[ensembl-dev] missing ID on call to variant_recoder

[Sage Hornung]

Hi,

I am making the following call (To localhost though not Ensembl)  http://grch37.rest.ensembl.org /variant_recoder/human/13:g.32893310A>G?content-type=application/json&fields=hgvsg,id<%20http:/grch37.rest.ensembl.org%20/variant_recoder/human/13:g.32893310A%3eG?content-type=application/json&fields=hgvsg,id> to a local ensemble setup. But I don't get an ID back in the response. I loaded the ensembl_stable_ids_100 database but its was the one I found here ftp://ftp.ensembl.org/pub/release-100/mysql/.

Here is what I get back using my local Ensembl  REST and Ensembl   DB . If I change to your DB it gives the ID back. Any idea what I am going wrong? Or how this should be configured differently? I am making my changes in the  ensembl_rest.conf file
[
    {
        "hgvsg": [
            "NC_000013.10:g.32893310A>G",
            "LRG_293:g.8694A>G"
        ],
        "input": "13:g.32893310A>G"
    }
]

I do see that pointing to the ensemble DB gives this when starting up the REST server
Species 'homo_sapiens' loaded from database 'homo_sapiens_core_100_37'
Species 'homo_sapiens' loaded from database 'homo_sapiens_cdna_100_37'
Species 'homo_sapiens' loaded from database 'homo_sapiens_otherfeatures_100_37'
Species 'homo_sapiens' loaded from database 'homo_sapiens_rnaseq_100_37'
homo_sapiens_variation_100_37 loaded
homo_sapiens_funcgen_100_37 loaded
ensembl_compara_100 loaded
No ancestral database found
ensembl_ontology_100 loaded
No taxonomy database found
No ensembl_metadata database found
No production database or adaptor found
ensembl_stable_ids_100 loaded

But it only finds the homo_sapiens_core DB when I point to my local DB (I definitely have the variation DB loaded )

Will only load v100 databases
Species 'homo_sapiens' loaded from database 'homo_sapiens_core_100_37'
No variation databases found
No funcgen databases found
No Compara databases found
No ancestral database found
No ontology database found
No taxonomy database found
No ensembl_metadata database found
No production database or adaptor found



Sage Hornung
Software Engineer
NeoGenomics Laboratories, Inc.
2131 Faraday Avenue, Carlsbad, CA 92008
Phone: 760.516.5114
Cell: 760.755.3930
sage.hornung at neogenomics.com<mailto:sage.hornung at neogenomics.com>
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