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<p>Hi Anja,</p>
<p>This is the part of the code that manages the queries:
<a class="moz-txt-link-freetext" href="https://github.com/opentargets/snp_to_gene/blob/master/snp_assignment.pl#L153-L179">https://github.com/opentargets/snp_to_gene/blob/master/snp_assignment.pl#L153-L179</a>.
If you look further down you will see that it cannot be a 429 code
as they are handled explicitly. I could add repeats in case of 400
codes if you think that it is the best solution. I have asked
about the memory allocation error because that is the one that
gets resolved if I try again but there are around 50 variants that
always give a 400 code even though they exist in Ensembl. One
example is rs1057518506 which is a <a moz-do-not-send="true"
href="https://www.ncbi.nlm.nih.gov/snp/rs1057518506">deletion
according to dbSNP</a>, is described as a <a
moz-do-not-send="true"
href="https://www.ensembl.org/Homo_sapiens/Variation/Explore?db=core;r=17:7220304-7221313;v=rs1057518506;vdb=variation;vf=371667648">frameshift
variant in Ensembl but it lacks alleles</a> and the <a
moz-do-not-send="true"
href="https://rest.ensembl.org/vep/human/id/rs1057518506?content-type=application/json">API
returns a 400 code saying that the length of the reference
allele is 0</a>. I am happy to share these cases with you if you
are interested in them.<br>
</p>
<p>I understand that using the POST endpoints would be a better
solution, at least because we could use a single query to retrieve
data about multiple variants thus reducing the burden on the API.
However,I am afraid that this is a piece of code that we run twice
every two months and it is not a priority for us to refactor it
unless you have a good reason for me to convince my managers.</p>
<p>Thank you,<br>
Asier<br>
</p>
<div class="moz-cite-prefix">On 21/08/2019 14:54, Anja Thormann
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:C2007FF7-7E3A-4349-8E3A-99A50B8C0E08@ebi.ac.uk">
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charset=windows-1252">
Hi Asier,
<div class=""><br class="">
</div>
<div class="">I would like to take a look at your script please. I
recommend for the first part that you use our VEP POST endpoints
for <a
href="https://rest.ensembl.org/documentation/info/vep_region_post"
class="" moz-do-not-send="true">region</a> and <a
href="https://rest.ensembl.org/documentation/info/vep_id_post"
class="" moz-do-not-send="true">id</a>. At this point I
recommend that you rerun your requests a few times on a 400
error and if the requests keep failing contact us with details
(variant id or region) of your failed requests. Can you rule out
that the error message has a 429 code due to too many requests?</div>
<div class=""><br class="">
</div>
<div class="">Thank you,</div>
<div class="">Anja<br class="">
<div class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On 21 Aug 2019, at 14:28, Asier Gonzalez
<<a href="mailto:gonzaleza@ebi.ac.uk" class=""
moz-do-not-send="true">gonzaleza@ebi.ac.uk</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class="">Hello Anja,<br class="">
<br class="">
Thank you for your email. This is an script that calls
both the id (/vep/human/id/) and region
(/vep/human/region/) endpoints depending on whether
the variant is defined by a rsID or a genomic
coordinates. It calls the API thousands of times using
GET requests, once per variant. I don't see any other
settings but I can point you to the few code lines
that control it on Github if you want to have a look
yourself.<br class="">
<br class="">
Please let me know if I can help. I just need to know
whether this is an expected behaviour as our script
retries calling the API if the response is a 5XX error
but it passes if it's a 400 as it should have been
caused by the query and retrying should not make any
difference.<br class="">
<br class="">
Best wishes,<br class="">
Asier<br class="">
<br class="">
On 21/08/2019 13:39, Anja Thormann wrote:<br class="">
<blockquote type="cite" class="">Dear Asier,<br
class="">
<br class="">
thank you for your feedback. Could you please let me
know which VEP endpoint and settings you use? If you
are using a POST endpoint, how many variant ids or
regions are you sending? I assume that the problem
happens at a point during the VEP calculation where
it is difficult to differentiate the cause of the
problem. But we will investigate further and
hopefully be able to provide a more accurate error
report.<br class="">
<br class="">
Best wishes,<br class="">
Anja<br class="">
<br class="">
<blockquote type="cite" class="">On 21 Aug 2019, at
12:47, Asier Gonzalez <<a
href="mailto:gonzaleza@ebi.ac.uk" class=""
moz-do-not-send="true">gonzaleza@ebi.ac.uk</a>>
wrote:<br class="">
<br class="">
Hi,<br class="">
<br class="">
I have an script that calls the VEP API for a few
thousand variants and does some processing. The
script captures HTTP errors and messages and I
have found a few cases where the 400 error is
accompanied by a "ERROR: Cannot allocate memory"
message. If I query the API again with the ids
that produced that error I get a results so I
understand that this is a temporary issue. I could
handle the 400 errors further to control these
cases but I wonder if it is an expected case or if
it an issue as it sounds as this should be an 5XX
error instead of a 400.<br class="">
<br class="">
Kind regards,<br class="">
Asier<br class="">
<br class="">
<br class="">
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</blockquote>
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