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Service URL for InterMine #72

Closed Meganmli closed 10 months ago

Meganmli commented 10 months ago

If it exists, what is the PombeMine service URL when trying to run this below in python v3?

from intermine.webservice import Service
service = Service({service_url})
gmicklem commented 10 months ago

Hi Megan,

I'm not sure of the context but you can find example service urls relating to the individual template queries (a) and by generating code from queries (b)

(a) Visit https://www.pombase.org/im/pombemine/templates

For instance for the first 10 rows of the template: Disease (MONDO) -> Genes

the service url is:

https://pombemine.rahtiapp.fi/pombemine/service/template/results?name=MONDO_disease_to_genes&constraint1=Gene.diseases.mondoTerm.parents.name&op1=eq&value1=Cornelia+de+Lange+syndrome&format=tab&size=10

and likewise for the template: All protein coding gene(s)

it is

https://pombemine.rahtiapp.fi/pombemine/service/template/results?name=protein_coding_genes&constraint1=Gene.description&op1=ne&value1=retrotransposable+element%2Ftransposon+Tf2-type&constraint2=Gene.description&op2=ne&value2=dubious&format=tab&size=10

(b) if you run a query (e.g. one of the template above), you can also generate code from the query results page using the button towards to the top right of the results table (default value of the drop-down is Python).

However instead of

https://pombemine.rahtiapp.fi/pombemine/service

this seems to be giving the service url as

http://localhost:8080/pombemine/service

which doesn't seem right.

I hope this helps.

Best wishes,

Gos

On Sep 21 2023, Megan Li wrote:

If it exists, what is the PombeMine service URL when trying to run this below in python v3?

from intermine.webservice import Service
service = Service({service_url})

-- Reply to this email directly or view it on GitHub: https://github.com/intermine/pombemine/issues/72 You are receiving this because you are subscribed to this thread.

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Meganmli commented 10 months ago

Hello! Sorry for not providing more context. I appreciate the detailed response!

https://pombemine.rahtiapp.fi/pombemine/service was exactly what I needed as http://localhost:8080/pombemine/service errored out when I tried to connect using this URL.

Thank you!

kimrutherford commented 10 months ago

Hi Megan.

I've also just added this as a more user friendly alias for the service URL: https://www.pombase.org/pombemine/service/ and I'll add that to the PomBase FAQ.

Thanks for helping out @gmicklem