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Replace the URL to DNAstack's decommissioned or soon-to-be-decommissioned data connect services #43

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merged 3 commits into from
Oct 24, 2023

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shiroyuki
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This PR is to replace the URL to DNAstack's decommissioned or soon-to-be-decommissioned data connect services.

Old endpoint Reason
https://data-connect-trino-public.prod.dnastack.com/ Soon to be decommissioned
https://ga4gh-search-adapter-presto-public.prod.dnastack.com/ Soon to be decommissioned

The new endpoint is https://data.publisher.dnastack.com/data-connect/.

NOTE: The tables have been replaced with the same/equivalent one.

@ianfore
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ianfore commented Feb 24, 2023

https://data.publisher.dnastack.com/data-connect/tables

gives the following error:

{
    "errors": [
        {
            "status": 401,
            "title": "Access Denied: HTTP 401: User does not have permission to access the table [system.metadata.catalogs]. [traceID: ffe755be6f7e249f | spanID: 52db90931f6929c2]",
            "details": "ffe755be6f7e249f: USER_ERROR: 4: PERMISSION_DENIED"
        }
    ],
    "error": {
        "status": 401,
        "title": "Access Denied: HTTP 401: User does not have permission to access the table [system.metadata.catalogs]. [traceID: ffe755be6f7e249f | spanID: 52db90931f6929c2]",
        "details": "ffe755be6f7e249f: USER_ERROR: 4: PERMISSION_DENIED"
    }
}

@shiroyuki
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@ianfore Sorry about that... I updated the hostname and some table names. It should be ok now.

@mbarkley
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@ianfore we think we've addressed the issue you reported when you last tried this. We'd love if you could try it out again, but if you don't have time, we'd still like to merge this change on Friday as the old table names will become unusable soon.

@mbarkley mbarkley merged commit 9fec2fd into ga4gh:main Oct 24, 2023
@ianfore
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ianfore commented Oct 25, 2023

@mbarkley . All I've had time to do at the moment is check the error I was getting before doesn't occur with the corrected endpoint.
https://publisher-data.prod.dnastack.com/data-connect

There are table name changes also, and haven't had a chance to look at all of those.
Same answer for the following PR on the fasp-scripts repo (probably less critical as fewer people rely on it, though it has many more table references)
ga4gh/fasp-scripts#37

@ianfore
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ianfore commented Oct 25, 2023

@mbarkley
I also hadn't checked whether the schema for the tables had been migrated correctly.

For notebook 2-3a the original table was
thousand_genomes.onek_genomes.sra_drs_files
See the schema that was previously provided in response to /table/thousand_genomes.onek_genomes.sra_drs_files/info at this commit

The replacement table on the new server seems to be:
collections.public_datasets.onek_genomes_sra_drs_files
The schema provided by the server is an autogenerated schema

The old server was making use of static json schema files that had been provided for specific datasets . These don't seem to have migrated to the new server. Or perhaps just not to the location on the new server where they would be expected to be found.

@shiroyuki shiroyuki deleted the data-connect-url-update branch October 26, 2023 19:00
@shiroyuki
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I am in the process of restoring the custom schema. As it involves fixing a bug on our backend service, it should be ready by the end of next week.

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3 participants