Class: Api::V2::QcFileResource

Inherits:
BaseResource
  • Object
show all
Defined in:
app/resources/api/v2/qc_file_resource.rb

Overview

Note:

Access this resource via the /api/v2/qc_files/ endpoint.

Note:

This resource cannot be modified after creation: its endpoint will not accept PATCH requests.

Note:

Known issue

Occasionally, encoding failures may occur resulting in 500 Internal Server errors mentioning from ASCII-8BIT to UTF-8. If this occurs, try re-requesting the resource without including the contents attribute, for example: /api/v2/qc_files/1?fields[qc_files]=filename,uuid,created_at

Provides a JSON:API representation of QcFile which contains the QC data previously added to a piece of Labware. The file contents are stored in the database using the DbFile model.

For more information about JSON:API see the JSON:API Specifications or look at the JSONAPI::Resources package for Sequencescape's implementation of the JSON:API standard.

Examples:

POST request

POST /api/v2/qc_files/
{
  "data": {
    "type": "qc_files",
    "attributes": {
      "filename": "a_test_file.csv",
      "contents": "Hello"
    },
    "relationships": {
      // "asset": {
      //   "data": {
      //     "type": "labware",
      //     "id": 26
      //   }
      // }
    }
  }
}

GET request for all QcFile resources

GET /api/v2/qc_files/

GET request for a QcFile with ID 123

GET /api/v2/qc_files/123/

GET request for all QcFile resources associated with a Plate with ID 123

GET /api/v2/plates/123/qc_files/

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Methods inherited from BaseResource

apply_includes, creatable_fields, default_includes, #fetchable_fields, inclusions, resolve_relationship_names_to_relations, updatable_fields

Instance Attribute Details

#content_type ⇒ String (readonly)

Returns The content type, or MIME type, of the QC file.

Returns:

  • (String) —

    The content type, or MIME type, of the QC file.



56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
 
# File 'app/resources/api/v2/qc_file_resource.rb', line 56

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

#contents ⇒ String

Returns the file contents as UTF-8.

Not all uploaded files contain encoding information, causing encoding errors on less-common characters. See background at https://yehudakatz.com/2010/05/05/ruby-1-9-encodings-a-primer-and-the-solution-for-rails/

Returns:

  • (String) —

    The contents of the QC file.



96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
 
# File 'app/resources/api/v2/qc_file_resource.rb', line 96

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

#created_at ⇒ DateTime (readonly)

Returns The date and time the QC file was created.

Returns:

  • (DateTime) —

    The date and time the QC file was created.



60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
 
# File 'app/resources/api/v2/qc_file_resource.rb', line 60

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

#filename ⇒ String

Returns The filename of the QC file. This can only be written once on creation.

Returns:

  • (String) —

    The filename of the QC file. This can only be written once on creation.



114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
 
# File 'app/resources/api/v2/qc_file_resource.rb', line 114

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

#labware ⇒ LabwareResource

Returns The Labware which this QcFile belongs to.

Returns:



76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
 
# File 'app/resources/api/v2/qc_file_resource.rb', line 76

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

#size ⇒ Integer (readonly)

Returns The size of the QC file in bytes.

Returns:

  • (Integer) —

    The size of the QC file in bytes.



64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
 
# File 'app/resources/api/v2/qc_file_resource.rb', line 64

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

#uuid ⇒ String (readonly)

Returns The UUID of the bulk transfers operation.

Returns:

  • (String) —

    The UUID of the bulk transfers operation.



68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
 
# File 'app/resources/api/v2/qc_file_resource.rb', line 68

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

Class Method Details

.create(context) ⇒ Object 



117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
 
# File 'app/resources/api/v2/qc_file_resource.rb', line 117

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

Instance Method Details

#filter_uuid ⇒ Object

Filter the QcFile resources by UUID.

Examples:

GET request with UUID filter

GET /api/v2/qc_files?filter[uuid]=12345678-1234-1234-1234-123456789012


86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
 
# File 'app/resources/api/v2/qc_file_resource.rb', line 86

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