Added tests

MANIFEST.in

@@ -10,7 +10,9 @@ include cwl_utils/cwlNodeEngineJSConsole.js
 include cwl_utils/cwlNodeEngineWithContext.js
 include testdata/*.cwl
 include testdata/*.yaml
+include testdata/*.yml
 include testdata/*.input
+include testdata/*.json
 include testdata/*.ttl
 include testdata/*.owl
 include testdata/checker_wf/*.cwl

testdata/dir4-job.yml

@@ -0,0 +1,9 @@
+inf:
+  class: File
+  location: hello.tar
+  secondaryFiles:
+    - class: File
+      location: index.py
+    - class: Directory
+      basename: xtestdir
+      location: testdir

testdata/env-job3.yaml

@@ -0,0 +1,6 @@
+in: "hello test env"
+cwl:requirements:
+ - class: EnvVarRequirement
+   envDef:
+     - envName: TEST_ENV
+       envValue: $(inputs.in)

testdata/formattest-job.json

@@ -0,0 +1,7 @@
+{
+    "input": {
+        "class": "File",
+        "location": "whale.txt",
+        "format": "edam:format_2330"
+    }
+}

testdata/nested-array-job.yml

@@ -0,0 +1 @@
+letters: [[a]]

tests/test_parser_utils.py

@@ -17,7 +17,6 @@
 import cwl_utils.parser.utils
 from cwl_utils.errors import WorkflowException
 from cwl_utils.parser import load_document_by_uri
-
 from .util import get_data
 
 
@@ -144,6 +143,36 @@ def test_v1_0_file_content_larger_than_64_kB() -> None:
     assert content == text[0 : cwl_utils.parser.cwl_v1_0_utils.CONTENT_LIMIT]
 
 
+def test_v_1_0_load_inputfile_with_format() -> None:
+    """Test that File object with the `format` field is correctly loaded with CWL v1.0."""
+    uri = Path(get_data("testdata/formattest2_v1_0.cwl")).resolve().as_uri()
+    cwl_obj = load_document_by_uri(uri)
+    uri = Path(get_data("testdata/formattest-job.json")).resolve().as_uri()
+    jobfile = cwl_utils.parser.utils.load_inputfile_by_uri(
+        "v1.0", uri, cwl_obj.loadingOptions
+    )
+    assert jobfile["input"].format == cwl_obj.inputs[0].format
+
+
+def test_v_1_0_load_inputfile_with_nested_array() -> None:
+    """Test that nested arrays are preserved when loading an input file with CWL v1.0."""
+    uri = Path(get_data("testdata/nested-array-job.yml")).resolve().as_uri()
+    jobfile = cwl_utils.parser.utils.load_inputfile_by_uri("v1.0", uri)
+    assert isinstance(jobfile["letters"], MutableSequence)
+    assert isinstance(jobfile["letters"][0], MutableSequence)
+    assert jobfile["letters"][0][0] == "a"
+
+
+def test_v_1_0_load_inputfile_with_secondary_files() -> None:
+    """Test that secondary files are treated as objects when loading an input file with CWL v1.0."""
+    uri = Path(get_data("testdata/dir4-job.yml")).resolve().as_uri()
+    jobfile = cwl_utils.parser.utils.load_inputfile_by_uri("v1.0", uri)
+    assert isinstance(jobfile["inf"].secondaryFiles[0], cwl_utils.parser.cwl_v1_0.File)
+    assert isinstance(
+        jobfile["inf"].secondaryFiles[1], cwl_utils.parser.cwl_v1_0.Directory
+    )
+
+
 def test_v1_0_stdout_to_file() -> None:
     """Test that stdout shortcut is converted to stdout parameter with CWL v1.0."""
     clt = cwl_utils.parser.cwl_v1_0.CommandLineTool(
@@ -423,6 +452,45 @@ def test_v1_1_file_content_larger_than_64_kB() -> None:
     assert content == text[0 : cwl_utils.parser.cwl_v1_1_utils.CONTENT_LIMIT]
 
 
+def test_v_1_1_load_inputfile_with_format() -> None:
+    """Test that File object with the `format` field is correctly loaded with CWL v1.1."""
+    uri = Path(get_data("testdata/formattest2_v1_1.cwl")).resolve().as_uri()
+    cwl_obj = load_document_by_uri(uri)
+    uri = Path(get_data("testdata/formattest-job.json")).resolve().as_uri()
+    jobfile = cwl_utils.parser.utils.load_inputfile_by_uri(
+        "v1.1", uri, cwl_obj.loadingOptions
+    )
+    assert jobfile["input"].format == cwl_obj.inputs[0].format
+
+
+def test_v_1_1_load_inputfile_with_nested_array() -> None:
+    """Test that nested arrays are preserved when loading an input file with CWL v1.1."""
+    uri = Path(get_data("testdata/nested-array-job.yml")).resolve().as_uri()
+    jobfile = cwl_utils.parser.utils.load_inputfile_by_uri("v1.1", uri)
+    assert isinstance(jobfile["letters"], MutableSequence)
+    assert isinstance(jobfile["letters"][0], MutableSequence)
+    assert jobfile["letters"][0][0] == "a"
+
+
+def test_v_1_1_load_inputfile_with_requirements() -> None:
+    """Test that an input file with the cwl:requirements directive is correctly loaded with CWL v1.1."""
+    uri = Path(get_data("testdata/env-job3.yaml")).resolve().as_uri()
+    jobfile = cwl_utils.parser.utils.load_inputfile_by_uri("v1.1", uri)
+    assert isinstance(
+        jobfile["cwl:requirements"][0], cwl_utils.parser.cwl_v1_1.EnvVarRequirement
+    )
+
+
+def test_v_1_1_load_inputfile_with_secondary_files() -> None:
+    """Test that secondary files are treated as objects when loading an input file with CWL v1.1."""
+    uri = Path(get_data("testdata/dir4-job.yml")).resolve().as_uri()
+    jobfile = cwl_utils.parser.utils.load_inputfile_by_uri("v1.1", uri)
+    assert isinstance(jobfile["inf"].secondaryFiles[0], cwl_utils.parser.cwl_v1_1.File)
+    assert isinstance(
+        jobfile["inf"].secondaryFiles[1], cwl_utils.parser.cwl_v1_1.Directory
+    )
+
+
 def test_v1_1_stdout_to_file() -> None:
     """Test that stdout shortcut is converted to stdout parameter with CWL v1.1."""
     clt = cwl_utils.parser.cwl_v1_1.CommandLineTool(
@@ -746,6 +814,45 @@ def test_v1_2_file_content_larger_than_64_kB() -> None:
             cwl_utils.parser.cwl_v1_2_utils.content_limit_respected_read(f)
 
 
+def test_v_1_2_load_inputfile_with_format() -> None:
+    """Test that File object with the `format` field is correctly loaded with CWL v1.2."""
+    uri = Path(get_data("testdata/formattest2.cwl")).resolve().as_uri()
+    cwl_obj = load_document_by_uri(uri)
+    uri = Path(get_data("testdata/formattest-job.json")).resolve().as_uri()
+    jobfile = cwl_utils.parser.utils.load_inputfile_by_uri(
+        "v1.2", uri, cwl_obj.loadingOptions
+    )
+    assert jobfile["input"].format == cwl_obj.inputs[0].format
+
+
+def test_v_1_2_load_inputfile_with_nested_array() -> None:
+    """Test that nested arrays are preserved when loading an input file with CWL v1.2."""
+    uri = Path(get_data("testdata/nested-array-job.yml")).resolve().as_uri()
+    jobfile = cwl_utils.parser.utils.load_inputfile_by_uri("v1.2", uri)
+    assert isinstance(jobfile["letters"], MutableSequence)
+    assert isinstance(jobfile["letters"][0], MutableSequence)
+    assert jobfile["letters"][0][0] == "a"
+
+
+def test_v_1_2_load_inputfile_with_requirements() -> None:
+    """Test that an input file with the cwl:requirements directive is correctly loaded with CWL v1.2."""
+    uri = Path(get_data("testdata/env-job3.yaml")).resolve().as_uri()
+    jobfile = cwl_utils.parser.utils.load_inputfile_by_uri("v1.2", uri)
+    assert isinstance(
+        jobfile["cwl:requirements"][0], cwl_utils.parser.cwl_v1_2.EnvVarRequirement
+    )
+
+
+def test_v_1_2_load_inputfile_with_secondary_files() -> None:
+    """Test that secondary files are treated as objects when loading an input file with CWL v1.2."""
+    uri = Path(get_data("testdata/dir4-job.yml")).resolve().as_uri()
+    jobfile = cwl_utils.parser.utils.load_inputfile_by_uri("v1.2", uri)
+    assert isinstance(jobfile["inf"].secondaryFiles[0], cwl_utils.parser.cwl_v1_2.File)
+    assert isinstance(
+        jobfile["inf"].secondaryFiles[1], cwl_utils.parser.cwl_v1_2.Directory
+    )
+
+
 def test_v1_2_stdout_to_file() -> None:
     """Test that stdout shortcut is converted to stdout parameter with CWL v1.2."""
     clt = cwl_utils.parser.cwl_v1_2.CommandLineTool(