Fix type annotations (faa752ed) · Commits · NDIP / Galaxy

lib/galaxy/datatypes/binary.py

+5 −5

Original line number	Diff line number	Diff line
		@@ -667,7 +667,7 @@ 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)

		def init_meta(self, dataset: HasMetadata, copy_from: Optional[HasMetadata] = None) -> None:
		Binary.init_meta(self, dataset, copy_from=copy_from)
		@@ -735,7 +735,7 @@ 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)
		except Exception:
		shutil.rmtree(tmp_dir, ignore_errors=True)
		raise
		@@ -932,9 +932,9 @@ 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())
		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())
		dataset.metadata.bam_index = index_file

		def sniff(self, filename: str) -> bool:
		@@ -1125,7 +1125,7 @@ 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())
		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 (
		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

test/unit/tool_shed/test_tool_panel_manager.py

+3 −2

Original line number	Diff line number	Diff line
		import os
		from typing import Optional

		from galaxy.app_unittest_utils.toolbox_support import (
		BaseToolBoxTestCase,
		@@ -71,7 +72,7 @@ class TestToolPanelManager(BaseToolBoxTestCase):

		def test_add_twice(self):
		self._init_dynamic_tool_conf()
		previous_guid = None
		previous_guid: Optional[str] = None
		for v in "1", "2", "3":
		self.__toolbox = self.get_new_toolbox()
		changeset = f"0123456789abcde{v}"
		@@ -107,7 +108,7 @@ class TestToolPanelManager(BaseToolBoxTestCase):
		# New GUID replaced old one in tool panel but both
		# appear in integrated tool panel.
		if previous_guid:
		assert (f"tool_{previous_guid}") not in section.panel_items() # type: ignore[unreachable]
		assert (f"tool_{previous_guid}") not in section.panel_items()
		assert (f"tool_{guid}") in self.toolbox._integrated_tool_panel["tid1"].panel_items()
		previous_guid = guid

tools/filters/axt_to_lav.py

+3 −2

Original line number	Diff line number	Diff line
		@@ -12,6 +12,7 @@ standard out; some statistics are written to standard error.
		from __future__ import print_function

		import sys
		from typing import Optional

		import bx.align.axt
		import bx.align.lav
		@@ -48,7 +49,7 @@ def main():

		# parse the command line

		primary = None
		primary: Optional[str] = None
		secondary = None
		silent = False

		@@ -74,7 +75,7 @@ def main():
		elif primary is None and val is None:
		primary = arg
		elif secondary is None and val is None:
		secondary = arg # type: ignore[unreachable]
		secondary = arg
		else:
		usage("unknown argument: %s" % arg)

tools/filters/gff_to_bed_converter.py

+11 −6

Original line number	Diff line number	Diff line
		@@ -2,11 +2,16 @@
		from __future__ import print_function

		import sys
		from typing import (
		List,
		Optional,
		Tuple,
		)

		from galaxy.datatypes.util.gff_util import parse_gff_attributes


		def get_bed_line(chrom, name, strand, blocks):
		def get_bed_line(chrom, name, strand, blocks: List[Tuple[int, int]]):
		"""Returns a BED line for given data."""

		if len(blocks) == 1:
		@@ -66,9 +71,9 @@ def __main__():
		first_skipped_line = 0
		i = 0
		cur_transcript_chrome = None
		cur_transcript_id = None
		cur_transcript_id: Optional[str] = None
		cur_transcript_strand = None
		cur_transcripts_blocks = [] # (start, end) for each block.
		cur_transcripts_blocks: List[Tuple[int, int]] = [] # (start, end) for each block.
		with open(output_name, "w") as out, open(input_name) as in_fh:
		for i, line in enumerate(in_fh):
		line = line.rstrip("\r\n")
		@@ -77,7 +82,7 @@ def __main__():
		# GFF format: chrom source, name, chromStart, chromEnd, score, strand, attributes
		elems = line.split("\t")
		start = str(int(elems[3]) - 1)
		coords = [int(start), int(elems[4])]
		coords = (int(start), int(elems[4]))
		strand = elems[6]
		if strand not in ["+", "-"]:
		strand = "+"
		@@ -92,7 +97,7 @@ def __main__():
		# Write previous transcript.
		if cur_transcript_id:
		# Write BED entry.
		out.write( # type: ignore[unreachable]
		out.write(
		get_bed_line(
		cur_transcript_chrome,
		cur_transcript_id,
		@@ -120,7 +125,7 @@ def __main__():
		# Write previous transcript.
		if cur_transcript_id:
		# Write BED entry.
		out.write( # type: ignore[unreachable]
		out.write(
		get_bed_line(
		cur_transcript_chrome, cur_transcript_id, cur_transcript_strand, cur_transcripts_blocks
		)