Force noLinkCheck=true when loading input file

common-workflow-language · Oct 20, 2023 · 294dd35 · 294dd35
1 parent 338e540
commit 294dd35
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Showing 3 changed files with 11 additions and 0 deletions.
diff --git a/cwl_utils/parser/cwl_v1_0_utils.py b/cwl_utils/parser/cwl_v1_0_utils.py
@@ -322,6 +322,7 @@ def load_inputfile(
         baseuri = cwl.file_uri(os.getcwd()) + "/"
     if loadingOptions is None:
         loadingOptions = cwl.LoadingOptions()
+    loadingOptions = cwl.LoadingOptions(copyfrom=loadingOptions, no_link_check=True)
     result, metadata = _inputfile_load(
         doc,
         baseuri,
@@ -343,6 +344,7 @@ def load_inputfile_by_string(
     if loadingOptions is None:
         loadingOptions = cwl.LoadingOptions(fileuri=uri)
 
+    loadingOptions = cwl.LoadingOptions(copyfrom=loadingOptions, no_link_check=True)
     result, metadata = _inputfile_load(
         result,
         uri,
@@ -362,6 +364,7 @@ def load_inputfile_by_yaml(
     if loadingOptions is None:
         loadingOptions = cwl.LoadingOptions(fileuri=uri)
 
+    loadingOptions = cwl.LoadingOptions(copyfrom=loadingOptions, no_link_check=True)
     result, metadata = _inputfile_load(
         yaml,
         uri,

diff --git a/cwl_utils/parser/cwl_v1_1_utils.py b/cwl_utils/parser/cwl_v1_1_utils.py
@@ -338,6 +338,8 @@ def load_inputfile(
         baseuri = cwl.file_uri(os.getcwd()) + "/"
     if loadingOptions is None:
         loadingOptions = cwl.LoadingOptions()
+
+    loadingOptions = cwl.LoadingOptions(copyfrom=loadingOptions, no_link_check=True)
     result, metadata = _inputfile_load(
         doc,
         baseuri,
@@ -359,6 +361,7 @@ def load_inputfile_by_string(
     if loadingOptions is None:
         loadingOptions = cwl.LoadingOptions(fileuri=uri)
 
+    loadingOptions = cwl.LoadingOptions(copyfrom=loadingOptions, no_link_check=True)
     result, metadata = _inputfile_load(
         result,
         uri,
@@ -378,6 +381,7 @@ def load_inputfile_by_yaml(
     if loadingOptions is None:
         loadingOptions = cwl.LoadingOptions(fileuri=uri)
 
+    loadingOptions = cwl.LoadingOptions(copyfrom=loadingOptions, no_link_check=True)
     result, metadata = _inputfile_load(
         yaml,
         uri,

diff --git a/cwl_utils/parser/cwl_v1_2_utils.py b/cwl_utils/parser/cwl_v1_2_utils.py
@@ -401,6 +401,8 @@ def load_inputfile(
         baseuri = cwl.file_uri(os.getcwd()) + "/"
     if loadingOptions is None:
         loadingOptions = cwl.LoadingOptions()
+
+    loadingOptions = cwl.LoadingOptions(copyfrom=loadingOptions, no_link_check=True)
     result, metadata = _inputfile_load(
         doc,
         baseuri,
@@ -422,6 +424,7 @@ def load_inputfile_by_string(
     if loadingOptions is None:
         loadingOptions = cwl.LoadingOptions(fileuri=uri)
 
+    loadingOptions = cwl.LoadingOptions(copyfrom=loadingOptions, no_link_check=True)
     result, metadata = _inputfile_load(
         result,
         uri,
@@ -441,6 +444,7 @@ def load_inputfile_by_yaml(
     if loadingOptions is None:
         loadingOptions = cwl.LoadingOptions(fileuri=uri)
 
+    loadingOptions = cwl.LoadingOptions(copyfrom=loadingOptions, no_link_check=True)
     result, metadata = _inputfile_load(
         yaml,
         uri,