Class: PlateBarcode

Inherits:
Object
  • Object
show all
Extended by:
Dev::PlateBarcode::CacheBarcodes
Defined in:
app/models/plate_barcode.rb

Overview

Class that handles the access to Baracoda to obtain new barcodes

Constant Summary

Constants included from Dev::PlateBarcode::CacheBarcodes

Dev::PlateBarcode::CacheBarcodes::MAX_SIZE_CACHE

Class Method Summary collapse

Methods included from Dev::PlateBarcode::CacheBarcodes

barcode_in_cache?, cache_barcode, data_cache, dev_cache_get_next_barcode, reset_cache, resize_cache

Class Method Details

._connection_scope(url, data = nil) ⇒ Object

Creates required objects to perform a call to the server so they can be reused inside the scope. Args:

  • url: string that contains the url to connect
  • data: object that we will POST to the url. If not defined it will be an empty POST. Yields:
  • http_connection - Net::HTTP instance to connect to the host/port
  • request - Net::HTTP::Post object that contains the params for the request like the body, headers, etc


93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
 
# File 'app/models/plate_barcode.rb', line 93

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

._retries_scope(retries, wait_timeout) ⇒ Object

Retries the number of times specified before calling the block. It sleeps wait_timeout in between calls except with the last call. Args:

  • retries - int, Number of times it will retry to use the block
  • wait_timeout - float. Time sleep in between calls to baracoda when connection is refused Yields: Nothing


73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
 
# File 'app/models/plate_barcode.rb', line 73

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

.create_barcode ⇒ Object

Creates a new single barcode in baracoda Returns:

  • Barcode instance, using Sequencescape22 format


16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
 
# File 'app/models/plate_barcode.rb', line 16

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

.create_barcode_with_text(text) ⇒ Object

Creates a new single barcode with a code text in baracoda Arguments: text - str with the code of up to 3 characters that will be appended after the prefix Returns:

  • Barcode instance, using Sequencescape22 format


27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
 
# File 'app/models/plate_barcode.rb', line 27

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

.create_child_barcodes(parent_barcode, count = 1) ⇒ Object

Creates a new group of child barcodes from a parent barcode. Args:

  • parent_barcode - String with the barcode we want to create children from
  • count - Number of children to create Returns:
  • Barcode instance, using Sequencescape22 format


38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
 
# File 'app/models/plate_barcode.rb', line 38

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

.fetch_response(url, data = nil, retries = 3, wait_timeout = 0.1) ⇒ Object

Obtain a record from Baracoda and retries the specified amount of time. If the number or retries is reached the method will raise an exception Args:

  • http_connection - Net::HTTP instance to connect to the host/port
  • request - Net::HTTP::Post object that contains the params for the request like the body, headers, etc
  • retries - int, defaults to 3. Number of times it will retry to call baracoda. After that time period it will raise exception
  • wait_timeout - float, defaults to 0.1 (100 ms). Time sleep in between calls to baracoda when connection is refused Returns:
  • Json parsed hash with the response from Baracoda
  • If no answers is obtained, it raises an exception


55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
 
# File 'app/models/plate_barcode.rb', line 55

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

.prefix ⇒ Object 



9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
 
# File 'app/models/plate_barcode.rb', line 9

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

.site ⇒ Object 



5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
 
# File 'app/models/plate_barcode.rb', line 5

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end