common-workflow-language · mr-c · Aug 19, 2022 · Aug 19, 2022 · mr-c · Aug 19, 2022
diff --git a/cwltool/singularity.py b/cwltool/singularity.py
@@ -184,7 +184,7 @@ def get_image(
             candidates.append(dockerRequirement["dockerImageId"])
             candidates.append(_normalize_image_id(dockerRequirement["dockerImageId"]))
             if is_version_3_or_newer():
-                candidates.append(_normalize_sif_id(dockerRequirement["dockerPull"]))
+                candidates.append(_normalize_sif_id(dockerRequirement["dockerImageId"]))
 
         targets = [os.getcwd()]
         if "CWL_SINGULARITY_CACHE" in os.environ:

diff --git a/tests/debian_image_id.cwl b/tests/debian_image_id.cwl
@@ -4,11 +4,11 @@ class: CommandLineTool
 
 requirements:
   DockerRequirement:
-    dockerImageId: 'debian.img'
+    dockerImageId: 'debian:stable-slim.img'
 
 inputs:
   message: string
 
 outputs: []
 
-baseCommand: echo
+baseCommand: echo
diff --git a/tests/debian_image_id2.cwl b/tests/debian_image_id2.cwl
@@ -0,0 +1,14 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+
+requirements:
+  DockerRequirement:
+    dockerImageId: 'docker.io_debian:stable-slim.sif'
+
+inputs:
+  message: string
+
+outputs: []
+
+baseCommand: echo
diff --git a/tests/echo-job.yaml b/tests/echo-job.yaml
@@ -1,5 +1,5 @@
 cwl:requirements:
  - class: DockerRequirement
-   dockerPull: docker.io/debian
+   dockerPull: docker.io/debian:stable-slim
 
 inp: "Howdy!"
diff --git a/tests/non_portable.cwl b/tests/non_portable.cwl
@@ -4,7 +4,7 @@ class: CommandLineTool
 
 requirements:
   DockerRequirement:
-    dockerPull: docker.io/debian
+    dockerPull: docker.io/debian:stable-slim
   InitialWorkDirRequirement:
     listing:
       - class: File

diff --git a/tests/non_portable2.cwl b/tests/non_portable2.cwl
@@ -4,7 +4,7 @@ class: CommandLineTool
 
 hints:
   DockerRequirement:
-    dockerPull: docker.io/debian
+    dockerPull: docker.io/debian:stable-slim
     dockerOutputDirectory: /var/spool/cwl
   InitialWorkDirRequirement:
     listing:

diff --git a/tests/portable.cwl b/tests/portable.cwl
@@ -4,7 +4,7 @@ class: CommandLineTool
 
 requirements:
   DockerRequirement:
-    dockerPull: docker.io/debian
+    dockerPull: docker.io/debian:stable-slim
     dockerOutputDirectory: /var/spool/cwl
   InitialWorkDirRequirement:
     listing:

diff --git a/tests/sing_pullfolder_test.cwl b/tests/sing_pullfolder_test.cwl
@@ -4,7 +4,7 @@ class: CommandLineTool
 
 requirements:
   DockerRequirement:
-    dockerPull: docker.io/debian
+    dockerPull: docker.io/debian:stable-slim
 
 inputs:
   message: string

diff --git a/tests/test_docker_info.py b/tests/test_docker_info.py
@@ -5,7 +5,7 @@
 def test_docker_mem() -> None:
     error_code, stdout, stderr = get_main_output(
         [
-            "--default-container=debian",
+            "--default-container=docker.io/debian:stable-slim",
             "--enable-ext",
             get_data("tests/wf/timelimit.cwl"),
             "--sleep_time",

diff --git a/tests/test_singularity.py b/tests/test_singularity.py
@@ -10,6 +10,7 @@
     get_main_output,
     needs_singularity,
     needs_singularity_2_6,
+    needs_singularity_3_or_newer,
     working_directory,
 )
 
@@ -107,7 +108,7 @@ def test_singularity_local(tmp_path: Path) -> None:
 
 
 @needs_singularity_2_6
-def test_singularity_docker_image_id_in_tool(tmp_path: Path) -> None:
+def test_singularity2_docker_image_id_in_tool(tmp_path: Path) -> None:
     workdir = tmp_path / "working_dir"
     workdir.mkdir()
     with working_directory(workdir):
@@ -128,3 +129,28 @@ def test_singularity_docker_image_id_in_tool(tmp_path: Path) -> None:
             ]
         )
         assert result_code1 == 0
+
+
+@needs_singularity_3_or_newer
+def test_singularity3_docker_image_id_in_tool(tmp_path: Path) -> None:
+    workdir = tmp_path / "working_dir"
+    workdir.mkdir()
+    with working_directory(workdir):
+        result_code, stdout, stderr = get_main_output(
+            [
+                "--singularity",
+                get_data("tests/sing_pullfolder_test.cwl"),
+                "--message",
+                "hello",
+            ]
+        )
+        assert result_code == 0
+        result_code1, stdout, stderr = get_main_output(
+            [
+                "--singularity",
+                get_data("tests/debian_image_id2.cwl"),
+                "--message",
+                "hello",
+            ]
+        )
+        assert result_code1 == 0
diff --git a/tests/test_tmpdir.py b/tests/test_tmpdir.py
@@ -45,7 +45,7 @@ def test_docker_commandLineTool_job_tmpdir_prefix(tmp_path: Path) -> None:
                     "requirements": [
                         {
                             "class": "DockerRequirement",
-                            "dockerPull": "docker.io/debian:stable",
+                            "dockerPull": "docker.io/debian:stable-slim",
                         }
                     ],
                 }
@@ -120,7 +120,7 @@ def test_dockerfile_tmpdir_prefix(
     assert DockerCommandLineJob.get_image(
         {
             "class": "DockerRequirement",
-            "dockerFile": "FROM debian:stable",
+            "dockerFile": "FROM debian:stable-slim",
             "dockerImageId": sys._getframe().f_code.co_name,
         },
         pull_image=True,

diff --git a/tests/test_udocker.py b/tests/test_udocker.py
@@ -56,7 +56,7 @@ def test_udocker_usage_should_not_write_cid_file(udocker: str, tmp_path: Path) -
             [
                 "--debug",
                 "--default-container",
-                "debian",
+                "debian:stable-slim",
                 "--user-space-docker-cmd=" + udocker,
                 get_data(test_file),
                 get_data(job_file),
@@ -79,7 +79,7 @@ def test_udocker_should_display_memory_usage(udocker: str, tmp_path: Path) -> No
         error_code, stdout, stderr = get_main_output(
             [
                 "--enable-ext",
-                "--default-container=debian",
+                "--default-container=debian:stable-slim",
                 "--user-space-docker-cmd=" + udocker,
                 get_data("tests/wf/timelimit.cwl"),
                 "--sleep_time",

diff --git a/tests/wf/1590.cwl b/tests/wf/1590.cwl
@@ -23,7 +23,7 @@
   "requirements": [
     {
       "class": "DockerRequirement",
-      "dockerPull": "debian:stretch-slim"
+      "dockerPull": "debian:stable-slim"
     }
   ],
   "stdout": "output"

diff --git a/tests/wf/cat-tool.cwl b/tests/wf/cat-tool.cwl
@@ -5,7 +5,7 @@ cwlVersion: v1.0
 
 hints:
   DockerRequirement:
-    dockerPull: docker.io/frolvlad/alpine-bash
+    dockerPull: docker.io/bash:4.4`
 
 inputs:
   file1: File

diff --git a/tests/wf/directory.cwl b/tests/wf/directory.cwl
@@ -8,7 +8,7 @@ doc: >
 
 hints:
   - class: DockerRequirement
-    dockerPull: docker.io/debian:8
+    dockerPull: docker.io/debian:stable-slim
 
 inputs:
     dir:

diff --git a/tests/wf/expect_packed.cwl b/tests/wf/expect_packed.cwl
@@ -6,7 +6,7 @@
             "hints": [
                 {
                     "class": "DockerRequirement",
-                    "dockerPull": "docker.io/debian:8"
+                    "dockerPull": "docker.io/debian:stable-slim"
                 }
             ],
             "inputs": [

diff --git a/tests/wf/expect_revsort_datetime_packed.cwl b/tests/wf/expect_revsort_datetime_packed.cwl
@@ -6,7 +6,7 @@
             "hints": [
                 {
                     "class": "DockerRequirement",
-                    "dockerPull": "docker.io/debian:8"
+                    "dockerPull": "docker.io/debian:stable-slim"
                 }
             ],
             "inputs": [

diff --git a/tests/wf/expect_trick_packed.cwl b/tests/wf/expect_trick_packed.cwl
@@ -62,7 +62,7 @@
             "hints": [
                 {
                     "class": "DockerRequirement",
-                    "dockerPull": "docker.io/debian:8"
+                    "dockerPull": "docker.io/debian:stable-slim"
                 }
             ],
             "inputs": [

diff --git a/tests/wf/iwdr_permutations.cwl b/tests/wf/iwdr_permutations.cwl
@@ -6,7 +6,7 @@ requirements:
     envDef:
       LC_ALL: C
   DockerRequirement:
-    dockerPull: docker.io/debian
+    dockerPull: docker.io/debian:stable-slim
   InitialWorkDirRequirement:
     listing:
       - entry: $(inputs.first)

diff --git a/tests/wf/literalfile.cwl b/tests/wf/literalfile.cwl
@@ -6,5 +6,5 @@ inputs:
 outputs: []
 requirements:
   DockerRequirement:
-    dockerPull: docker.io/debian:9
+    dockerPull: docker.io/debian:stable-slim
 arguments: [cat, $(inputs.a1)]
diff --git a/tests/wf/networkaccess-fail.cwl b/tests/wf/networkaccess-fail.cwl
@@ -3,7 +3,7 @@ class: CommandLineTool
 cwlVersion: v1.0
 requirements:
   DockerRequirement:
-    dockerPull: docker.io/python:3
+    dockerPull: docker.io/python:3-slim
   NetworkAccess:
     networkAccess: true
 inputs: []

diff --git a/tests/wf/networkaccess.cwl b/tests/wf/networkaccess.cwl
@@ -5,7 +5,7 @@ $namespaces:
   cwltool: "http://commonwl.org/cwltool#"
 requirements:
   DockerRequirement:
-    dockerPull: docker.io/python:3
+    dockerPull: docker.io/python:3-slim
   cwltool:NetworkAccess:
     networkAccess: true
 inputs: []

diff --git a/tests/wf/revsort.cwl b/tests/wf/revsort.cwl
@@ -11,7 +11,7 @@ cwlVersion: v1.0
 # in which the command line tools will execute.
 hints:
   - class: DockerRequirement
-    dockerPull: docker.io/debian:8
+    dockerPull: docker.io/debian:stable-slim
 
 
 # The inputs array defines the structure of the input object that describes

diff --git a/tests/wf/revsort_datetime.cwl b/tests/wf/revsort_datetime.cwl
@@ -11,7 +11,7 @@ cwlVersion: v1.0
 # in which the command line tools will execute.
 hints:
   - class: DockerRequirement
-    dockerPull: docker.io/debian:8
+    dockerPull: docker.io/debian:stable-slim
 
 
 # The inputs array defines the structure of the input object that describes

diff --git a/tests/wf/secret_wf.cwl b/tests/wf/secret_wf.cwl
@@ -7,7 +7,7 @@ hints:
   "cwltool:Secrets":
     secrets: [pw]
   DockerRequirement:
-    dockerPull: docker.io/debian:8
+    dockerPull: docker.io/debian:stable-slim
 inputs:
   pw: string
 outputs:

diff --git a/tests/wf/touch_tool.cwl b/tests/wf/touch_tool.cwl
@@ -5,7 +5,7 @@ class: CommandLineTool
 baseCommand: touch
 requirements:
   DockerRequirement:
-    dockerPull: docker.io/alpine
+    dockerPull: docker.io/alpine:latest
 inputs:
   message:
     type: string

diff --git a/tests/wf/trick_revsort.cwl b/tests/wf/trick_revsort.cwl
@@ -11,7 +11,7 @@ cwlVersion: v1.0
 # in which the command line tools will execute.
 hints:
   - class: DockerRequirement
-    dockerPull: docker.io/debian:8
+    dockerPull: docker.io/debian:stable-slim
 
 
 # The inputs array defines the structure of the input object that describes

diff --git a/tests/wf/updateval.cwl b/tests/wf/updateval.cwl
@@ -8,7 +8,7 @@ requirements:
         writable: true
 hints:
   DockerRequirement:
-    dockerPull: "docker.io/python:2.7.15-alpine3.7"
+    dockerPull: "docker.io/python:3-slim"
 inputs:
   r: File
   script:

diff --git a/tests/wf/updateval_inplace.cwl b/tests/wf/updateval_inplace.cwl
@@ -12,7 +12,7 @@ requirements:
     inplaceUpdate: true
 hints:
   DockerRequirement:
-    dockerPull: "docker.io/python:2.7.15-alpine3.7"
+    dockerPull: "docker.io/python:3-slim"
 inputs:
   r: File
   script:

diff --git a/tests/wf/workreuse-fail.cwl b/tests/wf/workreuse-fail.cwl
@@ -3,7 +3,7 @@ class: CommandLineTool
 cwlVersion: v1.0
 requirements:
   DockerRequirement:
-    dockerPull: docker.io/python:3
+    dockerPull: docker.io/python:3-slim
   WorkReuse:
     enableReuse: false
 inputs: []

diff --git a/tests/wf/workreuse.cwl b/tests/wf/workreuse.cwl
@@ -5,7 +5,7 @@ $namespaces:
   cwltool: "http://commonwl.org/cwltool#"
 requirements:
   DockerRequirement:
-    dockerPull: docker.io/python:3
+    dockerPull: docker.io/python:3-slim
   cwltool:WorkReuse:
     enableReuse: false
 inputs: []
-Original file line number
+Diff line change
@@ Expand Up / @@ -8,7 +8,7 @@ doc: > @@
     hints:
       - class: DockerRequirement
-        dockerPull: docker.io/debian:8
+        dockerPull: docker.io/debian:stable-slim
     inputs:
         dir:
@@ Expand Down @@