class GalaxyFileSystem():
def __init__(self, url, user):
u = urlsplit(url)
if u.scheme != 'http' and u.scheme != 'https':
raise ValueError("Invalid name node address")
self.url = urlunparse((u.scheme, u.netloc, '', '', '', ''))
self.localdir = ""
self.prefix = 'GalaxyFS'
self.lddaprefix = 'Libraries'
self.hdaprefix = 'Histories'
self.client = GalaxyInstance(self.url, user)
def normalize_path(self, path):
path = os.path.normpath(path)
if path.startswith(self.prefix):
path = path[len(self.prefix):]
while path and path[0] == os.sep:
path = path[1:]
return os.path.join(self.localdir, path)
def strip_root(self, path):
if path.startswith(self.url):
path = path[len(self.url):]
if not path.startswith(self.localdir):
raise 'Invalid hdfs path. It must start with the root directory'
if not path.startswith(self.localdir):
return path
return path[len(self.localdir):]
def make_fullpath(self, path):
path = self.normalize_path(path)
return os.path.join(self.prefix, path)
def create_folder(self, path):
try:
path = self.normalize_path(path)
parts = pathlib.Path(normalized_path).parts
if len(parts) > 3:
raise ValueError("Galaxy path may have maximum 3 parts.")
if parts[0] == self.lddaprefix:
id = self.client.libraries.create_library(parts[-1])
else:
id = self.client.histories.create_history(parts[-1])
parts[-1] = id
path = os.sep.join(parts)
return self.make_fullpath(path)
except:
return None
return path
def remove(self, path):
try:
path = self.normalize_path(path)
parts = pathlib.Path(normalized_path).parts
if len(parts) == 3:
raise ValueError("Galaxy path may have maximum 3 parts.")
if parts[0] == self.lddaprefix:
id = self.client.libraries.delete_library(library_id=parts[-1])
else:
id = self.client.histories.delete_history(history_id=parts[-1])
except Exception as e:
print(e)
def rename(self, oldpath, newpath):
try:
oldpath = self.normalize_path(oldpath)
newpath = self.normalize_path(newpath)
self.client.rename(oldpath, newpath)
except Exception as e:
print(e)
def get_files(self, path):
path = self.normalize_path(path)
files = []
for f in self.client.list(path):
status = self.client.status(join(path, f), False)
if status['type'] != "DIRECTORY":
files.append(f)
return files
def get_folders(self, path):
try:
path = self.normalize_path(path)
parts = pathlib.Path(normalized_path).parts
if len(parts) > 3:
raise ValueError("Galaxy path may have maximum 3 parts.")
if parts[0] == self.lddaprefix:
id = self.client.libraries.create_library(parts[-1])
else:
id = self.client.histories.create_history(parts[-1])
parts[-1] = id
path = os.sep.join(parts)
return self.make_fullpath(path)
except:
return []
return path
def exists(self, path):
return self.isdir(path) or self.ispath(path)
def isdir(self, path):
path = self.normalize_path(path)
return path == self.lddaprefix or path == self.hdaprefix
def isfile(self, path):
return not self.isdir(path) and self.name_from_id(path)
def read(self, path):
path = self.normalize_path(path)
with self.client.read(path) as reader:
return reader.read().decode('utf-8')
def write(self, path, content):
path = self.normalize_path(path)
self.client.write(path, content)
def name_from_id(self, path):
normalized_path = self.normalize_path(path)
parts = pathlib.Path(normalized_path).parts
if len(parts) == 0:
return ""
elif len(parts) == 1:
return self.lddaprefix if parts[
0] == self.lddaprefix else self.hdaprefix
elif len(parts) == 2:
info = self.client.libraries.get_libraries(
library_id=parts[1]
)[0] if parts[
0] == self.lddaprefix else self.client.histories.get_histories(
history_id=parts[1])[0]
else:
hda_or_ldda = 'ldda' if parts[0] == self.lddaprefix else 'hda'
info = self.client.datasets.show_dataset(
dataset_id=os.path.basename(normalized_path),
hda_ldda=hda_or_ldda)
if info:
return info['name']
def make_json(self, path):
normalized_path = self.normalize_path(path)
if not normalized_path:
return [
self.make_json(self.lddaprefix),
self.make_json(self.hdaprefix)
]
else:
data_json = {
'path': os.path.join(self.url, normalized_path),
'text': self.name_from_id(path)
}
parts = pathlib.Path(normalized_path).parts
if parts[0] == self.lddaprefix:
if len(parts) == 1:
data_json['folder'] = True
libraries = self.client.libraries.get_libraries()
data_json['nodes'] = [
self.make_json(os.path.join(path, fn['id']))
for fn in libraries
]
elif len(parts) == 2:
data_json['folder'] = True
#library = self.client.libraries.get_libraries(library_id = parts[1])
#data_json['nodes'] = [self.make_json(os.path.join(path, fn['id'])) for fn in libraries]
elif parts[0] == self.hdaprefix:
if len(parts) == 1:
data_json['folder'] = True
histories = self.client.histories.get_histories()
data_json['nodes'] = [
self.make_json(os.path.join(path, fn['id']))
for fn in histories
]
elif len(parts) == 2:
data_json['folder'] = True
datasets = self.client.histories.show_matching_datasets(
parts[1])
data_json['nodes'] = [
self.make_json(os.path.join(path, fn['id']))
for fn in datasets
]
return data_json
def save_upload(self, file, fullpath):
localpath = os.path.join(tempfile.gettempdir(),
os.path.basename(fullpath))
if os.path.isfile(localpath):
os.remove(localpath)
try:
file.save(localpath)
if isfile(fullpath):
fullpath = os.path.dirname(fullpath)
self.client.upload(self.normalize_path(fullpath), localpath, True)
except:
pass
def download(self, path):
path = self.normalize_path(path)
status = self.client.status(path, False)
if status is not None and status['type'] == "FILE":
localpath = os.path.join(tempfile.gettempdir(),
os.path.basename(path))
return self.client.download(path, localpath, True)
else:
return None
