add registry to dockerPull references

mr-c · mr-c · commit 6a7f35fa67a4 · 2021-09-21T13:17:17.000+02:00
diff --git a/tests/echo-job.yaml b/tests/echo-job.yaml
@@ -1,5 +1,5 @@
 cwl:requirements:
  - class: DockerRequirement
-   dockerPull: debian
+   dockerPull: docker.io/debian
 
 inp: "Howdy!"
diff --git a/tests/iwdr_bad_expr.cwl b/tests/iwdr_bad_expr.cwl
@@ -4,7 +4,7 @@ cwlVersion: v1.0
 
 requirements:
   DockerRequirement:
-      dockerPull: debian:stable-slim
+      dockerPull: docker.io/debian:stable-slim
   InlineJavascriptRequirement: {}
   InitialWorkDirRequirement:
     listing: |
diff --git a/tests/iwdr_dir_literal_real_file.cwl b/tests/iwdr_dir_literal_real_file.cwl
@@ -4,7 +4,7 @@ cwlVersion: v1.0
 
 requirements:
   DockerRequirement:
-      dockerPull: debian:stable-slim
+      dockerPull: docker.io/debian:stable-slim
   InlineJavascriptRequirement: {}
   InitialWorkDirRequirement:
     listing: |
diff --git a/tests/non_portable.cwl b/tests/non_portable.cwl
@@ -4,7 +4,7 @@ class: CommandLineTool
 
 requirements:
   DockerRequirement:
-    dockerPull: debian
+    dockerPull: docker.io/debian
   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: debian
+    dockerPull: docker.io/debian
     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: debian
+    dockerPull: docker.io/debian
     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: debian
+    dockerPull: docker.io/debian
 
 inputs:
   message: string
diff --git a/tests/test_tmpdir.py b/tests/test_tmpdir.py
@@ -42,7 +42,10 @@ def test_docker_commandLineTool_job_tmpdir_prefix(tmp_path: Path) -> None:
                     "inputs": [],
                     "outputs": [],
                     "requirements": [
-                        {"class": "DockerRequirement", "dockerPull": "debian:stable"}
+                        {
+                            "class": "DockerRequirement",
+                            "dockerPull": "docker.io/debian:stable",
+                        }
                     ],
                 }
             ),
diff --git a/tests/wf/910.cwl b/tests/wf/910.cwl
@@ -18,7 +18,7 @@ requirements:
 
 hints:
 - class: DockerRequirement
-  dockerPull: ubuntu
+  dockerPull: docker.io/ubuntu
 
 inputs: []
 
diff --git a/tests/wf/arguments.cwl b/tests/wf/arguments.cwl
@@ -5,7 +5,7 @@ class: CommandLineTool
 label: Example trivial wrapper for Java 9 compiler
 hints:
   DockerRequirement:
-    dockerPull: openjdk:9.0.1-11-slim
+    dockerPull: docker.io/openjdk:9.0.1-11-slim
 baseCommand: javac
 arguments: ["-d", $(runtime.outdir)]
 inputs:
diff --git a/tests/wf/cat-tool.cwl b/tests/wf/cat-tool.cwl
@@ -5,7 +5,7 @@ cwlVersion: v1.0
 
 hints:
   DockerRequirement:
-    dockerPull: frolvlad/alpine-bash
+    dockerPull: docker.io/frolvlad/alpine-bash
 
 inputs:
   file1: File
diff --git a/tests/wf/directory.cwl b/tests/wf/directory.cwl
@@ -8,7 +8,7 @@ doc: >
 
 hints:
   - class: DockerRequirement
-    dockerPull: debian:8
+    dockerPull: docker.io/debian:8
 
 inputs:
     dir:
diff --git a/tests/wf/expect_packed.cwl b/tests/wf/expect_packed.cwl
@@ -6,7 +6,7 @@
             "hints": [
                 {
                     "class": "DockerRequirement",
-                    "dockerPull": "debian:8"
+                    "dockerPull": "docker.io/debian:8"
                 }
             ],
             "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": "debian:8"
+                    "dockerPull": "docker.io/debian:8"
                 }
             ],
             "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": "debian:8"
+                    "dockerPull": "docker.io/debian:8"
                 }
             ],
             "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: debian
+    dockerPull: docker.io/debian
   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: debian:9
+    dockerPull: docker.io/debian:9
 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: python:3
+    dockerPull: docker.io/python:3
   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: python:3
+    dockerPull: docker.io/python:3
   cwltool:NetworkAccess:
     networkAccess: true
 inputs: []
diff --git a/tests/wf/operation/abstract-cosifer.cwl b/tests/wf/operation/abstract-cosifer.cwl
@@ -3,7 +3,7 @@ cwlVersion: v1.2
 
 requirements:
   DockerRequirement:
-    dockerPull: 'tsenit/cosifer:b4d5af45d2fc54b6bff2a9153a8e9054e560302e'
+    dockerPull: 'docker.io/tsenit/cosifer:b4d5af45d2fc54b6bff2a9153a8e9054e560302e'
 
 inputs:
   data_matrix:
diff --git a/tests/wf/operation/expect_operation-single_packed.cwl b/tests/wf/operation/expect_operation-single_packed.cwl
@@ -4,7 +4,7 @@
             "class": "Operation",
             "requirements": [
                 {
-                    "dockerPull": "tsenit/cosifer:b4d5af45d2fc54b6bff2a9153a8e9054e560302e",
+                    "dockerPull": "docker.io/tsenit/cosifer:b4d5af45d2fc54b6bff2a9153a8e9054e560302e",
                     "class": "DockerRequirement"
                 }
             ],
@@ -151,4 +151,4 @@
         }
     ],
     "cwlVersion": "v1.2"
-}
+}
diff --git a/tests/wf/packed-with-loadlisting.cwl b/tests/wf/packed-with-loadlisting.cwl
@@ -46,7 +46,7 @@
           "class": "CommandLineTool",
           "requirements": [
             {
-              "dockerPull": "debian:stretch-slim",
+              "dockerPull": "docker.io/debian:stretch-slim",
               "class": "DockerRequirement",
             },
             {
diff --git a/tests/wf/paramref_arguments_self.cwl b/tests/wf/paramref_arguments_self.cwl
@@ -24,7 +24,7 @@ steps:
       class: CommandLineTool
       hints:
         DockerRequirement:
-          dockerPull: everpeace/curl-jq
+          dockerPull: docker.io/everpeace/curl-jq
       inputs:
         self:
           type: File
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: debian:8
+    dockerPull: docker.io/debian:8
 
 
 # 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: debian:8
+    dockerPull: docker.io/debian:8
 
 
 # The inputs array defines the structure of the input object that describes
diff --git a/tests/wf/schemadef-bug-1473.cwl b/tests/wf/schemadef-bug-1473.cwl
@@ -151,7 +151,7 @@
             "doc": "Runs the BCL Convert application off standard architechture\n",
             "hints": [
                 {
-                    "dockerPull": "umccr/bcl-convert:3.7.5",
+                    "dockerPull": "docker.io/umccr/bcl-convert:3.7.5",
                     "class": "DockerRequirement"
                 },
                 {
@@ -400,7 +400,7 @@
             "doc": "Use before running bcl-convert workflow to ensure that the bclConvert workflow can run in parallel.\nSamples will be split into separate samplesheets based on their cycles specification\n",
             "hints": [
                 {
-                    "dockerPull": "umccr/alpine_pandas:latest-cwl",
+                    "dockerPull": "docker.io/umccr/alpine_pandas:latest-cwl",
                     "class": "DockerRequirement"
                 },
                 {
@@ -700,7 +700,7 @@
             "doc": "Documentation for custom-create-dummy-file v1.0.0\n",
             "hints": [
                 {
-                    "dockerPull": "alpine:latest",
+                    "dockerPull": "docker.io/alpine:latest",
                     "class": "DockerRequirement"
                 },
                 {
@@ -762,7 +762,7 @@
             "doc": "Producing QC report using interop matrix\n",
             "hints": [
                 {
-                    "dockerPull": "umccr/multiqc_dragen:1.2.1",
+                    "dockerPull": "docker.io/umccr/multiqc_dragen:1.2.1",
                     "class": "DockerRequirement"
                 },
                 {
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: debian:8
+    dockerPull: docker.io/debian:8
 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: alpine
+    dockerPull: docker.io/alpine
 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: debian:8
+    dockerPull: docker.io/debian:8
 
 
 # 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: "python:2.7.15-alpine3.7"
+    dockerPull: "docker.io/python:2.7.15-alpine3.7"
 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: "python:2.7.15-alpine3.7"
+    dockerPull: "docker.io/python:2.7.15-alpine3.7"
 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: python:3
+    dockerPull: docker.io/python:3
   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: python:3
+    dockerPull: docker.io/python:3
   cwltool:WorkReuse:
     enableReuse: false
 inputs: []

Original file line number	Diff line number	Diff line change
`@@ -6,7 +6,7 @@`
`6`	`6`	`"hints": [`
`7`	`7`	`{`
`8`	`8`	`"class": "DockerRequirement",`
`9`		`- "dockerPull": "debian:8"`
	`9`	`+ "dockerPull": "docker.io/debian:8"`
`10`	`10`	`}`
`11`	`11`	`],`
`12`	`12`	`"inputs": [`
Original file line number	Diff line number	Diff line change
`@@ -62,7 +62,7 @@`
`62`	`62`	`"hints": [`
`63`	`63`	`{`
`64`	`64`	`"class": "DockerRequirement",`
`65`		`- "dockerPull": "debian:8"`
	`65`	`+ "dockerPull": "docker.io/debian:8"`
`66`	`66`	`}`
`67`	`67`	`],`
`68`	`68`	`"inputs": [`
Original file line number	Diff line number	Diff line change
`@@ -4,7 +4,7 @@`
`4`	`4`	`"class": "Operation",`
`5`	`5`	`"requirements": [`
`6`	`6`	`{`
`7`		`- "dockerPull": "tsenit/cosifer:b4d5af45d2fc54b6bff2a9153a8e9054e560302e",`
	`7`	`+ "dockerPull": "docker.io/tsenit/cosifer:b4d5af45d2fc54b6bff2a9153a8e9054e560302e",`
`8`	`8`	`"class": "DockerRequirement"`
`9`	`9`	`}`
`10`	`10`	`],`
`@@ -151,4 +151,4 @@`
`151`	`151`	`}`
`152`	`152`	`],`
`153`	`153`	`"cwlVersion": "v1.2"`
`154`		`-}`
	`154`	`+}`
Original file line number	Diff line number	Diff line change
`@@ -46,7 +46,7 @@`
`46`	`46`	`"class": "CommandLineTool",`
`47`	`47`	`"requirements": [`
`48`	`48`	`{`
`49`		`- "dockerPull": "debian:stretch-slim",`
	`49`	`+ "dockerPull": "docker.io/debian:stretch-slim",`
`50`	`50`	`"class": "DockerRequirement",`
`51`	`51`	`},`
`52`	`52`	`{`
Original file line number	Diff line number	Diff line change
`@@ -151,7 +151,7 @@`
`151`	`151`	`"doc": "Runs the BCL Convert application off standard architechture\n",`
`152`	`152`	`"hints": [`
`153`	`153`	`{`
`154`		`- "dockerPull": "umccr/bcl-convert:3.7.5",`
	`154`	`+ "dockerPull": "docker.io/umccr/bcl-convert:3.7.5",`
`155`	`155`	`"class": "DockerRequirement"`
`156`	`156`	`},`
`157`	`157`	`{`
`@@ -400,7 +400,7 @@`
`400`	`400`	`"doc": "Use before running bcl-convert workflow to ensure that the bclConvert workflow can run in parallel.\nSamples will be split into separate samplesheets based on their cycles specification\n",`
`401`	`401`	`"hints": [`
`402`	`402`	`{`
`403`		`- "dockerPull": "umccr/alpine_pandas:latest-cwl",`
	`403`	`+ "dockerPull": "docker.io/umccr/alpine_pandas:latest-cwl",`
`404`	`404`	`"class": "DockerRequirement"`
`405`	`405`	`},`
`406`	`406`	`{`
`@@ -700,7 +700,7 @@`
`700`	`700`	`"doc": "Documentation for custom-create-dummy-file v1.0.0\n",`
`701`	`701`	`"hints": [`
`702`	`702`	`{`
`703`		`- "dockerPull": "alpine:latest",`
	`703`	`+ "dockerPull": "docker.io/alpine:latest",`
`704`	`704`	`"class": "DockerRequirement"`
`705`	`705`	`},`
`706`	`706`	`{`
`@@ -762,7 +762,7 @@`
`762`	`762`	`"doc": "Producing QC report using interop matrix\n",`
`763`	`763`	`"hints": [`
`764`	`764`	`{`
`765`		`- "dockerPull": "umccr/multiqc_dragen:1.2.1",`
	`765`	`+ "dockerPull": "docker.io/umccr/multiqc_dragen:1.2.1",`
`766`	`766`	`"class": "DockerRequirement"`
`767`	`767`	`},`
`768`	`768`	`{`