Class: HTTPClients::ENATaxaClient

Inherits:
BaseClient show all
Defined in:
lib/http_clients/ena_taxa_client.rb

Overview

Retrieves taxonomic information from the ENA taxonomy database.

Usage:

```rb
client = HTTPClients::ENATaxaClient.new
client.id_from_text('human') # returns 9606
client.name_from_id(9606) # returns 'homo sapiens'
````

API usage guide: https://ena-docs.readthedocs.io/en/latest/retrieval/programmatic-access/taxon-based-search.html Swagger docs: https://www.ebi.ac.uk/ena/taxonomy/rest/swagger-ui/index.html

Instance Method Summary collapse

Instance Method Details

#conn ⇒ Object 



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# File 'lib/http_clients/ena_taxa_client.rb', line 18

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

#taxon_from_id(id) ⇒ Hash

Returns the taxon information for a given ENA taxon ID.

Parameters:

  • id (Integer, String) —

    The ENA taxon ID (eg: 9606)

Returns:

  • (Hash) —

    A hash with 'taxId', 'scientificName', and 'commonName'.



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# File 'lib/http_clients/ena_taxa_client.rb', line 52

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

#taxon_from_text(suggestion) ⇒ Hash?

Returns the ENA taxon information for a given organism suggestion string.

Parameters:

  • suggestion (String) —

    The organism name or suggestion (e.g., 'human')

Returns:

  • (Hash, nil) —

    A hash with 'taxId', 'scientificName', and 'commonName' if found, or nil if not found.



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# File 'lib/http_clients/ena_taxa_client.rb', line 33

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