galaxyproject / galaxyproject/galaxy

Job handler need to be started for pasted upload to work

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kind/bug
Dominant language
Python
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Avg merge
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Merged PRs (30d)
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Description

If only the web handlers are online I'm seeing
```
Traceback (most recent call last):
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.7/shutil.py", line 566, in move
os.rename(src, real_dst)
FileNotFoundError: [Errno 2] No such file or directory: '/Users/mvandenb/src/galaxy/database/tmp/strio_url_paste_cqgopuo3' -> '/Users/mvandenb/src/galaxy/database/files/000/dataset_101.dat'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/Users/mvandenb/src/galaxy/tools/data_source/upload.py", line 326, in
__main__()
File "/Users/mvandenb/src/galaxy/tools/data_source/upload.py", line 319, in __main__
metadata.append(add_file(dataset, registry, output_path))
File "/Users/mvandenb/src/galaxy/tools/data_source/upload.py", line 151, in add_file
shutil.move(converted_path or dataset.path, output_path)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.7/shutil.py", line 580, in move
copy_function(src, real_dst)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.7/shutil.py", line 266, in copy2
copyfile(src, dst, follow_symlinks=follow_symlinks)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.7/shutil.py", line 120, in copyfile
with open(src, 'rb') as fsrc:
FileNotFoundError: [Errno 2] No such file or directory: '/Users/mvandenb/src/galaxy/database/tmp/strio_url_paste_cqgopuo3'
```

Contributor guide

Open the contributing guide

Research direction

Start with tools/data_source/upload.py, especially add_file around line 151 and __main__ around line 326, then reproduce a pasted upload with only the web handlers online. Trace why the temporary file is missing and define done as pasted uploads completing without the shown FileNotFoundError or clearly documenting the required handler.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
backend
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
42/100

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