snakemake.remote.EGA: NameError: name 'self' is not defined

Question

我想使用 snakemake 实用程序 (5.6.0) 来使用存储在 EGA 上的文件。首先我想尝试一下官方文档中写的代码，所以我尝试了这个：

import snakemake.remote.EGA as EGA

ega = EGA.RemoteProvider()

rule get_remote_file_ega:
   input:
       ega.remote("ega/dataset_id/foo.bam")
   output:
       "data/foo.bam"
   shell:
       "cp {input} {output}"

在执行脚本之前，我根据需要创建了环境变量（EGA_USERNAME 和 EGA_PASSWORD）。

然后我得到以下错误：

me:~/scripts$ snakemake -s test_ega.smk
Building DAG of jobs...
Traceback (most recent call last):
  File "/home/puissant/miniconda3/lib/python3.7/site-packages/snakemake/__init__.py", line 551, in snakemake
    export_cwl=export_cwl)
  File "/home/puissant/miniconda3/lib/python3.7/site-packages/snakemake/workflow.py", line 433, in execute
    dag.init()
  File "/home/puissant/miniconda3/lib/python3.7/site-packages/snakemake/dag.py", line 122, in init
    job = self.update([job], progress=progress)
  File "/home/puissant/miniconda3/lib/python3.7/site-packages/snakemake/dag.py", line 603, in update
    progress=progress)
  File "/home/puissant/miniconda3/lib/python3.7/site-packages/snakemake/dag.py", line 655, in update_
    missing_input = job.missing_input
  File "/home/puissant/miniconda3/lib/python3.7/site-packages/snakemake/jobs.py", line 396, in missing_input
    for f in self.input
  File "/home/puissant/miniconda3/lib/python3.7/site-packages/snakemake/jobs.py", line 397, in <genexpr>
    if not f.exists and not f in self.subworkflow_input)
  File "/home/puissant/miniconda3/lib/python3.7/site-packages/snakemake/io.py", line 208, in exists
    return self.exists_remote
  File "/home/puissant/miniconda3/lib/python3.7/site-packages/snakemake/io.py", line 119, in wrapper
    v = func(self, *args, **kwargs)
  File "/home/puissant/miniconda3/lib/python3.7/site-packages/snakemake/io.py", line 258, in exists_remote
    return self.remote_object.exists()
  File "/home/puissant/miniconda3/lib/python3.7/site-packages/snakemake/remote/EGA.py", line 173, in exists
    return self.parts.path in self.provider.get_files(self.parts.dataset)
  File "/home/puissant/miniconda3/lib/python3.7/site-packages/snakemake/remote/EGA.py", line 126, in get_files
    "data/metadata/datasets/{dataset}/files".format(dataset=dataset))
  File "/home/puissant/miniconda3/lib/python3.7/site-packages/snakemake/remote/EGA.py", line 96, in api_request
    headers["Authorization"] = "Bearer {}".format(self.token)
  File "/home/puissant/miniconda3/lib/python3.7/site-packages/snakemake/remote/EGA.py", line 77, in token
    self._login()
  File "/home/puissant/miniconda3/lib/python3.7/site-packages/snakemake/remote/EGA.py", line 45, in _login
    "client_id"    : self._client_id(),
  File "/home/puissant/miniconda3/lib/python3.7/site-packages/snakemake/remote/EGA.py", line 151, in _client_id
    return self._credentials("EGA_CLIENT_ID")
NameError: name 'self' is not defined

涉及的部分代码在那里（EGA.py第151行）：

1   @classmethod
2   def _client_id(cls):
3         return self._credentials("EGA_CLIENT_ID")

错误可能来自第 3 行的 "self" 而不是 "cls" 吗？因为在将其更改为 "cls" 后，错误移至下一个块，以相同的方式构建。我对python对象的理解有限，希望不要说出天大的废话

我是否忘记或误解了任何步骤？

Answer 1

你是对的，你应该使用 cls（这里大概代表 'class'）而不是 self。 self 通常是用于类实例的名称，即对象。如果您在函数的其他地方使用 self，则需要将它们切换为 cls。

snakemake.remote.EGA: NameError: name 'self' is not defined

snakemake.remote.EGA: NameError: name 'self' is not defined

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