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dieterich-lab / scimodom

Sci- ModoM: A quantitative database of transcriptome-wide high-throughput RNA modification sites
https://dieterich-lab.github.io/scimodom/
GNU Affero General Public License v3.0
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Delay between project creation and data upload will blow up the server #117

Closed eboileau closed 2 months ago

eboileau commented 3 months ago

Aims/objectives.

Adding a new selection on project creation will make this selection available e.g. for the Search, but if no data is added, this will blow up e.g. when trying to fetch the gene cache.

A clear and concise description of todo items.

I don't know how to handle this... temporarily, we can find all "weak" end-points and add exception handling...

HaraldWilhelmi commented 2 months ago

There are multiple issues we may run into:

eboileau commented 2 months ago

No assembly for taxa_id (NoResultFound when accessing /chroms)

While it make sense to handle such cases, if a user is able to choose a selection, then the corresponding assembly exists, so there is in principle no problem, but this is not necessarily the case if we use the API directly.

No annoation (KeyError on RNA_TYPE_TO_ANNOTATION_SOURCE_MAP when accessing /annotation)

Same as above, the rna_type is pre-defined, but...

So yes, in general, these exceptions should be handled in scimodom/api/utilities.py