Added stdstreams to file conversion utils (#144)

Author: GlassOfWhiskey

.gitignore

@@ -107,3 +107,7 @@ venv.bak/
 
 testenv*/
 pydocstyle_report.txt
+
+# PyCharm
+.idea/
+

cwl_utils/parser/cwl_v1_0_utils.py

@@ -0,0 +1,28 @@
+import hashlib
+
+from schema_salad.exceptions import ValidationException
+from schema_salad.utils import json_dumps
+
+from cwl_utils.parser.cwl_v1_0 import CommandLineTool, CommandOutputBinding
+
+
+def convert_stdstreams_to_files(clt: CommandLineTool) -> None:
+    for out in clt.outputs:
+        if out.type == 'stdout':
+            if out.outputBinding is not None:
+                raise ValidationException(
+                    "Not allowed to specify outputBinding when using stdout shortcut.")
+            if clt.stdout is None:
+                clt.stdout = str(hashlib.sha1(json_dumps(  # nosec
+                    clt.save(), sort_keys=True).encode('utf-8')).hexdigest())
+            out.type = 'File'
+            out.outputBinding = CommandOutputBinding(glob=clt.stdout)
+        elif out.type == 'stderr':
+            if out.outputBinding is not None:
+                raise ValidationException(
+                    "Not allowed to specify outputBinding when using stderr shortcut.")
+            if clt.stderr is None:
+                clt.stderr = str(hashlib.sha1(json_dumps(  # nosec
+                    clt.save(), sort_keys=True).encode('utf-8')).hexdigest())
+            out.type = 'File'
+            out.outputBinding = CommandOutputBinding(glob=clt.stderr)

cwl_utils/parser/cwl_v1_1_utils.py

@@ -0,0 +1,40 @@
+import hashlib
+from typing import cast
+
+from schema_salad.exceptions import ValidationException
+from schema_salad.utils import json_dumps
+
+from cwl_utils.parser.cwl_v1_1 import CommandLineTool, CommandOutputBinding
+
+
+def convert_stdstreams_to_files(clt: CommandLineTool) -> None:
+    for out in clt.outputs:
+        if out.type == 'stdout':
+            if out.outputBinding is not None:
+                raise ValidationException(
+                    "Not allowed to specify outputBinding when using stdout shortcut.")
+            if clt.stdout is None:
+                clt.stdout = str(hashlib.sha1(json_dumps(  # nosec
+                    clt.save(), sort_keys=True).encode('utf-8')).hexdigest())
+            out.type = 'File'
+            out.outputBinding = CommandOutputBinding(glob=clt.stdout)
+        elif out.type == 'stderr':
+            if out.outputBinding is not None:
+                raise ValidationException(
+                    "Not allowed to specify outputBinding when using stderr shortcut.")
+            if clt.stderr is None:
+                clt.stderr = str(hashlib.sha1(json_dumps(  # nosec
+                    clt.save(), sort_keys=True).encode('utf-8')).hexdigest())
+            out.type = 'File'
+            out.outputBinding = CommandOutputBinding(glob=clt.stderr)
+    for inp in clt.inputs:
+        if inp.type == 'stdin':
+            if inp.inputBinding is not None:
+                raise ValidationException(
+                    "Not allowed to specify unputBinding when using stdin shortcut.")
+            if clt.stdin is not None:
+                raise ValidationException(
+                    "Not allowed to specify stdin path when using stdin type shortcut.")
+            else:
+                clt.stdin = '$(inputs.%s.path)' % cast(str, inp.id).rpartition('#')[2].split('/')[-1]
+                inp.type = 'File'

cwl_utils/parser/cwl_v1_2_utils.py

@@ -0,0 +1,40 @@
+import hashlib
+from typing import cast
+
+from schema_salad.exceptions import ValidationException
+from schema_salad.utils import json_dumps
+
+from cwl_utils.parser.cwl_v1_2 import CommandLineTool, CommandOutputBinding
+
+
+def convert_stdstreams_to_files(clt: CommandLineTool) -> None:
+    for out in clt.outputs:
+        if out.type == 'stdout':
+            if out.outputBinding is not None:
+                raise ValidationException(
+                    "Not allowed to specify outputBinding when using stdout shortcut.")
+            if clt.stdout is None:
+                clt.stdout = str(hashlib.sha1(json_dumps(  # nosec
+                    clt.save(), sort_keys=True).encode('utf-8')).hexdigest())
+            out.type = 'File'
+            out.outputBinding = CommandOutputBinding(glob=clt.stdout)
+        elif out.type == 'stderr':
+            if out.outputBinding is not None:
+                raise ValidationException(
+                    "Not allowed to specify outputBinding when using stderr shortcut.")
+            if clt.stderr is None:
+                clt.stderr = str(hashlib.sha1(json_dumps(  # nosec
+                    clt.save(), sort_keys=True).encode('utf-8')).hexdigest())
+            out.type = 'File'
+            out.outputBinding = CommandOutputBinding(glob=clt.stderr)
+    for inp in clt.inputs:
+        if inp.type == 'stdin':
+            if inp.inputBinding is not None:
+                raise ValidationException(
+                    "Not allowed to specify unputBinding when using stdin shortcut.")
+            if clt.stdin is not None:
+                raise ValidationException(
+                    "Not allowed to specify stdin path when using stdin type shortcut.")
+            else:
+                clt.stdin = '$(inputs.%s.path)' % cast(str, inp.id).rpartition('#')[2].split('/')[-1]
+                inp.type = 'File'