DINA Ruby Gem
The DINA Consortium develops an open-source web-based information management system for natural history data that consists of several connected software components. At the core of the system is support for assembling, managing and sharing data associated with natural history collections and their curation ("collection management"). Target collections include zoological, botanical, geological and paleontological collections, living collections, biodiversity inventories, observation records, and molecular data.
This Ruby 3.2 gem abstracts the Keycloak configuration and JSON:API models for the DINA collection management system. It depends on the json_api_client where more documentation is available on how to create, update, query, and delete objects.
Disclaimer
The DINA APIs for each of its components are under rapid development and so too is this gem. The intent of the latter is to be as closely aligned with the most recent versions of the former. As such, this gem makes use of the DINA APIs via their single, frontend gateway.
Requirements & Dependencies
- ruby >= 3.3
- bundled dependencies: json_api_client (~> 1.22), keycloak (~> 3.2.1),
Install
$ gem install dinaConfiguration
All variables are required and most can be obtained from a DINA system administrator.
-
authorization_url,realm,client_id,user, andpassword: used in the Keycloak authentication handshake -
endpoint_url: the single DINA gateway to JSON:API models -
token_store_file: your local file that caches authentication token responses, which are thereafter automatically reused and updated as needed
require 'dina'
settings = {
authorization_url: "http://localhost/auth",
endpoint_url: "http://localhost/api",
realm: "dina",
client_id: "dina",
user: "username",
password: "password",
token_store_file: "config/token.json"
}
Dina.config = settingsInstantiate and Save a Person
person = Dina::Person.new
person.givenNames = "Peter"
person.familyNames = "Pipetter"
person.email = "email@email.com"
person.save
=> trueAlternatively, use the create method to save a Person without having to instantiate it first:
data = {
givenNames: "Peter",
familyNames: "pipetter",
email: "email@email.com"
}
person = Dina::Person.create(data)A new instance like person above sets and uses a default UUIDv7, which can be accessed as person.id.
Add an Identifier to a person Instance
identifier = Dina::Identifier.new
identifier.namespace = "WIKIDATA"
identifier.value = "http://www.wikidata.org/entity/Q163373"
identifier.save
=> true
person.identifiers = [ identifier ]
person.save
=> trueInstance objects (like identifier above) must be saved before they can be attached to related objects (like person above).
Query for a Person by Email Address
person = Dina::Person.find_by_email(email: "email@email.com").first
person.attributes
=>
{"type"=>"person",
"id"=>"017fe537-bb13-7c35-b52a-cb5490cce7be",
"displayName"=>"Pipetter, Peter",
"email"=>"email@email.com",
"createdBy"=>"username",
"createdOn"=>2022-11-25 17:23:09.262958 UTC,
"givenNames"=>"Peter",
"familyNames"=>"Pipetter",
"aliases"=>nil,
"webpage"=>nil,
"remarks"=>nil,
"identifiers"=>[]}Unlike typical ActiveRecord methods, find or find_by_* methods return an array and so you must additionally use .first or [0].
Delete a Person
person = Dina::Person.find("017fe537-bb13-7c35-b52a-cb5490cce7be").first
person.destroy
=> trueAdd an instance of a collection method to that of a collecting event
# Find a collection method or create one as you would a person or identifier above
collection_method = Dina::CollectionMethod.find("0189f7ea-ae2c-7809-8aeb-b819cf5e9e7f").first
collecting_event = Dina::CollectingEvent.new
collecting_event.group = "CNC"
collecting_event.collectionMethod = collection_method
collecting_event.save
=> trueUpload an Image File and its ObjectStore Metadata
file = Dina::File.new
file.group = "DAOM"
file.filePath = "/my-directory/my-file.jpg"
file.fileName = "what-i-want-it-called.jpg" # the Original Filename in the DINA UI
file.dcFormat = "image/jpeg"
file.save # also injects attributes from the server response like dateTimeDigitized below
=> true
metadata = Dina::ObjectStore.new
metadata.group = "DAOM"
metadata.dcType = "IMAGE"
metadata.dcFormat = "image/jpeg"
metadata.fileExtension = ".jpg"
metadata.fileIdentifier = file.id
date_time = Time.find_zone("America/New_York")
.parse(file.dateTimeDigitized)
.rfc3339.to_s
metadata.acDigitizationDate = date_time
metadata.save
=> trueSearch
payload = {
query: {
bool: {
must: [
{ term: { "data.attributes.managedAttributes.original_directory_name.keyword":"dc1.2021-08-19_15-42-15_e49ba1" } },
{ term: { "data.attributes.group":"dao" } }
]
}
},
size: 1
}
hits = Dina::Search.execute(index: "object_store", payload: payload)
=> [#<Dina::Search:@attributes={"type"=>"metadata", "id"=>"0189f7ea-ae2f-72b9-9be8-9c3e3e8abae8", "created_by"=>"s-dao", ... ]Search Counts
payload = {
query: {
bool: {
must: [
{ term: { "data.attributes.group":"dao" } }
]
}
}
}
hits = Dina::SearchCount.execute(index: "object_store", payload: payload)
hits.meta.count
=> 415425Search Autocomplete
WORK IN PROGRESS
Autocomplete against the dina_agent_index search index on the displayName property using supplied text, "Peter":
autocomplete = Dina::SearchAutoComplete.execute(index: "agent", autoCompleteField: "data.attributes.displayName", prefix: "Peter")Shortcut Endpoints
WORK IN PROGRESS
DINA has a handful of endpoints that operate outside the context of JSON:API. These are more performant GET requests to obtain specific items:
Summary Material Sample
Dina::Endpoint.material_sample_summary(id: '0189f7ea-ae2f-72b9-9be8-9c3e3e8abae8')Find UUID by Object Name
Dina::Endpoint.resource_name_identifier(name: "DAO123", type: "material-sample", group: "dao")
=> "0189f7ea-ae2f-72b9-9be8-9c3e3e8abae8Schema
To list available JSON:API Classes:
Dina.classesTo list available properties for a Class:
Dina::MaterialSample.propertiesTo list relationships and their cardinality for a Class:
Dina::MaterialSample.associationsConnection Errors
In the event there are SSL certificate verification issues, you can skip verification by adding the following to Dina.config:
verify_ssl: falseThe best approach is to incorporate SSL certificates in one's operating system or environment if the host uses self-signed certificates that cannot be verified.
Advanced
Flush the token from memory and save an empty token file
Dina.flushSupport
Bug reports can be filed at https://github.com/dshorthouse/dina/issues.
Copyright
Copyright © 2023 Government of Canada
Authors: David P. Shorthouse, Julia Douglas Freitas
License
dina is released under the MIT license.