本文整理汇总了Python中biokbase.workspace.client.Workspace.copy_object方法的典型用法代码示例。如果您正苦于以下问题：Python Workspace.copy_object方法的具体用法？Python Workspace.copy_object怎么用？Python Workspace.copy_object使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类biokbase.workspace.client.Workspace的用法示例。
在下文中一共展示了Workspace.copy_object方法的1个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: filter_genes
# 需要导入模块: from biokbase.workspace.client import Workspace [as 别名]
# 或者: from biokbase.workspace.client.Workspace import copy_object [as 别名]
#.........这里部分代码省略.........
## checking genelist
with open("{0}/{1}".format(self.RAWEXPR_DIR, self.GENELST_FN),'r') as glh:
gl = glh.readlines()
gl = [x.strip('\n') for x in gl]
if(len(gl) < 1) :
self.logger.error("No genes are selected")
return empty_results("Increase p_value or specify num_features", expr,self.__WS_URL, param, self.logger, ws)
#sys.exit(4)
## Upload FVE
# change workspace to be the referenced object's workspace_name because it may not be in the same working ws due to referencing
# Updates: change missing genome handling strategy by copying reference to working workspace
cmd_upload_expr = [self.TSV_2_FVE, '--workspace_service_url', self.__WS_URL,
'--object_name', param['out_expr_object_name'],
'--working_directory', self.FINAL_DIR,
'--input_directory', self.FLTRD_DIR,
'--output_file_name', self.FINAL_FN
]
tmp_ws = param['workspace_name']
if 'genome_ref' in expr:
obj_infos = ws.get_object_info_new({"objects": [{'ref':expr['genome_ref']}]})[0]
if len(obj_infos) < 1:
self.logger.error("Couldn't find {0} from the workspace".format(expr['genome_ref']))
raise Exception("Couldn't find {0} from the workspace".format(expr['genome_ref']))
#tmp_ws = "{0}".format(obj_infos[7])
self.logger.info("{0} => {1} / {2}".format(expr['genome_ref'], obj_infos[7], obj_infos[1]))
if obj_infos[7] != param['workspace_name']:
#we need to copy it from the other workspace
try:
self.logger.info("trying to copy the referenced genome object : {0}".format(expr['genome_ref']))
ws.copy_object({'from' : {'ref' : expr['genome_ref']},'to' : {'workspace': param['workspace_name'], 'name' : obj_infos[1]}})
# add genome_object_name only after successful copy
cmd_upload_expr.append('--genome_object_name')
cmd_upload_expr.append(obj_infos[1])
except:
# no permission or any issues... then, give up providing genome reference
self.logger.info("".join(traceback.format_exc()))
pass
else:
# it is local... we can simply add reference without copying genome
cmd_upload_expr.append('--genome_object_name')
cmd_upload_expr.append(obj_infos[1])
# updated ws name
cmd_upload_expr.append('--workspace_name')
cmd_upload_expr.append(tmp_ws)
self.logger.info(" ".join(cmd_upload_expr))
tool_process = subprocess.Popen(" ".join(cmd_upload_expr), stderr=subprocess.PIPE, shell=True, env=eenv)
stdout, stderr = tool_process.communicate()
if stdout is not None and len(stdout) > 0:
self.logger.info(stdout)
if stderr is not None and len(stderr) > 0:
self.logger.info(stderr)
with open("{0}/{1}".format(self.FINAL_DIR,self.FINAL_FN),'r') as et:
eo = json.load(et)
if 'description' not in expr: