Generic API search plugin

[Bjoernsen]

Let’s say, I have a gff3 track that includes the entries gene1, gene2, gene3. I can visualize and to search for them.

My issue is that I have a DB that includes many further alternative gene names (and locations) for the genes in my gff3, e.g. alt1 for gene1.

I would like to be able to search for alternative names. JBrowse2 should just jump to the gene1 location.

Therefore, I would have to set up an API endpoint that takes the query, searches the DB and returns the results in format that can directly be used within JBrowse2.

Now, I have 2 main issues:

• How should such a result look like?
• How should the corresponding JBrowse2 plugin look like?

Unfortunately, I am bad at writing Javascript. I tried to use copilot, but it did not work.

Would it make sense to create a generic search plugin where the user only configs the API endpoint and the search works out of the box (if the API endpoint response matches the defined structure?)

{
  "aggregateTextSearchAdapters": [
    {
      "type": "ApiSearchAdapter",
      "endpoint": "https://my/api/endpoint"
    }
  ]
}

[cmdcolin]

Hi there,
Here are a couple thoughts

Let’s say, I have a gff3 track that includes the entries gene1, gene2, gene3. I can visualize and to search for them...My issue is that I have a DB that includes many further alternative gene names (and locations) for the genes in my gff3, e.g. alt1 for gene1.

JBrowse is capable of handling indexing multiple gene aliases/synonyms with the normal "jbrowse text-index" command. For example, if a specific GFF3 field like "gene_synonyms" is a comma-separated list of gene synonyms, you can say "jbrowse text-index --attributes Name,ID,gene_synonyms"

If you are want to make a API anyways, it should be possible. I don't have an example of a custom search adapter that can hit a REST API yet but could make an example

I am a little wary of making a "built-in" plugin for this, as REST APIs for searching are often so variable and weird, that (IMO) people who want to use a REST API, who are often advanced users in the first place, can make a jbrowse plugin that queries the REST API in the way that they want to