How can I load data into database using activerecord - sql

Question

I have a ruby script that extracts information from a file (genbank) and I would like to load this data into the database. I have created the model and the schema and a connection script:
require 'active_record'
def establish_connection(db_location= "protein.db.sqlite3")
ActiveRecord::Base.establish_connection(
:adapter => "sqlite3",
:database => db_location,
:pool => 5,
:timeout => 5000
)
end
This is my script that outputs the data:
require 'rubygems'
require 'bio'
require 'snp_db_models'
establish_connection
snp_positions_file = File.open("snp_position.txt")
outfile = File.open("output.txt", "w")
genome_sequence = Bio::FlatFile.open(Bio::EMBL, "ref.embl").next_entry
snp_positions = Array.new
snp_positions_file.gets # header line
while line = snp_positions_file.gets
snp_details = line.chomp.split("\t")
snp_seq = snp_details[1]
snp_positions << snp_details[1].to_i
end
mean_snp_per_base = snp_positions.size/genome_sequence.sequence_length.to_f
puts "Mean snps per base: #{mean_snp_per_base}"
#outfile = File.open("/Volumes/DataRAID/Projects/GAS/fastq_files/bowtie_results/snp_annotation/genes_with_higher_snps.tsv", "w")
outfile.puts("CDS start\tCDS end\tStrand\tGene\tLocus_tag\tnote\tsnp_ID\ttranslation_seq\tProduct\tNo_of_snps_per_gene\tsnp_rate_vs_mean")
genome_sequence.features do |feature|
if feature.feature !~ /gene/i && feature.feature !~ /source/i
start_pos = feature.locations.locations.first.from
end_pos = feature.locations.locations.first.to
number_of_snps_in_gene = (snp_positions & (start_pos..end_pos).to_a).size # intersect finds number of times snp occurs within cds location
mean_snp_per_base_in_gene = number_of_snps_in_gene.to_f/(end_pos - start_pos)
outfile.print "#{start_pos}\t"
outfile.print "#{end_pos}\t"
if feature.locations.locations.first.strand == 1
outfile.print "forward\t"
else
outfile.print "reverse\t"
end
qualifiers = feature.to_hash
["gene", "locus_tag", "note", "snp_id", "translation", "product"].each do |qualifier|
if qualifiers.has_key?(qualifier) # if there is gene and product in the file
# puts "#{qualifier}: #{qualifiers[qualifier]}"
outfile.print "#{qualifiers[qualifier].join(",")}\t"
else
outfile.print " \t"
end
end
outfile.print "#{number_of_snps_in_gene}\t"
outfile.print "%.2f" % (mean_snp_per_base_in_gene/mean_snp_per_base)
outfile.puts
end
end
outfile.close
How can I load the data in outfile.txt into the database. Do I have to do something like marshall dump?
Thanks in advance
Mark

Answer 1

Your can write a rake task to do this. Save it in lib/tasks and give it a .rake extension.
desc "rake task to load data into db"
task :load_data_db => :environment do
...
end
Since the rails environment is loaded, you can access your Model directly as you would in any Rails model/controller. Of course, it'll connect to the database depending on the environment variable defined when you execute your rake task.

Answer 2

In a mere script, your models are unknown.
You have to define a minimum to use them as if in a Rails App. Simply declare them:
class Foo << ActiveRecord:Base
end
Otherwise, in a Rails context, use rake tasks which are aware of the Rails app details.