require 'active_record'
class SampleDatatable < AjaxDatatablesRails::Base
include SamplesHelper
ASSIGNED_SORT_COL = "assigned"
def initialize(view,
organization,
project = nil,
my_module = nil,
experiment = nil)
super(view)
@organization = organization
@project = project
@my_module = my_module
@experiment = experiment
end
# Define sortable columns, so 1st column will be sorted by attribute in sortable_columns[0]
def sortable_columns
sort_array = [
ASSIGNED_SORT_COL,
"Sample.name",
"SampleType.name",
"SampleGroup.name",
"Sample.created_at",
"User.full_name",
]
sort_array.push(*custom_fields_sort_by)
@sortable_columns ||= sort_array
end
# Define attributes on which we perform search
def searchable_columns
search_array = [
"Sample.name",
"SampleType.name",
"SampleGroup.name",
"Sample.created_at",
"User.full_name"
]
search_array.push(*custom_fields_sort_by)
@searchable_columns ||= filter_search_array search_array
end
private
# filters the search array by checking if the the column is visible
def filter_search_array input_array
param_index = 2
filtered_array =[]
input_array.each do |col|
unless params[:columns].to_a[param_index] == nil
filtered_array.push(col) unless params[:columns].to_a[param_index][1]["searchable"] == "false"
param_index += 1
end
end
filtered_array
end
# Get array of columns to sort by (for custom fields)
def custom_fields_sort_by
num_cf = CustomField.where(organization_id: @organization).count
array = []
for _ in 0..num_cf
array << "SampleCustomField.value"
end
array
end
# Returns json of current samples (already paginated)
def data
records.map do |record|
sample = {
"DT_RowId": record.id,
"1": assigned_cell(record),
"2": record.name,
"3": record.sample_type.nil? ? I18n.t("samples.table.no_type") : record.sample_type.name,
"4": record.sample_group.nil? ?
" " + I18n.t("samples.table.no_group") :
" " + record.sample_group.name,
"5": I18n.l(record.created_at, format: :full),
"6": record.user.full_name,
"sampleInfoUrl": Rails.application.routes.url_helpers.edit_sample_path(record.id),
"sampleUpdateUrl": Rails.application.routes.url_helpers.sample_path(record.id)
}
# Add custom attributes
record.sample_custom_fields.each do |scf|
sample[@cf_mappings[scf.custom_field_id]] = scf.value
end
sample
end
end
def assigned_cell(record)
@assigned_samples.include?(record) ?
" " :
" "
end
# Query database for records (this will be later paginated and filtered)
# after that "data" function will return json
def get_raw_records
samples = Sample
.includes(
:sample_type,
:sample_group,
:user,
:sample_custom_fields
)
.references(
:sample_type,
:sample_group,
:user,
:sample_custom_fields
)
.where(
organization: @organization
)
if @my_module
@assigned_samples = @my_module.samples
samples = samples.joins("LEFT OUTER JOIN sample_my_modules ON
(samples.id = sample_my_modules.sample_id AND
(sample_my_modules.my_module_id = #{@my_module.id.to_s} OR
sample_my_modules.id IS NULL))")
.references(:sample_my_modules)
elsif @project
@assigned_samples = @project.assigned_samples
ids = @project.my_modules_ids
if ids.blank?
samples = samples.joins('LEFT OUTER JOIN sample_my_modules ON
(samples.id = sample_my_modules.sample_id AND
sample_my_modules.id IS NULL)')
.references(:sample_my_modules)
else
samples = samples.joins("LEFT OUTER JOIN sample_my_modules ON
(samples.id = sample_my_modules.sample_id AND
(sample_my_modules.my_module_id IN (#{ids}) OR
sample_my_modules.id IS NULL))")
.references(:sample_my_modules)
end
elsif @experiment
@assigned_samples = @experiment.assigned_samples
ids = @experiment.my_modules.select(:id)
samples = samples.joins("LEFT OUTER JOIN sample_my_modules ON
(samples.id = sample_my_modules.sample_id AND
(sample_my_modules.my_module_id IN (#{ids.to_sql}) OR
sample_my_modules.id IS NULL))")
.references(:sample_my_modules)
end
# Make mappings of custom fields, so we have same id for every column
i = 7
@cf_mappings = {}
all_custom_fields.each do |cf|
@cf_mappings[cf.id] = i.to_s
i += 1
end
samples
end
# Override default behaviour
# Don't filter and paginate records when sorting by custom column - everything
# is done in sort_records method - you might ask why, well if you want the
# number of samples/all samples it's dependant upon sort_record query
def fetch_records
records = get_raw_records
records = sort_records(records) if params[:order].present?
escape_special_chars
records = filter_records(records) if params[:search].present? && (not (sorting_by_custom_column))
records = paginate_records(records) if (not (params[:length].present? && params[:length] == '-1')) && (not (sorting_by_custom_column))
records
end
# Override default sort method if needed
def sort_records(records)
if params[:order].present? and params[:order].length == 1
if sort_column(params[:order].values[0]) == ASSIGNED_SORT_COL
# If "assigned" column is sorted
if @my_module then
# Depending on the sort, order nulls first or
# nulls last on sample_my_modules association
records.order("sample_my_modules.id NULLS #{sort_null_direction(params[:order].values[0])}")
elsif @experiment
# A very elegant solution to sort assigned samples at a experiment level
# grabs the ids of samples which has a modules that belongs to this project
assigned = Sample
.joins('LEFT OUTER JOIN "sample_my_modules" ON "sample_my_modules"."sample_id" = "samples"."id"')
.joins('LEFT OUTER JOIN "my_modules" ON "my_modules"."id" = "sample_my_modules"."my_module_id"')
.where('"my_modules"."experiment_id" = ?', @experiment.id)
.where('"my_modules"."nr_of_assigned_samples" > 0')
.select('"samples"."id"')
.distinct
# grabs the ids that are not the previous one but are still of the same organization
unassigned = Sample
.where('"samples"."organization_id" = ?', @organization.id)
.where('"samples"."id" NOT IN (?)', assigned)
.select('"samples"."id"')
.distinct
# check the input param and merge the two arrays of ids
if params[:order].values[0]['dir'] == 'asc'
ids = assigned + unassigned
elsif params[:order].values[0]['dir'] == 'desc'
ids = unassigned + assigned
end
ids = ids.collect(&:id)
# order the records by input ids
order_by_index = ActiveRecord::Base.send(
:sanitize_sql_array,
["position((',' || samples.id || ',') in ?)",
ids.join(',') + ','] )
records.where(id: ids).order(order_by_index)
elsif @project
# A very elegant solution to sort assigned samples at a project level
# grabs the ids of samples which has a modules that belongs to this project
assigned = Sample
.joins('LEFT OUTER JOIN "sample_my_modules" ON "sample_my_modules"."sample_id" = "samples"."id"')
.joins('LEFT OUTER JOIN "my_modules" ON "my_modules"."id" = "sample_my_modules"."my_module_id"')
.joins('LEFT OUTER JOIN "experiments" ON "experiments"."id" = "my_modules"."experiment_id"')
.where('"experiments"."project_id" = ?', @project.id)
.where('"my_modules"."nr_of_assigned_samples" > 0')
.select('"samples"."id"')
.distinct
# grabs the ids that are not the previous one but are still of the same organization
unassigned = Sample
.where('"samples"."organization_id" = ?', @organization.id)
.where('"samples"."id" NOT IN (?)', assigned)
.select('"samples"."id"')
.distinct
# check the input param and merge the two arrays of ids
if params[:order].values[0]["dir"] == "asc"
ids = assigned + unassigned
elsif params[:order].values[0]["dir"] == "desc"
ids = unassigned + assigned
end
ids = ids.collect { |s| s.id }
# order the records by input ids
order_by_index = ActiveRecord::Base.send(:sanitize_sql_array,
["position((',' || samples.id || ',') in ?)", ids.join(',') + ','] )
records.where(id: ids).order(order_by_index)
end
elsif sorting_by_custom_column
# Check if have to filter samples first
if params[:search].present? and params[:search][:value].present?
# Couldn't force ActiveRecord to yield the same query as below because
# Rails apparently forgets to join stuff in subqueries -
# #justrailsthings
conditions = build_conditions_for(params[:search][:value])
filter_query = 'SELECT "samples"."id" FROM "samples"
LEFT OUTER JOIN "sample_custom_fields" ON "sample_custom_fields"."sample_id" = "samples"."id"
LEFT OUTER JOIN "sample_types" ON "sample_types"."id" = "samples"."sample_type_id"
LEFT OUTER JOIN "sample_groups" ON "sample_groups"."id" = "samples"."sample_group_id"
LEFT OUTER JOIN "users" ON "users"."id" = "samples"."user_id"
WHERE "samples"."organization_id" = ' + @organization.id.to_s + ' AND ' + conditions.to_sql
records = records.where("samples.id IN (#{filter_query})")
end
cf_id = all_custom_fields[params[:order].values[0]["column"].to_i - 7].id
dir = sort_direction(params[:order].values[0])
# Because samples can have multiple sample custom fields, we first group
# them by samples.id and inside that group we sort them by cf_id. Because
# we sort them ASC, sorted columns will be on top. Distinct then only
# takes the first row and cuts the rest of every group and voila we have
# 1 row for every sample, which are not sorted yet ...
records = records.select("DISTINCT ON (samples.id) *")
.order("samples.id, CASE WHEN sample_custom_fields.custom_field_id = #{cf_id} THEN 1 ELSE 2 END ASC")
# ... this little gem (pun intended) then takes the records query, sorts it again
# and paginates it. sq.t0_* are determined empirically and are crucial -
# imagine A -> B -> C transitive relation but where A and C are the
# same. Useless right? But not when you acknowledge that find_by_sql
# method does some funky stuff when your query spans multiple queries -
# Sample object might have id from SampleType, name from
# User ... chaos ensues basically. If something changes in db this might
# change.
formated_date = (I18n.t 'time.formats.datatables_date').gsub!(/^\"|\"?$/, '')
Sample.find_by_sql("SELECT sq.t0_r0 as id, sq.t0_r1 as name, to_char( sq.t0_r4, '#{ formated_date }' ) as created_at, sq.t0_r5, sq.t0_r6 as sample_group_id ,sq.t0_r7 as sample_type_id, sq.t0_r2 as user_id, sq.custom_field_id FROM (#{records.to_sql})
as sq ORDER BY CASE WHEN sq.custom_field_id = #{cf_id} THEN 1 ELSE 2 END #{dir}, sq.value #{dir}
LIMIT #{per_page} OFFSET #{offset}")
else
super(records)
end
else
super(records)
end
end
#(I18n.t('time.formats.datatables_date')).gsub("\"", '\'')
# A hack that overrides the new_search_contition method default behavior of the ajax-datatables-rails gem
# now the method checks if the column is the created_at and generate a custom SQL to parse
# it back to the caller method
def new_search_condition(column, value)
model, column = column.split('.')
model = model.constantize
formated_date = (I18n.t 'time.formats.datatables_date').gsub!(/^\"|\"?$/, '')
if column == 'created_at'
casted_column = ::Arel::Nodes::NamedFunction.new('CAST',
[ Arel.sql("to_char( samples.created_at, '#{ formated_date }' ) AS VARCHAR") ] )
else
casted_column = ::Arel::Nodes::NamedFunction.new('CAST',
[model.arel_table[column.to_sym].as(typecast)])
end
casted_column.matches("%#{value}%")
end
def sort_null_direction(item)
val = sort_direction(item)
val == "ASC" ? "LAST" : "FIRST"
end
def inverse_sort_direction(item)
val = sort_direction(item)
val == "ASC" ? "DESC" : "ASC"
end
def sorting_by_custom_column
params[:order].values[0]["column"].to_i > 6
end
# Escapes special characters in search query
def escape_special_chars
params[:search][:value] = ActiveRecord::Base
.send(:sanitize_sql_like,
params[:search][:value]) if params[:search]
.present?
end
end