worms-server 0.5.3

No feature changes. All dependencies were updates to the latest versions.

Full Changelog: 0.5.2...0.5.3

worms-server 0.5.2

Added an accepted query parameter to /descendants/:name. If accepted=true then only accepted scientific names are returned. If accepted=false (the default) then all names, both accepted and not accepted names are returned.

Full Changelog: 0.5.1...0.5.2

worms-server 0.5.1

I've made the following 3 changes to worms-server related to fathomnet/fathomnet-py#26

1. acceptedAphiaId

All taxa nodes now include an acceptedAphiaID field. Any endpoint that starts with taxa will return this field. This is the term WoRMS uses internally, not sure why they use valid_AphiaID in their service. Example https://fathomnet.org/worms/taxa/info/Swiftia%20pallida returns:

{
  "name": "Swiftia pallida",
  "rank": "Species",
  "aphiaId": 125401,
  "acceptedAphiaId": 1608729,
  "alternateNames": [
    "Nördliche Seefeder",
    "northern sea fan",
    "Northern sea fan coral",
    "corail pâle"
    ]
}

2. /names/aphiaid/{aphiaid}

I've also added a new /names/aphiaid/{aphiaid} endpoint. This aggregates alternativeNames from any other nodes that use the matched node as their accepted one.

https://fathomnet.org/worms/names/aphiaid/125401

{
    "aphiaId": 125401,
    "name": "Swiftia pallida",
    "acceptedName": "Callistephanus pallida",
    "alternateNames": [
        "Northern sea fan coral",
        "Nördliche Seefeder",
        "corail pâle",
        "northern sea fan"
    ]
}

https://fathomnet.org/worms/names/aphiaid/1608729

{
    "aphiaId": 1608729,
    "name": "Callistephanus pallida",
    "acceptedName": "Callistephanus pallida",
    "alternateNames": [
        "Northern sea fan coral",
        "Nördliche Seefeder",
        "Swiftia pallida",
        "Swiftia rosea pallida",
        "corail pâle",
        "northern sea fan"
    ]
}

3. synonyms has a new behavior

The contract is that the first item in the list is the accepted name. Before worms-server just found a node by its name and used the alternate names attached to the node. Now it finds the accepted node and expands the search to find outdated (non-accepted?) nodes.

https://fathomnet.org/worms/synonyms/Swiftia%20pallida

Before

[
  "Swiftia pallida",
  "Northern sea fan coral",
  "Nördliche Seefeder",
  "corail pâle",
  "northern sea fan"
]

Now

[
  "Callistephanus pallida",
  "Northern sea fan coral",
  "Nördliche Seefeder",
  "Swiftia pallida",
  "Swiftia rosea pallida",
  "corail pâle",
  "northern sea fan"
]

Full Changelog: 0.4.5...0.5.1

worms-server 0.4.5

• updated dependencies
• Add scoping rules to taxa/query/startswith endpoint. #4

worms-server 0.4.1

Changes

• Address #3
• Updated all dependencies to latest versions
• Fix a bug where valid aphiaIds where changed to negative values.

Full Changelog: 0.3.0...0.4.1

worms-server 0.3.0

I've added the ability to merge in custom branches with WoRMS. This is to accomodate adding geology/equipment/etc from the VARS knowledgebase. This release has been published to docker at https://hub.docker.com/repository/docker/mbari/worms-server

Full Changelog: 0.2.3...0.3.0