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Fix file name for extracted .gz/.bz2/.xz containers

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This commit is contained in:
RichardG867
2022-04-05 22:44:10 -03:00
parent 7fdd140583
commit e5b70934be
1 changed files with 18 additions and 8 deletions
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26
biostools/extractors.py
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@@ -96,6 +96,7 @@ class ApricotExtractor(Extractor):
# Return destination directory path.
return dest_dir
class ArchiveExtractor(Extractor):
"""Extract known archive types."""
@@ -108,9 +109,9 @@ class ArchiveExtractor(Extractor):
b'''Rar!\\x1A\\x07|''' # rar
b'''7z\\xBC\\xAF\\x27\\x1C|''' # 7z
b'''MSCF|''' # cab
b'''\\x1F\\x8B|''' # gzip
b'''(\\x1F\\x8B|''' # gzip
b'''BZh|''' # bzip2
b'''\\xFD7zXZ\\x00|''' # xz
b'''\\xFD7zXZ\\x00)|''' # xz
b'''LHA\\x20|''' # lha
b'''ZOO''' # zoo
)
@@ -178,13 +179,14 @@ class ArchiveExtractor(Extractor):
"""Extract an archive."""
# Stop if this is apparently not an archive.
if not self._signature_pattern.match(file_header):
match = self._signature_pattern.match(file_header)
if not match:
return False
# Do the actual extraction.
return self._extract_archive(file_path, dest_dir)
return self._extract_archive(file_path, dest_dir, rename=bool(match.group(1)))
def _extract_archive(self, file_path, dest_dir, remove=True):
def _extract_archive(self, file_path, dest_dir, remove=True, rename=False):
# Create destination directory and stop if it couldn't be created.
if not util.try_makedirs(dest_dir):
return True
@@ -221,9 +223,17 @@ class ArchiveExtractor(Extractor):
break
# Assume failure if nothing was extracted.
if len(os.listdir(dest_dir)) < 1:
files_extracted = os.listdir(dest_dir)
if len(files_extracted) < 1:
return False
# Rename single file if requested.
if rename and len(files_extracted) == 1:
try:
shutil.move(os.path.join(dest_dir, files_extracted[0]), os.path.join(dest_dir, os.path.splitext(os.path.basename(file_path))[0]))
except:
pass
# Remove archive file.
if remove:
try:
@@ -1124,7 +1134,7 @@ class ISOExtractor(ArchiveExtractor):
return False
# Extract this as an archive.
ret = self._extract_archive(file_path, dest_dir, False)
ret = self._extract_archive(file_path, dest_dir, remove=False)
# Some El Torito hard disk images have an MBR (Lenovo ThinkPad UEFI updaters).
# 7-Zip doesn't care about MBRs and just takes the El Torito sector count field
@@ -2006,7 +2016,7 @@ class VMExtractor(ArchiveExtractor):
# Extract image as an archive.
image_path = os.path.join(dest_dir, deps[0][1])
ret = self._extract_archive(image_path, dest_dir, False)
ret = self._extract_archive(image_path, dest_dir, remove=False)
if type(ret) == str and len(os.listdir(dest_dir)) > 1:
# Remove original file.
try: