def is_data_index_sample_file(file_path):
"""
Attempt to determine if a .sample file is appropriate for copying to ~/tool-data when
a tool shed repository is being installed into a Galaxy instance.
"""
# Currently most data index files are tabular, so check that first. We'll assume that
# if the file is tabular, it's ok to copy.
if is_column_based(file_path):
return True
# If the file is any of the following, don't copy it.
if checkers.check_html(file_path):
return False
if checkers.check_image(file_path):
return False
if checkers.check_binary(name=file_path):
return False
if checkers.is_bz2(file_path):
return False
if checkers.is_gzip(file_path):
return False
if checkers.check_zip(file_path):
return False
# Default to copying the file if none of the above are true.
return True
def is_data_index_sample_file(file_path):
"""
Attempt to determine if a .sample file is appropriate for copying to ~/tool-data when
a tool shed repository is being installed into a Galaxy instance.
"""
# Currently most data index files are tabular, so check that first. We'll assume that
# if the file is tabular, it's ok to copy.
if is_column_based(file_path):
return True
# If the file is any of the following, don't copy it.
if checkers.check_html(file_path):
return False
if checkers.check_image(file_path):
return False
if checkers.check_binary(name=file_path):
return False
if checkers.is_bz2(file_path):
return False
if checkers.is_gzip(file_path):
return False
if checkers.check_zip(file_path):
return False
# Default to copying the file if none of the above are true.
return True
def iszip( file_path ):
return checkers.check_zip( file_path )
if not chunk:
break
os.write( fd, chunk )
os.close( fd )
bzipped_file.close()
# Replace the bzipped file with the decompressed file if it's safe to do so
if dataset.type in ( 'server_dir', 'path_paste' ) or not in_place:
dataset.path = uncompressed
else:
shutil.move( uncompressed, dataset.path )
os.chmod(dataset.path, 0644)
dataset.name = dataset.name.rstrip( '.bz2' )
data_type = 'bz2'
if not data_type:
# See if we have a zip archive
is_zipped = check_zip( dataset.path )
if is_zipped:
if link_data_only == 'copy_files':
CHUNK_SIZE = 2 ** 20 # 1Mb
uncompressed = None
uncompressed_name = None
unzipped = False
z = zipfile.ZipFile( dataset.path )
for name in z.namelist():
if name.endswith('/'):
continue
if unzipped:
stdout = 'ZIP file contained more than one file, only the first file was added to Galaxy.'
break
fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_zip_' % dataset.dataset_id, dir=os.path.dirname( output_path ), text=False )
if sys.version_info[:2] >= ( 2, 6 ):
break
os.write(fd, chunk)
os.close(fd)
bzipped_file.close()
# Replace the bzipped file with the decompressed file if it's safe to do so
if dataset.type in ('server_dir',
'path_paste') or not in_place:
dataset.path = uncompressed
else:
shutil.move(uncompressed, dataset.path)
os.chmod(dataset.path, 0644)
dataset.name = dataset.name.rstrip('.bz2')
data_type = 'bz2'
if not data_type:
# See if we have a zip archive
is_zipped = check_zip(dataset.path)
if is_zipped:
if link_data_only == 'copy_files':
CHUNK_SIZE = 2**20 # 1Mb
uncompressed = None
uncompressed_name = None
unzipped = False
z = zipfile.ZipFile(dataset.path)
for name in z.namelist():
if name.endswith('/'):
continue
if unzipped:
stdout = 'ZIP file contained more than one file, only the first file was added to Galaxy.'
break
fd, uncompressed = tempfile.mkstemp(
prefix='data_id_%s_upload_zip_' %
def iszip(file_path):
return checkers.check_zip(file_path)
def main(archive,
archivename,
logfile,
logid,
workdir,
merge,
rm_header=0,
concat=''):
# create a temporary repository
# tmp_dir = tempfile.mkdtemp(dir=os.getcwd())
os.mkdir("decompress_files")
# open log file
mylog = open(logfile, "w")
is_gzipped, is_gzvalid = check_gzip(archive)
is_bzipped, is_bzvalid = check_bz2(archive)
# extract all files in a temp directory
# test if is a zip file
if check_zip(archive):
with zipfile.ZipFile(archive, 'r') as myarchive:
myarchive.extractall("decompress_files")
# test if is a tar file
elif tarfile.is_tarfile(archive):
mytarfile = tarfile.TarFile.open(archive)
mytarfile.extractall("decompress_files")
mytarfile.close()
# test if is a gzip file
elif is_gzipped and is_gzvalid:
mygzfile = gzip.open(archive, 'rb')
myungzippedfile = open(
"decompress_files/" +
os.path.splitext(os.path.basename(archivename))[0], 'wb', 2**20)
for i in iter(lambda: mygzfile.read(2**20), ''):
myungzippedfile.write(i)
myungzippedfile.close()
mygzfile.close()
elif is_bzipped and is_bzvalid:
mybzfile = bz2.BZ2File(archive, 'rb')
myunbzippedfile = open(
"decompress_files/" +
os.path.splitext(os.path.basename(archivename))[0], 'wb', 2**20)
for i in iter(lambda: mybzfile.read(2**20), ''):
myunbzippedfile.write(i)
myunbzippedfile.close()
mybzfile.close()
# test if merge is enable
if merge == "true":
mylog.write("Merge option is enabled with " + str(rm_header) +
" lines to deleted\n\n")
myfinalfile = open(concat, "w")
for myfile in listdirectory("decompress_files"):
myopenfile = open(myfile, "r")
nblinesremove = 0
mylog.write(
os.path.basename(myfile) +
" is extracted from the archive and is added into the result file\n"
)
for line in myopenfile:
# if not equal, don't write
if int(rm_header) != nblinesremove:
nblinesremove = nblinesremove + 1
else:
# write the line into the final file
myfinalfile.write(line)
myfinalfile.close()
shutil.rmtree("decompress_files")
else:
# if merge is disable
mylog.write("Merge option is disabled\n\n")
# move all files (recursively) in the working dir
for myfile in listdirectory("decompress_files"):
myfileclean = myfile.replace(" ", "\ ")
mylog.write(
os.path.basename(myfileclean) +
" is extracted from the archive \n")
fileext = os.path.splitext(myfile)[1].replace(".", "")
# if no extension
if fileext == '':
shutil.move(os.path.abspath(myfile),
os.path.abspath(myfile) + ".txt")
if fileext == 'fa':
shutil.move(os.path.abspath(myfile),
os.path.abspath(myfile).replace(".fa", ".fasta"))
if fileext == 'fq':
shutil.move(os.path.abspath(myfile),
os.path.abspath(myfile).replace(".fq", ".fastq"))
mylog.write(
"\nPlease refresh your history if all files are not present\n")
mylog.close()
