duplicate transcripts with gene2transcripts endpoint

[vidboda]

Describe the bug
For some genes, e.g. HYMAI, some transcripts (e.g. NR_002768.2) are duplicated in the json response

To Reproduce
curl -X 'GET' -H 'accept: application/json' 'http://YOURVVSERVER/VariantValidator/tools/gene2transcripts/HYMAI?content-type=application/json'

Expected behavior
Only one occurence of NR_002768.2

Screenshots

{                                                                                                                                                                                                    
  "current_name": "hydatidiform mole associated and imprinted",
  "current_symbol": "HYMAI",
  "hgnc": "HGNC:5326",
  "lovd_corrections": null,
  "lovd_messages": null,
  "previous_symbol": "",
  "requested_symbol": "HYMAI",
  "transcripts": [
    {
      "annotations": {
        "chromosome": "6",
        "db_xref": {
          "CCDS": null,
          "ensemblgene": null,
          "hgnc": "HGNC:5326",
          "ncbigene": "57061",
          "select": false
        },
        "ensembl_select": false,
        "mane_plus_clinical": false,
        "mane_select": false,
        "map": "6q24.2",
        "note": "hydatidiform mole associated and imprinted",
        "refseq_select": false,
        "variant": "0"
      },
      "coding_end": null,
      "coding_start": null,
      "description": "Homo sapiens hydatidiform mole associated and imprinted (HYMAI), long non-coding RNA",
      "genomic_spans": {
        "NC_000006.11": {
...
      },
      "length": 3815,
      "reference": "NR_002768.2",
      "translation": null
    },
    {
      "annotations": {
        "chromosome": "6",
        "db_xref": {
          "CCDS": null,
          "ensemblgene": null,
          "hgnc": "HGNC:5326",
          "ncbigene": "57061",
          "select": false
        },
        "ensembl_select": false,
        "mane_plus_clinical": false,
        "mane_select": false,
        "map": "6q24.2",
        "note": "hydatidiform mole associated and imprinted",
        "refseq_select": false,
        "variant": "0"
      },
      "coding_end": null,
      "coding_start": null,
      "description": "Homo sapiens hydatidiform mole associated and imprinted (HYMAI), long non-coding RNA",
      "genomic_spans": {
        "NC_000006.11": {
...
      },
      "length": 3815,
      "reference": "NR_002768.2",
      "translation": null
    },
...

[Peter-J-Freeman]

Thanks @vidboda. This endpoint is deprecated and will be removed at some point. I recommend switching to gene2transcripts_v2.

[ifokkema]

This endpoint is deprecated and will be removed at some point. I recommend switching to gene2transcripts_v2.

I have some notes somewhere about not being able to use v2 just yet... I'll have to dig those up, if you're considering removing v1. The LOVD/VV library still uses v1.

[Peter-J-Freeman]

I have some notes somewhere about not being able to use v2 just yet... I'll have to dig those up, if you're considering removing v1. The LOVD/VV library still uses v1.

Wont be remving it any time soon, especially now we have the new server with collaborator only access that you and @vidboda are on, but we are hiding it and recommending switching to v2 as the v1 is too slow and given the ever increasing number of transcripts we add each tine we db update, it will not work well for many genes now and is prone to taking up to 5 minutes to respond e.g. for BRCA1 which I think now has around 3 and a half billion transcripts in RefSeq. May be a slight over exageration