Unverified Commit 7c8d732e authored by Marius van den Beek's avatar Marius van den Beek Committed by GitHub
Browse files

Merge pull request #15439 from bernt-matthias/fix-looks-like-yaml-w-class 

[22.05] fix looks_like_yaml_or_cwl_with_class
parents bff1a04c 8ec08f66

lib/galaxy/tool_util/loader_directory.py

+2 −2
Original line number Diff line number Diff line
@@ -190,7 +190,7 @@ def looks_like_a_data_manager_xml(path): 


def as_dict_if_looks_like_yaml_or_cwl_with_class(path, classes):

    """

    get a dict from yaml file if it contains `class: CLASS`, where CLASS is

    get a dict from yaml file if it contains a line `class: CLASS`, where CLASS is

    any string given in CLASSES. must appear in the first 5k and also load

    properly in total.

    """
@@ -199,7 +199,7 @@ def as_dict_if_looks_like_yaml_or_cwl_with_class(path, classes): 
            start_contents = f.read(5 * 1024)

        except UnicodeDecodeError:

            return False, None

        if re.search(rf"\nclass:\s+({'|'.join(classes)})\s*\n", start_contents) is None:

        if re.search(rf"^class:\s+{'|'.join(classes)}\s*$", start_contents, re.MULTILINE) is None:

            return False, None



    with open(path) as f:

test/unit/tool_util/test_loader_directory.py

0 → 100644
+24 −0
Original line number Diff line number Diff line 
import tempfile



from galaxy.tool_util.loader_directory import is_a_yaml_with_class





def test_is_a_yaml_with_class():

    with tempfile.NamedTemporaryFile("w", suffix=".yaml") as tf:

        fname = tf.name

        tf.write(

            """class: GalaxyWorkflow

name: "Test Workflow"

inputs:

  - id: input1

outputs:

  - id: wf_output_1

    outputSource: first_cat/out_file1

steps:

  - tool_id: cat

    label: first_cat

    in:

      input1: input1"""

        )

        tf.flush()

        assert is_a_yaml_with_class(fname, ["GalaxyWorkflow"])