EVA-3605 Add Contig translation service #178
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apriltuesday
reviewed
Sep 9, 2024
eva-server/src/main/java/uk/ac/ebi/eva/server/ws/RegionWSServer.java
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eva-server/src/main/java/uk/ac/ebi/eva/server/ws/RegionWSServerV2.java
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eva-server/src/main/java/uk/ac/ebi/eva/server/ws/contigalias/ContigAliasService.java
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apriltuesday
approved these changes
Sep 11, 2024
| @@ -56,6 +61,8 @@ public GA4GHBeaconResponse beacon(@RequestParam("referenceName") String chromoso | |||
| @RequestParam("start") long start, | |||
| @RequestParam("allele") String allele, | |||
| @RequestParam("datasetIds") List<String> studies, | |||
| @RequestParam(name = "contigNamingConvention", required = false) | |||
| ContigNamingConvention contigNamingConvention, | |||
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Did we decide to change the GA4GH endpoints as well? Asking because I'm just not sure what the spec allows...
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The specs allow to have more parameters but not mandatory.
In any case we're not compliant with the spec already and the specs have moved on to Beacon v2.
tcezard
approved these changes
Sep 11, 2024
Comment on lines
111
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115
| public String translateContigFromInsdc(String genbankContig, ContigNamingConvention contigNamingConvention) { | ||
| if (contigNamingConvention == null) { | ||
| return ""; | ||
| } | ||
| String url = contigAliasUrl + CONTIG_ALIAS_CHROMOSOMES_GENBANK_ENDPOINT + genbankContig; |
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I know the endpoint is still called genbank but we should change it.
This is the INSDC accession and genbank can also issue a contig name that might be different from ENA's
Suggested change
| public String translateContigFromInsdc(String genbankContig, ContigNamingConvention contigNamingConvention) { | |
| if (contigNamingConvention == null) { | |
| return ""; | |
| } | |
| String url = contigAliasUrl + CONTIG_ALIAS_CHROMOSOMES_GENBANK_ENDPOINT + genbankContig; | |
| public String translateContigFromInsdc(String insdcContig, ContigNamingConvention contigNamingConvention) { | |
| if (contigNamingConvention == null) { | |
| return ""; | |
| } | |
| String url = contigAliasUrl + CONTIG_ALIAS_CHROMOSOMES_GENBANK_ENDPOINT + insdcContig; |
| @@ -56,6 +61,8 @@ public GA4GHBeaconResponse beacon(@RequestParam("referenceName") String chromoso | |||
| @RequestParam("start") long start, | |||
| @RequestParam("allele") String allele, | |||
| @RequestParam("datasetIds") List<String> studies, | |||
| @RequestParam(name = "contigNamingConvention", required = false) | |||
| ContigNamingConvention contigNamingConvention, | |||
There was a problem hiding this comment.
The specs allow to have more parameters but not mandatory.
In any case we're not compliant with the spec already and the specs have moved on to Beacon v2.
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