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AlexsLemonade / refinebio

Refine.bio harmonizes petabytes of publicly available biological data into ready-to-use datasets for cancer researchers and AI/ML scientists.
https://www.refine.bio/
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Fix downloader_no_op_tests MissingSchema exception #3214

Closed arkid15r closed 1 year ago

arkid15r commented 1 year ago

Context

In order to restore staging/prod deploy process CI/CD tests need to be fixed.

Problem or idea

2023-02-16 00:58:52,759 local data_refinery_workers.downloaders.sra ERROR [downloader_job: 9]: Exception caught while downloading file.
Traceback (most recent call last):
  File "/usr/local/lib/python3.8/dist-packages/data_refinery_common/utils.py", line 407, in download_file
    with requests.get(download_url, stream=True) as r:
  File "/usr/local/lib/python3.8/dist-packages/requests/api.py", line 73, in get
    return request("get", url, params=params, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/requests/api.py", line 59, in request
    return session.request(method=method, url=url, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/requests/sessions.py", line 573, in request
    prep = self.prepare_request(req)
  File "/usr/local/lib/python3.8/dist-packages/requests/sessions.py", line 484, in prepare_request
    p.prepare(
  File "/usr/local/lib/python3.8/dist-packages/requests/models.py", line 368, in prepare
    self.prepare_url(url, params)
  File "/usr/local/lib/python3.8/dist-packages/requests/models.py", line 439, in prepare_url
    raise MissingSchema(
requests.exceptions.MissingSchema: Invalid URL 'some_path': No scheme supplied. Perhaps you meant https://some_path?

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/lib/python3.8/dist-packages/data_refinery_common/utils.py", line 407, in download_file
    with requests.get(download_url, stream=True) as r:
  File "/usr/local/lib/python3.8/dist-packages/requests/api.py", line 73, in get
    return request("get", url, params=params, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/requests/api.py", line 59, in request
    return session.request(method=method, url=url, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/requests/sessions.py", line 573, in request
    prep = self.prepare_request(req)
  File "/usr/local/lib/python3.8/dist-packages/requests/sessions.py", line 484, in prepare_request
    p.prepare(
  File "/usr/local/lib/python3.8/dist-packages/requests/models.py", line 368, in prepare
    self.prepare_url(url, params)
  File "/usr/local/lib/python3.8/dist-packages/requests/models.py", line 439, in prepare_url
    raise MissingSchema(
requests.exceptions.MissingSchema: Invalid URL 'some_path': No scheme supplied. Perhaps you meant https://some_path?

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/lib/python3.8/dist-packages/data_refinery_common/utils.py", line 407, in download_file
    with requests.get(download_url, stream=True) as r:
  File "/usr/local/lib/python3.8/dist-packages/requests/api.py", line 73, in get
    return request("get", url, params=params, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/requests/api.py", line 59, in request
    return session.request(method=method, url=url, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/requests/sessions.py", line 573, in request
    prep = self.prepare_request(req)
  File "/usr/local/lib/python3.8/dist-packages/requests/sessions.py", line 484, in prepare_request
    p.prepare(
  File "/usr/local/lib/python3.8/dist-packages/requests/models.py", line 368, in prepare
    self.prepare_url(url, params)
  File "/usr/local/lib/python3.8/dist-packages/requests/models.py", line 439, in prepare_url
    raise MissingSchema(
requests.exceptions.MissingSchema: Invalid URL 'some_path': No scheme supplied. Perhaps you meant https://some_path?

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/lib/python3.8/dist-packages/data_refinery_common/utils.py", line 407, in download_file
    with requests.get(download_url, stream=True) as r:
  File "/usr/local/lib/python3.8/dist-packages/requests/api.py", line 73, in get
    return request("get", url, params=params, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/requests/api.py", line 59, in request
    return session.request(method=method, url=url, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/requests/sessions.py", line 573, in request
    prep = self.prepare_request(req)
  File "/usr/local/lib/python3.8/dist-packages/requests/sessions.py", line 484, in prepare_request
    p.prepare(
  File "/usr/local/lib/python3.8/dist-packages/requests/models.py", line 368, in prepare
    self.prepare_url(url, params)
  File "/usr/local/lib/python3.8/dist-packages/requests/models.py", line 439, in prepare_url
    raise MissingSchema(
requests.exceptions.MissingSchema: Invalid URL 'some_path': No scheme supplied. Perhaps you meant https://some_path?

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/lib/python3.8/dist-packages/data_refinery_common/utils.py", line 407, in download_file
    with requests.get(download_url, stream=True) as r:
  File "/usr/local/lib/python3.8/dist-packages/requests/api.py", line 73, in get
    return request("get", url, params=params, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/requests/api.py", line 59, in request
    return session.request(method=method, url=url, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/requests/sessions.py", line 573, in request
    prep = self.prepare_request(req)
  File "/usr/local/lib/python3.8/dist-packages/requests/sessions.py", line 484, in prepare_request
    p.prepare(
  File "/usr/local/lib/python3.8/dist-packages/requests/models.py", line 368, in prepare
    self.prepare_url(url, params)
  File "/usr/local/lib/python3.8/dist-packages/requests/models.py", line 439, in prepare_url
    raise MissingSchema(
requests.exceptions.MissingSchema: Invalid URL 'some_path': No scheme supplied. Perhaps you meant https://some_path?

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/lib/python3.8/dist-packages/data_refinery_common/utils.py", line 407, in download_file
    with requests.get(download_url, stream=True) as r:
  File "/usr/local/lib/python3.8/dist-packages/requests/api.py", line 73, in get
    return request("get", url, params=params, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/requests/api.py", line 59, in request
    return session.request(method=method, url=url, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/requests/sessions.py", line 573, in request
    prep = self.prepare_request(req)
  File "/usr/local/lib/python3.8/dist-packages/requests/sessions.py", line 484, in prepare_request
    p.prepare(
  File "/usr/local/lib/python3.8/dist-packages/requests/models.py", line 368, in prepare
    self.prepare_url(url, params)
  File "/usr/local/lib/python3.8/dist-packages/requests/models.py", line 439, in prepare_url
    raise MissingSchema(
requests.exceptions.MissingSchema: Invalid URL 'some_path': No scheme supplied. Perhaps you meant https://some_path?

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/lib/python3.8/dist-packages/data_refinery_common/utils.py", line 407, in download_file
    with requests.get(download_url, stream=True) as r:
  File "/usr/local/lib/python3.8/dist-packages/requests/api.py", line 73, in get
    return request("get", url, params=params, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/requests/api.py", line 59, in request
    return session.request(method=method, url=url, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/requests/sessions.py", line 573, in request
    prep = self.prepare_request(req)
  File "/usr/local/lib/python3.8/dist-packages/requests/sessions.py", line 484, in prepare_request
    p.prepare(
  File "/usr/local/lib/python3.8/dist-packages/requests/models.py", line 368, in prepare
    self.prepare_url(url, params)
  File "/usr/local/lib/python3.8/dist-packages/requests/models.py", line 439, in prepare_url
    raise MissingSchema(
requests.exceptions.MissingSchema: Invalid URL 'some_path': No scheme supplied. Perhaps you meant https://some_path?

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/lib/python3.8/dist-packages/data_refinery_common/utils.py", line 407, in download_file
    with requests.get(download_url, stream=True) as r:
  File "/usr/local/lib/python3.8/dist-packages/requests/api.py", line 73, in get
    return request("get", url, params=params, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/requests/api.py", line 59, in request
    return session.request(method=method, url=url, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/requests/sessions.py", line 573, in request
    prep = self.prepare_request(req)
  File "/usr/local/lib/python3.8/dist-packages/requests/sessions.py", line 484, in prepare_request
    p.prepare(
  File "/usr/local/lib/python3.8/dist-packages/requests/models.py", line 368, in prepare
    self.prepare_url(url, params)
  File "/usr/local/lib/python3.8/dist-packages/requests/models.py", line 439, in prepare_url
    raise MissingSchema(
requests.exceptions.MissingSchema: Invalid URL 'some_path': No scheme supplied. Perhaps you meant https://some_path?

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/lib/python3.8/dist-packages/data_refinery_common/utils.py", line 407, in download_file
    with requests.get(download_url, stream=True) as r:
  File "/usr/local/lib/python3.8/dist-packages/requests/api.py", line 73, in get
    return request("get", url, params=params, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/requests/api.py", line 59, in request
    return session.request(method=method, url=url, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/requests/sessions.py", line 573, in request
    prep = self.prepare_request(req)
  File "/usr/local/lib/python3.8/dist-packages/requests/sessions.py", line 484, in prepare_request
    p.prepare(
  File "/usr/local/lib/python3.8/dist-packages/requests/models.py", line 368, in prepare
    self.prepare_url(url, params)
  File "/usr/local/lib/python3.8/dist-packages/requests/models.py", line 439, in prepare_url
    raise MissingSchema(
requests.exceptions.MissingSchema: Invalid URL 'some_path': No scheme supplied. Perhaps you meant https://some_path?

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/user/data_refinery_workers/downloaders/sra.py", line 73, in _download_file_http
    download_file(download_url, target_file_path)
  File "/usr/local/lib/python3.8/dist-packages/data_refinery_common/utils.py", line 421, in download_file
    download_file(download_url, target_file_path, retry + 1)
  File "/usr/local/lib/python3.8/dist-packages/data_refinery_common/utils.py", line 421, in download_file
    download_file(download_url, target_file_path, retry + 1)
  File "/usr/local/lib/python3.8/dist-packages/data_refinery_common/utils.py", line 421, in download_file
    download_file(download_url, target_file_path, retry + 1)
  [Previous line repeated 6 more times]
  File "/usr/local/lib/python3.8/dist-packages/data_refinery_common/utils.py", line 423, in download_file
    raise e
  File "/usr/local/lib/python3.8/dist-packages/data_refinery_common/utils.py", line 407, in download_file
    with requests.get(download_url, stream=True) as r:
  File "/usr/local/lib/python3.8/dist-packages/requests/api.py", line 73, in get
    return request("get", url, params=params, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/requests/api.py", line 59, in request
    return session.request(method=method, url=url, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/requests/sessions.py", line 573, in request
    prep = self.prepare_request(req)
  File "/usr/local/lib/python3.8/dist-packages/requests/sessions.py", line 484, in prepare_request
    p.prepare(
  File "/usr/local/lib/python3.8/dist-packages/requests/models.py", line 368, in prepare
    self.prepare_url(url, params)
  File "/usr/local/lib/python3.8/dist-packages/requests/models.py", line 439, in prepare_url
    raise MissingSchema(
requests.exceptions.MissingSchema: Invalid URL 'some_path': No scheme supplied. Perhaps you meant https://some_path?
2023-02-16 00:58:52,767 local data_refinery_workers.downloaders.utils INFO [failure_reason: Exception caught while downloading file\n Invalid URL 'some_path': No scheme supplied. Perhaps you meant https://some_path?] [downloader_job: 9] [downloader_task: ]: Downloader job failed!
2023-02-16 00:58:52,778 local data_refinery_workers.downloaders.utils ERROR [downloader_job: 9] [downloader_task: ]: Downloader job failed without having failure_reason set. FIX ME!!!!!!!!
F2023-02-16 00:58:53,096 local data_refinery_workers.downloaders.sra DEBUG [downloader_job: 10]: Downloading file from some_path to /tmp/doomed using HTTP.
2023-02-16 01:09:41,536 local data_refinery_workers.downloaders.sra ERROR [downloader_job: 10]: Exception caught while downloading file.
Traceback (most recent call last):
  File "/usr/local/lib/python3.8/dist-packages/data_refinery_common/utils.py", line 407, in download_file
    with requests.get(download_url, stream=True) as r:
  File "/usr/local/lib/python3.8/dist-packages/requests/api.py", line 73, in get
    return request("get", url, params=params, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/requests/api.py", line 59, in request
    return session.request(method=method, url=url, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/requests/sessions.py", line 573, in request
    prep = self.prepare_request(req)
  File "/usr/local/lib/python3.8/dist-packages/requests/sessions.py", line 484, in prepare_request
    p.prepare(
  File "/usr/local/lib/python3.8/dist-packages/requests/models.py", line 368, in prepare
    self.prepare_url(url, params)
  File "/usr/local/lib/python3.8/dist-packages/requests/models.py", line 439, in prepare_url
    raise MissingSchema(
requests.exceptions.MissingSchema: Invalid URL 'some_path': No scheme supplied. Perhaps you meant https://some_path?

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/lib/python3.8/dist-packages/data_refinery_common/utils.py", line 407, in download_file
    with requests.get(download_url, stream=True) as r:
  File "/usr/local/lib/python3.8/dist-packages/requests/api.py", line 73, in get
    return request("get", url, params=params, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/requests/api.py", line 59, in request
    return session.request(method=method, url=url, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/requests/sessions.py", line 573, in request
    prep = self.prepare_request(req)
  File "/usr/local/lib/python3.8/dist-packages/requests/sessions.py", line 484, in prepare_request
    p.prepare(
  File "/usr/local/lib/python3.8/dist-packages/requests/models.py", line 368, in prepare
    self.prepare_url(url, params)
  File "/usr/local/lib/python3.8/dist-packages/requests/models.py", line 439, in prepare_url
    raise MissingSchema(
requests.exceptions.MissingSchema: Invalid URL 'some_path': No scheme supplied. Perhaps you meant https://some_path?

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/lib/python3.8/dist-packages/data_refinery_common/utils.py", line 407, in download_file
    with requests.get(download_url, stream=True) as r:
  File "/usr/local/lib/python3.8/dist-packages/requests/api.py", line 73, in get
    return request("get", url, params=params, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/requests/api.py", line 59, in request
    return session.request(method=method, url=url, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/requests/sessions.py", line 573, in request
    prep = self.prepare_request(req)
  File "/usr/local/lib/python3.8/dist-packages/requests/sessions.py", line 484, in prepare_request
    p.prepare(
  File "/usr/local/lib/python3.8/dist-packages/requests/models.py", line 368, in prepare
    self.prepare_url(url, params)
  File "/usr/local/lib/python3.8/dist-packages/requests/models.py", line 439, in prepare_url
    raise MissingSchema(
requests.exceptions.MissingSchema: Invalid URL 'some_path': No scheme supplied. Perhaps you meant https://some_path?

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/lib/python3.8/dist-packages/data_refinery_common/utils.py", line 407, in download_file
    with requests.get(download_url, stream=True) as r:
  File "/usr/local/lib/python3.8/dist-packages/requests/api.py", line 73, in get
    return request("get", url, params=params, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/requests/api.py", line 59, in request
    return session.request(method=method, url=url, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/requests/sessions.py", line 573, in request
    prep = self.prepare_request(req)
  File "/usr/local/lib/python3.8/dist-packages/requests/sessions.py", line 484, in prepare_request
    p.prepare(
  File "/usr/local/lib/python3.8/dist-packages/requests/models.py", line 368, in prepare
    self.prepare_url(url, params)
  File "/usr/local/lib/python3.8/dist-packages/requests/models.py", line 439, in prepare_url
    raise MissingSchema(
requests.exceptions.MissingSchema: Invalid URL 'some_path': No scheme supplied. Perhaps you meant https://some_path?

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/lib/python3.8/dist-packages/data_refinery_common/utils.py", line 407, in download_file
    with requests.get(download_url, stream=True) as r:
  File "/usr/local/lib/python3.8/dist-packages/requests/api.py", line 73, in get
    return request("get", url, params=params, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/requests/api.py", line 59, in request
    return session.request(method=method, url=url, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/requests/sessions.py", line 573, in request
    prep = self.prepare_request(req)
  File "/usr/local/lib/python3.8/dist-packages/requests/sessions.py", line 484, in prepare_request
    p.prepare(
  File "/usr/local/lib/python3.8/dist-packages/requests/models.py", line 368, in prepare
    self.prepare_url(url, params)
  File "/usr/local/lib/python3.8/dist-packages/requests/models.py", line 439, in prepare_url
    raise MissingSchema(
requests.exceptions.MissingSchema: Invalid URL 'some_path': No scheme supplied. Perhaps you meant https://some_path?

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/lib/python3.8/dist-packages/data_refinery_common/utils.py", line 407, in download_file
    with requests.get(download_url, stream=True) as r:
  File "/usr/local/lib/python3.8/dist-packages/requests/api.py", line 73, in get
    return request("get", url, params=params, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/requests/api.py", line 59, in request
    return session.request(method=method, url=url, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/requests/sessions.py", line 573, in request
    prep = self.prepare_request(req)
  File "/usr/local/lib/python3.8/dist-packages/requests/sessions.py", line 484, in prepare_request
    p.prepare(
  File "/usr/local/lib/python3.8/dist-packages/requests/models.py", line 368, in prepare
    self.prepare_url(url, params)
  File "/usr/local/lib/python3.8/dist-packages/requests/models.py", line 439, in prepare_url
    raise MissingSchema(
requests.exceptions.MissingSchema: Invalid URL 'some_path': No scheme supplied. Perhaps you meant https://some_path?

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/lib/python3.8/dist-packages/data_refinery_common/utils.py", line 407, in download_file
    with requests.get(download_url, stream=True) as r:
  File "/usr/local/lib/python3.8/dist-packages/requests/api.py", line 73, in get
    return request("get", url, params=params, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/requests/api.py", line 59, in request
    return session.request(method=method, url=url, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/requests/sessions.py", line 573, in request
    prep = self.prepare_request(req)
  File "/usr/local/lib/python3.8/dist-packages/requests/sessions.py", line 484, in prepare_request
    p.prepare(
  File "/usr/local/lib/python3.8/dist-packages/requests/models.py", line 368, in prepare
    self.prepare_url(url, params)
  File "/usr/local/lib/python3.8/dist-packages/requests/models.py", line 439, in prepare_url
    raise MissingSchema(
requests.exceptions.MissingSchema: Invalid URL 'some_path': No scheme supplied. Perhaps you meant https://some_path?

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/lib/python3.8/dist-packages/data_refinery_common/utils.py", line 407, in download_file
    with requests.get(download_url, stream=True) as r:
  File "/usr/local/lib/python3.8/dist-packages/requests/api.py", line 73, in get
    return request("get", url, params=params, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/requests/api.py", line 59, in request
    return session.request(method=method, url=url, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/requests/sessions.py", line 573, in request
    prep = self.prepare_request(req)
  File "/usr/local/lib/python3.8/dist-packages/requests/sessions.py", line 484, in prepare_request
    p.prepare(
  File "/usr/local/lib/python3.8/dist-packages/requests/models.py", line 368, in prepare
    self.prepare_url(url, params)
  File "/usr/local/lib/python3.8/dist-packages/requests/models.py", line 439, in prepare_url
    raise MissingSchema(
requests.exceptions.MissingSchema: Invalid URL 'some_path': No scheme supplied. Perhaps you meant https://some_path?

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/lib/python3.8/dist-packages/data_refinery_common/utils.py", line 407, in download_file
    with requests.get(download_url, stream=True) as r:
  File "/usr/local/lib/python3.8/dist-packages/requests/api.py", line 73, in get
    return request("get", url, params=params, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/requests/api.py", line 59, in request
    return session.request(method=method, url=url, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/requests/sessions.py", line 573, in request
    prep = self.prepare_request(req)
  File "/usr/local/lib/python3.8/dist-packages/requests/sessions.py", line 484, in prepare_request
    p.prepare(
  File "/usr/local/lib/python3.8/dist-packages/requests/models.py", line 368, in prepare
    self.prepare_url(url, params)
  File "/usr/local/lib/python3.8/dist-packages/requests/models.py", line 439, in prepare_url
    raise MissingSchema(
requests.exceptions.MissingSchema: Invalid URL 'some_path': No scheme supplied. Perhaps you meant https://some_path?

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/user/data_refinery_workers/downloaders/sra.py", line 73, in _download_file_http
    download_file(download_url, target_file_path)
  File "/usr/local/lib/python3.8/dist-packages/data_refinery_common/utils.py", line 421, in download_file
    download_file(download_url, target_file_path, retry + 1)
  File "/usr/local/lib/python3.8/dist-packages/data_refinery_common/utils.py", line 421, in download_file
    download_file(download_url, target_file_path, retry + 1)
  File "/usr/local/lib/python3.8/dist-packages/data_refinery_common/utils.py", line 421, in download_file
    download_file(download_url, target_file_path, retry + 1)
  [Previous line repeated 6 more times]
  File "/usr/local/lib/python3.8/dist-packages/data_refinery_common/utils.py", line 423, in download_file
    raise e
  File "/usr/local/lib/python3.8/dist-packages/data_refinery_common/utils.py", line 407, in download_file
    with requests.get(download_url, stream=True) as r:
  File "/usr/local/lib/python3.8/dist-packages/requests/api.py", line 73, in get
    return request("get", url, params=params, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/requests/api.py", line 59, in request
    return session.request(method=method, url=url, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/requests/sessions.py", line 573, in request
    prep = self.prepare_request(req)
  File "/usr/local/lib/python3.8/dist-packages/requests/sessions.py", line 484, in prepare_request
    p.prepare(
  File "/usr/local/lib/python3.8/dist-packages/requests/models.py", line 368, in prepare
    self.prepare_url(url, params)
  File "/usr/local/lib/python3.8/dist-packages/requests/models.py", line 439, in prepare_url
    raise MissingSchema(
requests.exceptions.MissingSchema: Invalid URL 'some_path': No scheme supplied. Perhaps you meant https://some_path?

Solution or next step

Fix requests.exceptions.MissingSchema exception

arkid15r commented 1 year ago

The data doesn't seem to exist anymore - https://github.com/AlexsLemonade/refinebio/blob/c4b4a6ad9392b911eec754c81b50a0b05b5f4d41/workers/data_refinery_workers/downloaders/test_sra.py#L67

Commented out for now. Need guidance regarding permanent fix.

davidsmejia commented 1 year ago

The data doesn't seem to exist anymore -

https://github.com/AlexsLemonade/refinebio/blob/c4b4a6ad9392b911eec754c81b50a0b05b5f4d41/workers/data_refinery_workers/downloaders/test_sra.py#L67

Commented out for now. Need guidance regarding permanent fix.

Moved to AWS https://www.ncbi.nlm.nih.gov/Traces/index.html?view=run_browser&acc=SRR9117853&display=data-access

arkid15r commented 1 year ago

Implemented in https://github.com/AlexsLemonade/refinebio/pull/3231