small changes in bosh input/output specs; adding tests with workflows

Author: djarecka

pydra/engine/boutiques.py

@@ -130,7 +130,7 @@ def _prepare_input_spec(self):
                 tp = ty.List[tp]
 
             mdata = {
-                "help_string": input["description"],
+                "help_string": input.get("description", None) or input["name"],
                 "mandatory": not input["optional"],
                 "argstr": input.get("command-line-flag", None),
             }
@@ -152,7 +152,7 @@ def _prepare_output_spec(self):
                 output["path-template"],
             )
             mdata = {
-                "help_string": output["description"],
+                "help_string": output.get("description", None) or output["name"],
                 "mandatory": not output["optional"],
                 "output_file_template": path_template,
             }
@@ -181,6 +181,7 @@ def _input_file(self, state_ind, ind=None):
             # adding to the json file if specified by the user
             if value is not attr.NOTHING and value != "NOTHING":
                 if is_local_file(f):
+                    value = Path(value)
                     self.bindings.extend(["-v", f"{value.parent}:{value.parent}:ro"])
                     value = str(value)
 

pydra/engine/tests/test_boutiques.py

@@ -3,24 +3,37 @@
 from pathlib import Path
 import pytest
 
+from ..core import Workflow
+from ..submitter import Submitter
 from ..boutiques import BoshTask
+from .utils import result_no_submitter, result_submitter
 
 need_bosh_docker = pytest.mark.skipif(
     shutil.which("docker") is None
     or sp.call(["docker", "info"] or sp.call(["bosh", "version"])),
     reason="requires docker and bosh",
 )
 
+if bool(shutil.which("sbatch")):
+    Plugins = ["cf", "slurm"]
+else:
+    Plugins = ["cf"]
+
+Infile = Path(__file__).resolve().parent / "data_tests" / "test.nii.gz"
+
 
 @need_bosh_docker
 @pytest.mark.parametrize(
     "maskfile", ["test_brain.nii.gz", "test_brain", "test_brain.nii"]
 )
-def test_boutiques_1(maskfile):
+@pytest.mark.parametrize("results_function", [result_no_submitter, result_submitter])
+@pytest.mark.parametrize("plugin", Plugins)
+def test_boutiques_1(maskfile, plugin, results_function):
+    """ simple task to run fsl.bet using BoshTask"""
     btask = BoshTask(name="NA", zenodo="zenodo.1482743")
-    btask.inputs.infile = Path(__file__).resolve().parent / "data_tests" / "test.nii.gz"
+    btask.inputs.infile = Infile
     btask.inputs.maskfile = maskfile
-    res = btask()
+    res = results_function(btask, plugin)
 
     assert res.output.return_code == 0
 
@@ -30,3 +43,76 @@ def test_boutiques_1(maskfile):
     # other files should also have proper names, but they do not exist
     assert res.output.out_outskin_off.name == "test_brain_outskin_mesh.off"
     assert not res.output.out_outskin_off.exists()
+
+
+@need_bosh_docker
+@pytest.mark.parametrize(
+    "maskfile", ["test_brain.nii.gz", "test_brain", "test_brain.nii"]
+)
+@pytest.mark.parametrize("plugin", Plugins)
+def test_boutiques_wf_1(maskfile, plugin):
+    """ wf with one task that runs fsl.bet using BoshTask"""
+    wf = Workflow(name="wf", input_spec=["maskfile", "infile"])
+    wf.inputs.maskfile = maskfile
+    wf.inputs.infile = Infile
+
+    wf.add(
+        BoshTask(
+            name="bet",
+            zenodo="zenodo.1482743",
+            infile=wf.lzin.infile,
+            maskfile=wf.lzin.maskfile,
+        )
+    )
+
+    wf.set_output([("outfile", wf.bet.lzout.outfile)])
+
+    with Submitter(plugin=plugin) as sub:
+        wf(submitter=sub)
+
+    res = wf.result()
+    assert res.output.outfile.name == "test_brain.nii.gz"
+    assert res.output.outfile.exists()
+
+
+@need_bosh_docker
+@pytest.mark.parametrize(
+    "maskfile", ["test_brain.nii.gz", "test_brain", "test_brain.nii"]
+)
+@pytest.mark.parametrize("plugin", Plugins)
+def test_boutiques_wf_2(maskfile, plugin):
+    """ wf with two tasks that run fsl.bet and fsl.stats using BoshTask"""
+    wf = Workflow(name="wf", input_spec=["maskfile", "infile"])
+    wf.inputs.maskfile = maskfile
+    wf.inputs.infile = Infile
+
+    wf.add(
+        BoshTask(
+            name="bet",
+            zenodo="zenodo.1482743",
+            infile=wf.lzin.infile,
+            maskfile=wf.lzin.maskfile,
+        )
+    )
+    wf.add(
+        BoshTask(
+            name="stat",
+            zenodo="zenodo.3240521",
+            input_file=wf.bet.lzout.outfile,
+            v=True,
+        )
+    )
+
+    wf.set_output(
+        [("outfile_bet", wf.bet.lzout.outfile), ("out_stat", wf.stat.lzout.output)]
+    )
+
+    with Submitter(plugin=plugin) as sub:
+        wf(submitter=sub)
+
+    res = wf.result()
+    assert res.output.outfile_bet.name == "test_brain.nii.gz"
+    assert res.output.outfile_bet.exists()
+
+    assert res.output.out_stat.name == "output.txt"
+    assert res.output.out_stat.exists()

pydra/engine/tests/test_shelltask.py

@@ -11,27 +11,14 @@
 from ..submitter import Submitter
 from ..core import Workflow
 from ..specs import ShellOutSpec, ShellSpec, SpecInfo, File
+from .utils import result_no_submitter, result_submitter
 
 if bool(shutil.which("sbatch")):
     Plugins = ["cf", "slurm"]
 else:
     Plugins = ["cf"]
 
 
-def result_no_submitter(shell_task, plugin=None):
-    """ helper function to return result when running without submitter """
-    return shell_task()
-
-
-def result_submitter(shell_task, plugin):
-    """ helper function to return result when running with submitter
-        with specific plugin
-    """
-    with Submitter(plugin=plugin) as sub:
-        shell_task(submitter=sub)
-    return shell_task.result()
-
-
 @pytest.mark.parametrize("results_function", [result_no_submitter, result_submitter])
 @pytest.mark.parametrize("plugin", Plugins)
 def test_shell_cmd_1(plugin, results_function):

pydra/engine/tests/utils.py

@@ -4,10 +4,25 @@
 from pathlib import Path
 
 from ..core import Workflow
+from ..submitter import Submitter
 from ... import mark
 from ..specs import File
 
 
+def result_no_submitter(shell_task, plugin=None):
+    """ helper function to return result when running without submitter """
+    return shell_task()
+
+
+def result_submitter(shell_task, plugin):
+    """ helper function to return result when running with submitter
+        with specific plugin
+    """
+    with Submitter(plugin=plugin) as sub:
+        shell_task(submitter=sub)
+    return shell_task.result()
+
+
 @mark.task
 def fun_addtwo(a):
     import time