Merge pull request #66 from simleo/container_img

Add ContainerImage

requirements.txt

@@ -1,6 +1,6 @@
 bdbag>=1.4.1
 click~=8.1
-cwl-utils>=0.27
+cwl-utils==0.29
 cwlprov==0.1.1
 networkx==3.1
 prov>=1.5.1

setup.cfg

@@ -32,7 +32,7 @@ python_requires=>=3.8, <4
 install_requires=
     bdbag>=1.4.1
     click~=8.1
-    cwl-utils>=0.27
+    cwl-utils==0.29
     cwlprov==0.1.1
     networkx==3.1
     prov>=1.5.1

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):

tests/test_utils.py

@@ -0,0 +1,42 @@
+# Copyright 2023 CRS4.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from runcrate.utils import parse_img
+
+
+def test_parse_img():
+    assert parse_img("python") == {
+        "registry": "docker.io",
+        "name": "python"
+    }
+    assert parse_img("python:3.12") == {
+        "registry": "docker.io",
+        "name": "python",
+        "tag": "3.12"
+    }
+    assert parse_img("josiah/python:3.11") == {
+        "registry": "docker.io",
+        "name": "josiah/python",
+        "tag": "3.11"
+    }
+    assert parse_img("quay.io/josiah/python:3.11") == {
+        "registry": "quay.io",
+        "name": "josiah/python",
+        "tag": "3.11"
+    }
+    assert parse_img("python@sha256:7b8d65a924f596eb65306214f559253c468336bcae09fd575429774563460caf") == {
+        "registry": "docker.io",
+        "name": "python",
+        "sha256": "7b8d65a924f596eb65306214f559253c468336bcae09fd575429774563460caf"
+    }