From ea26057b531851c445e28c3f141929258c1361d6 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <1330696+mr-c@users.noreply.github.com>
Date: Sat, 4 Nov 2023 11:57:47 +0100
Subject: [PATCH 1/2] abstract CWL test: recusively validate

Fixes: #51
---
 tests/test_export_abstract.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/test_export_abstract.py b/tests/test_export_abstract.py
index a1ebe67..a984c93 100644
--- a/tests/test_export_abstract.py
+++ b/tests/test_export_abstract.py
@@ -5,10 +5,10 @@
     getdefault,
     LoadingContext,
 )
+from cwltool.load_tool import recursive_resolve_and_validate_document
 from cwltool.main import (
     default_loader,
     fetch_document,
-    resolve_and_validate_document,
     tool_resolver,
 )
 
@@ -140,7 +140,7 @@ def _run_example(as_dict, out=None):
     )
     loadingContext.resolver = getdefault(loadingContext.resolver, tool_resolver)
     loadingContext, workflowobj, uri = fetch_document(out, loadingContext)
-    loadingContext, uri = resolve_and_validate_document(
+    loadingContext, uri = recursive_resolve_and_validate_document(
         loadingContext,
         workflowobj,
         uri,

From 33c7572c322779787b6d941603d0bfa6153c88b9 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Tue, 16 Apr 2024 18:42:07 +0200
Subject: [PATCH 2/2] partial fix for valid CWL abstract export

---
 dev-requirements.txt          | 4 ++--
 gxformat2/abstract.py         | 8 ++++++--
 tests/example_wfs.py          | 6 ++++++
 tests/test_export_abstract.py | 2 +-
 4 files changed, 15 insertions(+), 5 deletions(-)

diff --git a/dev-requirements.txt b/dev-requirements.txt
index 3b1a54f..eac118f 100644
--- a/dev-requirements.txt
+++ b/dev-requirements.txt
@@ -1,7 +1,7 @@
 # Optional dependencies
 schema-salad[pycodegen]
-# Needs to validate v1.2
-cwltool>=3.0.20200807132242
+# Needs to validate v1.2, recursive_resolve_and_validate_document
+cwltool>=3.0.20201117141248
 
 
 mypy
diff --git a/gxformat2/abstract.py b/gxformat2/abstract.py
index 847b9f8..3b34540 100644
--- a/gxformat2/abstract.py
+++ b/gxformat2/abstract.py
@@ -82,14 +82,18 @@ def _format2_step_to_abstract(format2_step, requirements):
         step_run = {
             "class": "Operation",
             "doc": format2_step.get("doc", ""),
-            "inputs": {},  # TODO
-            "outputs": {},  # TODO
+            "inputs": _format2_wfstep_inputs_to_abstract(format2_step),
+            "outputs": { out: "Any" for out in format2_step["out"] }
         }
         abstract_step["run"] = step_run
     abstract_step["in"] = _format2_in_to_abstract(format2_step.get("in", []))
     abstract_step["out"] = _format2_out_to_abstract(format2_step)
     return abstract_step
 
+def _format2_wfstep_inputs_to_abstract(format2_step):
+    if "in" in format2_step:
+        return { name: "Any" for name in format2_step["in"].keys() }
+    return {}
 
 def _format2_in_to_abstract(in_dict):
     """Convert Format2 'in' dict for step into CWL abstract 'in' dict."""
diff --git a/tests/example_wfs.py b/tests/example_wfs.py
index cb641d5..23a8d46 100644
--- a/tests/example_wfs.py
+++ b/tests/example_wfs.py
@@ -18,6 +18,8 @@
     doc: cat doc
     in:
       input1: the_input
+    out:
+      out_file1: {}
 """
 
 WORKFLOW_WITH_REPEAT = """
@@ -100,6 +102,8 @@
         mapping:
           - type: list_identifiers
             columns: [0, 1]
+    out:
+      output: {}
   random_lines:
     tool_id: random_lines1
     state:
@@ -109,6 +113,8 @@
       seed_source:
         seed_source_selector: set_seed
         seed: asdf
+    out:
+      out_file1: {}
 """
 
 RUNTIME_INPUTS = """
diff --git a/tests/test_export_abstract.py b/tests/test_export_abstract.py
index a984c93..b56dce1 100644
--- a/tests/test_export_abstract.py
+++ b/tests/test_export_abstract.py
@@ -140,7 +140,7 @@ def _run_example(as_dict, out=None):
     )
     loadingContext.resolver = getdefault(loadingContext.resolver, tool_resolver)
     loadingContext, workflowobj, uri = fetch_document(out, loadingContext)
-    loadingContext, uri = recursive_resolve_and_validate_document(
+    loadingContext, uri, process = recursive_resolve_and_validate_document(
         loadingContext,
         workflowobj,
         uri,