Unpin json-api-resource and fix associations

The update to jsonapi-resources 0.10.6 broke the loading of tubes
for pacbio library and pool resources.

This appears to be related to the addition of the configuration option
`use_related_resource_records_for_joins`

cerebris/jsonapi-resources#1381

This is failing to function correctly in this case.

By specifying the relationship explicitly, we disable this
behaviour, and everything behaves as expected.

I still haven't quite managed to get to the bottom of
the problem. It may be we need to disable the behaviour
globally.

Author: James Glover

Gemfile

@@ -10,7 +10,7 @@ gem 'bunny'
 gem 'exception_notification'
 # 0.10.5 Results in MySQL syntax error on several tests when run against a MySQL
 # There is a 'monkey patch' for this in config/intializers/jsonapi_resources:15-63
-gem 'jsonapi-resources', '=0.10.5'
+gem 'jsonapi-resources'
 gem 'mysql2'
 gem 'puma', '~> 4.3' # Use Puma as the app server
 gem 'rack-cors' # Use Rack CORS for handling CORS, making cross-origin AJAX possible

Gemfile.lock

@@ -101,15 +101,15 @@ GEM
       activesupport (>= 5.0)
     i18n (1.10.0)
       concurrent-ruby (~> 1.0)
-    jsonapi-resources (0.10.5)
+    jsonapi-resources (0.10.7)
       activerecord (>= 4.1)
       concurrent-ruby
       railties (>= 4.1)
     listen (3.1.5)
       rb-fsevent (~> 0.9, >= 0.9.4)
       rb-inotify (~> 0.9, >= 0.9.7)
       ruby_dep (~> 1.2)
-    loofah (2.16.0)
+    loofah (2.17.0)
       crass (~> 1.0.2)
       nokogiri (>= 1.5.9)
     mail (2.7.1)
@@ -265,7 +265,7 @@ DEPENDENCIES
   database_cleaner
   exception_notification
   factory_bot_rails
-  jsonapi-resources (= 0.10.5)
+  jsonapi-resources
   listen (>= 3.0.5, < 3.2)
   mysql2
   pry-rails

app/resources/v1/pacbio/library_resource.rb

@@ -10,7 +10,11 @@ class LibraryResource < JSONAPI::Resource
                  :insert_size, :created_at, :deactivated_at, :source_identifier
 
       has_one :request, always_include_optional_linkage_data: true
-      has_one :tube
+      # If we don't specify the relation_name here, jsonapi-resources
+      # attempts to use_related_resource_records_for_joins
+      # In this case I can see it using container_associations
+      # so seems to be linking the wrong tube relationship.
+      has_one :tube, relation_name: :tube
       has_one :tag, always_include_optional_linkage_data: true
       has_one :pool, always_include_optional_linkage_data: true
       has_one :source_well, relation_name: :source_well, class_name: 'Well'

app/resources/v1/pacbio/pool_resource.rb

@@ -6,7 +6,11 @@ module Pacbio
     class PoolResource < JSONAPI::Resource
       model_name 'Pacbio::Pool'
 
-      has_one :tube
+      # If we don't specify the relation_name here, jsonapi-resources
+      # attempts to use_related_resource_records_for_joins
+      # In this case I can see it using container_associations
+      # so seems to be linking the wrong tube relationship.
+      has_one :tube, relation_name: :tube
       has_many :libraries
 
       attributes :volume, :concentration, :template_prep_kit_box_barcode,