Unverified Commit 318aa579 authored by Nicola Soranzo's avatar Nicola Soranzo
Browse files

Fix type annotations for pysam 0.23.0 

Partial backport of commit faa752ed
to fix test_galaxy_packages tests.
For lines where the `type: ignore` comment is not needed any more,
here we add `unused-ignore` instead of removing the comment, so
that the (non-package) mypy tests don't fail (since those still
use an older pysam).

When merging forward, choose removing the comment (i.e. the dev
version).
parent 1dcfdecb

lib/galaxy/datatypes/binary.py

+5 −5
Original line number Diff line number Diff line
@@ -570,7 +570,7 @@ class BamNative(CompressedArchive, _BamOrSam): 
        :param split_files: List of bam file paths to merge

        :param output_file: Write merged bam file to this location

        """

        pysam.merge("-O", "BAM", output_file, *split_files)  # type: ignore[attr-defined]

        pysam.merge("-O", "BAM", output_file, *split_files)  # type: ignore[attr-defined, unused-ignore]



    def init_meta(self, dataset: HasMetadata, copy_from: Optional[HasMetadata] = None) -> None:

        Binary.init_meta(self, dataset, copy_from=copy_from)
@@ -638,7 +638,7 @@ class BamNative(CompressedArchive, _BamOrSam): 
            [f"-@{slots}", file_name, "-T", tmp_sorted_dataset_file_name_prefix, "-O", "BAM", "-o", sorted_file_name]

        )

        try:

            pysam.sort(*sort_args)  # type: ignore[attr-defined]

            pysam.sort(*sort_args)  # type: ignore[attr-defined, unused-ignore]

        except Exception:

            shutil.rmtree(tmp_dir, ignore_errors=True)

            raise
@@ -835,9 +835,9 @@ class Bam(BamNative): 
            )

        if index_flag == "-b":

            # IOError: No such file or directory: '-b' if index_flag is set to -b (pysam 0.15.4)

            pysam.index("-o", index_file.get_file_name(), dataset.get_file_name())  # type: ignore [attr-defined]

            pysam.index("-o", index_file.get_file_name(), dataset.get_file_name())  # type: ignore[attr-defined, unused-ignore]

        else:

            pysam.index(index_flag, "-o", index_file.get_file_name(), dataset.get_file_name())  # type: ignore [attr-defined]

            pysam.index(index_flag, "-o", index_file.get_file_name(), dataset.get_file_name())  # type: ignore[attr-defined, unused-ignore]

        dataset.metadata.bam_index = index_file



    def sniff(self, filename: str) -> bool:
@@ -1028,7 +1028,7 @@ class CRAM(Binary): 


    def set_index_file(self, dataset: HasFileName, index_file) -> bool:

        try:

            pysam.index("-o", index_file.get_file_name(), dataset.get_file_name())  # type: ignore [attr-defined]

            pysam.index("-o", index_file.get_file_name(), dataset.get_file_name())  # type: ignore[attr-defined, unused-ignore]

            return True

        except Exception as exc:

            log.warning("%s, set_index_file Exception: %s", self, exc)

test/unit/data/datatypes/test_bam.py

+7 −3
Original line number Diff line number Diff line 
import json



from pysam import (  # type: ignore[attr-defined]

from pysam import (  # type: ignore[attr-defined, unused-ignore]

    AlignmentFile,

    view,

)
@@ -16,8 +16,12 @@ from .util import ( 
def test_merge_bam():

    with get_input_files("1.bam", "1.bam") as input_files, get_tmp_path() as outpath:

        Bam.merge(input_files, outpath)

        alignment_count_output = int(view("-c", outpath).strip())

        alignment_count_input = int(view("-c", input_files[0]).strip()) * 2

        ret = view("-c", outpath)

        assert isinstance(ret, str)

        alignment_count_output = int(ret.strip())

        ret = view("-c", input_files[0])

        assert isinstance(ret, str)

        alignment_count_input = int(ret.strip()) * 2

        assert alignment_count_input == alignment_count_output