def install_annotation_files(anno_root_dir, dl_files=False, extra=None):
"""Download required annotation files.
"""
# create the full gemini data path based on
# the root dir the user provided
if anno_root_dir.endswith(("gemini/data", "gemini/data/", "gemini_data")):
anno_dir = anno_root_dir
elif anno_root_dir.endswith(("gemini", "gemini/")):
anno_dir = os.path.join(anno_root_dir, "data")
else:
anno_dir = os.path.join(anno_root_dir, "gemini", "data")
cur_config = read_gemini_config(allow_missing=True)
cur_config["annotation_dir"] = os.path.abspath(anno_dir)
cur_config["versions"] = anno_versions
write_gemini_config(cur_config)
if dl_files:
if not os.path.exists(anno_dir):
os.makedirs(anno_dir)
if not os.path.isdir(anno_dir):
sys.exit(anno_dir + " is not a valid directory.")
_check_dependencies()
to_dl = anno_files[:]
if extra:
to_dl += [extra_anno_files[x] for x in extra]
_download_anno_files("https://s3.amazonaws.com/gemini-annotations",
to_dl, anno_dir, cur_config)
def install_annotation_files(anno_root_dir, dl_files=False, extra=None):
"""Download required annotation files.
"""
# create the full gemini data path based on
# the root dir the user provided
if anno_root_dir.endswith(("gemini/data", "gemini/data/", "gemini_data")):
anno_dir = anno_root_dir
elif anno_root_dir.endswith(("gemini", "gemini/")):
anno_dir = os.path.join(anno_root_dir, "data")
else:
anno_dir = os.path.join(anno_root_dir, "gemini", "data")
cur_config = read_gemini_config(allow_missing=True)
cur_config["annotation_dir"] = os.path.abspath(anno_dir)
cur_config["versions"] = anno_versions
write_gemini_config(cur_config)
if dl_files:
if not os.path.exists(anno_dir):
os.makedirs(anno_dir)
if not os.path.isdir(anno_dir):
sys.exit(anno_dir + " is not a valid directory.")
_check_dependencies()
to_dl = anno_files[:]
if extra:
to_dl += [extra_anno_files[x] for x in extra]
_download_anno_files("https://s3.amazonaws.com/gemini-annotations",
to_dl, anno_dir, cur_config)
def install_annotation_files(anno_root_dir):
"""Download required annotation files.
"""
# create the full gemini data path based on
# the root dir the user provided
if anno_root_dir.endswith(("gemini", "gemini/")):
anno_dir = os.path.join(anno_root_dir, "data")
else:
anno_dir = os.path.join(anno_root_dir, "gemini", "data")
if not os.path.exists(anno_dir):
os.makedirs(anno_dir)
cur_config = read_gemini_config(allow_missing=True)
# download and install each of the annotation files
for orig in anno_files:
if orig.endswith(".gz"):
dls = [orig, "%s.tbi" % orig]
else:
dls = [orig]
for dl in dls:
url = "http://people.virginia.edu/~arq5x/files/gemini/annotations/{fname}".format(fname=dl)
_download_to_dir(url, anno_dir, anno_versions.get(orig, 1),
cur_config.get("versions", {}).get(orig, 1))
cur_config["annotation_dir"] = anno_dir
cur_config["versions"] = anno_versions
write_gemini_config(cur_config)
def _download_anno_files(base_url, file_names, anno_dir, cur_config):
"""Download and install each of the annotation files
"""
for orig in file_names:
if orig.endswith(".gz"):
dls = [orig, "%s.tbi" % orig]
else:
dls = [orig]
for dl in dls:
url = "{base_url}/{fname}".format(fname=dl, base_url=base_url)
_download_to_dir(url, anno_dir, anno_versions.get(orig, 1),
cur_config.get("versions", {}).get(orig, 1))
cur_config["annotation_dir"] = anno_dir
cur_config["versions"] = anno_versions
write_gemini_config(cur_config)
def _download_anno_files(base_url, file_names, anno_dir, cur_config):
"""Download and install each of the annotation files
"""
cur_config["annotation_dir"] = os.path.abspath(anno_dir)
cur_config["versions"] = anno_versions
write_gemini_config(cur_config)
for orig in file_names:
if orig.endswith(".gz"):
dls = [orig, "%s.tbi" % orig]
else:
dls = [orig]
for dl in dls:
url = "{base_url}/{fname}".format(fname=dl, base_url=base_url)
_download_to_dir(url, anno_dir, anno_versions.get(orig, 1),
cur_config.get("versions", {}).get(orig, 1))
def install_annotation_files(anno_root_dir):
"""Download required annotation files.
"""
# create the full gemini data path based on
# the root dir the user provided
if anno_root_dir.endswith(("gemini", "gemini/")):
anno_dir = os.path.join(anno_root_dir, "data")
else:
anno_dir = os.path.join(anno_root_dir, "gemini", "data")
if not os.path.exists(anno_dir):
os.makedirs(anno_dir)
cur_config = read_gemini_config(allow_missing=True)
cur_config["annotation_dir"] = anno_dir
write_gemini_config(cur_config)
# download and install each of the annotation files
for dl in anno_files:
url = "http://people.virginia.edu/~arq5x/files/gemini/annotations/{fname}".format(
fname=dl)
_download_to_dir(url, anno_dir)