Implemented --version call in PROV as well as tests

Author: Ryan Cali

pydra/engine/audit.py

@@ -171,7 +171,6 @@ def audit_check(self, flag):
 
     def audit_task(self, task):
         import subprocess as sp
-
         label = task.name
         if hasattr(task.inputs, "executable"):
             command = task.cmdline
@@ -187,13 +186,15 @@ def audit_task(self, task):
             software = command.split()[0]
             software = software + " " + "--version"
             # take the first word of command as the name of the executable (this may not always be the case)
-            version_cmd = (
-                sp.run(software, shell=True, check=True, stdout=sp.PIPE)
-                .stdout.decode("utf-8")
-                .splitlines()[0]
-            )
+            version_cmd = (sp.run(software, shell=True, stdout=sp.PIPE).stdout.decode("utf-8"))
+            try:
+                version_cmd = version_cmd.splitlines()[0]
+
+            except IndexError:
+                version_cmd = None
+
         else:
-            software = None
+            version_cmd = None
 
         start_message = {
             "@id": self.aid,
@@ -202,7 +203,7 @@ def audit_task(self, task):
             "Command": command,
             "StartedAtTime": now(),
             # "Used": input_file,
-            "AssociatedWith": version_cmd,
+            "AssociatedWith": version_cmd
         }
 
         # new code to be added here for i/o tracking - WIP

pydra/engine/tests/test_task.py

@@ -1003,9 +1003,10 @@ def testfunc(a: int, b: float = 0.1) -> ty.NamedTuple("Output", [("out", float)]
     for file in glob(str(message_path) + "/*.jsonld"):
         with open(file, "r") as f:
             data = json.load(f)
-            if "label" in data:
+            print(data)
+            if "Label" in data:
                 json_content.append(True)
-                assert "testfunc" == data["label"]
+                assert "testfunc" == data["Label"]
     assert any(json_content)
 
 
@@ -1031,16 +1032,46 @@ def test_audit_shellcommandtask(tmpdir):
     for file in glob(str(message_path) + "/*.jsonld"):
         with open(file, "r") as f:
             data = json.load(f)
-            if "label" in data:
+            print(data)
+            if "Label" in data:
                 label_content.append(True)
-            if "command" in data:
+            if "Command" in data:
                 command_content.append(True)
-                assert "ls -l" == data["command"]
+                assert "ls -l" == data["Command"]
 
     print(command_content)
     assert any(label_content)
 
 
+
+
+def test_audit_shellcommandtask_version(tmpdir):
+    cmd = "mrcat"
+    shelly = ShellCommandTask(
+        name="shelly",
+        executable=cmd,
+        audit_flags=AuditFlag.PROV,
+        messengers=FileMessenger(),
+    )
+
+    import subprocess as sp
+    import glob
+    shelly.cache_dir = tmpdir
+    shelly()
+    message_path = tmpdir / shelly.checksum / "messages"
+    # go through each jsonld file in message_path and check if the label field exists
+    version_content = []
+    for file in glob.glob(str(message_path) + "/*.jsonld"):
+        with open(file, "r") as f:
+            data = json.load(f)
+            if "AssociatedWith" in data:
+                if "== mrcat 3.0.3 ==" in data["AssociatedWith"]:
+                    version_content.append(True)
+
+    
+    assert any(version_content)
+
+
 def test_audit_prov_messdir_1(tmpdir, use_validator):
     """customized messenger dir"""