Hi,

I'm rewriting my galaxy-api-tools project to use bioblend. I can't
believe I missed it the first time around.

I'm a little confused reading about LibraryDatasetDatasetAssociation
(ldda), LibraryDataset (ld) and HistoryDatasetAssociation (hda). I
found something in the wiki[1] but is not helping enough.

I guess my question is, let's say I use any of
bioblend.galaxy.libraries.upload_*() fucntions[2] to upload a file to
a data library, the json response for that is something that looks
like this:
[{'url': '/api/libraries/ca4f6513e2849358/contents/e70b6e37a29da1c1',
'id': 'e70b6e37a29da1c1', 'name': '1.fastq'}]

Now let's say I use bioblend.galaxy.tools.upload_file()[2] and upload
a file to a history, the json response for that looks like:
{'outputs': [{'misc_blurb': None, 'peek': '<table cellspacing="0"
cellpadding="3"></table>', 'uuid': None, 'hda_ldda': 'hda',
'data_type': 'auto', 'deleted': False, 'history_id':
'6eafbc3efd020327', 'purged': False, 'state': 'queued', 'name':
'1.fastq', 'visible': True, 'genome_build': '?', 'model_class':
'HistoryDatasetAssociation', 'hid': 5, 'file_size': 0,
'metadata_data_lines': None, 'file_ext': 'auto', 'id':
'c3e7863ed8b6cf9e', 'misc_info': None, 'metadata_dbkey': '?'}]}

Which 'src' setting should I use for
bioblend.galaxy.workflows.run_workflow()'s[2] {'<input>': {'id':
<encoded dataset ID>, 'src': '[ldda, ld, hda]'}?

If I have to guess {'<input>': {'id': 'e70b6e37a29da1c1', 'src':
'ldda'} for the first one and {'<input>': {'id': 'c3e7863ed8b6cf9e',
'src': 'hda'} for the second one. That leaves out 'ld', when do I have
to use that one?

Finally and as a comment. I think the inconsistency on what to expect
after delivering a payload to the API makes it hard to use these
responses. See this issue[3] I submitted to bioblend but it seems is
actually Galaxy who is at fault.

[1]http://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20and%20Datasets
[2]http://bioblend.readthedocs.org/en/latest/api_docs/galaxy/all.html
[3]https://github.com/afgane/bioblend/issues/40

Thanks,
Carlos
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