Attempt to escape cwl evaluating bash as javascript

aefee505 · Timo Millenaar · a58db939 · a58db939 · a58db939 · aefee505
Commit aefee505 authored 10 months ago by Timo Millenaar
--- a/compress_pipeline.png
+++ b/compress_pipeline.png
--- a/download_and_compress_pipeline.png
+++ b/download_and_compress_pipeline.png
--- a/steps/combine_inspect_dataset.cwl
+++ b/steps/combine_inspect_dataset.cwl
@@ -8,7 +8,8 @@ requirements:
  - class: InlineJavascriptRequirement
 hints:
  - class: DockerRequirement
-    dockerPull: git.astron.nl:5000/ldv/lofar_quality:latest
+    # dockerPull: git.astron.nl:5000/ldv/lofar_quality:latest
+    dockerPull: localhost/lofar_quality_lofarstman:latest
  - class: NetworkAccess
    networkAccess: true
 inputs: 

--- a/steps/create_inspect_dataset.cwl
+++ b/steps/create_inspect_dataset.cwl
@@ -8,7 +8,8 @@ requirements:
  - class: InlineJavascriptRequirement
 hints:
  - class: DockerRequirement
-    dockerPull: git.astron.nl:5000/ldv/lofar_quality:latest
+    # dockerPull: git.astron.nl:5000/ldv/lofar_quality:latest
+    dockerPull: localhost/lofar_quality_lofarstman:latest
  - class: NetworkAccess
    networkAccess: true
 inputs: 

--- a/steps/extract_quality_metrics.cwl
+++ b/steps/extract_quality_metrics.cwl
@@ -16,6 +16,7 @@ requirements:
 hints:
  - class: DockerRequirement
    dockerPull: git.astron.nl:5000/ldv/lofar_quality:latest
+    # dockerPull: localhost/lofar_quality_lofarstman
  - class: NetworkAccess
    networkAccess: true
 inputs: 

--- a/steps/fetch_data.cwl
+++ b/steps/fetch_data.cwl
@@ -32,6 +32,6 @@ requirements:
            globus-url-copy $turl - | tar -xvf -
          else
            echo "Downloading $1 with srmcp"
-            srmcp $1 file:////`pwd`/$(basename $1)
-            tar -xvf $(basename $1)
+            srmcp $1 file:////`pwd`/\$(basename $1)
+            tar -xvf \$(basename $1)
          fi