confusion about linked organism values in preview

[mpoelchau]

This might be a non-issue, just trying to confirm. When creating a linked record from assembly (ID 557018) to the organism table, here's the key/value list:

THe documentation states that the value of each field should take me to the corresponding record at NCBI. When I click on the organism value, it leads me here, which doesn't seem to contain any information about the organism: http://ontologies.berkeleybop.org/#NCBITaxon:57918

[bradfordcondon]

i actually resolved this issue in core. here's the update:

/**
 * Update the NCBITaxon DB entry.
 */
function tripal_chado_update_7337(){

  chado_insert_db(array(
    'name' => 'NCBITaxon',
    'description' => 'NCBI organismal classification.',
    'url' => 'http://www.berkeleybop.org/ontologies/ncbitaxon/',
    'urlprefix' => 'https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id={accession}',
  ));
}

so assuming we use urlprefix instead of url (we do) this should work. The fact taht the url is wrong for you just means tripal core should be updated on the droplet. I'll do that now.

yep, when running updatedb:

drush updatedb
 Tripal_chado  7336  Use correct contact field when linked via linker table.
 Tripal_chado  7337  Update the NCBITaxon DB entry.
 Tripal        7313  Adds a tripal_storage_api setting to all field storage details

7337 is the update that will fix this.

i updated core on the droplet and this is fixed.