Closed chinchliff closed 10 years ago
This is done and should be stable as of commit ccde8f199d583bd440a0aa47fe85940028ac3668.
There are three ways to access deprecated ids.
1 The contextQueryForNames service now has an option to include deprecated ids in the results.
Example:
curl -X POST http://localhost:7474/db/data/ext/TNRS/graphdb/contextQueryForNames -H "content-type:application/json" -d '{"queryString":"Metopidae","includeDubious":true,includeDeprecated":true}'
Results:
{
"governing_code" : "undefined",
"unambiguous_name_ids" : [ "Metopidae" ],
"unmatched_name_ids" : [ ],
"matched_name_ids" : [ "Metopidae" ],
"context" : "All life",
"includes_deprecated_ids" : true,
"includes_dubious_names" : true,
"taxonomy" : {
"author" : "open tree of life project",
"weburl" : "https://github.com/OpenTreeOfLife/opentree/wiki/Open-Tree-Taxonomy",
"source" : "ott2.6"
},
"results" : [ {
"id" : "Metopidae",
"matches" : [ {
"is_deprecated" : false,
"dubious_name" : false,
"is_synonym" : false,
"flags" : [ "SIBLING_LOWER", "TATTERED" ],
"is_perfect_match" : false,
"search_string" : "metopidae",
"score" : 1.0,
"is_approximate_match" : false,
"is_homonym" : true,
"matched_ott_id" : 5342013,
"matched_node_id" : 2754493,
"rank" : "",
"matched_name" : "Metopidae",
"unique_name" : "Metopidae (family in order Armophorida)",
"nomenclature_code" : "ICN",
"synonym_or_homonym_status" : "known"
}, {
"is_deprecated" : false,
"dubious_name" : true,
"is_synonym" : false,
"flags" : [ "HIDDEN", "SIBLING_LOWER", "TATTERED", "TATTERED_INHERITED" ],
"is_perfect_match" : false,
"search_string" : "metopidae",
"score" : 1.0,
"is_approximate_match" : false,
"is_homonym" : true,
"matched_ott_id" : 5342015,
"matched_node_id" : 2755117,
"rank" : "",
"matched_name" : "Metopidae",
"unique_name" : "Metopidae (family in order Heterotrichida)",
"nomenclature_code" : "ICN",
"synonym_or_homonym_status" : "known"
}, {
"is_deprecated" : true,
"matched_node_id" : 3135045,
"flags" : [ "DEPRECATED" ],
"matched_name" : "Metopidae",
"is_perfect_match" : true,
"score" : 1.0,
"search_string" : "metopidae",
"is_approximate_match" : false,
"matched_ott_id" : 5342016
} ]
} ]
}
2 The getTaxonInfo service will find and return deprecated taxa:
Example:
curl -X POST http://localhost:7474/db/data/ext/OTTServices/graphdb/getTaxonInfo -H "content-type:application/json" -d '{"ottId":5342016}'
Results:
{
"ot:ottId" : 5342016,
"flags" : [ "DEPRECATED" ],
"source_info" : "irmng:113432",
"ot:ottTaxonName" : "Metopidae",
"reason" : "unresolved/blocked",
"node_id" : 3135045
}
3 There is a new service that will return information about all the deprecated taxa in the database.
Example:
curl -X POST http://localhost:7474/db/data/ext/OTTServices/graphdb/getDeprecatedTaxa
Result:
[ {
"ot:ottId" : 5286014,
"source_info" : "if:293729",
"ot:ottTaxonName" : "Bogoriellomyces subpersicinae",
"reason" : "different-division"
},
...
{
"ot:ottId" : 5298479,
"source_info" : "if:413285,gbif:5448851",
"ot:ottTaxonName" : "Lacrymaria atricha",
"reason" : "different-division"
} ]
Need to import the deprecated ids from Jonathan and have a service to query them.