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Merge pull request #725 from okriuchykhin/ok_SCI_1409

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Fix datatables [SCI-1409]
This commit is contained in:
okriuchykhin 2017-07-03 15:47:19 +02:00 committed by GitHub
parent 1b2884c1b7 b234c07c13
commit 2e24e6b73a
10 changed files with 300 additions and 313 deletions
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40
app/datatables/custom_datatable.rb Normal file
View file

@ -0,0 +1,40 @@
class CustomDatatable < AjaxDatatablesRails::Base
private
def dt_params
@dt_params ||=
params.permit(:assigned, :draw, :length, :start, search: %i(value regex))
.to_h
end
def columns_params
@columns_params ||= params.require(:columns).permit!.to_h
end
def order_params
@order_params ||=
params.require(:order).require('0').permit(:column, :dir).to_h
end
def fetch_records
records = get_raw_records
records = sort_records(records) if order_params.present?
records = filter_records(records) if dt_params[:search].present?
records = paginate_records(records) unless dt_params[:length].present? &&
dt_params[:length] == '-1'
records
end
def sort_records(records)
sort_by = "#{sort_column(order_params)} #{sort_direction(order_params)}"
records.order(sort_by)
end
def generate_sortable_displayed_columns
@sortable_displayed_columns = []
columns_params.each_value do |col|
@sortable_displayed_columns << col[:data] if col[:orderable] == 'true'
end
@sortable_displayed_columns
end
end

12
app/datatables/load_from_repository_protocols_datatable.rb
View file

@ -1,4 +1,4 @@
class LoadFromRepositoryProtocolsDatatable < AjaxDatatablesRails::Base
class LoadFromRepositoryProtocolsDatatable < CustomDatatable
# Needed for sanitize_sql_like method
include ActiveRecord::Sanitization::ClassMethods
include InputSanitizeHelper
@ -57,10 +57,10 @@ class LoadFromRepositoryProtocolsDatatable < AjaxDatatablesRails::Base
# See https://github.com/antillas21/ajax-datatables-rails/issues/112
def as_json(options = {})
{
:draw => params[:draw].to_i,
:recordsTotal => get_raw_records.length,
:recordsFiltered => filter_records(get_raw_records).length,
:data => data
draw: dt_params[:draw].to_i,
recordsTotal: get_raw_records.length,
recordsFiltered: filter_records(get_raw_records).length,
data: data
}
end
@ -166,7 +166,7 @@ class LoadFromRepositoryProtocolsDatatable < AjaxDatatablesRails::Base
def build_conditions_for(query)
# Inner query to retrieve list of protocol IDs where concatenated
# protocol keywords string, or user's full_name contains searched query
search_val = params[:search][:value]
search_val = dt_params[:search][:value]
records_having = get_raw_records_base.having(
::Arel::Nodes::NamedFunction.new(
'CAST',

2
app/datatables/protocol_linked_children_datatable.rb
View file

@ -1,4 +1,4 @@
class ProtocolLinkedChildrenDatatable < AjaxDatatablesRails::Base
class ProtocolLinkedChildrenDatatable < CustomDatatable
def_delegator :@view, :link_to
def_delegator :@view, :protocols_my_module_path

12
app/datatables/protocols_datatable.rb
View file

@ -1,4 +1,4 @@
class ProtocolsDatatable < AjaxDatatablesRails::Base
class ProtocolsDatatable < CustomDatatable
# Needed for sanitize_sql_like method
include ActiveRecord::Sanitization::ClassMethods
include InputSanitizeHelper
@ -48,10 +48,10 @@ class ProtocolsDatatable < AjaxDatatablesRails::Base
# See https://github.com/antillas21/ajax-datatables-rails/issues/112
def as_json(options = {})
{
:draw => params[:draw].to_i,
:recordsTotal => get_raw_records.length,
:recordsFiltered => filter_records(get_raw_records).length,
:data => data
draw: dt_params[:draw].to_i,
recordsTotal: get_raw_records.length,
recordsFiltered: filter_records(get_raw_records).length,
data: data
}
end
@ -229,7 +229,7 @@ class ProtocolsDatatable < AjaxDatatablesRails::Base
def build_conditions_for(query)
# Inner query to retrieve list of protocol IDs where concatenated
# protocol keywords string, or user's full_name contains searched query
search_val = params[:search][:value]
search_val = dt_params[:search][:value]
records_having = get_raw_records_base.having(
::Arel::Nodes::NamedFunction.new(
'CAST',

170
app/datatables/repository_datatable.rb
View file

@ -1,6 +1,6 @@
require 'active_record'
class RepositoryDatatable < AjaxDatatablesRails::Base
class RepositoryDatatable < CustomDatatable
include ActionView::Helpers::TextHelper
include SamplesHelper
include InputSanitizeHelper
@ -79,9 +79,9 @@ class RepositoryDatatable < AjaxDatatablesRails::Base
param_index = 2
filtered_array = []
input_array.each do |col|
next if params[:columns].to_a[param_index].nil?
next if columns_params.to_a[param_index].nil?
params_col =
params[:columns].to_a.find { |v| v[1]['data'] == param_index.to_s }
columns_params.to_a.find { |v| v[1]['data'] == param_index.to_s }
filtered_array.push(col) unless params_col[1]['searchable'] == 'false'
param_index += 1
end
@ -166,7 +166,7 @@ class RepositoryDatatable < AjaxDatatablesRails::Base
)
.joins(:created_by)
.where(repository: @repository)
return @assigned_rows if params[:assigned] == 'assigned'
return @assigned_rows if dt_params[:assigned] == 'assigned'
else
@assigned_rows = repository_rows.joins(
'INNER JOIN my_module_repository_rows ON
@ -183,10 +183,11 @@ class RepositoryDatatable < AjaxDatatablesRails::Base
# number of samples/all samples it's dependant upon sort_record query
def fetch_records
records = get_raw_records
records = filter_records(records) if params[:search].present?
records = sort_records(records) if params[:order].present?
records = paginate_records(records) unless params[:length].present? &&
params[:length] == '-1'
records = filter_records(records) if dt_params[:search].present? &&
dt_params[:search][:value].present?
records = sort_records(records) if order_params.present?
records = paginate_records(records) unless dt_params[:length].present? &&
dt_params[:length] == '-1'
escape_special_chars
records
end
@ -195,10 +196,7 @@ class RepositoryDatatable < AjaxDatatablesRails::Base
# NOTE: Function assumes the provided records/rows are only from the current
# repository!
def filter_records(repo_rows)
return repo_rows unless params[:search].present? &&
params[:search][:value].present?
search_val = params[:search][:value]
search_val = dt_params[:search][:value]
filtered_rows = repo_rows.find_by_sql(
"SELECT DISTINCT repository_rows.*
FROM repository_rows
@ -232,123 +230,43 @@ class RepositoryDatatable < AjaxDatatablesRails::Base
# Override default sort method if needed
def sort_records(records)
if params[:order].present? && params[:order].length == 1
if sort_column(params[:order].values[0]) == ASSIGNED_SORT_COL
# If "assigned" column is sorted
direction = sort_null_direction(params[:order].values[0])
if @my_module
# Depending on the sort, order nulls first or
# nulls last on repository_cells association
records.joins(
"LEFT OUTER JOIN my_module_repository_rows ON
(repository_rows.id = my_module_repository_rows.repository_row_id
AND (my_module_repository_rows.my_module_id = #{@my_module.id} OR
my_module_repository_rows.id IS NULL))"
).order("my_module_repository_rows.id NULLS #{direction}")
else
records.joins(
'LEFT OUTER JOIN my_module_repository_rows ON
(repository_rows.id = my_module_repository_rows.repository_row_id)'
).order("my_module_repository_rows.id NULLS #{direction}")
end
elsif sorting_by_custom_column
# Check if have to filter records first
# if params[:search].present? && 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 "users" ON "users"."id" = "repository_row"."user_id"
# WHERE "samples"."team_id" = #{@team.id} AND #{conditions.to_sql})
#
# records = records.where("samples.id IN (#{filter_query})")
# end
ci = sortable_displayed_columns[
params[:order].values[0][:column].to_i - 1
]
column_id = @columns_mappings.key((ci.to_i + 1).to_s)
dir = sort_direction(params[:order].values[0])
# Because repository records can have multiple custom cells,
# we first group them by samples.id and inside that group we sort them by column_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 (repository_rows.id) *')
# .order("repository_rows.id, CASE WHEN repository_cells.repository_column_id = #{column_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, s, sq.t0_r2 as user_id, sq.custom_field_id FROM (#{records.to_sql})
# as sq ORDER BY CASE WHEN sq.custom_field_id = #{column_id} THEN 1 ELSE 2 END #{dir}, sq.value #{dir}
# LIMIT #{per_page} OFFSET #{offset}")
if sort_column(order_params) == ASSIGNED_SORT_COL
# If "assigned" column is sorted
direction = sort_null_direction(order_params)
if @my_module
# Depending on the sort, order nulls first or
# nulls last on repository_cells association
return records if dt_params[:assigned] == 'assigned'
records.joins(
"LEFT OUTER JOIN (SELECT repository_cells.repository_row_id,
repository_text_values.data AS value FROM repository_cells
INNER JOIN repository_text_values
ON repository_text_values.id = repository_cells.value_id
WHERE repository_cells.repository_column_id = #{column_id}) AS values
ON values.repository_row_id = repository_rows.id"
).order("values.value #{dir}")
"LEFT OUTER JOIN my_module_repository_rows ON
(repository_rows.id = my_module_repository_rows.repository_row_id
AND (my_module_repository_rows.my_module_id = #{@my_module.id} OR
my_module_repository_rows.id IS NULL))"
).order("my_module_repository_rows.id NULLS #{direction}")
else
super(records)
records.joins(
'LEFT OUTER JOIN my_module_repository_rows ON
(repository_rows.id = my_module_repository_rows.repository_row_id)'
).order("my_module_repository_rows.id NULLS #{direction}")
end
elsif sorting_by_custom_column
ci = sortable_displayed_columns[order_params[:column].to_i - 1]
column_id = @columns_mappings.key((ci.to_i + 1).to_s)
dir = sort_direction(order_params)
records.joins(
"LEFT OUTER JOIN (SELECT repository_cells.repository_row_id,
repository_text_values.data AS value FROM repository_cells
INNER JOIN repository_text_values
ON repository_text_values.id = repository_cells.value_id
WHERE repository_cells.repository_column_id = #{column_id}) AS values
ON values.repository_row_id = repository_rows.id"
).order("values.value #{dir}")
else
super(records)
end
end
# 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 model == SampleCustomField
# # Find visible (searchable) custom field IDs, and only perform filter
# # on those custom fields
# searchable_cfs = params[:columns].select do |_, v|
# v['searchable'] == 'true' && @cf_mappings.values.include?(v['data'])
# end
# cfmi = @cf_mappings.invert
# cf_ids = searchable_cfs.map { |_, v| cfmi[v['data']] }
#
# # Do an ILIKE on 'value', as well as make sure to only include
# # custom fields that have 'custom_field_id' among visible custom fields
# casted_column = ::Arel::Nodes::NamedFunction.new(
# 'CAST',
# [model.arel_table[column.to_sym].as(typecast)]
# )
# casted_column = casted_column.matches("%#{value}%")
# casted_column = casted_column.and(
# model.arel_table['custom_field_id'].in(cf_ids)
# )
# casted_column
# elsif column == 'created_at'
# casted_column = ::Arel::Nodes::NamedFunction.new('CAST',
# [ Arel.sql("to_char( samples.created_at, '#{ formated_date }' ) AS VARCHAR") ] )
# casted_column.matches("%#{sanitize_sql_like(value)}%")
# else
# casted_column = ::Arel::Nodes::NamedFunction.new('CAST',
# [model.arel_table[column.to_sym].as(typecast)])
# casted_column.matches("%#{sanitize_sql_like(value)}%")
# end
# end
def sort_null_direction(item)
val = sort_direction(item)
val == 'ASC' ? 'LAST' : 'FIRST'
@ -360,15 +278,15 @@ class RepositoryDatatable < AjaxDatatablesRails::Base
end
def sorting_by_custom_column
sort_column(params[:order].values[0]) == 'repository_cells.value'
sort_column(order_params) == 'repository_cells.value'
end
# Escapes special characters in search query
def escape_special_chars
if params[:search].present?
params[:search][:value] = ActiveRecord::Base
.__send__(:sanitize_sql_like,
params[:search][:value])
if dt_params[:search].present?
dt_params[:search][:value] = ActiveRecord::Base
.__send__(:sanitize_sql_like,
dt_params[:search][:value])
end
end

353
app/datatables/sample_datatable.rb
View file

@ -1,6 +1,6 @@
require 'active_record'
class SampleDatatable < AjaxDatatablesRails::Base
class SampleDatatable < CustomDatatable
include ActionView::Helpers::TextHelper
include SamplesHelper
include InputSanitizeHelper
@ -49,7 +49,8 @@ class SampleDatatable < AjaxDatatablesRails::Base
@user = user
end
# Define sortable columns, so 1st column will be sorted by attribute in sortable_columns[0]
# Define sortable columns, so 1st column will be sorted
# by attribute in sortable_columns[0]
def sortable_columns
sort_array = [
ASSIGNED_SORT_COL,
@ -86,9 +87,9 @@ class SampleDatatable < AjaxDatatablesRails::Base
param_index = 2
filtered_array = []
input_array.each do |col|
next if params[:columns].to_a[param_index].nil?
next if dt_params.to_a[param_index].nil?
params_col =
params[:columns].to_a.find { |v| v[1]['data'] == param_index.to_s }
columns_params.to_a.find { |v| v[1]['data'] == param_index.to_s }
filtered_array.push(col) unless params_col[1]['searchable'] == 'false'
param_index += 1
end
@ -139,9 +140,11 @@ class SampleDatatable < AjaxDatatablesRails::Base
end
def assigned_cell(record)
@assigned_samples.include?(record) ?
"<span class='circle'>&nbsp;</span>" :
if @assigned_samples.include?(record)
"<span class='circle'>&nbsp;</span>"
else
"<span class='circle disabled'>&nbsp;</span>"
end
end
def sample_group_cell(record)
@ -159,21 +162,21 @@ class SampleDatatable < AjaxDatatablesRails::Base
# 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(
team: @team
)
.includes(
:sample_type,
:sample_group,
:user,
:sample_custom_fields
)
.references(
:sample_type,
:sample_group,
:user,
:sample_custom_fields
)
.where(
team: @team
)
if @my_module
@assigned_samples = @my_module.samples
@ -184,7 +187,7 @@ class SampleDatatable < AjaxDatatablesRails::Base
#{@my_module.id} OR
sample_my_modules.id IS NULL))")
.references(:sample_my_modules)
if params[:assigned] == 'assigned'
if dt_params[:assigned] == 'assigned'
samples = samples.where('"sample_my_modules"."id" > 0')
end
elsif @project
@ -203,7 +206,7 @@ class SampleDatatable < AjaxDatatablesRails::Base
sample_my_modules.id IS NULL))")
.references(:sample_my_modules)
end
if params[:assigned] == 'assigned'
if dt_params[:assigned] == 'assigned'
samples = samples.joins('LEFT OUTER JOIN "my_modules" ON
"my_modules"."id" =
"sample_my_modules"."my_module_id"')
@ -221,8 +224,8 @@ class SampleDatatable < AjaxDatatablesRails::Base
(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)
if params[:assigned] == 'assigned'
.references(:sample_my_modules)
if dt_params[:assigned] == 'assigned'
samples = samples.joins('LEFT OUTER JOIN "my_modules" ON
"my_modules"."id" =
"sample_my_modules"."my_module_id"')
@ -249,154 +252,177 @@ class SampleDatatable < AjaxDatatablesRails::Base
# 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?
records = sort_records(records) if order_params.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))
unless sorting_by_custom_column
records = filter_records(records) if dt_params[:search].present?
records = paginate_records(records) unless dt_params[:length].present? &&
dt_params[:length] == '-1'
end
records
end
# Override default sort method if needed
def sort_records(records)
if params[:order].present? && 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
if sort_column(order_params) == ASSIGNED_SORT_COL
# If "assigned" column is sorted
if @my_module
# 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(order_params)}"
)
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 team
unassigned = Sample
.where('"samples"."team_id" = ?', @team.id)
.where('"samples"."id" NOT IN (?)', assigned)
.select('"samples"."id"')
.distinct
# grabs the ids that are not the previous one but are still
# of the same team
unassigned = Sample.where('"samples"."team_id" = ?', @team.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 team
unassigned = Sample
.where('"samples"."team_id" = ?', @team.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)
# check the input param and merge the two arrays of ids
if order_params['dir'] == 'asc'
ids = assigned + unassigned
elsif order_params['dir'] == 'desc'
ids = unassigned + assigned
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"."team_id" = #{@team.id} AND #{conditions.to_sql})
ids = ids.collect(&:id)
records = records.where("samples.id IN (#{filter_query})")
# 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 ones
# but are still of the same team
unassigned = Sample
.where('"samples"."team_id" = ?', @team.id)
.where('"samples"."id" NOT IN (?)', assigned)
.select('"samples"."id"')
.distinct
# check the input param and merge the two arrays of ids
if order_params['dir'] == 'asc'
ids = assigned + unassigned
elsif order_params['dir'] == 'desc'
ids = unassigned + assigned
end
ids = ids.collect(&:id)
ci = sortable_displayed_columns[
params[:order].values[0][:column].to_i - 1
]
cf_id = @cf_mappings.key((ci.to_i + 1).to_s)
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)
# 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 dt_params[:search].present? && dt_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(dt_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"."team_id" = #{@team.id} AND #{conditions.to_sql})
records = records.where("samples.id IN (#{filter_query})")
end
ci = sortable_displayed_columns[
order_params[:column].to_i - 1
]
cf_id = @cf_mappings.key((ci.to_i + 1).to_s)
dir = sort_direction(order_params)
# 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
end
# 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
# 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!(/^\"|\"?$/, '')
formated_date = I18n.t('time.formats.datatables_date')
.gsub!(/^\"|\"?$/, '')
if model == SampleCustomField
# Find visible (searchable) custom field IDs, and only perform filter
# on those custom fields
searchable_cfs = params[:columns].select do |_, v|
searchable_cfs = columns_params.select do |_, v|
v['searchable'] == 'true' && @cf_mappings.values.include?(v['data'])
end
cfmi = @cf_mappings.invert
@ -414,36 +440,43 @@ class SampleDatatable < AjaxDatatablesRails::Base
)
casted_column
elsif column == 'created_at'
casted_column = ::Arel::Nodes::NamedFunction.new('CAST',
[ Arel.sql("to_char( samples.created_at, '#{ formated_date }' ) AS VARCHAR") ] )
casted_column = ::Arel::Nodes::NamedFunction.new(
'CAST',
[Arel.sql(
"to_char( samples.created_at, '#{formated_date}' ) AS VARCHAR"
)]
)
casted_column.matches("%#{sanitize_sql_like(value)}%")
else
casted_column = ::Arel::Nodes::NamedFunction.new('CAST',
[model.arel_table[column.to_sym].as(typecast)])
casted_column = ::Arel::Nodes::NamedFunction.new(
'CAST',
[model.arel_table[column.to_sym].as(typecast)]
)
casted_column.matches("%#{sanitize_sql_like(value)}%")
end
end
def sort_null_direction(item)
val = sort_direction(item)
val == "ASC" ? "LAST" : "FIRST"
val == 'ASC' ? 'LAST' : 'FIRST'
end
def inverse_sort_direction(item)
val = sort_direction(item)
val == "ASC" ? "DESC" : "ASC"
val == 'ASC' ? 'DESC' : 'ASC'
end
def sorting_by_custom_column
sort_column(params[:order].values[0]) == 'sample_custom_fields.value'
sort_column(order_params) == 'sample_custom_fields.value'
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?
if dt_params[:search].present?
dt_params[:search][:value] =
ActiveRecord::Base.__send__(:sanitize_sql_like,
dt_params[:search][:value])
end
end
def new_sort_column(item)
@ -452,7 +485,7 @@ class SampleDatatable < AjaxDatatablesRails::Base
.split('.')
return model if model == ASSIGNED_SORT_COL
col = [model.constantize.table_name, column].join('.')
[model.constantize.table_name, column].join('.')
end
def generate_sortable_displayed_columns

2
app/datatables/team_users_datatable.rb
View file

@ -1,4 +1,4 @@
class TeamUsersDatatable < AjaxDatatablesRails::Base
class TeamUsersDatatable < CustomDatatable
include InputSanitizeHelper
include ActiveRecord::Sanitization::ClassMethods

18
app/datatables/teams_datatable.rb
View file

@ -1,4 +1,4 @@
class TeamsDatatable < AjaxDatatablesRails::Base
class TeamsDatatable < CustomDatatable
include InputSanitizeHelper
def_delegator :@view, :link_to
@ -56,16 +56,12 @@ class TeamsDatatable < AjaxDatatablesRails::Base
# Overwrite default sort method to handle custom members column
# which is calculated in code and not present in DB
def sort_records(records)
if params[:order].present? && params[:order].length == 1
if sort_column(params[:order].values[0]) == MEMEBERS_SORT_COL
records = records.sort_by(&proc { |ut| ut.team.users.count })
if params[:order].values[0]['dir'] == 'asc'
return records
elsif params[:order].values[0]['dir'] == 'desc'
return records.reverse
end
else
super(records)
if sort_column(order_params) == MEMEBERS_SORT_COL
records = records.sort_by(&proc { |ut| ut.team.users.count })
if order_params['dir'] == 'asc'
return records
elsif order_params['dir'] == 'desc'
return records.reverse
end
else
super(records)

2
app/models/my_module.rb
View file

@ -299,7 +299,7 @@ class MyModule < ApplicationRecord
if !final.include?(my_module)
final << my_module
end
modules.push(*my_module.my_module_antecessors.flatten)
modules.push(*my_module.my_module_antecessors)
end
final
end

2
app/views/shared/_secondary_navigation.html.erb
View file

@ -199,7 +199,7 @@
<ul class="dropdown-menu repositories-dropdown-menu" aria-labelledby="repositoriesDropdownMenuLink">
<% @my_module.experiment.project.team.repositories.order(created_at: :asc).each do |repository| %>
<li>
<a class="dropdown-item" href="<%= repository_my_module_url(repository_id: repository) %>" title="<%= repository.name %>">
<a class="dropdown-item" href="<%= repository_my_module_url(id: @my_module, repository_id: repository) %>" title="<%= repository.name %>">
<%= truncate(repository.name) %>
</a>
</li>