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Only top ten lines in result #5

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prince26121991 opened this issue Sep 12, 2023 · 8 comments
Open

Only top ten lines in result #5

prince26121991 opened this issue Sep 12, 2023 · 8 comments

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@prince26121991
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prince26121991 commented Sep 12, 2023

Hi, I am trying to run this tool using R using examples given on homepage of this repository. But every time I am getting only 10 variants only. Here is the code I am using:
query_obj_to_json(regionQuery(contig = '20', start=1, end=70000))

This is the command I used for collecting output:
sink("test.txt")
query_obj_to_json(regionQuery(contig = '20', start=1, end=70000))
sink()

That's the output I am getting:
test.txt

@quemeb
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quemeb commented Sep 13, 2023

Hi, Prince26121991,
Thanks for bringing this to our attention. We recently moved our query to use ElasticSearch. It seems the package was built before using ElasticSearch. By default, Elasticsearch returns only the first 10 results for a query. The issue has been fixed and a pull request has been opened so the output reflects all annotations present. Let us know if you have any other issues with the package.
Thank you,

@prince26121991
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Can you please tell me, what do I need to do to implement these changes? I forced resinstalled this library but still I am getting same result. Am I missing something here?

@quemeb
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quemeb commented Sep 13, 2023

The package hasn't been updated, yet. Hopefully, it will be done by the end of the day (PST). I am relatively new to the team so I don't have permission to change the code directly. The new update should handle the problem without any issues. I will make another comment here once the package has been updated. You aren't missing anything. Thank you for your patience.

@quemeb
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quemeb commented Sep 13, 2023

The package has been updated. Please give it a try and let us know if you have any issues. Thank you.

@prince26121991
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prince26121991 commented Sep 28, 2023

Ok so I retried it today, but now this is giving different error i.e. "requested time out error. I am running first example .
`library(AnnoQR)

q = init_query_js_body()

ex = exists_filter("ANNOVAR_ensembl_Effect")

q = add_query_filter(q, ex)

variants = perform_search(q)

variants`

getting error after this line
variants = perform_search(q)

Error in curl::curl_fetch_memory(url, handle = handle) :
Timeout was reached: [bioghost2.usc.edu:3403] Failed to connect to bioghost2.usc.edu port 3403 after 10002 ms: Timeout was reached

@quemeb
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quemeb commented Sep 28, 2023

The API must have been down, I ran into the same timeout when I tried it a bit ago. I've restarted the API and it seems to be working correctly now. Let me know if you are able to run it!

@prince26121991
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prince26121991 commented Sep 28, 2023

Same code giving following error now:

Error in perform_search(q) : Bad Request (HTTP 400).

@prince26121991
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