Merge branch '19109-upload-secondary' refs #19109

[arvados.git] / sdk / cwl / arvados_cwl / runner.py

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 50b3bb94d8934c1234220c25a3aa6bfb1a3075a0..f232178c5d5400ab90aad300d2f1d2d70909b98d 100644 (file)
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -129,6 +129,9 @@ def set_secondary(fsaccess, builder, inputschema, secondaryspec, primary, discov
             set_secondary(fsaccess, builder, i, secondaryspec, primary, discovered)
         return
 
             set_secondary(fsaccess, builder, i, secondaryspec, primary, discovered)
         return
 

+    if inputschema == "File":
+        inputschema = {"type": "File"}
+

     if isinstance(inputschema, basestring):
         sd = search_schemadef(inputschema, reversed(builder.hints+builder.requirements))
         if sd:
     if isinstance(inputschema, basestring):
         sd = search_schemadef(inputschema, reversed(builder.hints+builder.requirements))
         if sd:


@@ -164,10 +167,13 @@ def set_secondary(fsaccess, builder, inputschema, secondaryspec, primary, discov
             set_secondary(fsaccess, builder, {"type": inputschema["items"]}, secondaryspec, p, discovered)
 
     elif (inputschema["type"] == "File" and
             set_secondary(fsaccess, builder, {"type": inputschema["items"]}, secondaryspec, p, discovered)
 
     elif (inputschema["type"] == "File" and

-          secondaryspec and

           isinstance(primary, Mapping) and
           isinstance(primary, Mapping) and

-          primary.get("class") == "File" and
-          "secondaryFiles" not in primary):
+          primary.get("class") == "File"):
+
+        if "secondaryFiles" in primary or not secondaryspec:
+            # Nothing to do.
+            return
+

         #
         # Found a file, check for secondaryFiles
         #
         #
         # Found a file, check for secondaryFiles
         #


@@ -175,9 +181,9 @@ def set_secondary(fsaccess, builder, inputschema, secondaryspec, primary, discov
         primary["secondaryFiles"] = secondaryspec
         for i, sf in enumerate(aslist(secondaryspec)):
             if builder.cwlVersion == "v1.0":
         primary["secondaryFiles"] = secondaryspec
         for i, sf in enumerate(aslist(secondaryspec)):
             if builder.cwlVersion == "v1.0":

-                pattern = builder.do_eval(sf, context=primary)
+                pattern = sf

             else:
             else:

-                pattern = builder.do_eval(sf["pattern"], context=primary)
+                pattern = sf["pattern"]

             if pattern is None:
                 continue
             if isinstance(pattern, list):
             if pattern is None:
                 continue
             if isinstance(pattern, list):


@@ -214,7 +220,20 @@ def set_secondary(fsaccess, builder, inputschema, secondaryspec, primary, discov
                     "Expression must return list, object, string or null")
 
             if pattern is not None:
                     "Expression must return list, object, string or null")
 
             if pattern is not None:

-                sfpath = substitute(primary["location"], pattern)
+                if "${" in pattern or "$(" in pattern:
+                    sfname = builder.do_eval(pattern, context=primary)
+                else:
+                    sfname = substitute(primary["basename"], pattern)
+
+                if sfname is None:
+                    continue
+
+                p_location = primary["location"]
+                if "/" in p_location:
+                    sfpath = (
+                        p_location[0 : p_location.rindex("/") + 1]
+                        + sfname
+                    )

 
             required = builder.do_eval(required, context=primary)
 
 
             required = builder.do_eval(required, context=primary)