toil 8.2.0__py3-none-any.whl → 9.1.0__py3-none-any.whl

toil/test/batchSystems/test_slurm.py

@@ -6,6 +6,8 @@ import logging
 import pytest
 import sys
 
+from datetime import datetime, timedelta
+
 import toil.batchSystems.slurm
 from toil.batchSystems.abstractBatchSystem import (
     EXIT_STATUS_UNAVAILABLE_VALUE,
@@ -22,10 +24,25 @@ logger = logging.getLogger(__name__)
 # TODO: Come up with a better way to mock the commands then monkey-patching the
 # command-calling functions.
 
+# To convincingly test jobs in the past relative to the time Toil goes looking
+# for them, we give our fake jobs times relative to the module load time, which
+# we hope is not days and days away from the time the tests actually run.
+JOB_BASE_TIME = datetime.now().astimezone(None) - timedelta(days=5)
+
+def call_either(args, **_) -> str:
+    """
+    Pretend to call either sacct or scontrol as appropriate.
+    """
+    if args[0] == "sacct":
+        return call_sacct(args)
+    elif args[0] == "scontrol":
+        return call_scontrol(args)
+    else:
+        raise RuntimeError(f"Cannot fake command call: {args}")
 
 def call_sacct(args, **_) -> str:
     """
-    The arguments passed to `call_command` when executing `sacct` are:
+    The arguments passed to `call_command` when executing `sacct` are something like:
     ['sacct', '-n', '-j', '<comma-separated list of job-ids>', '--format',
     'JobIDRaw,State,ExitCode', '-P', '-S', '1970-01-01']
     The multi-line output is something like::
@@ -36,6 +53,7 @@ def call_sacct(args, **_) -> str:
         1236|FAILED|0:2
         1236.extern|COMPLETED|0:0
     """
+    logger.info("sacct call: %s", args)
     if sum(len(a) for a in args) > 1000:
         # Simulate if the argument list is too long
         raise OSError(errno.E2BIG, "Argument list is too long")
@@ -51,11 +69,58 @@ def call_sacct(args, **_) -> str:
         789868: "789868|PENDING|0:0\n",
         789869: "789869|COMPLETED|0:0\n789869.batch|COMPLETED|0:0\n789869.extern|COMPLETED|0:0\n",
     }
-    job_ids = [int(job_id) for job_id in args[3].split(",")]
+    # And time we say the job was at
+    job_time = {
+        609663: JOB_BASE_TIME + timedelta(days=1),
+        754725: JOB_BASE_TIME + timedelta(days=1),
+        765096: JOB_BASE_TIME + timedelta(days=2),
+        767925: JOB_BASE_TIME + timedelta(days=2),
+        785023: JOB_BASE_TIME + timedelta(days=3),
+        789456: JOB_BASE_TIME + timedelta(days=3),
+        789724: JOB_BASE_TIME + timedelta(days=4),
+        789868: JOB_BASE_TIME + timedelta(days=4),
+        789869: JOB_BASE_TIME + timedelta(days=4),
+    }
+
+    # See if they asked for a job list
+    try:
+        j_index = args.index('-j')
+        job_ids = [int(job_id) for job_id in args[j_index + 1].split(",")]
+    except ValueError:
+        # We're not restricting to a list of jobs.
+        job_ids = list(sacct_info.keys())
+    # See if they asked for start or end times
+    try:
+        flag_index = args.index('-S')
+        begin_time = datetime.fromisoformat(args[flag_index + 1]).astimezone(None)
+    except ValueError:
+        # By default, Slurm uses today at midnight
+        begin_time = datetime.now().astimezone(None).replace(
+            hour=0,
+            minute=0,
+            second=0,
+            microsecond=0,
+            fold=0
+        )
+    try:
+        flag_index = args.index('-E')
+        end_time = datetime.fromisoformat(args[flag_index + 1]).astimezone(None)
+    except ValueError:
+        end_time = None
+
     stdout = ""
     # Glue the fake outputs for the request job-ids together in a single string
     for job_id in job_ids:
-        stdout += sacct_info.get(job_id, "")
+        if job_id not in sacct_info:
+            # Not a job we know of.
+            continue
+        if begin_time is not None and begin_time > job_time[job_id]:
+            # Skip this job as being too early
+            continue
+        if end_time is not None and end_time < job_time[job_id]:
+            # Skip this job as being too late
+            continue
+        stdout += sacct_info[job_id]
     return stdout
 
 
@@ -64,8 +129,11 @@ def call_scontrol(args, **_) -> str:
     The arguments passed to `call_command` when executing `scontrol` are:
     ``['scontrol', 'show', 'job']`` or ``['scontrol', 'show', 'job', '<job-id>']``
     """
+    logger.info("scontrol call: %s", args)
     job_id = int(args[3]) if len(args) > 3 else None
     # Fake output per fake job-id.
+    # scontrol only shows recent jobs, so we have fewer/different jobs here
+    # than for sacct.
     scontrol_info = {
         787204: textwrap.dedent(
             """\
@@ -211,6 +279,9 @@ class FakeBatchSystem(BatchSystemSupport):
 
     def __init__(self):
         super().__init__(self.__fake_config(), float("inf"), sys.maxsize, sys.maxsize)
+        # Pretend to be a workflow that started before we pretend the jobs
+        # we pretend to have ran.
+        self.start_time = JOB_BASE_TIME - timedelta(hours=2)
 
     def getWaitDuration(self):
         return 10
@@ -358,14 +429,14 @@ class SlurmTest(ToilTest):
     ###
 
     def test_getJobExitCode_job_exists(self):
-        self.monkeypatch.setattr(toil.batchSystems.slurm, "call_command", call_sacct)
+        self.monkeypatch.setattr(toil.batchSystems.slurm, "call_command", call_either)
         job_id = "785023"  # FAILED
         expected_result = (127, BatchJobExitReason.FAILED)
         result = self.worker.getJobExitCode(job_id)
         assert result == expected_result, f"{result} != {expected_result}"
 
     def test_getJobExitCode_job_not_exists(self):
-        self.monkeypatch.setattr(toil.batchSystems.slurm, "call_command", call_sacct)
+        self.monkeypatch.setattr(toil.batchSystems.slurm, "call_command", call_either)
         job_id = "1234"  # Non-existent
         expected_result = None
         result = self.worker.getJobExitCode(job_id)
@@ -379,7 +450,7 @@ class SlurmTest(ToilTest):
         self.monkeypatch.setattr(
             self.worker, "_getJobDetailsFromSacct", call_sacct_raises
         )
-        self.monkeypatch.setattr(toil.batchSystems.slurm, "call_command", call_scontrol)
+        self.monkeypatch.setattr(toil.batchSystems.slurm, "call_command", call_either)
         job_id = "787204"  # COMPLETED
         expected_result = (0, BatchJobExitReason.FINISHED)
         result = self.worker.getJobExitCode(job_id)
@@ -393,7 +464,7 @@ class SlurmTest(ToilTest):
         self.monkeypatch.setattr(
             self.worker, "_getJobDetailsFromSacct", call_sacct_raises
         )
-        self.monkeypatch.setattr(toil.batchSystems.slurm, "call_command", call_scontrol)
+        self.monkeypatch.setattr(toil.batchSystems.slurm, "call_command", call_either)
         job_id = "1234"  # Non-existent
         try:
             _ = self.worker.getJobExitCode(job_id)
@@ -407,21 +478,21 @@ class SlurmTest(ToilTest):
     ###
 
     def test_coalesce_job_exit_codes_one_exists(self):
-        self.monkeypatch.setattr(toil.batchSystems.slurm, "call_command", call_sacct)
+        self.monkeypatch.setattr(toil.batchSystems.slurm, "call_command", call_either)
         job_ids = ["785023"]  # FAILED
         expected_result = [(127, BatchJobExitReason.FAILED)]
         result = self.worker.coalesce_job_exit_codes(job_ids)
         assert result == expected_result, f"{result} != {expected_result}"
 
     def test_coalesce_job_exit_codes_one_not_exists(self):
-        self.monkeypatch.setattr(toil.batchSystems.slurm, "call_command", call_sacct)
+        self.monkeypatch.setattr(toil.batchSystems.slurm, "call_command", call_either)
         job_ids = ["1234"]  # Non-existent
         expected_result = [None]
         result = self.worker.coalesce_job_exit_codes(job_ids)
         assert result == expected_result, f"{result} != {expected_result}"
 
     def test_coalesce_job_exit_codes_many_all_exist(self):
-        self.monkeypatch.setattr(toil.batchSystems.slurm, "call_command", call_sacct)
+        self.monkeypatch.setattr(toil.batchSystems.slurm, "call_command", call_either)
         job_ids = [
             "754725",  # TIMEOUT,
             "789456",  # FAILED,
@@ -440,8 +511,26 @@ class SlurmTest(ToilTest):
         result = self.worker.coalesce_job_exit_codes(job_ids)
         assert result == expected_result, f"{result} != {expected_result}"
 
+    def test_coalesce_job_exit_codes_mix_sacct_scontrol(self):
+        self.monkeypatch.setattr(toil.batchSystems.slurm, "call_command", call_either)
+        job_ids = [
+            "609663",  # FAILED, in sacct only
+            "789869",  # COMPLETED, in sacct only
+            "787204",  # COMPLETED, in scontrol only
+            "789724",  # RUNNING, in scontrol only
+        ]
+        # RUNNING and PENDING jobs should return None
+        expected_result = [
+            (130, BatchJobExitReason.FAILED),
+            (0, BatchJobExitReason.FINISHED),
+            (0, BatchJobExitReason.FINISHED),
+            None
+        ]
+        result = self.worker.coalesce_job_exit_codes(job_ids)
+        assert result == expected_result, f"{result} != {expected_result}"
+
     def test_coalesce_job_exit_codes_some_exists(self):
-        self.monkeypatch.setattr(toil.batchSystems.slurm, "call_command", call_sacct)
+        self.monkeypatch.setattr(toil.batchSystems.slurm, "call_command", call_either)
         job_ids = [
             "609663",  # FAILED (SIGINT)
             "767925",  # FAILED,
@@ -468,7 +557,7 @@ class SlurmTest(ToilTest):
         self.monkeypatch.setattr(
             self.worker, "_getJobDetailsFromSacct", call_sacct_raises
         )
-        self.monkeypatch.setattr(toil.batchSystems.slurm, "call_command", call_scontrol)
+        self.monkeypatch.setattr(toil.batchSystems.slurm, "call_command", call_either)
         job_ids = ["787204"]  # COMPLETED
         expected_result = [(0, BatchJobExitReason.FINISHED)]
         result = self.worker.coalesce_job_exit_codes(job_ids)
@@ -482,7 +571,7 @@ class SlurmTest(ToilTest):
         self.monkeypatch.setattr(
             self.worker, "_getJobDetailsFromSacct", call_sacct_raises
         )
-        self.monkeypatch.setattr(toil.batchSystems.slurm, "call_command", call_scontrol)
+        self.monkeypatch.setattr(toil.batchSystems.slurm, "call_command", call_either)
         job_ids = ["1234"]  # Non-existent
         try:
             _ = self.worker.coalesce_job_exit_codes(job_ids)
@@ -644,5 +733,5 @@ class SlurmTest(ToilTest):
         self.assertTrue(detector("-B"))
         self.assertFalse(detector("--no-bazz"))
         self.assertFalse(detector("--foo-bar=--bazz-only"))
-       
+
 

toil/test/cwl/cwlTest.py

@@ -45,9 +45,11 @@ from toil.cwl.utils import (
     download_structure,
     visit_cwl_class_and_reduce,
     visit_top_cwl_class,
+    remove_redundant_mounts
 )
 from toil.fileStores import FileID
 from toil.fileStores.abstractFileStore import AbstractFileStore
+from toil.job import WorkerImportJob
 from toil.lib.threading import cpu_count
 from toil.test import (
     get_data,
@@ -1112,12 +1114,13 @@ def cwl_v1_0_spec(tmp_path: Path) -> Generator[Path]:
     finally:
         pass  # no cleanup
 
-
+@pytest.mark.integrative
+@pytest.mark.conformance
 @needs_cwl
 @needs_online
 @pytest.mark.cwl
 @pytest.mark.online
-class TestCWLv10:
+class TestCWLv10Conformance:
     """
     Run the CWL 1.0 conformance tests in various environments.
     """
@@ -1295,11 +1298,13 @@ def cwl_v1_1_spec(tmp_path: Path) -> Generator[Path]:
         pass  # no cleanup
 
 
+@pytest.mark.integrative
+@pytest.mark.conformance
 @needs_cwl
 @needs_online
 @pytest.mark.cwl
 @pytest.mark.online
-class TestCWLv11:
+class TestCWLv11Conformance:
     """
     Run the CWL 1.1 conformance tests in various environments.
     """
@@ -1383,11 +1388,13 @@ def cwl_v1_2_spec(tmp_path: Path) -> Generator[Path]:
         pass  # no cleanup
 
 
+@pytest.mark.integrative
+@pytest.mark.conformance
 @needs_cwl
 @needs_online
 @pytest.mark.cwl
 @pytest.mark.online
-class TestCWLv12:
+class TestCWLv12Conformance:
     """
     Run the CWL 1.2 conformance tests in various environments.
     """
@@ -1525,7 +1532,7 @@ class TestCWLv12:
         TOIL_WES_ENDPOINT=http://localhost:8080 \
         TOIL_WES_USER=test \
         TOIL_WES_PASSWORD=password \
-        python -m pytest src/toil/test/cwl/cwlTest.py::TestCWLv12::test_wes_server_cwl_conformance -vv --log-level INFO --log-cli-level INFO
+        python -m pytest src/toil/test/cwl/cwlTest.py::TestCWLv12Conformance::test_wes_server_cwl_conformance -vv --log-level INFO --log-cli-level INFO
         """
         endpoint = os.environ.get("TOIL_WES_ENDPOINT")
         extra_args = [f"--wes_endpoint={endpoint}"]
@@ -1906,6 +1913,134 @@ def test_visit_cwl_class_and_reduce() -> None:
     assert up_child_count == 2
 
 
+@needs_cwl
+@pytest.mark.cwl
+@pytest.mark.cwl_small
+def test_trim_mounts_op_nonredundant() -> None:
+    """
+    Make sure we don't remove all non-duplicate listings
+    """
+    s: CWLObjectType = {"class": "Directory", "basename": "directory", "listing": [{"class": "File", "basename": "file", "contents": "hello world"}]}
+    remove_redundant_mounts(s)
+
+    # nothing should have been removed
+    assert isinstance(s['listing'], list)
+    assert len(s['listing']) == 1
+
+@needs_cwl
+@pytest.mark.cwl
+@pytest.mark.cwl_small
+def test_trim_mounts_op_redundant() -> None:
+    """
+    Make sure we remove all duplicate listings
+    """
+    s: CWLObjectType = {
+        "class": "Directory",
+        "location": "file:///home/heaucques/Documents/toil/test_dir",
+        "basename": "test_dir",
+        "listing": [
+            {
+                "class": "Directory",
+                "location": "file:///home/heaucques/Documents/toil/test_dir/nested_dir",
+                "basename": "nested_dir",
+                "listing": [],
+                "path": "/home/heaucques/Documents/toil/test_dir/nested_dir"
+            },
+            {
+                "class": "File",
+                "location": "file:///home/heaucques/Documents/toil/test_dir/test_file",
+                "basename": "test_file",
+                "size": 0,
+                "nameroot": "test_file",
+                "nameext": "",
+                "path": "/home/heaucques/Documents/toil/test_dir/test_file",
+                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709"
+            }
+        ],
+        "path": "/home/heaucques/Documents/toil/test_dir"
+    }
+    remove_redundant_mounts(s)
+
+    # everything should have been removed
+    assert isinstance(s['listing'], list)
+    assert len(s['listing']) == 0
+
+@needs_cwl
+@pytest.mark.cwl
+@pytest.mark.cwl_small
+def test_trim_mounts_op_partially_redundant() -> None:
+    """
+    Make sure we remove only the redundant listings in the CWL object and leave nonredundant listings intact
+    """
+    s: CWLObjectType = {
+        "class": "Directory",
+        "location": "file:///home/heaucques/Documents/toil/test_dir",
+        "basename": "test_dir",
+        "listing": [
+            {
+                "class": "Directory",
+                "location": "file:///home/heaucques/Documents/thing",
+                "basename": "thing2",
+                "listing": [],
+                "path": "/home/heaucques/Documents/toil/thing2"
+            },
+            {
+                "class": "File",
+                "location": "file:///home/heaucques/Documents/toil/test_dir/test_file",
+                "basename": "test_file",
+                "size": 0,
+                "nameroot": "test_file",
+                "nameext": "",
+                "path": "/home/heaucques/Documents/toil/test_dir/test_file",
+                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709"
+            }
+        ],
+        "path": "/home/heaucques/Documents/toil/test_dir"
+    }
+    remove_redundant_mounts(s)
+
+    # everything except the nested directory should be removed
+    assert isinstance(s['listing'], list)
+    assert len(s['listing']) == 1
+
+@needs_cwl
+@pytest.mark.cwl
+@pytest.mark.cwl_small
+def test_trim_mounts_op_mixed_urls_and_paths() -> None:
+    """
+    Ensure we remove redundant listings in certain edge cases
+    """
+    # Edge cases around encoding:
+    # Ensure URL decoded file URIs match the bare path equivalent. Both of these paths should have the same shared directory
+    s: CWLObjectType = {"class": "Directory", "basename": "123", "location": "file:///tmp/%25/123", "listing": [{"class": "File", "path": "/tmp/%/123/456", "basename": "456"}]}
+    remove_redundant_mounts(s)
+    assert isinstance(s['listing'], list)
+    assert len(s['listing']) == 0
+
+@needs_cwl
+@pytest.mark.cwl
+@pytest.mark.cwl_small
+def test_trim_mounts_op_decodable_paths() -> None:
+    """"""
+    # Ensure path names don't get unnecessarily decoded
+    s: CWLObjectType = {"class": "Directory", "basename": "dir", "path": "/tmp/cat%2Ftag/dir", "listing": [{"class": "File", "path": "/tmp/cat/tag/dir/file", "basename": "file"}]}
+    remove_redundant_mounts(s)
+    assert isinstance(s['listing'], list)
+    assert len(s['listing']) == 1
+
+@needs_cwl
+@pytest.mark.cwl
+@pytest.mark.cwl_small
+def test_trim_mounts_op_multiple_encodings() -> None:
+    # Ensure differently encoded URLs are properly decoded
+    s: CWLObjectType = {"class": "Directory", "basename": "dir", "location": "file:///tmp/cat%2Ftag/dir", "listing": [{"class": "File", "location": "file:///tmp/cat%2ftag/dir/file", "basename": "file"}]}
+    remove_redundant_mounts(s)
+    assert isinstance(s['listing'], list)
+    assert len(s['listing']) == 0
+
+
+
+
 @needs_cwl
 @pytest.mark.cwl
 @pytest.mark.cwl_small
@@ -2010,12 +2145,16 @@ def test_import_on_workers() -> None:
 
     with get_data("test/cwl/download.cwl") as cwl_file:
         with get_data("test/cwl/directory/directory/file.txt") as file_path:
+            # To make sure we see every job issued with a leader log message
+            # that we can then detect for the test, we need to turn off
+            # chaining.
             args = [
                 "--runImportsOnWorkers",
                 "--importWorkersDisk=10MiB",
                 "--realTimeLogging=True",
                 "--logLevel=INFO",
                 "--logColors=False",
+                "--disableChaining=True",
                 str(cwl_file),
                 "--input",
                 str(file_path),
@@ -2024,6 +2163,29 @@ def test_import_on_workers() -> None:
 
         assert detector.detected is True
 
+@needs_cwl
+@pytest.mark.cwl
+@pytest.mark.cwl_small
+def test_missing_tmpdir_and_tmp_outdir(tmp_path: Path) -> None:
+    """
+    tmpdir_prefix and tmp_outdir_prefix do not need to exist prior to running the workflow
+    """
+    tmpdir_prefix = os.path.join(tmp_path, "tmpdir/blah")
+    tmp_outdir_prefix = os.path.join(tmp_path, "tmp_outdir/blah")
+
+    assert not os.path.exists(os.path.dirname(tmpdir_prefix))
+    assert not os.path.exists(os.path.dirname(tmp_outdir_prefix))
+    with get_data("test/cwl/echo_string.cwl") as cwl_file:
+        cmd = [
+            "toil-cwl-runner",
+            f"--jobStore=file:{tmp_path / 'jobstore'}",
+            "--strict-memory-limit",
+            f'--tmpdir-prefix={tmpdir_prefix}',
+            f'--tmp-outdir-prefix={tmp_outdir_prefix}',
+            str(cwl_file),
+        ]
+        p = subprocess.run(cmd)
+        assert p.returncode == 0
 
 # StreamHandler is generic, _typeshed doesn't exist at runtime, do a bit of typing trickery, see https://github.com/python/typeshed/issues/5680
 if TYPE_CHECKING:
@@ -2036,7 +2198,7 @@ else:
 
 class ImportWorkersMessageHandler(_stream_handler):
     """
-    Detect the import workers log message and set a flag.
+    Detect whether any WorkerImportJob jobs ran during a workflow.
     """
 
     def __init__(self) -> None:
@@ -2045,7 +2207,18 @@ class ImportWorkersMessageHandler(_stream_handler):
         super().__init__(sys.stderr)
 
     def emit(self, record: logging.LogRecord) -> None:
-        if (record.msg % record.args).startswith(
-            "Issued job 'CWLImportJob' CWLImportJob"
+        # We get the job name from the class since we already started failing
+        # this test once due to it being renamed.
+        try:
+            formatted = record.getMessage()
+        except TypeError as e:
+            # The log message has the wrong number of items for its fields.
+            # Complain in a way we could figure out.
+            raise RuntimeError(
+                f"Log message {record.msg} has wrong number of "
+                f"fields in {record.args}"
+            ) from e
+        if formatted.startswith(
+            f"Issued job '{WorkerImportJob.__name__}'"
         ):
             self.detected = True

toil/test/cwl/staging_cat.cwl

@@ -0,0 +1,27 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: CommandLineTool
+baseCommand: [ "bash", "run.sh" ]
+
+requirements:
+  DockerRequirement: # <- this is the part that causes the error
+    dockerPull: ubuntu:latest
+  InitialWorkDirRequirement:
+    listing:
+      - entryname: some_dir # <- put all the input files into a dir
+        writable: true
+        entry: "$({class: 'Directory', listing: inputs.input_files})"
+      - entryname: run.sh
+        entry: |-
+          for i in \$(find some_dir -type f); do cat \$i ; done
+
+stdout: output.txt
+
+inputs:
+  input_files:
+    type: File[]
+
+outputs:
+  output_file:
+    type: stdout

toil/test/cwl/staging_make_file.cwl

@@ -0,0 +1,25 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: CommandLineTool
+baseCommand: [ "bash", "run.sh" ]
+
+stdout: output.txt
+
+requirements:
+  InitialWorkDirRequirement:
+    listing:
+      - entryname: run.sh
+        entry: |-
+          echo "$1"
+
+inputs:
+  sampleId:
+    type: string
+    inputBinding:
+      position: 1
+
+outputs:
+  output_file:
+    type: stdout
+

toil/test/cwl/staging_workflow.cwl

@@ -0,0 +1,43 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: Workflow
+requirements:
+  MultipleInputFeatureRequirement: {}
+  ScatterFeatureRequirement: {}
+  StepInputExpressionRequirement: {}
+  InlineJavascriptRequirement: {}
+  SubworkflowFeatureRequirement: {}
+
+inputs:
+  samples:
+    type:
+      type: array
+      items:
+        type: record
+        fields:
+          sampleId: string
+
+steps:
+  make_file:
+    run: staging_make_file.cwl
+    scatter: sample
+    in:
+      sample: samples
+      sampleId:
+        valueFrom: ${ return inputs.sample['sampleId']; }
+    out:
+      [ output_file ]
+
+  gather_files:
+    run: staging_cat.cwl
+    in:
+      input_files: make_file/output_file
+    out:
+      [ output_file ]
+
+outputs:
+  output_file:
+    type: File
+    outputSource: gather_files/output_file
+

toil/test/cwl/zero_default.cwl

@@ -0,0 +1,61 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.2
+class: Workflow
+requirements:
+  MultipleInputFeatureRequirement: {}
+  InlineJavascriptRequirement: {}
+inputs:
+  valueA:
+    type: int?
+    default: 0
+  valueB:
+    type: int?
+  someFile:
+    type: File?
+steps:
+  prev_step:
+    run:
+      class: ExpressionTool
+      requirements:
+        InlineJavascriptRequirement: {}
+      inputs:
+        someFile:
+          type: File
+      outputs:
+        valueA:
+          type: int
+      expression: |
+        ${
+          return {valueA: 1};
+        }
+    in:
+      someFile: someFile
+    out: [valueA]
+    when: $(inputs.someFile != null)
+    
+  main_step:
+    run:
+      class: ExpressionTool
+      requirements:
+        InlineJavascriptRequirement: {}
+      inputs:
+        valueA:
+          type: int
+      outputs:
+        valueA:
+          type: int
+      expression: |
+        ${
+          return {valueA: inputs.valueA};
+        }
+    in:
+      valueA:
+        source: [prev_step/valueA, valueA]
+        pickValue: first_non_null
+    out: [valueA]
+outputs:
+  valueA:
+    type: int
+    outputSource: main_step/valueA
+
+