def handler(self, args):
access_token = args.access_token
project = get_active_project()
oauth2_section = DEFAULT_OAUTH2_SECTION
token_section = DEFAULT_TOKEN_SECTION
config = read_config(project)
if not access_token:
access_token = config_get(config.get, token_section,
'access_token')
endpoint = config_get(config.get, oauth2_section, 'endpoint')
api = API(access_token, endpoint=endpoint, timeout=18.)
try:
result = api.aggregate_omics_data(args.data_element_id,
args.time_dimension,
args.start_time,
end_time=args.end_time,
biosample_id=args.biosample_id,
interval=args.interval,
periods=args.periods)
except APIError as e:
output('[red]请求失败：[/red]')
output_json(e.result)
sys.exit(1)
output('[green]请求成功：[/green]')
output_json(result, cls=ModelEncoder)
def handler(self, args):
access_token = args.access_token
filepath = args.filepath
project = get_active_project()
oauth2_section = DEFAULT_OAUTH2_SECTION
token_section = DEFAULT_TOKEN_SECTION
config = read_config(project)
if not access_token:
access_token = config_get(config.get, token_section,
'access_token')
endpoint = config_get(config.get, oauth2_section, 'endpoint')
api = API(access_token, endpoint=endpoint, timeout=18.)
if not posixpath.isfile(filepath):
output('[red]只能上传文件[/red]')
sys.exit(1)
filename = args.filename
cmk_id = args.cmk_id
if not filename:
filename = posixpath.split(filepath)[1]
message = '正在上传文件 {}'.format(filepath)
with console.status(message, spinner='earth'):
try:
with open(filepath, 'rb') as fp:
object_name = api.upload(filename, fp, cmk_id=cmk_id)
except APIError as e:
output('[red]请求失败：[/red]')
output_json(e.result)
sys.exit(1)
output('[green]文件上传成功，存储位置：[/green]{}'.format(object_name))
def upload_model_expfs(self, args):
home = get_home()
project = get_active_project()
config_path = self.get_model_config_path()
config = get_config_parser(config_path)
section_name = DEFAULT_MODEL_SECTION
model_id = config_get(config.get, section_name, 'model_id')
oauth2_section = DEFAULT_OAUTH2_SECTION
token_section = DEFAULT_TOKEN_SECTION
config = read_config(project)
access_token = config_get(config.get, token_section, 'access_token')
endpoint = config_get(config.get, oauth2_section, 'endpoint')
api = API(access_token,
endpoint=endpoint,
timeout=DEFAULT_MODEL_TIMEOUT)
try:
result = api.upload_model_expfs(model_id, 'uploadtest.zip')
except APIError as e:
output('[red]上传模型扩展集失败：[/red]')
output_json(e.result)
sys.exit(1)
task_id = result.task_id
output('上传模型扩展集任务：{}'.format(task_id))
task_path = join(home, '.bge', 'expfs.task_id')
with open(task_path, 'w') as f:
f.write(task_id)
output('上传模型扩展集任务返回结果：')
progress = self._wait_model_task(api, task_id, task_path)
if 'SUCCESS' == progress:
output('[green]模型 {} 上传模型扩展集成功。'.format(model_id))
elif 'FAILURE' == progress:
output('[red]模型 {} 上传模型扩展集失败。'.format(model_id))
elif 'REVOKED' == progress:
output('[white]模型 {} 上传模型扩展集任务已被撤销。'.format(model_id))
def release_doc(self, args):
project = get_active_project()
config = read_config(project)
access_token = config_get(
config.get, DEFAULT_TOKEN_SECTION, 'access_token')
endpoint = config_get(config.get, DEFAULT_OAUTH2_SECTION, 'endpoint')
api = API(
access_token, endpoint=endpoint, timeout=DEFAULT_MODEL_TIMEOUT)
input_value = input('？请输入需要发布的 json 文件路径：')
if input_value:
if not exists(input_value):
output('[red]文件路径：{} 有误，请检查。[/red]'.format(input_value))
sys.exit(1)
doc_data = json.load(open(input_value))
doc_tab = doc_data['doc_tab']
model_id = doc_data['model_id']
doc_content = doc_data['doc_content']
try:
result = api.upload_model_doc(doc_tab, model_id, doc_content)
except APIError as e:
output('[red]模型文档上传失败：[/red]')
output_json(e.result)
sys.exit(1)
output('模型文档上传结果：')
output_json(result)
else:
output('[red]请输入需要预览的文档路径[/red]')
sys.exit(1)
def handler(self, args):
access_token = args.access_token
namespace = args.namespace
biosample_id = args.biosample_id
project = get_active_project()
oauth2_section = DEFAULT_OAUTH2_SECTION
token_section = DEFAULT_TOKEN_SECTION
config = read_config(project)
if not access_token:
access_token = config_get(config.get, token_section,
'access_token')
endpoint = config_get(config.get, oauth2_section, 'endpoint')
api = API(access_token, endpoint=endpoint, timeout=18.)
try:
result = api.get_data_items(namespace,
biosample_id,
collection_id=args.collection_id,
data_element_ids=args.data_element_ids,
next_page=args.next_page)
except APIError as e:
output('[red]请求失败：[/red]')
output_json(e.result)
sys.exit(1)
output('[green]请求成功：[/green]')
output_json(result, cls=ModelEncoder)
def list_projects(args=None):
active_project = get_active_project()
config_dir = get_config_dir()
projects = []
for filename in os.listdir(config_dir):
name, ext = splitext(filename)
if ext != '.ini':
continue
projects.append(name)
projects.sort()
table = Table(
title='通过 bge workon <NAME> 切换生效配置',
expand=True,
show_header=True,
header_style="magenta"
)
table.add_column(
"项目",
justify="center",
style="dim"
)
table.add_column("使用中", justify="center")
if active_project in projects:
table.add_row(
active_project,
'Y',
style="green",
)
for project in projects:
if project == active_project:
continue
table.add_row(project, '-')
console.print(table)
def handler(self, args):
access_token = args.access_token
data_element_id = args.data_element_id
project = get_active_project()
oauth2_section = DEFAULT_OAUTH2_SECTION
token_section = DEFAULT_TOKEN_SECTION
config = read_config(project)
if not access_token:
access_token = config_get(config.get, token_section,
'access_token')
endpoint = config_get(config.get, oauth2_section, 'endpoint')
api = API(access_token, endpoint=endpoint, timeout=18.)
try:
result = api.get_range_stream(data_element_id,
biosample_id=args.biosample_id,
start_time=args.start_time,
end_time=args.end_time,
sort_direction=args.sort_direction,
next_page=args.next_page,
limit=args.limit)
except APIError as e:
output('[red]请求失败：[/red]')
output_json(e.result)
sys.exit(1)
output('[green]请求成功：[/green]')
output_json(result, cls=ModelEncoder)
def handler(self, args):
access_token = args.access_token
biosample_id = args.biosample_id
catalog = args.catalog
data_type = args.data_type
project = get_active_project()
oauth2_section = DEFAULT_OAUTH2_SECTION
token_section = DEFAULT_TOKEN_SECTION
config = read_config(project)
if not access_token:
access_token = config_get(config.get, token_section,
'access_token')
endpoint = config_get(config.get, oauth2_section, 'endpoint')
api = API(access_token, endpoint=endpoint, timeout=18.)
try:
result = api.get_gene_abundance(biosample_id,
catalog,
data_type,
ids=args.ids,
next_page=args.next_page,
limit=args.limit)
except APIError as e:
output('[red]请求失败：[/red]')
output_json(e.result)
sys.exit(1)
output('[green]请求成功：[/green]')
output_json(result, cls=ModelEncoder)
def show_project(self, args):
project = args.project
if not project:
project = get_active_project()
project = project.lower()
config_path = get_config_path(project)
title = 'BGE 开放平台 Python SDK 配置文件'
output_file(config_path, title=title, subtitle=config_path)
def run_model(self, args):
params = {}
if args.file:
filepath = args.file
if not exists(filepath):
output('文件不存在：{}'.format(filepath))
sys.exit(1)
if isdir(filepath):
output('存在文件夹：{}'.format(filepath))
sys.exit(1)
with open(filepath, 'r') as fp:
params = json.load(fp)
elif args.args:
params = dict(args.args)
draft = args.draft
test = args.test
project = get_active_project()
config_path = self.get_model_config_path()
config = get_config_parser(config_path)
section_name = DEFAULT_MODEL_SECTION
model_id = config_get(config.get, section_name, 'model_id')
oauth2_section = DEFAULT_OAUTH2_SECTION
token_section = DEFAULT_TOKEN_SECTION
config = read_config(project)
access_token = config_get(config.get, token_section, 'access_token')
endpoint = config_get(config.get, oauth2_section, 'endpoint')
api = API(access_token,
endpoint=endpoint,
timeout=DEFAULT_MODEL_TIMEOUT)
try:
if draft is True:
result = api.invoke_draft_model(model_id, **params)
elif test is True:
port = args.port
api = API(access_token,
endpoint='{}:{}'.format(TEST_SERVER_ENDPOINT, port),
timeout=DEFAULT_MODEL_TIMEOUT)
result = api.invoke_model(model_id, **params)
else:
result = api.invoke_model(model_id, **params)
except APIError as e:
output('[red]模型运行失败：[/red]')
output_json(e.result)
sys.exit(1)
output('[green]模型返回值：[/green]')
output_json(result.json())
def remove_project(self, args):
project = args.project.lower()
activate_project = get_active_project()
if activate_project == project:
output(
'[red]无法删除正在使用的配置，请先使用 bge workon 切换至其他项目[/red]'
)
sys.exit(1)
config_path = get_config_path(project)
if not confirm(prompt='确认删除配置项目 {}？'.format(project)):
output('已取消删除')
sys.exit(0)
try:
os.unlink(config_path)
except (IOError, OSError):
pass
output('[green]成功删除配置项目[/green] {}'.format(project))
def model_versions(self, args):
limit = args.limit
next_page = args.next_page
project = get_active_project()
config_path = self.get_model_config_path()
config = get_config_parser(config_path)
section_name = DEFAULT_MODEL_SECTION
model_id = config_get(config.get, section_name, 'model_id')
oauth2_section = DEFAULT_OAUTH2_SECTION
token_section = DEFAULT_TOKEN_SECTION
config = read_config(project)
access_token = config_get(config.get, token_section, 'access_token')
endpoint = config_get(config.get, oauth2_section, 'endpoint')
api = API(access_token,
endpoint=endpoint,
timeout=DEFAULT_MODEL_TIMEOUT)
try:
result = api.model_versions(model_id,
limit=limit,
next_page=next_page)
except APIError as e:
output('[red]获取模型版本列表失败：[/red]')
output_json(e.result)
sys.exit(1)
output('第 {} 页，模型 {} 已发布版本：'.format(next_page or 1, model_id))
output('...')
length = None
items = result['result']
for item in items:
version = item['version']
message = item['message']
create_time = datetime.fromtimestamp(item['create_time'])
if length is None:
length = len(str(version))
output('发布时间：{}，版本号：{}，发布记录：{}'.format(create_time,
str(version).rjust(length),
message))
output('...')
size = len(items)
if size == 0 or size < limit or next_page == result['next_page']:
output('下一页：无')
else:
output('下一页：{}'.format(result['next_page']))
def handler(self, args):
access_token = args.access_token
project = get_active_project()
oauth2_section = DEFAULT_OAUTH2_SECTION
token_section = DEFAULT_TOKEN_SECTION
config = read_config(project)
if not access_token:
access_token = config_get(config.get, token_section,
'access_token')
endpoint = config_get(config.get, oauth2_section, 'endpoint')
api = API(access_token, endpoint=endpoint, timeout=18.)
try:
result = api.get_user()
except APIError as e:
output('[red]请求失败：[/red]')
output_json(e.result)
sys.exit(1)
output('[green]请求成功：[/green]')
output_json(result, cls=ModelEncoder)
def handler(self, args):
project = get_active_project()
config_path = get_config_path(project)
config_parser = get_config_parser(config_path)
oauth2_section = constants.DEFAULT_OAUTH2_SECTION
client_id = config_get(config_parser.get, oauth2_section, 'client_id')
client_secret = config_get(config_parser.get, oauth2_section,
'client_secret')
endpoint = config_get(config_parser.get, oauth2_section, 'endpoint')
redirect_uri = args.redirect_uri
oauth2 = OAuth2(client_id,
client_secret,
endpoint=endpoint,
timeout=60.)
authorization_url = oauth2.get_authorization_url(redirect_uri,
state=args.state,
scopes=args.scopes)
output('授权页面地址为：{}'.format(authorization_url))
output('浏览器启动中...')
webbrowser.open(authorization_url, new=1, autoraise=False)
output('请在浏览器登录并完成授权，复制跳转后页面链接的 code 参数并关闭浏览器。\n')
while True:
code = Prompt.ask('请输入浏览器回调地址携带的参数 [cyan]code[/cyan]')
code = code.strip()
if code:
break
output('[red]参数 code 不能为空[/red]')
try:
token_result = oauth2.exchange_authorization_code(
code, redirect_uri=redirect_uri)
except APIError as e:
output('[red]令牌获取出错：[/red]')
output_json(e.result)
sys.exit(1)
self._write_token_config(project, token_result)
output('[green]令牌内容如下[/green]')
content = []
for key in [
'access_token', 'token_type', 'expires_in', 'scope',
'refresh_token'
]:
content.append('{} = {}'.format(key, token_result[key]))
output_syntax('\n'.join(content), lexer='INI')
def handler(self, args):
access_token = args.access_token
object_name = args.object_name
mode = args.mode
project = get_active_project()
oauth2_section = DEFAULT_OAUTH2_SECTION
token_section = DEFAULT_TOKEN_SECTION
config = read_config(project)
if not access_token:
access_token = config_get(config.get, token_section,
'access_token')
endpoint = config_get(config.get, oauth2_section, 'endpoint')
api = API(access_token, endpoint=endpoint, timeout=18.)
filename = posixpath.split(object_name)[1]
if filename == '':
output('[red]下载失败，object_name 不是文件：{}[/red]'.format(
repr(object_name)))
sys.exit(1)
if posixpath.exists(filename):
basename, suffix = posixpath.splitext(filename)
i = 1
while True:
new_basename = '{} ({})'.format(basename, i)
filename = ''.join((new_basename, suffix))
if not posixpath.exists(filename):
break
i += 1
message = '正在下载 {}'.format(object_name)
with console.status(message, spinner='earth'):
try:
with open(filename, mode) as fp:
api.download(object_name,
fp,
region=args.region,
expiration_time=args.expiration_time,
chunk_size=args.chunk_size)
except APIError as e:
output('[red]请求失败：[/red]')
output_json(e.result)
sys.exit(1)
output('[green]文件下载成功：[/green]{}'.format(filename))
def handler(self, args):
access_token = args.access_token
project = get_active_project()
oauth2_section = DEFAULT_OAUTH2_SECTION
token_section = DEFAULT_TOKEN_SECTION
config = read_config(project)
if not access_token:
access_token = config_get(config.get, token_section,
'access_token')
endpoint = config_get(config.get, oauth2_section, 'endpoint')
api = API(access_token, endpoint=endpoint, timeout=18.)
dirpath = args.dirpath
cmk_id = args.cmk_id
files = []
for filename in os.listdir(dirpath):
filepath = join(dirpath, filename)
if isfile(filepath):
files.append(filepath)
if not files:
output('[red]文件夹中没有可上传的文件[/red]')
sys.exit(1)
message = '正在上传目录 {}'.format(dirpath)
with console.status(message, spinner='earth'):
try:
object_names = api.upload_dir(dirpath, cmk_id=cmk_id)
except APIError as e:
output('[red]请求失败：[/red]')
output_json(e.result)
sys.exit(1)
output('[green]文件上传成功：[/green]')
table = Table(title="文件列表",
expand=True,
show_header=True,
header_style="magenta")
table.add_column("序号", style="cyan", no_wrap=True)
table.add_column("存储位置", style="magenta", overflow='fold')
for i, object_name in enumerate(object_names, 1):
table.add_row(str(i), object_name)
console.print(table)
def handler(self, args):
project = get_active_project()
config_path = get_config_path(project)
config_parser = get_config_parser(config_path)
oauth2_section = constants.DEFAULT_OAUTH2_SECTION
client_id = config_get(config_parser.get, oauth2_section, 'client_id')
client_secret = config_get(
config_parser.get, oauth2_section, 'client_secret')
endpoint = config_get(config_parser.get, oauth2_section, 'endpoint')
oauth2 = OAuth2(
client_id, client_secret, endpoint=endpoint, timeout=60.)
try:
token_result = oauth2.get_credentials_token()
except APIError as e:
output('[red]令牌获取出错：[/red]')
output_json(e.result)
sys.exit(1)
self._write_token_config(project, token_result)
console.rule('[green]令牌内容如下[/green]')
content = []
for key in ['access_token', 'token_type', 'expires_in', 'scope']:
content.append('{} = {}'.format(key, token_result[key]))
output_syntax('\n'.join(content), lexer='INI')
def rollback_model(self, args):
version = args.version
home = get_home()
project = get_active_project()
config_path = self.get_model_config_path()
config = get_config_parser(config_path)
section_name = DEFAULT_MODEL_SECTION
model_id = config_get(config.get, section_name, 'model_id')
oauth2_section = DEFAULT_OAUTH2_SECTION
token_section = DEFAULT_TOKEN_SECTION
config = read_config(project)
access_token = config_get(config.get, token_section, 'access_token')
endpoint = config_get(config.get, oauth2_section, 'endpoint')
api = API(access_token,
endpoint=endpoint,
timeout=DEFAULT_MODEL_TIMEOUT)
try:
result = api.rollback_model(model_id, version)
except APIError as e:
output('[red]模型回滚失败：[/red]')
output_json(e.result)
sys.exit(1)
task_id = result.task_id
output('模型回滚任务：{}'.format(task_id))
task_path = join(home, '.bge', 'task_id')
with open(task_path, 'w') as f:
f.write(task_id)
progress = self._wait_model_task(api, task_id, task_path)
if 'SUCCESS' == progress:
output('[green]模型 {} 灰度版已成功回滚至版本 {}。[/green]'.format(
model_id, version))
elif 'FAILURE' == progress:
output('[red]模型 {} 灰度回滚至版本 {} 失败。任务结果：{}[/red]'.format(
model_id, version, result))
elif 'REVOKED' == progress:
output('[white]模型 {} 灰度回滚至版本 {} 任务已被撤销失败。[/white]'.format(
model_id, version))
def publish_model(self, args):
"""发布模型到稳定版"""
message = args.message
project = get_active_project()
config_path = self.get_model_config_path()
config = get_config_parser(config_path)
section_name = DEFAULT_MODEL_SECTION
model_id = config_get(config.get, section_name, 'model_id')
oauth2_section = DEFAULT_OAUTH2_SECTION
token_section = DEFAULT_TOKEN_SECTION
config = read_config(project)
access_token = config_get(config.get, token_section, 'access_token')
endpoint = config_get(config.get, oauth2_section, 'endpoint')
api = API(access_token,
endpoint=endpoint,
timeout=DEFAULT_MODEL_TIMEOUT)
try:
result = api.publish_model(model_id, message)
except APIError as e:
output('[red]模型发布失败：[/red]')
output_json(e.result)
sys.exit(1)
output('[green]模型 {} 稳定版已成功发布。\n版本号：{}。[/green]'.format(
model_id, result['version']))
def handler(self, args):
access_token = args.access_token
params = vars(args)
for field in NOT_PARAM_FIELDS:
params.pop(field, None)
project = get_active_project()
oauth2_section = DEFAULT_OAUTH2_SECTION
token_section = DEFAULT_TOKEN_SECTION
config = read_config(project)
if not access_token:
access_token = config_get(config.get, token_section, 'access_token')
endpoint = config_get(config.get, oauth2_section, 'endpoint')
api = API(access_token, endpoint=endpoint, timeout=18.)
try:
result = api.get_samples(**params)
except APIError as e:
output('[red]请求失败：[/red]')
output_json(e.result)
sys.exit(1)
output('[green]请求成功：[/green]')
output_json(
result,
cls=ModelEncoder
)
def handler(self, args):
project = get_active_project()
output('当前正在配置 {}：\n'.format(project))
config_path = get_config_path(project, check_exists=False)
self._new_project(config_path)
def deploy_model(self, args):
"""部署模型"""
ignore_source = args.ignore_source
home = get_home()
project = get_active_project()
config_path = self.get_model_config_path()
config = get_config_parser(config_path)
section_name = DEFAULT_MODEL_SECTION
model_id = config_get(config.get, section_name, 'model_id')
timestr = datetime.now().strftime('%Y%m%d%H%M%S%f')
randstr = uuid4().hex
zip_filename = '{}.{}.{}.zip'.format(model_id, timestr, randstr)
params = {}
params['runtime'] = config_get(config.get, section_name, 'runtime')
params['memory_size'] = config_get(config.getint, section_name,
'memory_size')
params['timeout'] = config_get(config.getint, section_name, 'timeout')
oauth2_section = DEFAULT_OAUTH2_SECTION
token_section = DEFAULT_TOKEN_SECTION
config = read_config(project)
access_token = config_get(config.get, token_section, 'access_token')
endpoint = config_get(config.get, oauth2_section, 'endpoint')
api = API(access_token,
endpoint=endpoint,
timeout=DEFAULT_MODEL_TIMEOUT)
object_name = None
if not ignore_source:
ignore_path = join(home, BGE_IGNORE_FILE)
if not exists(ignore_path):
output('未发现 .bgeignore 文件，初始化 {} ...'.format(ignore_path))
open(ignore_path, 'w').write(BGEIGNORE_TEMPLATE)
minify_path = join(home, BGE_MINIFY_FILE)
if not exists(minify_path):
output('未发现 .bgeminify 文件，初始化 {} ...'.format(minify_path))
open(minify_path, 'w').write(BGEMINIFY_TEMPLATE)
output('开始打包模型源码...')
zip_tmpdir = join(home, '.bge', 'tmp')
if not exists(zip_tmpdir):
os.makedirs(zip_tmpdir)
with tempfile.NamedTemporaryFile(suffix='.zip',
prefix='model-',
dir=zip_tmpdir,
delete=False) as tmp:
with zipfile.ZipFile(tmp.name, 'w', ZIP_COMPRESSION) as zf:
self._zip_codedir(home, zf)
tmp.flush()
tmp.seek(0, 2)
size = tmp.tell()
tmp.seek(0)
human_size = human_byte(size)
if size > 100 * 1024 * 1024:
output('打包后 zip 文件大小为 {}，最大限制 100MB'.format(human_size))
exit(1)
output('打包成功：{}'.format(tmp.name))
output('文件大小：{}'.format(human_size))
output('开始上传模型源码...')
try:
object_name = api.upload(zip_filename, tmp)
except APIError as e:
output('[red]上传模型源码失败：[/red]')
output_json(e.result)
sys.exit(1)
output('[green]上传成功[green]')
with console.status('模型部署中...', spinner='earth'):
try:
result = api.deploy_model(model_id,
object_name=object_name,
**params)
except APIError as e:
output('[red]部署模型失败：[/red]')
output_json(e.result)
sys.exit(1)
task_id = result.task_id
output('模型部署任务：{}'.format(task_id))
task_path = join(home, '.bge', 'task_id')
with open(task_path, 'w') as f:
f.write(task_id)
output('模型部署任务返回结果：')
progress = self._wait_model_task(api, task_id, task_path)
if 'SUCCESS' == progress:
output('[green]模型 {} 灰度部署成功。'.format(model_id))
elif 'FAILURE' == progress:
output('[red]模型 {} 灰度部署失败。任务结果：{}'.format(model_id, result))
elif 'REVOKED' == progress:
output('[white]模型 {} 灰度部署任务已被撤销。'.format(model_id))
