scinote-web/app/models/organization.rb

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class Organization < ActiveRecord::Base
# Not really MVC-compliant, but we just use it for logger
# output in space_taken related functions
include ActionView::Helpers::NumberHelper
auto_strip_attributes :name, :description, nullify: false
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validates :name,
length: { minimum: Constants::NAME_MIN_LENGTH,
maximum: Constants::NAME_MAX_LENGTH }
validates :description, length: { maximum: Constants::TEXT_MAX_LENGTH }
validates :space_taken, presence: true
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belongs_to :created_by, :foreign_key => 'created_by_id', :class_name => 'User'
belongs_to :last_modified_by, foreign_key: 'last_modified_by_id', class_name: 'User'
has_many :user_organizations, inverse_of: :organization, dependent: :destroy
has_many :users, through: :user_organizations
has_many :samples, inverse_of: :organization
has_many :samples_tables, inverse_of: :organization, dependent: :destroy
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has_many :sample_groups, inverse_of: :organization
has_many :sample_types, inverse_of: :organization
has_many :logs, inverse_of: :organization
has_many :projects, inverse_of: :organization
has_many :custom_fields, inverse_of: :organization
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has_many :protocols, inverse_of: :organization, dependent: :destroy
has_many :protocol_keywords, inverse_of: :organization, dependent: :destroy
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# Based on file's extension opens file (used for importing)
def self.open_spreadsheet(file)
filename = file.original_filename
file_path = file.path
if file.class == Paperclip::Attachment and file.is_stored_on_s3?
fa = file.fetch
file_path = fa.path
end
case File.extname(filename)
when ".csv" then
Roo::CSV.new(file_path, extension: :csv)
when ".tdv" then
Roo::CSV.new(file_path, nil, :ignore, csv_options: {col_sep: "\t"})
when ".txt" then
# This assumption is based purely on biologist's habits
Roo::CSV.new(file_path, csv_options: {col_sep: "\t"})
when ".xls" then
Roo::Excel.new(file_path)
when ".xlsx" then
Roo::Excelx.new(file_path)
else
raise TypeError
end
end
# Writes to user log
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def log(message)
final = "[%s] %s" % [Time.current.to_s, message]
logs.create(message: final)
end
# Imports samples into db
# -1 == sample_name,
# -2 == sample_type,
# -3 == sample_group
# TODO: use constants
def import_samples(sheet, mappings, user)
errors = []
nr_of_added = 0
total_nr = 0
# First let's query for all custom_fields we're refering to
custom_fields = []
sname_index = -1
stype_index = -1
sgroup_index = -1
mappings.each.with_index do |(k, v), i|
if v == "-1"
# Fill blank space, so our indices stay the same
custom_fields << nil
sname_index = i
elsif v == "-2"
custom_fields << nil
stype_index = i
elsif v == "-3"
custom_fields << nil
sgroup_index = i
else
cf = CustomField.find_by_id(v)
# Even if doesn't exist we add nil value in order not to destroy our
# indices
custom_fields << cf
end
end
# Now we can iterate through sample data and save stuff into db
(2..sheet.last_row).each do |i|
error = []
total_nr += 1
sample = Sample.new(
name: sheet.row(i)[sname_index],
organization_id: id,
user: user
)
if sample.save
sheet.row(i).each.with_index do |value, index|
# We need to have sample saved before messing with custom fields (they
# need sample id)
if index == stype_index
stype = SampleType.where(name: value, organization_id: id).take();
if stype
sample.sample_type = stype
else
sample.create_sample_type(
name: value,
organization_id: id
)
end
sample.save
elsif index == sgroup_index
sgroup = SampleGroup.where(name: value, organization_id: id).take();
if sgroup
sample.sample_group = sgroup
else
sample.create_sample_group(
name: value,
organization_id: id
)
end
sample.save
elsif value and mappings[index.to_s].strip.present? and index != sname_index
if custom_fields[index]
# we're working with CustomField
scf = SampleCustomField.new(
sample_id: sample.id,
custom_field_id: custom_fields[index].id,
value: value
)
if !scf.save
error << scf.errors.messages
end
else
# This custom_field does not exist
error << {"#{mappings[index]}": "Does not exists"}
end
end
end
else
error << sample.errors.messages
end
if error.present?
errors << { "#{i}": error}
else
nr_of_added += 1
end
end
if errors.count > 0 then
return {
status: :error,
errors: errors,
nr_of_added: nr_of_added,
total_nr: total_nr
}
else
return {
status: :ok,
nr_of_added: nr_of_added,
total_nr: total_nr
}
end
end
def to_csv(samples, headers)
require "csv"
# Parse headers (magic numbers should be refactored - see
# sample-datatable.js)
header_names = []
headers.each do |header|
if header == "-1"
header_names << I18n.t("samples.table.sample_name")
elsif header == "-2"
header_names << I18n.t("samples.table.sample_type")
elsif header == "-3"
header_names << I18n.t("samples.table.sample_group")
elsif header == "-4"
header_names << I18n.t("samples.table.added_by")
elsif header == "-5"
header_names << I18n.t("samples.table.added_on")
else
cf = CustomField.find_by_id(header)
if cf
header_names << cf.name
else
header_names << nil
end
end
end
CSV.generate do |csv|
csv << header_names
samples.each do |sample|
sample_row = []
headers.each do |header|
if header == "-1"
sample_row << sample.name
elsif header == "-2"
sample_row << (sample.sample_type.nil? ? I18n.t("samples.table.no_type") : sample.sample_type.name)
elsif header == "-3"
sample_row << (sample.sample_group.nil? ? I18n.t("samples.table.no_group") : sample.sample_group.name)
elsif header == "-4"
sample_row << sample.user.full_name
elsif header == "-5"
sample_row << I18n.l(sample.created_at, format: :full)
else
scf = SampleCustomField.where(
custom_field_id: header,
sample_id: sample.id
).take
if scf
sample_row << scf.value
else
sample_row << nil
end
end
end
csv << sample_row
end
end
end
# Get all header fields for samples (used in importing for mappings - dropdowns)
def get_available_sample_fields
fields = {};
# First and foremost add sample name
fields["-1"] = I18n.t("samples.table.sample_name")
fields["-2"] = I18n.t("samples.table.sample_type")
fields["-3"] = I18n.t("samples.table.sample_group")
# Add all other custom fields
CustomField.where(organization_id: id).order(:created_at).each do |cf|
fields[cf.id] = cf.name
end
fields
end
# (re)calculate the space taken by this organization
def calculate_space_taken
st = 0
projects.includes(
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experiments: {
my_modules: {
protocols: { steps: :assets },
results: { result_asset: :asset }
}
}
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).find_each do |project|
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project.project_my_modules.find_each do |my_module|
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my_module.protocol.steps.find_each do |step|
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step.assets.find_each { |asset| st += asset.estimated_size }
end
my_module.results.find_each do |result|
if result.is_asset then
st += result.asset.estimated_size
end
end
end
end
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# project.experiments.each |experiment|
self.space_taken = [st, Constants::MINIMAL_ORGANIZATION_SPACE_TAKEN].max
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Rails::logger.info "Organization #{self.id}: " +
"space (re)calculated to: " +
"#{self.space_taken}B (#{number_to_human_size(self.space_taken)})"
end
# Take specified amount of bytes
def take_space(space)
orig_space = self.space_taken
self.space_taken += space
Rails::logger.info "Organization #{self.id}: " +
"space taken: " +
"#{orig_space}B + #{space}B = " +
"#{self.space_taken}B (#{number_to_human_size(self.space_taken)})"
end
# Release specified amount of bytes
def release_space(space)
orig_space = self.space_taken
self.space_taken = [space_taken - space,
Constants::MINIMAL_ORGANIZATION_SPACE_TAKEN].max
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Rails::logger.info "Organization #{self.id}: " +
"space released: " +
"#{orig_space}B - #{space}B = " +
"#{self.space_taken}B (#{number_to_human_size(self.space_taken)})"
end
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def protocol_keywords_list
ProtocolKeyword.where(organization: self).pluck(:name)
end
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end