rake task to create queries via CLI

[thomasvangurp]

Although bio-miga/miga#87 was fixed, the dataset does not show up as a query dataset where I would expect it.

when i run

miga add -P test/ -D Test_Xanthomonas_hortorum_pv_pelargonii_query2 \
-t genome -q --description "Test query 2" -i assembly \"/6_db_ssd/primer_tool/Xanthomonas/internal/NBC-76_Xanthomonas_hortorum_pv._pelargonii.fna.gz" \
-v -d

this will add the dataset to Test, but the q that is preceding reqular query datasets names is missing:

More importantly, while the dataset shows up as a reference, it does not show up as a query in the admin panel for queries. Whereas the dataset is marked as [Qry] i can only find it in the References list.

Ideally, I would like the ability to add this dataset as a query to one or multiple users, such that users can see that they requested this query and when.

[lmrodriguezr]

When you say "the admin panel" do you mean in the Web app?

Unfortunately, datasets added directly from the command-line will not be recognized by the web app as queries. The reason is that when you submit a query through the web app, the app has its own (quickly accessible) database where it register the dataset.

Is there a reason why you want to create the dataset from the command line as opposed to submitting it directly through the web app? If there is a common use case here, we could implement this functionality.

[thomasvangurp]

Hi @lmrodriguezr,

When you say "the admin panel" do you mean in the Web app?
Yes, that is what i mean.

I'd like to add a query dataset programmatically using a script and have it visible in the web-interface. We regularly assemble complete bacterial genomes that we'd like to classify. This happens using an automated pipeline. We would like to send the users that requested to get the genome sequenced a link to the query page in the MIGA web app.

Ideally, we can assign a query to a certain user such that user get's an overview of the genomes that he requested.

It would be great if this functionality could be implemented!

[lmrodriguezr]

Yes, that's a feature we could indeed implement!
However, it would be have to be implemented on the web server side, so I'll transfer this issue to the Web interface codebase.