Using api to report errors

usegalaxy.org support
1

Hi!What should I do?I’m using bioblend’s api to keep showing this:
File “C:\Users\dongge\PycharmProjects\宏基因组分析\meta.py”, line 75, in main
dataset_1 = gi.tools.upload_file(Input1_forward, history_id=history_id, file_type=‘fastqsanger.gz’)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “C:\Users\dongge\AppData\Local\Programs\Python\Python311\Lib\site-packages\bioblend\galaxy\tools_init_.py”, line 497, in upload_file
uploader.upload()
File “C:\Users\dongge\AppData\Local\Programs\Python\Python311\Lib\site-packages\tusclient\uploader\uploader.py”, line 45, in upload
self.upload_chunk()
File “C:\Users\dongge\AppData\Local\Programs\Python\Python311\Lib\site-packages\tusclient\uploader\uploader.py”, line 59, in upload_chunk
self._do_request()
File “C:\Users\dongge\AppData\Local\Programs\Python\Python311\Lib\site-packages\tusclient\uploader\uploader.py”, line 88, in _do_request
self._retry_or_cry(error)
File “C:\Users\dongge\AppData\Local\Programs\Python\Python311\Lib\site-packages\tusclient\uploader\uploader.py”, line 102, in _retry_or_cry
raise error
File “C:\Users\dongge\AppData\Local\Programs\Python\Python311\Lib\site-packages\tusclient\uploader\uploader.py”, line 85, in _do_request
self.request.perform()
File “C:\Users\dongge\AppData\Local\Programs\Python\Python311\Lib\site-packages\tusclient\request.py”, line 92, in perform
raise TusUploadFailed(error)
tusclient.exceptions.TusUploadFailed: HTTPSConnectionPool(host=‘usegalaxy.org’, port=443): Max retries exceeded with url: /api/upload/resumable_upload/a13f13579af4acb8a20a5f71d0785059 (Caused by SSLError(SSLEOFError(8, ‘EOF occurred in violation of protocol (_ssl.c:2423)’)))

2

Hi @chenqiang

Just as a guess – is the compression state of the files Ok? Meaning, they are actually of the datatype fastqsangergz ? What happens if you try to load the uncompressed version? Do the files load via the Upload tool directly (as a cross-check)? Is there anything else special about the data that you could share?

I’ve also cross-posted this over to the chat group for Bioblend. Please feel free to join, and they may reply here or there. You're invited to talk on Matrix

3

Just a guess, but I’m wondering if you are specifying gi = galaxy.GalaxyInstance(url="usegalaxy.org", key="..." rather than gi = galaxy.GalaxyInstance(url="https://usegalaxy.org", key="..."? i.e. the url without https

4

I tried the above method, but I still can’t.
Traceback (most recent call last):
File “C:\Users\dongge\PycharmProjects\宏基因组分析\16s分析.py”, line 162, in
main()
File “C:\Users\dongge\AppData\Local\Programs\Python\Python311\Lib\site-packages\gooey\python_bindings\gooey_decorator.py”, line 134, in
return lambda *args, **kwargs: func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File “C:\Users\dongge\PycharmProjects\宏基因组分析\16s分析.py”, line 87, in main
dataset_2 = gi.tools.upload_file(Input1_reverse, history_id=history_id, file_type=‘fastqillumina.gz’)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “C:\Users\dongge\AppData\Local\Programs\Python\Python311\Lib\site-packages\bioblend\galaxy\tools_init_.py”, line 497, in upload_file
uploader.upload()
File “C:\Users\dongge\AppData\Local\Programs\Python\Python311\Lib\site-packages\tusclient\uploader\uploader.py”, line 45, in upload
self.upload_chunk()
File “C:\Users\dongge\AppData\Local\Programs\Python\Python311\Lib\site-packages\tusclient\uploader\uploader.py”, line 59, in upload_chunk
self._do_request()
File “C:\Users\dongge\AppData\Local\Programs\Python\Python311\Lib\site-packages\tusclient\uploader\uploader.py”, line 88, in _do_request
self._retry_or_cry(error)
File “C:\Users\dongge\AppData\Local\Programs\Python\Python311\Lib\site-packages\tusclient\uploader\uploader.py”, line 102, in _retry_or_cry
raise error
File “C:\Users\dongge\AppData\Local\Programs\Python\Python311\Lib\site-packages\tusclient\uploader\uploader.py”, line 85, in _do_request
self.request.perform()
File “C:\Users\dongge\AppData\Local\Programs\Python\Python311\Lib\site-packages\tusclient\request.py”, line 92, in perform
raise TusUploadFailed(error)
tusclient.exceptions.TusUploadFailed: HTTPSConnectionPool(host=‘usegalaxy.eu’, port=443): Max retries exceeded with url: /api/upload/resumable_upload/793e99c4-3751-49e8-a544-67a9e297068a (Caused by SSLError(SSLEOFError(8, ‘EOF occurred in violation of protocol (_ssl.c:2423)’)))

5

Sorry, I’m not sure.

It might not be a problem related to BioBlend or Galaxy. There’s a lot of stuff online about such errors, e.g. ssl - Python requests.exceptions.SSLError: EOF occurred in violation of protocol - Stack Overflow