convert cwlprov:image

Author: simleo

src/runcrate/convert.py

@@ -35,7 +35,7 @@
 from rocrate.rocrate import ROCrate
 
 from .constants import PROFILES_BASE, PROFILES_VERSION, TERMS_NAMESPACE
-from .utils import as_list
+from .utils import as_list, parse_img
 
 
 WORKFLOW_BASENAME = "packed.cwl"
@@ -61,6 +61,8 @@
 
 WROC_PROFILE_VERSION = "1.0"
 
+DOCKER_IMG_TYPE = "https://w3id.org/ro/terms/workflow-run#DockerImage"
+
 
 def convert_cwl_type(cwl_type):
     if isinstance(cwl_type, list):
@@ -503,9 +505,24 @@ def to_wf_p(k):
         action["endTime"] = activity.end().time.isoformat()
         action["object"] = self.add_action_params(crate, activity, to_wf_p, "usage")
         action["result"] = self.add_action_params(crate, activity, to_wf_p, "generation")
+        self.add_container_images(crate, action, activity)
         for job in activity.steps():
             self.add_action(crate, job, parent_instrument=instrument)
 
+    def add_container_images(self, crate, action, activity):
+        images = set()
+        for assoc in activity.association():
+            for agent in activity.provenance.prov_doc.get_record(assoc.agent_id):
+                images |= agent.get_attribute("cwlprov:image")
+        for im in images:
+            properties = parse_img(im)
+            properties.update({
+                "@type": "ContainerImage",
+                "additionalType": {"@id": DOCKER_IMG_TYPE}
+            })
+            roc_img = crate.add(ContextEntity(crate, properties=properties))
+            action.append_to("containerImage", roc_img, compact=True)
+
     def add_action_params(self, crate, activity, to_wf_p, ptype="usage"):
         action_params = []
         all_roles = set()

src/runcrate/utils.py

@@ -17,3 +17,39 @@ def as_list(value):
     if isinstance(value, list):
         return value
     return [value]
+
+
+def parse_img_name(img_name):
+    parts = img_name.split("/")
+    if len(parts) == 3:
+        registry = parts[0]
+        name = "/".join(parts[1:])
+    else:
+        registry = "docker.io"
+        name = "/".join(parts)
+    return registry, name
+
+
+def parse_img(img_str):
+    """\
+    Parse image string following the docker pull syntax NAME[:TAG|@DIGEST].
+    CWL's DockerRequirement also accepts HTTP URLs for docker load.
+    """
+    parsed = {}
+    if img_str.startswith("http://") or img_str.startswith("https://"):
+        return img_str
+    parts = img_str.rsplit("@", 1)
+    if len(parts) == 2:
+        parsed["registry"], parsed["name"] = parse_img_name(parts[0])
+        algo, digest = parts[1].split(":", 1)
+        assert algo == "sha256"
+        parsed[algo] = digest
+        return parsed
+    parts = img_str.rsplit(":", 1)
+    if len(parts) == 2:
+        parsed["registry"], parsed["name"] = parse_img_name(parts[0])
+        parsed["tag"] = parts[1]
+        return parsed
+    assert len(parts) == 1
+    parsed["registry"], parsed["name"] = parse_img_name(parts[0])
+    return parsed

tests/test_cwlprov_crate_builder.py

@@ -182,6 +182,16 @@ def test_revsort(data_dir, tmpdir):
         metadata = json.load(f)
     context = metadata['@context']
     assert TERMS_NAMESPACE in context
+    # Docker image
+    for action in crate.get_by_type("CreateAction"):
+        if action is wf_action:
+            continue
+        assert "containerImage" in action
+        img = action["containerImage"]
+        assert img.type == "ContainerImage"
+        assert img["additionalType"] == "https://w3id.org/ro/terms/workflow-run#DockerImage"
+        assert img["name"] == "debian"
+        assert img["tag"] == "8"
 
 
 def test_no_input(data_dir, tmpdir):