PWD" --bindhome $(udocker.py create "ubuntu:latest") /bin/bash -c "bwa --this --that"
             '''

modules/nextflow/src/test/groovy/nextflow/executor/OarExecutorTest.groovy

@@ -270,8 +270,8 @@ class OarExecutorTest extends Specification {
         when:
         def executor = [:] as OarExecutor
         then:
-        executor.queueStatusCommand(null) == ['sh','-c', "oarstat -f | egrep '(Job_Id:|state =)' ".toString()]
-        executor.queueStatusCommand('xxx') == ['sh','-c', "oarstat -f xxx | egrep '(Job_Id:|state =)' ".toString()]
+        executor.queueStatusCommand(null) == ['sh','-c', "oarstat -f | grep -E '(Job_Id:|state =)' ".toString()]
+        executor.queueStatusCommand('xxx') == ['sh','-c', "oarstat -f xxx | grep -E '(Job_Id:|state =)' ".toString()]
 
     }
 

modules/nextflow/src/test/groovy/nextflow/executor/PbsExecutorTest.groovy

@@ -280,8 +280,8 @@ class PbsExecutorTest extends Specification {
         def executor = [:] as PbsExecutor
 
         expect:
-        executor.queueStatusCommand(null) == ['bash','-c', "set -o pipefail; qstat -f -1 | { egrep '(Job Id:|job_state =)' || true; }"]
-        executor.queueStatusCommand('xxx') == ['bash','-c', "set -o pipefail; qstat -f -1 xxx | { egrep '(Job Id:|job_state =)' || true; }"]
+        executor.queueStatusCommand(null) == ['bash','-c', "set -o pipefail; qstat -f -1 | { grep -E '(Job Id:|job_state =)' || true; }"]
+        executor.queueStatusCommand('xxx') == ['bash','-c', "set -o pipefail; qstat -f -1 xxx | { grep -E '(Job Id:|job_state =)' || true; }"]
         executor.queueStatusCommand('xxx').each { assert it instanceof String }
     }
 

modules/nextflow/src/test/groovy/nextflow/executor/PbsProExecutorTest.groovy

@@ -153,8 +153,8 @@ class PbsProExecutorTest extends Specification {
         def executor = [:] as PbsProExecutor
 
         expect:
-		executor.queueStatusCommand(null) == ['bash','-c', "set -o pipefail; qstat -f \$( qstat -B | egrep -v '(^Server|^---)' | awk -v ORS=' ' '{print \"@\"\$1}' ) | { egrep '(Job Id:|job_state =)' || true; }"]
-        executor.queueStatusCommand('xxx') == ['bash','-c', "set -o pipefail; qstat -f xxx | { egrep '(Job Id:|job_state =)' || true; }"]
+		executor.queueStatusCommand(null) == ['bash','-c', "set -o pipefail; qstat -f \$( qstat -B | grep -E -v '(^Server|^---)' | awk -v ORS=' ' '{print \"@\"\$1}' ) | { grep -E '(Job Id:|job_state =)' || true; }"]
+        executor.queueStatusCommand('xxx') == ['bash','-c', "set -o pipefail; qstat -f xxx | { grep -E '(Job Id:|job_state =)' || true; }"]
         executor.queueStatusCommand('xxx').each { assert it instanceof String }
     }
 

modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper-with-trace.txt

@@ -15,12 +15,12 @@ nxf_tree() {
 
     pstat() {
         local x_pid=$1
-        local STATUS=$(2> /dev/null < /proc/$1/status egrep 'Vm|ctxt')
+        local STATUS=$(2> /dev/null < /proc/$1/status grep -E 'Vm|ctxt')
 
         if [ $? = 0 ]; then
         local  x_vsz=$(echo "$STATUS" | grep VmSize | awk '{print $2}' || echo -n '0')
         local  x_rss=$(echo "$STATUS" | grep VmRSS | awk '{print $2}' || echo -n '0')
-        local x_peak=$(echo "$STATUS" | egrep 'VmPeak|VmHWM' | sed 's/^.*:\s*//' | sed 's/[\sa-zA-Z]*$//' | tr '\n' ' ' || echo -n '0 0')
+        local x_peak=$(echo "$STATUS" | grep -E 'VmPeak|VmHWM' | sed 's/^.*:\s*//' | sed 's/[\sa-zA-Z]*$//' | tr '\n' ' ' || echo -n '0 0')
         local x_pmem=$(awk -v rss=$x_rss -v mem_tot=$mem_tot 'BEGIN {printf "%.0f", rss/mem_tot*100*10}' || echo -n '0')
         local vol_ctxt=$(echo "$STATUS" | grep '\bvoluntary_ctxt_switches' | awk '{print $2}' || echo -n '0')
         local inv_ctxt=$(echo "$STATUS" | grep '\bnonvoluntary_ctxt_switches' | awk '{print $2}' || echo -n '0')

tests/checks/dynamic-storedir.nf/.checks

@@ -33,7 +33,7 @@ rm my_*
 echo ''
 $NXF_RUN | tee stdout
 
-[[ `grep 'INFO' .nextflow.log | egrep -c '\[skipping\] Stored process > foo'` == 4 ]] || false
+[[ `grep 'INFO' .nextflow.log | grep -E -c '\[skipping\] Stored process > foo'` == 4 ]] || false
 
 grep "Result $PWD/cache/omega/result.txt" stdout
 grep "Result $PWD/cache/delta/result.txt" stdout
@@ -58,7 +58,7 @@ rm my_*
 echo ''
 $NXF_RUN -resume | tee stdout
 
-[[ `grep 'INFO' .nextflow.log | egrep -c '\[skipping\] Stored process > foo'` == 4 ]] || false
+[[ `grep 'INFO' .nextflow.log | grep -E -c '\[skipping\] Stored process > foo'` == 4 ]] || false
 
 grep "Result $PWD/cache/omega/result.txt" stdout
 grep "Result $PWD/cache/delta/result.txt" stdout

tests/checks/error.nf/.checks

@@ -8,7 +8,7 @@ $NXF_RUN -c .config | tee stdout
 [[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > task1'` == 3 ]] || false
 [[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > task2'` == 3 ]] || false
 
-[[ `grep 'NOTE' .nextflow.log | egrep -c "Process .* terminated with an error exit status"` == 3 ]] || false
+[[ `grep 'NOTE' .nextflow.log | grep -E -c "Process .* terminated with an error exit status"` == 3 ]] || false
 
 
 #
@@ -20,4 +20,4 @@ $NXF_RUN -c .config -resume | tee stdout
 [[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > task1'` == 3 ]] || false
 [[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > task2'` == 3 ]] || false
 
-[[ `grep 'NOTE' .nextflow.log | egrep -c "Process .* terminated with an error exit status"` == 3 ]] || false
+[[ `grep 'NOTE' .nextflow.log | grep -E -c "Process .* terminated with an error exit status"` == 3 ]] || false