ga4gh / ga4gh/htsget-refserver
invalid JSON being returned
- Dominant language
- Go
- Stars
- 12
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- 4
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Description
We currently have the docker (1.4.1) running htsget-refsever. We are unable to get it to return results.
We have added in a config file:
`docker container run -d -p 3000:3000 -v /red/project/src:/usr/src/app/config ga4gh/htsget-refserver:1.4.1 ./htsget-refserver -config /red/project/src/config.json`
Starting the docker is fine. The contents of the config file, we have taken from the Readme of this repo, so it currently looks like:
```
{
"htsgetConfig": {
"reads": {
"enabled": true,
"dataSourceRegistry": {
"sources": [
{
"pattern": "^tabulamuris\\.(?P10X.*)$",
"path": "https://s3.amazonaws.com/czbiohub-tabula-muris/10x_bam_files/{accession}_possorted_genome.bam"
},
{
"pattern": "^tabulamuris\\.(?P.*)$",
"path": "https://s3.amazonaws.com/czbiohub-tabula-muris/facs_bam_files/{accession}.mus.Aligned.out.sorted.bam"
}
]
}
"serviceInfo": {
"id": "demo.reads",
"name": "htsget demo reads",
"description": "serve alignment data via htsget",
"organization": {
"name": "Example Org",
"url": "https://exampleorg.com"
},
"contactUrl": "mailto:nobody@exampleorg.com",
"documentationUrl": "https://htsget.exampleorg.com/docs",
"createdAt": "2021-01-01T09:00:00Z",
"updatedAt": "2021-01-01T09:00:00Z",
"environment": "test",
"version": "1.0.0"
}
}
}
}
```
When attempting to access this using what I am presuming is a correctly formed htsget request, I get the following:
```
$ htsget https://s3.amazonaws.com/czbiohub-tabula-muris/ --reference-name=2 --start=1000 --end=2000 -O NA12878_2.bam
/home/bcurran/bin/miniconda3/envs/ga4gh/bin/htsget: error: The server returned invalid JSON; the first non whitespace byte should be '{' but is = '<
```
Is this a problem with the underlying data set or is there something in the code that is failing to translate something?
Thanks
Ben.
Contributor guide
No contributing guide indexed for this repository
Research direction
Start with the README configuration and the supplied config.json, then reproduce the issue using the ./htsget-refserver Docker command and htsget request shown. Check whether the configured service starts and whether the request reaches the local server rather than the S3 URL. Done means the request returns valid htsget JSON instead of an HTML response.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- docker, go
- Domain
- api, backend
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100