js_sandbox: use smaller node:alpine image

Author: mr-c

.github/workflows/ci-tests.yml

@@ -124,6 +124,15 @@ jobs:
           wget --no-verbose https://github.com/sylabs/singularity/releases/download/v3.10.4/singularity-ce_3.10.4-jammy_amd64.deb
           sudo apt-get install -y ./singularity-ce_3.10.4-jammy_amd64.deb
 
+      - name: pull some containers
+        run: |
+          export CWL_SINGULARITY_CACHE=$(echo $GITHUB_WORKSPACE)/singularity_cache
+          mkdir -p ${CWL_SINGULARITY_CACHE}
+          singularity pull --name ${CWL_SINGULARITY_CACHE}/node_alpine.sif docker://docker.io/node:alpine
+          ls -lh ${CWL_SINGULARITY_CACHE}
+          echo ${CWL_SINGULARITY_CACHE}
+          echo "CWL_SINGULARITY_CACHE=${CWL_SINGULARITY_CACHE}" >> $GITHUB_ENV
+
       - name: Set up Python
         uses: actions/setup-python@v4
         with:

Makefile

@@ -152,7 +152,7 @@ diff-cover.html: coverage.xml
 
 ## test                   : run the cwl-utils test suite
 test: $(PYSOURCES)
-	python -m pytest -rs ${PYTEST_EXTRA}
+	python -m pytest -rsx ${PYTEST_EXTRA}
 
 ## testcov                : run the cwl-utils test suite and collect coverage
 testcov: $(PYSOURCES)

cwl_utils/cwl_v1_0_expression_refactor.py

@@ -190,7 +190,7 @@ def etool_to_cltool(
     )
     listing = [cwl.Dirent(entryname="expression.js", entry=contents, writable=None)]
     iwdr = cwl.InitialWorkDirRequirement(listing)
-    containerReq = cwl.DockerRequirement(dockerPull="node:slim")
+    containerReq = cwl.DockerRequirement(dockerPull="node:alpine")
     softwareHint = cwl.SoftwareRequirement(
         packages=[cwl.SoftwarePackage(package="nodejs")]
     )

cwl_utils/cwl_v1_1_expression_refactor.py

@@ -190,7 +190,7 @@ def etool_to_cltool(
     )
     listing = [cwl.Dirent(entryname="expression.js", entry=contents, writable=None)]
     iwdr = cwl.InitialWorkDirRequirement(listing)
-    containerReq = cwl.DockerRequirement(dockerPull="node:slim")
+    containerReq = cwl.DockerRequirement(dockerPull="node:alpine")
     softwareHint = cwl.SoftwareRequirement(
         packages=[cwl.SoftwarePackage(package="nodejs")]
     )

cwl_utils/cwl_v1_2_expression_refactor.py

@@ -190,7 +190,7 @@ def etool_to_cltool(
     )
     listing = [cwl.Dirent(entryname="expression.js", entry=contents, writable=None)]
     iwdr = cwl.InitialWorkDirRequirement(listing)
-    containerReq = cwl.DockerRequirement(dockerPull="node:slim")
+    containerReq = cwl.DockerRequirement(dockerPull="node:alpine")
     softwareHint = cwl.SoftwareRequirement(
         packages=[cwl.SoftwarePackage(package="nodejs")]
     )

cwl_utils/sandboxjs.py

@@ -307,7 +307,7 @@ def new_js_proc(
 
         if nodejs is None or nodejs is not None and required_node_version is False:
             try:
-                nodeimg = "docker.io/node:slim"
+                nodeimg = "docker.io/node:alpine"
                 if container_engine == "singularity":
                     nodeimg = f"docker://{nodeimg}"
 
@@ -322,10 +322,14 @@ def new_js_proc(
                         singularity_cache = os.environ.get("CWL_SINGULARITY_CACHE")
                         if singularity_cache:
                             singularityimgs = glob.glob(
-                                singularity_cache + "/node_slim.sif"
+                                singularity_cache + "/node_alpine.sif"
                             )
                         else:
-                            singularityimgs = glob.glob(os.getcwd() + "/node_slim.sif")
+                            singularityimgs = glob.glob(
+                                os.getcwd() + "/node_alpine.sif"
+                            )
+                        if singularityimgs:
+                            nodeimg = singularityimgs[0]
                     else:
                         raise Exception(
                             f"Unknown container_engine: {container_engine}."
@@ -338,7 +342,7 @@ def new_js_proc(
                         len(dockerimgs.split("\n")) <= 1
                     )
                     if need_singularity or need_docker or force_docker_pull:
-                        # pull node:slim docker container
+                        # pull node:alpine docker container
                         nodejs_pull_commands = [container_engine, "pull"]
                         if force_docker_pull:
                             nodejs_pull_commands.append("--force")
@@ -400,15 +404,15 @@ def new_js_proc(
                     pass
                 else:
                     raise
-            except subprocess.CalledProcessError:
-                pass
+            except subprocess.CalledProcessError as e:
+                _logger.debug("Error while attempting to run nodejs: %s", e)
 
         # docker failed and nodejs not on system
         if nodejs is None:
             raise JavascriptException(
                 "NodeJSEngine requires Node.js engine to evaluate and validate "
                 "Javascript expressions, but couldn't find it.  Tried {trynodes}, "
-                f"{container_engine} run node:slim".format(
+                f"{container_engine} run node:alpine".format(
                     trynodes=", ".join(trynodes), container_engine=container_engine
                 )
             )

tests/test_js_sandbox.py

@@ -154,7 +154,7 @@ def test_singularity_cache(tmp_path: Path, monkeypatch: pytest.MonkeyPatch) -> N
             )
             == 42 * 23
         )
-        assert (cache_path / "node_slim.sif").exists()
+        assert (cache_path / "node_alpine.sif").exists()
 
 
 def test_caches_js_processes(mocker: Any) -> None: