def all_remote_versions(self):
"""
Get all Versions from catalogue archive plus latest version.
:return: list of variables of the type DataSourceVersion
"""
# get from release catalogue archive
archive_path = posixpath.join(self.BASEURL, self.BASEPATH, 'archive')
file_list = downloader.list_ftp_dir(archive_path)
# get names of release catalogue files
release_catalog_list = set(
[x.name for x in file_list if 'RefSeq-release' in x.name])
# get release numbers from names
# RefSeq-release20.catalog.gz => 20
version_numbers = [
int(x.split('-')[1].split('.')[0].replace('release', ''))
for x in release_catalog_list
]
# put in DataSourceVersion, add latest
ds_versions = [DataSourceVersion(x) for x in version_numbers]
ds_versions.append(self.latest_remote_version())
return ds_versions
def latest_remote_version(self):
"""
Versions are named with 'year_month', e.g. '2016_01'.
Data is parsed from 'RELEASE.metalink' file in 'current_release' directory of FTP server.
:return: Latest remote version.
:rtype: DataSourceVersion
"""
current_release_path = posixpath.join(self.UNIPROT_BASEURL,
self.UNIPROT_CURRENT_BASEPATH)
release_file = posixpath.join(current_release_path, 'RELEASE.metalink')
# read XML file from server into string
release_metalink_xml = downloader.get_single_file_ftp(
release_file).read().decode()
# replace xml namespace thing to avoid dealing with namespaces
release_metalink_xml = release_metalink_xml.replace(
' xmlns="', ' xmlnamespace="')
# parse XML
tree = ElementTree.fromstring(release_metalink_xml)
version = tree.find('version').text
return DataSourceVersion(self._date_from_name(version))
def latest_remote_version(self):
"""
Get number of latest release from ftp://ftp.ncbi.nlm.nih.gov/refseq/release/RELEASE_NUMBER.
:return: DataSourceVersion of latest remote version
"""
# returns a BytesIO object
release_file = downloader.get_single_file_ftp(
'ftp://ftp.ncbi.nlm.nih.gov/refseq/release/RELEASE_NUMBER')
# to get the text simply 'read' and 'decode'
release_number = int(release_file.read().decode().rstrip())
return DataSourceVersion(release_number)
def all_remote_versions(self):
"""
Get all versions available on miRBase FTP server.
All versions are a directory in /pub/mirbase.
:return: List of DataSourceVersions available on server.
:rtype: list(DataSourceVersion)
"""
versions = [DataSourceVersion(x) for x in VERSION_2_URL]
return versions
def all_remote_versions(self):
"""
Get all versions available on miRBase FTP server.
All versions are a directory in /pub/mirbase.
:return: List of DataSourceVersions available on server.
:rtype: list(DataSourceVersion)
"""
ftp_list = downloader.list_ftp_dir(self.mirbase_baseurl,
path=self.mirbase_basepath)
versions = [DataSourceVersion(x.name) for x in ftp_list]
return versions
def latest_remote_version(self):
"""
Only the latest version is accessible.
"""
return DataSourceVersion('03-2018')