dina 0.4.1.0 → 0.4.2.0
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- checksums.yaml +4 -4
- data/lib/dina/json_api_client_patch.rb +11 -0
- data/lib/dina/models/{identifier.rb → agent/identifier.rb} +3 -1
- data/lib/dina/models/{organization.rb → agent/organization.rb} +1 -1
- data/lib/dina/models/{person.rb → agent/person.rb} +1 -1
- data/lib/dina/models/{collecting_event.rb → material_sample/collecting_event.rb} +1 -1
- data/lib/dina/models/{collecting_method.rb → material_sample/collecting_method.rb} +1 -1
- data/lib/dina/models/{collection.rb → material_sample/collection.rb} +1 -1
- data/lib/dina/models/{collection_sequence_generator.rb → material_sample/collection_sequence_generator.rb} +1 -1
- data/lib/dina/models/{material_sample.rb → material_sample/material_sample.rb} +1 -1
- data/lib/dina/models/{organism.rb → material_sample/organism.rb} +1 -1
- data/lib/dina/models/{preparation_method.rb → material_sample/preparation_method.rb} +1 -1
- data/lib/dina/models/{preparation_type.rb → material_sample/preparation_type.rb} +1 -1
- data/lib/dina/models/{project.rb → material_sample/project.rb} +1 -1
- data/lib/dina/models/{protocol.rb → material_sample/protocol.rb} +1 -1
- data/lib/dina/models/{derivative.rb → object_store/derivative.rb} +1 -1
- data/lib/dina/models/{file.rb → object_store/file.rb} +0 -0
- data/lib/dina/models/{object_store.rb → object_store/object_store.rb} +1 -1
- data/lib/dina/models/{object_store_managed_attribute.rb → object_store/object_store_managed_attribute.rb} +1 -1
- data/lib/dina/models/{object_subtype.rb → object_store/object_subtype.rb} +1 -1
- data/lib/dina/models/sequence/index_set.rb +19 -0
- data/lib/dina/models/sequence/molecular_sample.rb +19 -0
- data/lib/dina/models/sequence/ngs_workflow.rb +19 -0
- data/lib/dina/models/sequence/pcr_batch.rb +19 -0
- data/lib/dina/models/sequence/pcr_primer.rb +19 -0
- data/lib/dina/models/sequence/product.rb +19 -0
- data/lib/dina/models/sequence/region.rb +19 -0
- data/lib/dina/models/sequence/thermocycler_profile.rb +19 -0
- data/lib/dina/models/{storage_unit.rb → storage/storage_unit.rb} +1 -1
- data/lib/dina/models/{storage_unit_type.rb → storage/storage_unit_type.rb} +1 -1
- data/lib/dina/models/{transaction.rb → transaction/transaction.rb} +1 -1
- data/lib/dina/version.rb +1 -1
- metadata +32 -23
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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1
1
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---
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2
2
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SHA256:
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3
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-
metadata.gz:
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4
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-
data.tar.gz:
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3
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+
metadata.gz: 868b096ec196f62ae6cf4507cadf08c277b26f462957873140abc93ecf88a1a6
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|
4
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+
data.tar.gz: 26c127ec2bf4e6e9c990b4361aff69d1ce9f6a5e578ae01065472e8ede524bf5
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|
5
5
|
SHA512:
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|
6
|
-
metadata.gz:
|
|
7
|
-
data.tar.gz:
|
|
6
|
+
metadata.gz: 9fcd3ceca0594b95caaea14870a0ff6ebc9284fab58eac5e98bd236c04e8235b4fb542c720cba9c394b63b719a4883642f82e0871b347a9a18c5225c8e42e5b6
|
|
7
|
+
data.tar.gz: 95d262c72d8955a9eb944886efcd0784af500f4f8235846bc062a69d5128652e0af0260d85f7243bd608e8d2bd3f895a309cc752baac6b742282f84db658f88e
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|
@@ -0,0 +1,11 @@
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|
|
1
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+
# Monkeypatch the data method because the relations urls in the DINA JSON:API spec are incorrectly formed through its frontend proxy
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2
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+
module JsonApiClient
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3
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+
module Associations
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4
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+
class BaseAssociation
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5
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+
def data(url)
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|
6
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+
url.sub!("/api/v1/", "/api/#{association_class.requestor.instance_variable_get(:@klass).endpoint_path}")
|
|
7
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+
from_result_set(association_class.requestor.linked(url))
|
|
8
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+
end
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|
9
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+
end
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|
10
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+
end
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11
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+
end
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@@ -1,4 +1,4 @@
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1
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-
require_rel 'base_model'
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|
1
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+
require_rel '../base_model'
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|
2
2
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3
3
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module Dina
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4
4
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class Identifier < BaseModel
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|
@@ -8,6 +8,8 @@ module Dina
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8
8
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property :createdBy, type: :string
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|
9
9
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property :createdOn, type: :time
|
|
10
10
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|
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11
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+
belongs_to :person, shallow_path: true, class_name: "Person"
|
|
12
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+
|
|
11
13
|
def self.endpoint_path
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|
12
14
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"agent-api/"
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|
13
15
|
end
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File without changes
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@@ -0,0 +1,19 @@
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1
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+
require_rel '../base_model'
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2
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+
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|
3
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+
module Dina
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|
4
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+
class IndexSet < BaseModel
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|
5
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+
property :id, type: :string, default: SecureRandom.uuid
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|
6
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+
property :group, type: :string
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|
7
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+
|
|
8
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+
validates_presence_of :group, message: "group is required"
|
|
9
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+
|
|
10
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+
def self.endpoint_path
|
|
11
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+
"seqdb-api/"
|
|
12
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+
end
|
|
13
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+
|
|
14
|
+
def self.table_name
|
|
15
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+
"index-set"
|
|
16
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+
end
|
|
17
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+
|
|
18
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+
end
|
|
19
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+
end
|
|
@@ -0,0 +1,19 @@
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|
|
1
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+
require_rel '../base_model'
|
|
2
|
+
|
|
3
|
+
module Dina
|
|
4
|
+
class MolecularSample < BaseModel
|
|
5
|
+
property :id, type: :string, default: SecureRandom.uuid
|
|
6
|
+
property :group, type: :string
|
|
7
|
+
|
|
8
|
+
validates_presence_of :group, message: "group is required"
|
|
9
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+
|
|
10
|
+
def self.endpoint_path
|
|
11
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+
"seqdb-api/"
|
|
12
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+
end
|
|
13
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+
|
|
14
|
+
def self.table_name
|
|
15
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+
"molecular-sample"
|
|
16
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+
end
|
|
17
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+
|
|
18
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+
end
|
|
19
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+
end
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|
@@ -0,0 +1,19 @@
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1
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+
require_rel '../base_model'
|
|
2
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+
|
|
3
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+
module Dina
|
|
4
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+
class NgsWorkflow < BaseModel
|
|
5
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+
property :id, type: :string, default: SecureRandom.uuid
|
|
6
|
+
property :group, type: :string
|
|
7
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+
|
|
8
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+
validates_presence_of :group, message: "group is required"
|
|
9
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+
|
|
10
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+
def self.endpoint_path
|
|
11
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+
"seqdb-api/"
|
|
12
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+
end
|
|
13
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+
|
|
14
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+
def self.table_name
|
|
15
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+
"chain"
|
|
16
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+
end
|
|
17
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+
|
|
18
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+
end
|
|
19
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+
end
|
|
@@ -0,0 +1,19 @@
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|
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1
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+
require_rel '../base_model'
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|
2
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+
|
|
3
|
+
module Dina
|
|
4
|
+
class PcrBatch < BaseModel
|
|
5
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+
property :id, type: :string, default: SecureRandom.uuid
|
|
6
|
+
property :group, type: :string
|
|
7
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+
|
|
8
|
+
validates_presence_of :group, message: "group is required"
|
|
9
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+
|
|
10
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+
def self.endpoint_path
|
|
11
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+
"seqdb-api/"
|
|
12
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+
end
|
|
13
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+
|
|
14
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+
def self.table_name
|
|
15
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+
"pcr-batch"
|
|
16
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+
end
|
|
17
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+
|
|
18
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+
end
|
|
19
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+
end
|
|
@@ -0,0 +1,19 @@
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|
|
1
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+
require_rel '../base_model'
|
|
2
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+
|
|
3
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+
module Dina
|
|
4
|
+
class PcrPrimer < BaseModel
|
|
5
|
+
property :id, type: :string, default: SecureRandom.uuid
|
|
6
|
+
property :group, type: :string
|
|
7
|
+
|
|
8
|
+
validates_presence_of :group, message: "group is required"
|
|
9
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+
|
|
10
|
+
def self.endpoint_path
|
|
11
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+
"seqdb-api/"
|
|
12
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+
end
|
|
13
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+
|
|
14
|
+
def self.table_name
|
|
15
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+
"pcr-primer"
|
|
16
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+
end
|
|
17
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+
|
|
18
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+
end
|
|
19
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+
end
|
|
@@ -0,0 +1,19 @@
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|
|
1
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+
require_rel '../base_model'
|
|
2
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+
|
|
3
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+
module Dina
|
|
4
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+
class Product < BaseModel
|
|
5
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+
property :id, type: :string, default: SecureRandom.uuid
|
|
6
|
+
property :group, type: :string
|
|
7
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+
|
|
8
|
+
validates_presence_of :group, message: "group is required"
|
|
9
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+
|
|
10
|
+
def self.endpoint_path
|
|
11
|
+
"seqdb-api/"
|
|
12
|
+
end
|
|
13
|
+
|
|
14
|
+
def self.table_name
|
|
15
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+
"product"
|
|
16
|
+
end
|
|
17
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+
|
|
18
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+
end
|
|
19
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+
end
|
|
@@ -0,0 +1,19 @@
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|
|
1
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+
require_rel '../base_model'
|
|
2
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+
|
|
3
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+
module Dina
|
|
4
|
+
class Region < BaseModel
|
|
5
|
+
property :id, type: :string, default: SecureRandom.uuid
|
|
6
|
+
property :group, type: :string
|
|
7
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+
|
|
8
|
+
validates_presence_of :group, message: "group is required"
|
|
9
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+
|
|
10
|
+
def self.endpoint_path
|
|
11
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+
"seqdb-api/"
|
|
12
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+
end
|
|
13
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+
|
|
14
|
+
def self.table_name
|
|
15
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+
"region"
|
|
16
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+
end
|
|
17
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+
|
|
18
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+
end
|
|
19
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+
end
|
|
@@ -0,0 +1,19 @@
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|
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1
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+
require_rel '../base_model'
|
|
2
|
+
|
|
3
|
+
module Dina
|
|
4
|
+
class ThermocyclerProfile < BaseModel
|
|
5
|
+
property :id, type: :string, default: SecureRandom.uuid
|
|
6
|
+
property :group, type: :string
|
|
7
|
+
|
|
8
|
+
validates_presence_of :group, message: "group is required"
|
|
9
|
+
|
|
10
|
+
def self.endpoint_path
|
|
11
|
+
"seqdb-api/"
|
|
12
|
+
end
|
|
13
|
+
|
|
14
|
+
def self.table_name
|
|
15
|
+
"thermocycler-profile"
|
|
16
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+
end
|
|
17
|
+
|
|
18
|
+
end
|
|
19
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+
end
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data/lib/dina/version.rb
CHANGED
metadata
CHANGED
|
@@ -1,14 +1,14 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: dina
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 0.4.
|
|
4
|
+
version: 0.4.2.0
|
|
5
5
|
platform: ruby
|
|
6
6
|
authors:
|
|
7
7
|
- David P. Shorthouse
|
|
8
8
|
autorequire:
|
|
9
9
|
bindir: bin
|
|
10
10
|
cert_chain: []
|
|
11
|
-
date: 2022-12-
|
|
11
|
+
date: 2022-12-05 00:00:00.000000000 Z
|
|
12
12
|
dependencies:
|
|
13
13
|
- !ruby/object:Gem::Dependency
|
|
14
14
|
name: json_api_client
|
|
@@ -155,33 +155,42 @@ files:
|
|
|
155
155
|
- lib/dina/components/georeference_assertion.rb
|
|
156
156
|
- lib/dina/components/shipment.rb
|
|
157
157
|
- lib/dina/exceptions.rb
|
|
158
|
+
- lib/dina/json_api_client_patch.rb
|
|
158
159
|
- lib/dina/models/acquisition_event.rb
|
|
160
|
+
- lib/dina/models/agent/identifier.rb
|
|
161
|
+
- lib/dina/models/agent/organization.rb
|
|
162
|
+
- lib/dina/models/agent/person.rb
|
|
159
163
|
- lib/dina/models/assemblage.rb
|
|
160
164
|
- lib/dina/models/attachment.rb
|
|
161
165
|
- lib/dina/models/base_model.rb
|
|
162
|
-
- lib/dina/models/collecting_event.rb
|
|
163
|
-
- lib/dina/models/collecting_method.rb
|
|
164
|
-
- lib/dina/models/collection.rb
|
|
165
|
-
- lib/dina/models/collection_sequence_generator.rb
|
|
166
|
-
- lib/dina/models/derivative.rb
|
|
167
|
-
- lib/dina/models/file.rb
|
|
168
|
-
- lib/dina/models/identifier.rb
|
|
169
166
|
- lib/dina/models/institution.rb
|
|
170
167
|
- lib/dina/models/managed_attribute.rb
|
|
171
|
-
- lib/dina/models/material_sample.rb
|
|
172
|
-
- lib/dina/models/
|
|
173
|
-
- lib/dina/models/
|
|
174
|
-
- lib/dina/models/
|
|
175
|
-
- lib/dina/models/
|
|
176
|
-
- lib/dina/models/
|
|
177
|
-
- lib/dina/models/
|
|
178
|
-
- lib/dina/models/
|
|
179
|
-
- lib/dina/models/
|
|
180
|
-
- lib/dina/models/
|
|
181
|
-
- lib/dina/models/
|
|
182
|
-
- lib/dina/models/
|
|
183
|
-
- lib/dina/models/
|
|
184
|
-
- lib/dina/models/
|
|
168
|
+
- lib/dina/models/material_sample/collecting_event.rb
|
|
169
|
+
- lib/dina/models/material_sample/collecting_method.rb
|
|
170
|
+
- lib/dina/models/material_sample/collection.rb
|
|
171
|
+
- lib/dina/models/material_sample/collection_sequence_generator.rb
|
|
172
|
+
- lib/dina/models/material_sample/material_sample.rb
|
|
173
|
+
- lib/dina/models/material_sample/organism.rb
|
|
174
|
+
- lib/dina/models/material_sample/preparation_method.rb
|
|
175
|
+
- lib/dina/models/material_sample/preparation_type.rb
|
|
176
|
+
- lib/dina/models/material_sample/project.rb
|
|
177
|
+
- lib/dina/models/material_sample/protocol.rb
|
|
178
|
+
- lib/dina/models/object_store/derivative.rb
|
|
179
|
+
- lib/dina/models/object_store/file.rb
|
|
180
|
+
- lib/dina/models/object_store/object_store.rb
|
|
181
|
+
- lib/dina/models/object_store/object_store_managed_attribute.rb
|
|
182
|
+
- lib/dina/models/object_store/object_subtype.rb
|
|
183
|
+
- lib/dina/models/sequence/index_set.rb
|
|
184
|
+
- lib/dina/models/sequence/molecular_sample.rb
|
|
185
|
+
- lib/dina/models/sequence/ngs_workflow.rb
|
|
186
|
+
- lib/dina/models/sequence/pcr_batch.rb
|
|
187
|
+
- lib/dina/models/sequence/pcr_primer.rb
|
|
188
|
+
- lib/dina/models/sequence/product.rb
|
|
189
|
+
- lib/dina/models/sequence/region.rb
|
|
190
|
+
- lib/dina/models/sequence/thermocycler_profile.rb
|
|
191
|
+
- lib/dina/models/storage/storage_unit.rb
|
|
192
|
+
- lib/dina/models/storage/storage_unit_type.rb
|
|
193
|
+
- lib/dina/models/transaction/transaction.rb
|
|
185
194
|
- lib/dina/models/user.rb
|
|
186
195
|
- lib/dina/search/base_search.rb
|
|
187
196
|
- lib/dina/search/search.rb
|