EVA-3501 - adding new endpoint for parsing fasta file data #80
Conversation
nitin-ebi
changed the title
| @@ -86,4 +87,27 @@ public Optional<Map<String, Object>> getAllPossibleSeqColExtendedData(String acc | |||
|
|
|||
| return Optional.of(seqColResultData); | |||
| } | |||
|
|
|||
| public Optional<Map<String, Object>> getAllPossibleSeqColExtendedData(String insdcAccession, String fastFileContent) throws IOException { | |||
There was a problem hiding this comment.
This being a generic function for any fasta file, I'm not sure it makes sense to put it in NCBISeqColDataSource.java
| public Optional<AssemblySequenceEntity> getAssemblySequencesByAccession(String insdcAccession, String fastFileContent) throws IOException { | ||
| AssemblySequenceEntity assemblySequenceEntity; | ||
| try (InputStream stream = new ByteArrayInputStream(fastFileContent.getBytes())) { | ||
| NCBIAssemblySequenceReader reader = readerFactory.build(stream, insdcAccession); |
There was a problem hiding this comment.
We'll probably have to refactor this since NCBIAssemblySequenceReader is actually pretty generic and does not need to be attached to 'NCBI' prefix
| @ApiResponse(responseCode = "500", description = "Server Error") | ||
| }) | ||
| @PutMapping(value = "/seqcols/fasta/{insdcAccession}") | ||
| public ResponseEntity<?> fetchAndInsertSeqColByParsingFastFile(@PathVariable(value = "insdcAccession") String insdcAccession, @RequestBody String fastFileContent) { |
There was a problem hiding this comment.
I don't think the string parameter is being used anywhere. It is here to comply with the current object structure.
I guess we should at least change the variant name (and the doc) to make clear it does not have to be an INSDC assembly accession.
There was a problem hiding this comment.
I agree, it's not being used in the calculations but since we are using a lot of existing code that requires this value, I left it as it is. Was named insdcAccession, since it ultimately sets the insdcAccession value of AssemblySequenceEntity.
I have updated the parameter name to just accession.
|
Sorry, I didn't mean to commit the change, just to suggest |
src/main/java/uk/ac/ebi/eva/evaseqcol/controller/admin/AdminController.java
Outdated
Show resolved
Hide resolved
src/main/java/uk/ac/ebi/eva/evaseqcol/service/SeqColService.java
Outdated
Show resolved
Hide resolved
nitin-ebi
force-pushed
the
compliance-test
branch
from
fcc5307
to
91cc475
Compare
To be discussed in stand-upThe idea for this PR was to get the functionality working without modifying too much of the existing code (easier to remove the new changes if needed). |
src/main/java/uk/ac/ebi/eva/evaseqcol/entities/SeqColExtendedDataEntity.java
Outdated
Show resolved
Hide resolved
No description provided.