Error when trying to get ids of workflow outputs about bioblend

[stvlar]

I'm using the most recent release v21.09

[davelopez]

I quickly checked and /api/datasets/{dataset_id} should return a dictionary not a list. Otherwise, https://github.com/galaxyproject/bioblend/blob/v0.16.0/bioblend/_tests/TestGalaxyDatasets.py#L84 should be failing too right? I'm confused too...

[simonbray]

Hi @stvlar,

It seems the result returned by the Galaxy API has changed, I wasn't aware of that.

Probably the best solution is to change the line after the invocation to something like the following:

results_id = gi.invocations.show_invocation(results_run['id'])['outputs']

[stvlar]

Thank you for your response that worked!
Also I'm getting an error releated to
gi.datasets.download_dataset(id_str, file_path=result_path, maxwait=max_timeout)

This is the error message

TypeError at /tool/
list indices must be integers or slices, not str

This is the traceback

Traceback (most recent call last):
  File "/home/stella/.local/lib/python3.8/site-packages/django/core/handlers/exception.py", line 47, in inner
    response = get_response(request)
  File "/home/stella/.local/lib/python3.8/site-packages/django/core/handlers/base.py", line 181, in _get_response
    response = wrapped_callback(request, *callback_args, **callback_kwargs)
  File "/home/stella/pasteur/app/views.py", line 198, in tool
    gi.datasets.download_dataset(id_str, file_path=result_path, maxwait=max_timeout)
  File "/home/stella/.local/lib/python3.8/site-packages/bioblend/galaxy/datasets/__init__.py", line 92, in download_dataset
    dataset = self.wait_for_dataset(dataset_id, maxwait=maxwait, check=False)
  File "/home/stella/.local/lib/python3.8/site-packages/bioblend/galaxy/datasets/__init__.py", line 385, in wait_for_dataset
    state = dataset['state']

Exception Type: TypeError at /tool/
Exception Value: list indices must be integers or slices, not str
```
`

Again this is the first time this has been an issue for me so I'm a bit lost

[simonbray]

That is quite strange. The error is on this line: https://github.com/galaxyproject/bioblend/blob/v0.16.0/bioblend/galaxy/datasets/__init__.py#L385

So it would suggest that the show_dataset() method (used on line 384 above) is returning a list, rather than a dict as expected.

Can you check if that is really the case?

[stvlar]

As far as I can see it is returning a dictionary

`

dataset | [{'create_time': ...',   
'dataset_id': '...',  
'deleted': False,   
'extension': 'auto',   
'hid': 187,   
'history_content_type': 'dataset',   
'history_id': '..',   
'id': '...',   
'name': '...',   
'purged': False,   
'state': 'queued',   
'tags': [],   
'type': 'file',   
'type_id': 'dataset',   
'update_time': '....',   
'url': '....',   
'visible': True},
-- | --

`

[simonbray]

[{

Looks like a list of dicts to me?

@davelopez maybe you have some idea here? 😕

[simonbray]

@stvlar are you using a particular Galaxy version?

[stvlar]

[{

Looks like a list of dicts to me?

@davelopez maybe you have some idea here? confused

yes there were more dicts there I just left them out since the only difference between them was the input file and the time

[mvdbeek]

It seems the result returned by the Galaxy API has changed, I wasn't aware of that.

We should not be changing the API, which endpoint do you think has changed the response ? I'd also assume both the bioblend tests and Galaxy tests would be failing if that was the case. Does the invocation in question maybe not have any outputs ? What was the original exception ?

[stvlar]

@mvdbeek

What was the original exception ?

The original exception was a KeyError with 'outputs' being the exception value

the original problem was this line
results_id = results_run['outputs']

[mvdbeek]

Can you paste it please together with the response ? And ideally a reproducible example

[stvlar]

@mvdbeek
this is the original traceback

Traceback (most recent call last):
  File "/home/stella/.local/lib/python3.8/site-packages/django/core/handlers/exception.py", line 47, in inner
    response = get_response(request)
  File "/home/stella/.local/lib/python3.8/site-packages/django/core/handlers/base.py", line 181, in _get_response
    response = wrapped_callback(request, *callback_args, **callback_kwargs)
  File "/home/stella/project/app/views.py", line 195, in tool
    results_id = results_run['outputs']

Exception Type: KeyError at /tool/
Exception Value: 'outputs'

Request Method: | POST
Request URL : http://127.0.0.1:8000/tool/
Django Version : 3.2.11
Exception Type : KeyError
Exception Value : 'outputs'
Exception Location : /home/stella/project/app/views.py, line 195, in tool
Python Executable : /usr/bin/python3
Python Version : 3.8.10
Python Path : ['/home/stella/project',  '/usr/lib/python38.zip',  '/usr/lib/python3.8',  '/usr/lib/python3.8/lib-dynload',  '/home/stella/.local/lib/python3.8/site-packages',  '/usr/local/lib/python3.8/dist-packages',  '/usr/lib/python3/dist-packages',  '/usr/lib/python3.8/dist-packages',  '/home/stella/project']
Server time : Fri, 21 Jan 2022 12:40:56 +0000

the code is in my original question

Unfortunately I can't send a reproducible example for confidentiality reasons