Add ENA metadata seed file

db/seeds/016_ena_upload.seeds.rb

@@ -0,0 +1,63 @@
+# Custom Date dataType tailored to what ENA expects
+ena_iso_date_type = SampleAttributeType.find_or_initialize_by(title: 'ENA collection date')
+ena_iso_date_type.update(base_type: Seek::Samples::BaseType::STRING,
+                         regexp: '^(?:[12]\d{3}(?:-(?:0[1-9]|1[0-2])(?:-(?:0[1-9]|[12]\d|3[01]))?)?(?:T\d{2}:\d{2}(?::\d{2})?Z?(?:[+-]\d{1,2})?)?(?:\/\d{4}-(?:\d{2}-(?:\d{2}(?:T\d{2}:\d{2}(?::\d{2})?Z?(?:[+-]\d{1,2})?)?)?)?)?)?$|^not collected$|^not provided$|^restricted access$|^missing: control sample$|^missing: sample group$|^missing: synthetic construct$|^missing: lab stock$|^missing: third party data$|^missing: data agreement established pre-2023$|^missing: endangered species$|^missing: human-identifiable$',
+                         placeholder: '2015 or 2015-01 or 2015-01-01')
+
+# General functionalities
+def create_sample_controlled_vocab_terms_attributes(array)
+  attributes = []
+  array.each do |type|
+    attributes << { label: type }
+  end
+  attributes
+end
+
+existing_study_types = ['Whole Genome Sequencing', 'Metagenomics', 'Transcriptome Analysis', 'Resequencing',
+                        'Epigenetics', 'Synthetic Genomics', 'Forensic or Paleo-genomics', 'Gene Regulation Study',
+                        'Cancer Genomics', 'Population Genomics', 'RNASeq', 'Exome Sequencing',
+                        'Pooled Clone Sequencing', 'Transcriptome Sequencing', 'Other']
+
+disable_authorization_checks do
+  # Study
+  unless ExtendedMetadataType.where(title: 'ENA Sample Metadata', supported_type: 'Study').any?
+    study_emt = ExtendedMetadataType.new(title: 'ENA Sample Metadata', supported_type: 'Study')
+    study_emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'ena_sample_alias_prefix', required: true,
+                                                                                sample_attribute_type: SampleAttributeType.find_by(title: 'String'),
+                                                                                label: 'ENA sample alias prefix')
+    study_emt.save!
+  end
+
+  study_type_cv = SampleControlledVocab.where(title: 'ENA Study Types').first_or_create!(sample_controlled_vocab_terms_attributes: create_sample_controlled_vocab_terms_attributes(existing_study_types))
+
+  # Assay
+  unless ExtendedMetadataType.where(title: 'ENA Study metadata', supported_type: 'Assay').any?
+    assay_cmt = ExtendedMetadataType.new(title: 'ENA Study metadata', supported_type: 'Assay')
+    assay_cmt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'ena_study_title', required: true,
+                                                                  sample_attribute_type: SampleAttributeType.find_by(title: 'String'), label: 'ENA study title',
+                                                                  description: 'Title of the study as would be used in a publication.')
+    assay_cmt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'study_type', required: true,
+                                                                  sample_attribute_type: SampleAttributeType.find_by(title: 'Controlled Vocabulary'),
+                                                                  sample_controlled_vocab: study_type_cv,
+                                                                  description: 'The STUDY_TYPE presents a controlled vocabulary for expressing the overall purpose of the study.',
+                                                                  label: 'ENA Study Type')
+    assay_cmt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'new_study_type', required: false,
+                                                                  sample_attribute_type: SampleAttributeType.find_by(title: 'String'), label: 'New Study Type',
+                                                                  description: 'Specify a new Study Type here if "Other" was chosen as "ENA Study Type".')
+    assay_cmt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'ena_study_abstract', required: true,
+                                                                  sample_attribute_type: SampleAttributeType.find_by(title: 'Text'), label: 'ENA study abstract',
+                                                                  description: 'Briefly describes the goals, purpose, and scope of the Study.  This need not be listed if it can be inherited from a referenced publication.')
+    assay_cmt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'assay_stream', required: true,
+                                                                  sample_attribute_type: SampleAttributeType.find_by(title: 'String'),
+                                                                  description: 'This is the name that will be transferred to the ISA JSON. Example: "My assay" will be defined as "a_my_assay.txt" in the ISA JSON',
+                                                                  label: 'Name Assay Stream')
+    assay_cmt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'ena_study_alias_prefix', required: true,
+                                                                  sample_attribute_type: SampleAttributeType.find_by(title: 'String'), label: 'ENA study alias prefix')
+    assay_cmt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'ena_experiment_alias_prefix', required: true,
+                                                                  sample_attribute_type: SampleAttributeType.find_by(title: 'String'), label: 'ENA experiment alias prefix')
+    assay_cmt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'ena_run_alias_prefix', required: true,
+                                                                  sample_attribute_type: SampleAttributeType.find_by(title: 'String'), label: 'ENA run alias prefix')
+    assay_cmt.save!
+  end
+end
+puts 'Seeded ENA extended metadata'