GitLab

We upgraded the uploader code for API v1 to use the new JSON field names, matching the Java model. Anno project already sends the new JSON:

[
 { 
    "instituteCode": ...,
    "accessionNumber": ....,
    "taxonomy": { "genus": .... } }
 ...
]

Updating accession data works well, but we forgot to fix the code for deleteAccessions. It still receives @RequestBody List<AccessionHeaderJson> batch.

Please update the delete code (implementation should be based on upsert code):

ObjectReader reader = objectMapper.readerFor(Accession.class);

Date batchDate = new Date();
final List<Accession> accessions = new ArrayList<>(updates.size());
final List<AccessionOpResponse> responses = new ArrayList<>(updates.size());
List<Accession> toSave = new ArrayList<>(updates.size());

for (JsonNode accn : updates) {
  LOG.trace("Received: {}", accn);
  try {
    Accession accession = reader.readValue(accn);
    if (accession.getInstituteCode() == null || (accession.getDoi() == null && accession.getAccessionNumber() == null)) {
      throw new InvalidApiUsageException("instituteCode, accessionNumber OR doi missing in " + accn);
    }
    accessions.add(accession);
    responses.add(new AccessionOpResponse(accession.getInstituteCode(), accession.getAccessionNumber(), accession.getTaxonomy().getGenus()));
  } catch (IOException e) {
    LOG.error("Could not parse input: {}", e.getMessage(), e);
    accessions.add(null); // need to match get(index) with responses and updates
    responses.add(new AccessionOpResponse(accn.get("instituteCode").asText(), accn.get("accessionNumber").asText(), accn.get("taxonomy").get("genus").asText())
      .setResult(new UpsertResult(UpsertResult.Type.ERROR)).setError(e.getMessage()));
  }
}

LOG.debug("Processsed incoming JSON for {} accessions in {}ms", updates.size(), stopWatch.getTime());

List<Accession> existingAccessions = accessionRepository.find(! institute.hasUniqueAcceNumbs(), accessions);
LOG.debug("Have {} accessions for update and {} exist in {}ms", accessions.size(), existingAccessions.size(), stopWatch.getTime());

// Add code to remove existing accessions
// Missing accessions should have OP error message set to "Record not found"