add tests

mr-c · mr-c · commit 59139ba3cc9e · 2023-05-26T10:48:00.000+02:00
diff --git a/testdata/v1.0/params_inc.yml b/testdata/v1.0/params_inc.yml
@@ -0,0 +1,120 @@
+  - id: t1
+    type: Any
+    outputBinding:
+      outputEval: $(inputs)
+  - id: t2
+    type: Any
+    outputBinding:
+      outputEval: $(inputs.bar)
+  - id: t3
+    type: Any
+    outputBinding:
+      outputEval: $(inputs['bar'])
+  - id: t4
+    type: Any
+    outputBinding:
+      outputEval: $(inputs["bar"])
+
+  - id: t5
+    type: Any
+    outputBinding:
+      outputEval: $(inputs.bar.baz)
+  - id: t6
+    type: Any
+    outputBinding:
+      outputEval: $(inputs['bar'].baz)
+  - id: t7
+    type: Any
+    outputBinding:
+      outputEval: $(inputs['bar']["baz"])
+  - id: t8
+    type: Any
+    outputBinding:
+      outputEval: $(inputs.bar['baz'])
+
+  - id: t9
+    type: Any
+    outputBinding:
+      outputEval: $(inputs.bar['b az'])
+  - id: t10
+    type: Any
+    outputBinding:
+      outputEval: $(inputs.bar['b\'az'])
+  - id: t11
+    type: Any
+    outputBinding:
+      outputEval: $(inputs.bar["b'az"])
+  - id: t12
+    type: "null"
+    outputBinding:
+      outputEval: $(inputs.bar['b"az'])
+
+  - id: t13
+    type: Any
+    outputBinding:
+      outputEval: -$(inputs.bar.baz)
+  - id: t14
+    type: Any
+    outputBinding:
+      outputEval: -$(inputs['bar'].baz)
+  - id: t15
+    type: Any
+    outputBinding:
+      outputEval: -$(inputs['bar']["baz"])
+  - id: t16
+    type: Any
+    outputBinding:
+      outputEval: -$(inputs.bar['baz'])
+
+  - id: t17
+    type: Any
+    outputBinding:
+      outputEval: $(inputs.bar.baz) $(inputs.bar.baz)
+  - id: t18
+    type: Any
+    outputBinding:
+      outputEval: $(inputs['bar'].baz) $(inputs['bar'].baz)
+  - id: t19
+    type: Any
+    outputBinding:
+      outputEval: $(inputs['bar']["baz"]) $(inputs['bar']["baz"])
+  - id: t20
+    type: Any
+    outputBinding:
+      outputEval: $(inputs.bar['baz']) $(inputs.bar['baz'])
+
+  - id: t21
+    type: Any
+    outputBinding:
+      outputEval: $(inputs.bar['b az']) $(inputs.bar['b az'])
+  - id: t22
+    type: Any
+    outputBinding:
+      outputEval: $(inputs.bar['b\'az']) $(inputs.bar['b\'az'])
+  - id: t23
+    type: Any
+    outputBinding:
+      outputEval: $(inputs.bar["b'az"]) $(inputs.bar["b'az"])
+  - id: t24
+    type: Any
+    outputBinding:
+      outputEval: $(inputs.bar['b"az']) $(inputs.bar['b"az'])
+
+  - id: t25
+    type: Any
+    outputBinding:
+      outputEval: $(inputs.bar.buz[1])
+  - id: t26
+    type: Any
+    outputBinding:
+      outputEval: $(inputs.bar.buz[1]) $(inputs.bar.buz[1])
+
+  - id: t27
+    type: "null"
+    outputBinding:
+      outputEval: $(null)
+
+  - id: t28
+    type: int
+    outputBinding:
+      outputEval: $(inputs.bar.buz.length)
diff --git a/testdata/v1.0/subdir/params.cwl b/testdata/v1.0/subdir/params.cwl
@@ -0,0 +1,19 @@
+class: CommandLineTool
+cwlVersion: v1.0
+hints:
+  ResourceRequirement:
+    ramMin: 8
+inputs:
+  bar:
+    type: Any
+    default: {
+          "baz": "zab1",
+          "b az": 2,
+          "b'az": true,
+          'b"az': null,
+          "buz": ['a', 'b', 'c']
+        }
+
+outputs: {"$import": ../params_inc.yml}
+
+baseCommand: "true"
diff --git a/testdata/v1.1/params_inc.yml b/testdata/v1.1/params_inc.yml
@@ -0,0 +1,120 @@
+- id: t1
+  type: Any
+  outputBinding:
+    outputEval: $(inputs)
+- id: t2
+  type: Any
+  outputBinding:
+    outputEval: $(inputs.bar)
+- id: t3
+  type: Any
+  outputBinding:
+    outputEval: $(inputs['bar'])
+- id: t4
+  type: Any
+  outputBinding:
+    outputEval: $(inputs["bar"])
+
+- id: t5
+  type: Any
+  outputBinding:
+    outputEval: $(inputs.bar.baz)
+- id: t6
+  type: Any
+  outputBinding:
+    outputEval: $(inputs['bar'].baz)
+- id: t7
+  type: Any
+  outputBinding:
+    outputEval: $(inputs['bar']["baz"])
+- id: t8
+  type: Any
+  outputBinding:
+    outputEval: $(inputs.bar['baz'])
+
+- id: t9
+  type: Any
+  outputBinding:
+    outputEval: $(inputs.bar['b az'])
+- id: t10
+  type: Any
+  outputBinding:
+    outputEval: $(inputs.bar['b\'az'])
+- id: t11
+  type: Any
+  outputBinding:
+    outputEval: $(inputs.bar["b'az"])
+- id: t12
+  type: "null"
+  outputBinding:
+    outputEval: $(inputs.bar['b"az'])
+
+- id: t13
+  type: Any
+  outputBinding:
+    outputEval: -$(inputs.bar.baz)
+- id: t14
+  type: Any
+  outputBinding:
+    outputEval: -$(inputs['bar'].baz)
+- id: t15
+  type: Any
+  outputBinding:
+    outputEval: -$(inputs['bar']["baz"])
+- id: t16
+  type: Any
+  outputBinding:
+    outputEval: -$(inputs.bar['baz'])
+
+- id: t17
+  type: Any
+  outputBinding:
+    outputEval: $(inputs.bar.baz) $(inputs.bar.baz)
+- id: t18
+  type: Any
+  outputBinding:
+    outputEval: $(inputs['bar'].baz) $(inputs['bar'].baz)
+- id: t19
+  type: Any
+  outputBinding:
+    outputEval: $(inputs['bar']["baz"]) $(inputs['bar']["baz"])
+- id: t20
+  type: Any
+  outputBinding:
+    outputEval: $(inputs.bar['baz']) $(inputs.bar['baz'])
+
+- id: t21
+  type: Any
+  outputBinding:
+    outputEval: $(inputs.bar['b az']) $(inputs.bar['b az'])
+- id: t22
+  type: Any
+  outputBinding:
+    outputEval: $(inputs.bar['b\'az']) $(inputs.bar['b\'az'])
+- id: t23
+  type: Any
+  outputBinding:
+    outputEval: $(inputs.bar["b'az"]) $(inputs.bar["b'az"])
+- id: t24
+  type: Any
+  outputBinding:
+    outputEval: $(inputs.bar['b"az']) $(inputs.bar['b"az'])
+
+- id: t25
+  type: Any
+  outputBinding:
+    outputEval: $(inputs.bar.buz[1])
+- id: t26
+  type: Any
+  outputBinding:
+    outputEval: $(inputs.bar.buz[1]) $(inputs.bar.buz[1])
+
+- id: t27
+  type: "null"
+  outputBinding:
+    outputEval: $(null)
+
+- id: t28
+  type: int
+  outputBinding:
+    outputEval: $(inputs.bar.buz.length)
diff --git a/testdata/v1.1/subdir/params.cwl b/testdata/v1.1/subdir/params.cwl
@@ -0,0 +1,18 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.1
+class: CommandLineTool
+requirements:
+  NetworkAccess:
+    networkAccess: true
+  LoadListingRequirement:
+    loadListing: deep_listing
+hints:
+  ResourceRequirement:
+    ramMin: 8
+inputs:
+  bar:
+    type: Any
+    default: {"baz": "zab1", "b az": 2, "b'az": true, 'b"az': null, "buz": ['a', 'b',
+        'c']}
+baseCommand: "true"
+outputs: {"$import": ../params_inc.yml}
diff --git a/tests/test_import.py b/tests/test_import.py
@@ -0,0 +1,31 @@
+import filecmp
+from pathlib import Path
+
+from cwlupgrader.main import load_cwl_document, main, upgrade_document
+import pytest
+import logging
+from .util import get_data
+import re
+
+def test_import_parent_directory(tmp_path: Path, caplog: pytest.LogCaptureFixture) -> None:
+    """Confirm that $import to a superior directory still preserves the directory structure."""
+    caplog.set_level(logging.WARN)
+    out_dir = tmp_path/"out"
+    out_dir.mkdir()
+    doc = load_cwl_document(get_data("testdata/v1.0/subdir/params.cwl"))
+    upgraded = upgrade_document(doc, out_dir, out_dir, "v1.1")
+    expected = load_cwl_document(get_data("testdata/v1.1/subdir/params.cwl"))
+    assert upgraded == expected
+    assert len(caplog.records) == 1
+    assert re.search(re.escape(f"Writing file, '{tmp_path}/params_inc.yml', outside of the output directory, '{out_dir}'."), caplog.records[0].getMessage())
+
+def test_import_parent_directory_safe(tmp_path: Path, caplog: pytest.LogCaptureFixture) -> None:
+    """Confirm no warning when $import to a superior directory (but still in the current working directory) still preserves the directory structure."""
+    caplog.set_level(logging.WARN)
+    out_dir = tmp_path/"out"
+    out_dir.mkdir()
+    doc = load_cwl_document(get_data("testdata/v1.0/subdir/params.cwl"))
+    upgraded = upgrade_document(doc, out_dir, tmp_path, "v1.1")
+    expected = load_cwl_document(get_data("testdata/v1.1/subdir/params.cwl"))
+    assert upgraded == expected
+    assert len(caplog.records) == 0
