From f3c55a9d293d46064bb75e44765aa0223b4a57a2 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Thu, 25 May 2023 19:04:19 +0200
Subject: [PATCH] Unpin and upgrade cwl-utils version

---
 .github/dependabot.yml  | 16 ++++++++++++++++
 requirements.txt        |  2 +-
 setup.cfg               |  2 +-
 src/runcrate/convert.py | 37 +++++++++++++++++++------------------
 4 files changed, 37 insertions(+), 20 deletions(-)
 create mode 100644 .github/dependabot.yml

diff --git a/.github/dependabot.yml b/.github/dependabot.yml
new file mode 100644
index 0000000..c0a96e6
--- /dev/null
+++ b/.github/dependabot.yml
@@ -0,0 +1,16 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://help.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "pip" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "daily"
+  # Maintain dependencies for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "daily"
diff --git a/requirements.txt b/requirements.txt
index 97f6f54..0fcd5d7 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,6 +1,6 @@
 bdbag>=1.4.1
 click~=8.1
-cwl-utils==0.13
+cwl-utils>=0.27
 cwlprov==0.1.1
 networkx==2.8
 prov>=1.5.1
diff --git a/setup.cfg b/setup.cfg
index 7bc0931..af27bfd 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -32,7 +32,7 @@ python_requires=>=3.8, <4
 install_requires=
     bdbag>=1.4.1
     click~=8.1
-    cwl-utils==0.13
+    cwl-utils>=0.27
     cwlprov==0.1.1
     networkx==2.8
     prov>=1.5.1
diff --git a/src/runcrate/convert.py b/src/runcrate/convert.py
index 2cbd53c..2df565f 100644
--- a/src/runcrate/convert.py
+++ b/src/runcrate/convert.py
@@ -25,7 +25,7 @@
 import networkx as nx
 import prov.model
 from bdbag.bdbagit import BDBag
-from cwl_utils.parser import load_document_by_yaml
+from cwl_utils.parser import ProcessRequirement, load_document_by_yaml
 from cwlprov.prov import Entity, Provenance
 from cwlprov.ro import ResearchObject
 from cwlprov.utils import first
@@ -95,16 +95,12 @@ def is_structured(cwl_type):
     if is_structured(cwl_p.type):
         properties["multipleValues"] = "True"
     if hasattr(cwl_p, "default"):
-        try:
-            default_type = cwl_p.default["class"]
-        except (TypeError, KeyError):
-            if not is_structured(cwl_p.type) and cwl_p.default is not None:
-                properties["defaultValue"] = str(cwl_p.default)
-        else:
-            if default_type in ("File", "Directory"):
-                default = cwl_p.default.get("location", cwl_p.default.get("path"))
-                if default:
-                    properties["defaultValue"] = default
+        if hasattr(cwl_p.default, "class_") and cwl_p.default.class_ in ("File", "Directory"):
+            default = cwl_p.default.location or cwl_p.default.path
+            if default:
+                properties["defaultValue"] = default
+        elif not is_structured(cwl_p.type) and cwl_p.default is not None:
+            properties["defaultValue"] = str(cwl_p.default)
         # TODO: support more cases
     if getattr(cwl_p.type, "type", None) == "enum":
         properties["valuePattern"] = "|".join(_.rsplit("/", 1)[-1] for _ in cwl_p.type.symbols)
@@ -163,7 +159,7 @@ def get_workflow(wf_path):
         ns = n.pop("$namespaces", {})
         if ns:
             json_wf.setdefault("$namespaces", {}).update(ns)
-    defs = load_document_by_yaml(json_wf, wf_path.absolute().as_uri())
+    defs = load_document_by_yaml(json_wf, wf_path.absolute().as_uri(), load_all=True)
     if not isinstance(defs, list):
         defs = [defs]
     def_map = {}
@@ -362,13 +358,18 @@ def add_tool(self, crate, workflow, cwl_tool):
             properties["@type"] = "SoftwareApplication"
         if hasattr(cwl_tool, "intent") and cwl_tool.intent:
             properties["featureList"] = cwl_tool.intent
+        if hasattr(cwl_tool, "requirements") and cwl_tool.requirements:
+            for req in cwl_tool.requirements:
+                if req.class_ == "ResourceRequirement":
+                    ramMin = req.ramMin
+                    if ramMin:
+                        properties["memoryRequirements"] = f"{int(ramMin)} MiB"
         if hasattr(cwl_tool, "hints") and cwl_tool.hints:
-            hints_map = {_["class"]: _ for _ in cwl_tool.hints}
-            rreq = hints_map.get("ResourceRequirement")
-            if rreq:
-                ramMin = rreq.get("ramMin")
-                if ramMin:
-                    properties["memoryRequirements"] = f"{int(ramMin)} MiB"
+            for req in cwl_tool.hints:
+                if isinstance(req, ProcessRequirement) and req.class_ == "ResourceRequirement":
+                    ramMin = req.ramMin
+                    if ramMin:
+                        properties["memoryRequirements"] = f"{int(ramMin)} MiB"
         tool = crate.add(ContextEntity(crate, tool_id, properties=properties))
         tool["input"] = self.add_params(crate, cwl_tool.inputs)
         tool["output"] = self.add_params(crate, cwl_tool.outputs)