Merge pull request #2858 from broadinstitute/cjl_centaur_additions

Reinstate a whole bunch of centaur tests. Let the shoes drop...!
broadinstitute · Nov 15, 2017 · 12a6717 · 12a6717
2 parents daf5827 + 488f589
commit 12a6717
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Showing 74 changed files with 61 additions and 96 deletions.
diff --git a/backend/src/main/scala/cromwell/backend/io/GlobFunctions.scala b/backend/src/main/scala/cromwell/backend/io/GlobFunctions.scala
@@ -8,16 +8,15 @@ import common.validation.ErrorOr.ErrorOr
 import wom.values._
 import wom.expression.IoFunctionSet
 import wom.graph.TaskCallNode
-import wom.types.WomAnyType
 import wom.values.WomGlobFile
 
 trait GlobFunctions extends IoFunctionSet {
 
   def callContext: CallContext
 
   def findGlobOutputs(call: TaskCallNode, jobDescriptor: BackendJobDescriptor): ErrorOr[List[WomGlobFile]] =
-    call.callable.outputs.flatTraverse[ErrorOr, WomGlobFile] {
-      _.expression.evaluateFiles(jobDescriptor.localInputs, this, WomAnyType) map {
+    call.callable.outputs.flatTraverse[ErrorOr, WomGlobFile] { outputDefinition =>
+      outputDefinition.expression.evaluateFiles(jobDescriptor.localInputs, this, outputDefinition.womType) map {
         _.toList collect { case glob: WomGlobFile => glob }
       }
     }

diff --git a/centaur/src/main/resources/integrationTestCases/arrays.test b/centaur/src/main/resources/integrationTestCases/arrays.test
@@ -1,4 +1,3 @@
-ignore: true
 name: arrays
 testFormat: workflowsuccess
 

diff --git a/centaur/src/main/resources/standardTestCases/aliased_subworkflows.test b/centaur/src/main/resources/standardTestCases/aliased_subworkflows.test
@@ -1,4 +1,4 @@
-ignore: true
+ignore: true # Depends on #2615
 name: aliased_subworkflows
 testFormat: workflowsuccess
 tags: [import, subworkflow, alias]

diff --git a/centaur/src/main/resources/standardTestCases/array_io.test b/centaur/src/main/resources/standardTestCases/array_io.test
@@ -1,4 +1,5 @@
-ignore: true
+ignore: true # depends on 2864
+
 name: array_io
 testFormat: workflowsuccess
 

diff --git a/centaur/src/main/resources/standardTestCases/array_literal_locations.test b/centaur/src/main/resources/standardTestCases/array_literal_locations.test
@@ -1,7 +1,3 @@
-ignore: true
-# This test exercises a shortcoming in parsing array literals in WDL which never worked in any version of Cromwell, but
-# probably should.
-
 name: array_literal_locations
 testFormat: workflowsuccess
 
@@ -14,6 +10,6 @@ metadata {
   workflowName: array_literal_locations
   status: Succeeded
   "outputs.array_literal_locations.array_literal_locations_i.out": "0:1:2"
-  "outputs.array_literal_locations.array_literal_locations_ii.0.out": "0"
-  "outputs.array_literal_locations.array_literal_locations_ii.1.out": "1"
+  "outputs.array_literal_locations.array_literal_locations_ii.out.0": "0"
+  "outputs.array_literal_locations.array_literal_locations_ii.out.1": "1"
 }
diff --git a/.../src/main/resources/standardTestCases/array_literal_locations/array_literal_locations.wdl b/.../src/main/resources/standardTestCases/array_literal_locations/array_literal_locations.wdl
@@ -5,7 +5,7 @@ task array_literal_locations_i {
       echo ${sep=":" array} > out
     }
     runtime { docker: "ubuntu:latest" }
-    output { File out = "out" }
+    output { String out = read_string("out") }
 }
 
 task array_literal_locations_ii {
@@ -17,7 +17,7 @@ task array_literal_locations_ii {
         docker: "ubuntu:latest"
         continueOnReturnCode: [ 0, 1, 2 ]
     }
-    output { File out = "out" }
+    output { String out = read_string("out") }
 }
 
 workflow array_literal_locations {

diff --git a/centaur/src/main/resources/standardTestCases/arrays_scatters_ifs.test b/centaur/src/main/resources/standardTestCases/arrays_scatters_ifs.test
@@ -1,4 +1,3 @@
-ignore: true
 name: arrays_scatters_ifs
 testFormat: workflowsuccess
 

diff --git a/centaur/src/main/resources/standardTestCases/backendWithNoDocker.test b/centaur/src/main/resources/standardTestCases/backendWithNoDocker.test
@@ -1,4 +1,3 @@
-ignore: true
 name: backendWithNoDocker
 backends: [LocalNoDocker]
 testFormat: runtwiceexpectingcallcaching

diff --git a/centaur/src/main/resources/standardTestCases/cacheBetweenWf.test b/centaur/src/main/resources/standardTestCases/cacheBetweenWf.test
@@ -1,4 +1,3 @@
-ignore: true
 name: cacheBetweenWF
 testFormat: runtwiceexpectingcallcaching
 

diff --git a/centaur/src/main/resources/standardTestCases/cacheWithinWF.test b/centaur/src/main/resources/standardTestCases/cacheWithinWF.test
@@ -1,4 +1,3 @@
-ignore: true
 name: cacheWithinWF
 testFormat: workflowsuccess
 

diff --git a/centaur/src/main/resources/standardTestCases/call_cache_capoeira_jes.test b/centaur/src/main/resources/standardTestCases/call_cache_capoeira_jes.test
@@ -1,4 +1,3 @@
-ignore: true
 name: call_cache_capoeira_jes
 testFormat: workflowsuccess
 backends: [Jes, Local]

diff --git a/centaur/src/main/resources/standardTestCases/call_cache_capoeira_local.test b/centaur/src/main/resources/standardTestCases/call_cache_capoeira_local.test
@@ -1,4 +1,3 @@
-ignore: true
 name: call_cache_capoeira_local
 testFormat: workflowsuccess
 backends: [Local]

diff --git a/centaur/src/main/resources/standardTestCases/call_cache_capoeira_tes.test b/centaur/src/main/resources/standardTestCases/call_cache_capoeira_tes.test
@@ -1,4 +1,3 @@
-ignore: true
 name: call_cache_capoeira_tes
 testFormat: workflowsuccess
 backends: [TES]

diff --git a/centaur/src/main/resources/standardTestCases/circular_dependencies.test b/centaur/src/main/resources/standardTestCases/circular_dependencies.test
@@ -1,3 +1,4 @@
+# Ignored because of #1934
 ignore: true
 name: circular_dependencies
 testFormat: workflowfailure

diff --git a/centaur/src/main/resources/standardTestCases/complex_types_files.test b/centaur/src/main/resources/standardTestCases/complex_types_files.test
@@ -1,4 +1,3 @@
-ignore: true
 name: complex_types_files
 testFormat: workflowsuccess
 

diff --git a/centaur/src/main/resources/standardTestCases/composedenginefunctions.test b/centaur/src/main/resources/standardTestCases/composedenginefunctions.test
@@ -1,4 +1,3 @@
-ignore: true
 name: composedenginefunctions
 testFormat: workflowsuccess
 

diff --git a/centaur/src/main/resources/standardTestCases/conditionals.lots_of_nesting.test b/centaur/src/main/resources/standardTestCases/conditionals.lots_of_nesting.test
@@ -1,4 +1,5 @@
-ignore: true
+ignore: true # Depends on #2615
+
 name: lots_of_nesting
 testFormat: workflowsuccess
 tags: [ conditionals ]

diff --git a/centaur/src/main/resources/standardTestCases/conditionals.subworkflows_in_ifs.test b/centaur/src/main/resources/standardTestCases/conditionals.subworkflows_in_ifs.test
@@ -1,4 +1,4 @@
-ignore: true
+ignore: true # Depends on #2615
 name: subworkflows_in_ifs
 testFormat: workflowsuccess
 tags: [ conditionals ]

diff --git a/centaur/src/main/resources/standardTestCases/confirm_preemptible.test b/centaur/src/main/resources/standardTestCases/confirm_preemptible.test
@@ -1,4 +1,3 @@
-ignore: true
 name: confirm_preemptible
 testFormat: workflowsuccess
 backends: [Jes]

diff --git a/centaur/src/main/resources/standardTestCases/cont_while_possible_scatter.test b/centaur/src/main/resources/standardTestCases/cont_while_possible_scatter.test
@@ -1,4 +1,3 @@
-ignore: true
 name: cont_while_possible_scatter
 testFormat: workflowfailure
 backends: [Local]

diff --git a/centaur/src/main/resources/standardTestCases/custom_mount_point.test b/centaur/src/main/resources/standardTestCases/custom_mount_point.test
@@ -1,4 +1,3 @@
-ignore: true
 name: custom_mount_point
 testFormat: workflowsuccess
 backends: [Jes]

diff --git a/centaur/src/main/resources/standardTestCases/declarations_as_nodes.test b/centaur/src/main/resources/standardTestCases/declarations_as_nodes.test
@@ -1,4 +1,3 @@
-ignore: true
 name: declarations_as_nodes
 testFormat: workflowsuccess
 

diff --git a/centaur/src/main/resources/standardTestCases/defined_function.test b/centaur/src/main/resources/standardTestCases/defined_function.test
@@ -1,4 +1,4 @@
-ignore: true
+ignore: true # Depends on 2861
 name: defined_function
 testFormat: workflowsuccess
 

diff --git a/centaur/src/main/resources/standardTestCases/docker_hash_dockerhub_private.test b/centaur/src/main/resources/standardTestCases/docker_hash_dockerhub_private.test
@@ -1,4 +1,3 @@
-ignore: true
 name: docker_hash_dockerhub_private
 testFormat: workflowsuccess
 backends: [Jes]

diff --git a/centaur/src/main/resources/standardTestCases/docker_hash_gcr.test b/centaur/src/main/resources/standardTestCases/docker_hash_gcr.test
@@ -1,4 +1,3 @@
-ignore: true
 name: docker_hash_gcr
 testFormat: workflowsuccess
 

diff --git a/centaur/src/main/resources/standardTestCases/docker_hash_gcr_private.test b/centaur/src/main/resources/standardTestCases/docker_hash_gcr_private.test
@@ -1,4 +1,3 @@
-ignore: true
 name: docker_hash_gcr_private
 testFormat: workflowsuccess
 backends: [Jes]

diff --git a/centaur/src/main/resources/standardTestCases/dontCacheToFailedJobs.test b/centaur/src/main/resources/standardTestCases/dontCacheToFailedJobs.test
@@ -1,4 +1,3 @@
-ignore: true
 name: dont_cache_to_failed_jobs
 testFormat: runfailingtwiceexpectingnocallcaching
 

diff --git a/centaur/src/main/resources/standardTestCases/final_call_logs_dir_jes.test b/centaur/src/main/resources/standardTestCases/final_call_logs_dir_jes.test
@@ -1,4 +1,3 @@
-ignore: true
 # Tests that a runtime option to save call logs is copying said logs appropriately.
 
 name: final_call_logs_dir_jes

diff --git a/centaur/src/main/resources/standardTestCases/final_call_logs_dir_tes.test b/centaur/src/main/resources/standardTestCases/final_call_logs_dir_tes.test
@@ -1,4 +1,3 @@
-ignore: true
 # Tests that a runtime option to save call logs is copying said logs appropriately.
 
 name: final_call_logs_dir_tes

diff --git a/centaur/src/main/resources/standardTestCases/fofn_caching.test b/centaur/src/main/resources/standardTestCases/fofn_caching.test
@@ -1,4 +1,4 @@
-ignore: true
+ignore: true # Depends on 2864
 name: fofn_caching
 testFormat: runtwiceexpectingcallcaching
 backends: [Jes-Caching-No-Copy]

diff --git a/centaur/src/main/resources/standardTestCases/gcs_underscore_bucket.test b/centaur/src/main/resources/standardTestCases/gcs_underscore_bucket.test
@@ -1,4 +1,3 @@
-ignore: true
 name: gcs_underscore_bucket
 testFormat: workflowsuccess
 backends: [Jes]

diff --git a/centaur/src/main/resources/standardTestCases/globbingindex.test b/centaur/src/main/resources/standardTestCases/globbingindex.test
@@ -1,4 +1,4 @@
-ignore: true
+ignore: true # depends on 2901
 name: globbingindex
 testFormat: workflowsuccess
 

diff --git a/centaur/src/main/resources/standardTestCases/if_then_else_expressions.test b/centaur/src/main/resources/standardTestCases/if_then_else_expressions.test
@@ -1,4 +1,4 @@
-ignore: true
+ignore: true # Depends on #2861
 name: if_then_else_expressions
 testFormat: workflowsuccess
 

diff --git a/centaur/src/main/resources/standardTestCases/input_localization.test b/centaur/src/main/resources/standardTestCases/input_localization.test
@@ -1,4 +1,3 @@
-ignore: true
 # Tests that on a shared filesystem Cromwell is correctly localizing input files coming from the same as
 # well as different directories. Tests both docker and non-docker
 

diff --git a/centaur/src/main/resources/standardTestCases/input_mirror.test b/centaur/src/main/resources/standardTestCases/input_mirror.test
@@ -1,4 +1,3 @@
-ignore: true
 name: input_mirror
 testFormat: workflowsuccess
 

diff --git a/centaur/src/main/resources/standardTestCases/inter_scatter_dependencies.test b/centaur/src/main/resources/standardTestCases/inter_scatter_dependencies.test
@@ -1,4 +1,4 @@
-ignore: true
+ignore: true # Depends on #2898
 name: inter_scatter_dependencies
 testFormat: workflowsuccess
 

diff --git a/centaur/src/main/resources/standardTestCases/invalid_runtime_attributes.test b/centaur/src/main/resources/standardTestCases/invalid_runtime_attributes.test
@@ -1,4 +1,4 @@
-ignore: true
+ignore: true # Depends on 2904
 name: invalid_runtime_attributes
 testFormat: workflowfailure
 
@@ -8,6 +8,7 @@ files {
 }
 
 metadata {
-    "failures.0.message": "Runtime validation failed"
-    "failures.0.causedBy.0.message": "Task invalid_runtime_attributes has an invalid runtime attribute continueOnReturnCode = \"oops\""
+    "workflowName": "invalid_runtime_attributes_wf"
+    "failures.0.message": "Workflow failed"
+    "failures.0.causedBy.0.causedBy.0.message": "Expecting continueOnReturnCode runtime attribute to be either a Boolean, a String 'true' or 'false', or an Array[Int]"
 }
diff --git a/centaur/src/main/resources/standardTestCases/invalidate_bad_caches_jes.test b/centaur/src/main/resources/standardTestCases/invalidate_bad_caches_jes.test
@@ -1,4 +1,3 @@
-ignore: true
 name: invalidate_bad_caches_jes
 testFormat: workflowsuccess
 backends: [Jes]

diff --git a/centaur/src/main/resources/standardTestCases/invalidate_bad_caches_jes_no_copy.test b/centaur/src/main/resources/standardTestCases/invalidate_bad_caches_jes_no_copy.test
@@ -1,4 +1,3 @@
-ignore: true
 name: invalidate_bad_caches_jes_no_copy
 testFormat: workflowsuccess
 backends: [Jes-Caching-No-Copy]

diff --git a/centaur/src/main/resources/standardTestCases/invalidate_bad_caches_local.test b/centaur/src/main/resources/standardTestCases/invalidate_bad_caches_local.test
@@ -1,4 +1,5 @@
-ignore: true
+ignore: true # Depends on #2905
+
 name: invalidate_bad_caches_local
 testFormat: workflowsuccess
 backends: [Local]

diff --git a/centaur/src/main/resources/standardTestCases/jes_labels.test b/centaur/src/main/resources/standardTestCases/jes_labels.test
@@ -1,4 +1,3 @@
-ignore: true
 name: jes_labels
 testFormat: workflowsuccess
 tags: [ labels ]

diff --git a/centaur/src/main/resources/standardTestCases/local_gcs.test b/centaur/src/main/resources/standardTestCases/local_gcs.test
@@ -1,4 +1,3 @@
-ignore: true
 name: local_gcs
 testFormat: workflowsuccess
 backends: [Jes, Local]

diff --git a/centaur/src/main/resources/standardTestCases/missing_input_failure.test b/centaur/src/main/resources/standardTestCases/missing_input_failure.test
@@ -1,4 +1,3 @@
-ignore: true
 name: missing_input_failure
 testFormat: workflowfailure
 backends: [Jes]
@@ -11,8 +10,6 @@ files {
 metadata {
     workflowName: missing_input_failure
     status: Failed
-    "failures.0.message": "Couldn't resolve all inputs for missing_input_failure.hello at index None."
-    "failures.0.causedBy.0.message": "Input evaluation for Call missing_input_failure.hello failed."
-    "failures.0.causedBy.0.causedBy.0.message": "addressee"
-    "failures.0.causedBy.0.causedBy.0.causedBy.0.message": "nonexistingbucket/path/doesnt/exist"
+    "failures.0.message": "Workflow failed"
+    "failures.0.causedBy.0.message": "gs://nonexistingbucket/path/doesnt/exist"
 }
diff --git a/centaur/src/main/resources/standardTestCases/missing_optional_output.test b/centaur/src/main/resources/standardTestCases/missing_optional_output.test
@@ -1,4 +1,3 @@
-ignore: true
 name: missing_optional_output
 testFormat: workflowfailure
 
@@ -7,7 +6,7 @@ files {
 }
 
 metadata {
-  workflowName: missing_optional_output
   status: Failed
-  "failures.0.message": "out_except_undeclared is not declared as an output of the task x.\nMake sure to declare it as an output to be able to use it in the workflow."
+  "failures.0.message": "Workflow input processing failed"
+  "failures.0.causedBy.0.message": "No input x.out_except_undeclared found evaluating inputs for expression x.out_except_undeclared"
 }
diff --git a/centaur/src/main/resources/standardTestCases/monitoring_log.test b/centaur/src/main/resources/standardTestCases/monitoring_log.test
@@ -1,4 +1,3 @@
-ignore: true
 # Test to confirm the output of the monitoring script will be written to a monitoring.log file
 
 name: monitoring_log

diff --git a/centaur/src/main/resources/standardTestCases/no_new_calls.test b/centaur/src/main/resources/standardTestCases/no_new_calls.test
@@ -1,4 +1,5 @@
-ignore: true
+ignore: true # Depends on #2865
+
 #Currently failing since the workflow fails without completing task 'shouldSucceed'
 #and no information about tasks that weren't started.
 

diff --git a/centaur/src/main/resources/standardTestCases/optional_declarations.test b/centaur/src/main/resources/standardTestCases/optional_declarations.test
@@ -1,5 +1,3 @@
-ignore: true
-
 name: optional_declarations
 testFormat: workflowsuccess
 

diff --git a/centaur/src/main/resources/standardTestCases/optional_parameter.test b/centaur/src/main/resources/standardTestCases/optional_parameter.test
@@ -1,4 +1,4 @@
-ignore: true
+ignore: true # Reinstate with #2860
 # Tests interactions with an optional parameter. Supplying no value at all, using a default value and supplying a value
 
 name: optional_parameter

diff --git a/centaur/src/main/resources/standardTestCases/passingfiles.test b/centaur/src/main/resources/standardTestCases/passingfiles.test
@@ -1,4 +1,3 @@
-ignore: true
 name: passingfiles
 testFormat: workflowsuccess
 

diff --git a/centaur/src/main/resources/standardTestCases/public_http_import.test b/centaur/src/main/resources/standardTestCases/public_http_import.test
@@ -1,4 +1,4 @@
-ignore: true
+ignore: true # Depends on #2615
 name: public_http_import
 testFormat: workflowsuccess
 tags: [import, subworkflow, alias]

diff --git a/centaur/src/main/resources/standardTestCases/recursive_imports.test b/centaur/src/main/resources/standardTestCases/recursive_imports.test
@@ -1,4 +1,4 @@
-ignore: true
+ignore: true # Depends on #2615
 name: recursive_imports
 testFormat: workflowsuccess
 

diff --git a/centaur/src/main/resources/standardTestCases/referencingpreviousinputsandoutputs.test b/centaur/src/main/resources/standardTestCases/referencingpreviousinputsandoutputs.test
@@ -1,4 +1,3 @@
-ignore: true
 name: referencingpreviousinputsandoutputs
 testFormat: workflowsuccess
 

diff --git a/centaur/src/main/resources/standardTestCases/refresh_token.test b/centaur/src/main/resources/standardTestCases/refresh_token.test
@@ -1,4 +1,5 @@
-ignore: true
+ignore: true # Depends on 2862
+
 name: refresh_token
 testFormat: workflowsuccess
 backends: [Jes-Refresh]

diff --git a/centaur/src/main/resources/standardTestCases/refresh_token_failure.test b/centaur/src/main/resources/standardTestCases/refresh_token_failure.test
@@ -1,4 +1,3 @@
-ignore: true
 name: refresh_token_failure
 testFormat: workflowfailure
 backends: [Jes-Refresh]

diff --git a/centaur/src/main/resources/standardTestCases/refresh_token_no_auth_bucket.test b/centaur/src/main/resources/standardTestCases/refresh_token_no_auth_bucket.test
@@ -1,4 +1,4 @@
-ignore: true
+ignore: true # Depends on 2862
 name: refresh_token_no_auth_bucket
 testFormat: workflowfailure
 backends: [Jes-Refresh]

diff --git a/centaur/src/main/resources/standardTestCases/refresh_token_sub_workflow.test b/centaur/src/main/resources/standardTestCases/refresh_token_sub_workflow.test
@@ -1,4 +1,4 @@
-ignore: true
+ignore: true # Ignored because it requires subworkflows
 name: refresh_token_sub_workflow
 testFormat: workflowsuccess
 backends: [Jes-Refresh]

diff --git a/centaur/src/main/resources/standardTestCases/restart.restart_jes_with_recover.test b/centaur/src/main/resources/standardTestCases/restart.restart_jes_with_recover.test
@@ -1,4 +1,5 @@
-ignore: true
+ignore: true # Depends on #2866
+
 name: restart_jes_with_recover
 testFormat: CromwellRestartWithRecover
 callMark: cromwell_restart.cromwell_killer

diff --git a/centaur/src/main/resources/standardTestCases/restart.restart_local_with_recover.test b/centaur/src/main/resources/standardTestCases/restart.restart_local_with_recover.test
@@ -1,4 +1,5 @@
-ignore: true
+ignore: true # Depends on 2866
+
 name: restart_local_with_recover
 testFormat: CromwellRestartWithRecover
 callMark: cromwell_restart.cromwell_killer

diff --git a/centaur/src/main/resources/standardTestCases/restart.restart_tes_without_recover.test b/centaur/src/main/resources/standardTestCases/restart.restart_tes_without_recover.test
@@ -1,4 +1,5 @@
-ignore: true
+ignore: true # Depends on 2866
+
 name: restart_tes_without_recover
 testFormat: CromwellRestartWithoutRecover
 callMark: cromwell_restart.cromwell_killer