Fix failing tests

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
nextflow-io · Feb 10, 2024 · c4c6182 · c4c6182
1 parent 1d97d49
commit c4c6182
Show file tree

Hide file tree

Showing 4 changed files with 10 additions and 9 deletions.
diff --git a/modules/nextflow/src/main/resources/nextflow/executor/command-env.txt b/modules/nextflow/src/main/resources/nextflow/executor/command-env.txt
@@ -30,5 +30,6 @@ nxf_eval_cmd() {
         (IFS=$'\n' read -r -d '' _ERRNO_; return ${_ERRNO_});
     } < <((printf '\0%s\0%d\0' "$(((({ shift 2; "${@}"; echo "${?}" 1>&3-; } | tr -d '\0' 1>&4-) 4>&2- 2>&1- | tr -d '\0' 1>&4-) 3>&1- | exit "$(cat)") 4>&1-)" "${?}" 1>&2) 2>&1)
 }
+
 ## reset/create command env file
 echo '' > {{env_file}}
diff --git a/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
@@ -1131,7 +1131,7 @@ class BashWrapperBuilderTest extends Specification {
             set +e
             cd "$NXF_TASK_WORKDIR"
             
-            nxf_catch() {
+            nxf_eval_cmd() {
                 {
                     IFS=$'\\n' read -r -d '' "${1}";
                     IFS=$'\\n' read -r -d '' "${2}";
@@ -1163,7 +1163,7 @@ class BashWrapperBuilderTest extends Specification {
             set +e
             cd "$NXF_TASK_WORKDIR"
             
-            nxf_catch() {
+            nxf_eval_cmd() {
                 {
                     IFS=$'\\n' read -r -d '' "${1}";
                     IFS=$'\\n' read -r -d '' "${2}";
@@ -1176,7 +1176,7 @@ class BashWrapperBuilderTest extends Specification {
             echo FOO="${FOO[@]}" >> .command.env
             echo /FOO/ >> .command.env
             #
-            nxf_catch STDOUT STDERR this --cmd
+            nxf_eval_cmd STDOUT STDERR this --cmd
             status=$?
             if [ $status -eq 0 ]; then
               echo THIS="$STDOUT" >> .command.env
@@ -1186,7 +1186,7 @@ class BashWrapperBuilderTest extends Specification {
               echo /THIS/=exit:$status >> .command.env
             fi
             #
-            nxf_catch STDOUT STDERR other --cmd
+            nxf_eval_cmd STDOUT STDERR other --cmd
             status=$?
             if [ $status -eq 0 ]; then
               echo THAT="$STDOUT" >> .command.env

diff --git a/modules/nextflow/src/test/groovy/nextflow/processor/TaskProcessorTest.groovy b/modules/nextflow/src/test/groovy/nextflow/processor/TaskProcessorTest.groovy
@@ -984,7 +984,7 @@ class TaskProcessorTest extends Specification {
         processor.collectOutEnvMap(workDir, [cmd_out_1: 'foo --this', cmd_out_2: 'bar --that'])
         then:
         def e = thrown(ProcessEvalException)
-        e.message == 'Unable to evaluate command output'
+        e.message == 'Unable to evaluate output'
         e.command == 'bar --that'
         e.output == 'This is an error message\nfor unknown reason'
         e.status == 100

diff --git a/modules/nextflow/src/test/groovy/nextflow/script/params/TupleOutParamTest.groovy b/modules/nextflow/src/test/groovy/nextflow/script/params/TupleOutParamTest.groovy
@@ -179,12 +179,12 @@ class TupleOutParamTest extends Dsl2Spec {
         outs[0].inner[1].getName() == 'BAR'
     }
 
-    def 'should create tuple of cmd' () {
+    def 'should create tuple of eval' () {
         setup:
         def text = '''
             process hola {
               output:
-                tuple cmd('this --one'), cmd("$other --two")
+                tuple eval('this --one'), eval("$other --two")
               
               /echo command/ 
             }
@@ -208,11 +208,11 @@ class TupleOutParamTest extends Dsl2Spec {
         outs[0].inner.size() == 2
         and:
         outs[0].inner[0] instanceof CmdEvalParam
-        outs[0].inner[0].getName() =~ /nxf_out_cmd_\d+/
+        outs[0].inner[0].getName() =~ /nxf_out_eval_\d+/
         (outs[0].inner[0] as CmdEvalParam).getTarget(binding) == 'this --one'
         and:
         outs[0].inner[1] instanceof CmdEvalParam
-        outs[0].inner[1].getName() =~ /nxf_out_cmd_\d+/
+        outs[0].inner[1].getName() =~ /nxf_out_eval_\d+/
         (outs[0].inner[1] as CmdEvalParam).getTarget(binding) == 'tool --two'
 
     }