Merge remote-tracking branch 'origin/master' into singularity23_fix

Author: mr-c

cwltool/command_line_tool.py

@@ -440,7 +440,7 @@ def rm_pending_output_callback(output_callbacks, jobcachepending,
                             else:
                                 et["entryname"] = None
                             et["writable"] = t.get("writable", False)
-                            if et[u"entry"]:
+                            if et[u"entry"] is not None:
                                 ls.append(et)
                     else:
                         initwd_item = builder.do_eval(t)
@@ -797,7 +797,12 @@ def collect_output(self,
             adjustFileObjs(r, revmap)
 
             if not r and optional:
-                return None
+                # Don't convert zero or empty string to None
+                if r in [0, '']:
+                    return r
+                # For [] or None, return None
+                else:
+                    return None
 
         if (not empty_and_optional and isinstance(schema["type"], MutableMapping)
                 and schema["type"]["type"] == "record"):

setup.py

@@ -57,7 +57,7 @@
           'ruamel.yaml >= 0.12.4, <= 0.15.77',
           'rdflib >= 4.2.2, < 4.3.0',
           'shellescape >= 3.4.1, < 3.5',
-          'schema-salad >= 4.1, < 5',
+          'schema-salad >= 4.2, < 5',
           'mypy-extensions',
           'six >= 1.9.0',  # >= 1.9.0 required by prov
           'psutil',

tests/test_examples.py

@@ -920,3 +920,14 @@ def test_v1_0_position_expression():
         ['--debug', get_data(test_file), get_data(test_job)])
     assert "is not int" in stderr, stderr
     assert error_code == 1
+
+
+@windows_needs_docker
+def test_optional_numeric_output_0():
+    test_file = "tests/wf/optional-numerical-output-0.cwl"
+    error_code, stdout, stderr = get_main_output(
+        [get_data(test_file)])
+
+    assert "completed success" in stderr
+    assert error_code == 0
+    assert json.loads(stdout)['out'] == 0

tests/test_iwdr.py

@@ -3,7 +3,7 @@
 from cwltool.main import main
 from cwltool import load_tool
 from .util import (get_data, get_windows_safe_factory, windows_needs_docker,
-                   needs_docker, temp_dir, needs_singularity)
+                   needs_docker, temp_dir, needs_singularity, get_main_output)
 
 @windows_needs_docker
 def test_newline_in_entry():
@@ -14,6 +14,16 @@ def test_newline_in_entry():
     echo = factory.make(get_data("tests/wf/iwdr-entry.cwl"))
     assert echo(message="hello") == {"out": "CONFIGVAR=hello\n"}
 
+
+@needs_docker
+def test_empty_file_creation():
+    """
+    test that empty file can be created in InitialWorkingDirectory
+    """
+    err_code, _, _ = get_main_output([get_data("tests/wf/iwdr-empty.cwl")])
+    assert err_code == 0
+
+
 @needs_docker
 def test_iwdr_permutations():
     saved_tempdir = tempfile.tempdir

tests/wf/iwdr-empty.cwl

@@ -0,0 +1,14 @@
+#!/usr/bin/env cwl-runner
+
+class: CommandLineTool
+cwlVersion: v1.0
+baseCommand: ["cat", "empty_file"]
+
+requirements:
+  InitialWorkDirRequirement:
+    listing:
+      - entryname: empty_file
+        entry: ""
+
+inputs: []
+outputs: []

tests/wf/optional-numerical-output-0.cwl

@@ -0,0 +1,16 @@
+cwlVersion: v1.0
+class: CommandLineTool
+baseCommand:
+  - echo
+  - "0"
+stdout: a.txt
+requirements:
+- class: InlineJavascriptRequirement
+inputs: []
+outputs:
+  out:
+    type: float?
+    outputBinding:
+      glob: "a.txt"
+      loadContents: true
+      outputEval: "${\n    return parseFloat(self[0].contents);\n}"