archive biom: back changes #3202
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| Additionally, study artifacts have 5 different states: sandboxed, awaiting_approval, | ||
| private, public and archived. A sandboxed artifact has all operational | ||
| capabilities in the system but is not publicly available, allowing for quick | ||
| integration with other studies but at the same time keeping it private so the |
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I think using 'private' in this sentence might be confusing, since it's not the same meaning as the 'private' state for study artifacts. The text on 'awaiting_approval' was also a little confusing. Here are some suggested changes in the context of the text as a whole:
Additionally, study artifacts have 5 different states: sandboxed,
awaiting_approval, private, public and archived. A sandboxed artifact has all
operational capabilities in the system but is not publicly available, allowing
for quick integration with other studies but at the same time keeping it hidden
so the user can improve the analysis.
Once a user is satisfied with their analysis, they can request to upgrade their
project's status to 'private'; this confers additional benefits to the project,
including permanent space in the repository. During this time, an administrator
will validate their study and its status will change to 'awaiting_approval'.
At this stage in Qiita the whole study (including all processed data) is
private. This process is completely automatic via the Graphical User Interface
(GUI). Currently sequence data is deposited for permanent storage to the
European Nucleotide Archive (ENA), part of the European Bioinformatics
Institute (EBI). When the user is ready, usually when the main manuscript of
the study is ready for publication, the user can request for the artifact to be
made 'public', both in Qiita and the permanent repository, Figure 2. Finally,
when new processing algorithms are available, the older BIOM artifacts are
'archived', for long term storage.
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| def artifact_visibilities_to_skip(): | ||
| return tuple([qdb.util.convert_to_id('archived', "visibility")]) |
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A new function for one line of code seems a little excessive. However I appreciate the readability. Not sure I would suggest unfolding it.
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I tried adding as a global variable in the artifact.py and as a member of the Artifact object but turns out that this is not possible because the code will try to initialize those variables when the code is initiated (and there is no database) so it fails, for example.
qiita_db/artifact.py
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| QiitaDBOperationNotPermittedError | ||
| If the artifact is not public | ||
| If the artifact_type is not BIOM | ||
| If the artifact belowns to an analysis |
qiita_db/artifact.py
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| 'Only non raw artifacts can be archived') | ||
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| # let's find all ancestors that can be deleted (it has parents and no | ||
| # ancestors, and delete them |
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ancestors -> descendants?
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it's actually both but added extra info to make it clearer
3 participants
This adds the possibility to archive BIOM files and delete their log files.