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Merge pull request #524 from okriuchykhin/ok_SCI_1046

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Add team_id field to assets and tables [SCI-1046]
This commit is contained in:
okriuchykhin 2017-03-24 14:48:16 +01:00 committed by GitHub
parent 804fb2fec9 d2c8e9a395
commit 71dc6921fb
11 changed files with 98 additions and 15 deletions
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4
app/controllers/protocols_controller.rb
View file

@ -521,7 +521,9 @@ class ProtocolsController < ApplicationController
transaction_error = false
Protocol.transaction do
begin
import_into_existing(@protocol, @protocol_json, current_user)
import_into_existing(
@protocol, @protocol_json, current_user, current_team
)
rescue Exception
transaction_error = true
raise ActiveRecord:: Rollback

2
app/controllers/result_assets_controller.rb
View file

@ -29,6 +29,7 @@ class ResultAssetsController < ApplicationController
@asset = Asset.new(result_params[:asset_attributes])
@asset.created_by = current_user
@asset.last_modified_by = current_user
@asset.team = current_team
@result = Result.new(
user: current_user,
my_module: @my_module,
@ -98,6 +99,7 @@ class ResultAssetsController < ApplicationController
asset = Asset.find_by_id(update_params[:asset_attributes][:id])
asset.created_by = current_user
asset.last_modified_by = current_user
asset.team = current_team
@result.asset = asset
end

4
app/controllers/result_tables_controller.rb
View file

@ -31,6 +31,7 @@ class ResultTablesController < ApplicationController
def create
@table = Table.new(result_params[:table_attributes])
@table.created_by = current_user
@table.team = current_team
@table.last_modified_by = current_user
@result = Result.new(
user: current_user,
@ -92,6 +93,7 @@ class ResultTablesController < ApplicationController
update_params = result_params
@result.last_modified_by = current_user
@result.table.last_modified_by = current_user
@result.table.team = current_team
@result.assign_attributes(update_params)
flash_success = t("result_tables.update.success_flash",
module: @my_module.name)
@ -218,6 +220,4 @@ class ResultTablesController < ApplicationController
]
)
end
end

20
app/controllers/steps_controller.rb
View file

@ -33,6 +33,14 @@ class StepsController < ApplicationController
@step.protocol = @protocol
@step.user = current_user
@step.last_modified_by = current_user
@step.assets.each do |asset|
asset.created_by = current_user
asset.team = current_team
end
@step.tables.each do |table|
table.created_by = current_user
table.team = current_team
end
# Update default checked state
@step.checklists.each do |checklist|
@ -133,6 +141,18 @@ class StepsController < ApplicationController
@step.assign_attributes(step_params_all)
@step.last_modified_by = current_user
@step.assets.each do |asset|
asset.created_by = current_user if asset.new_record?
asset.last_modified_by = current_user unless asset.new_record?
asset.team = current_team
end
@step.tables.each do |table|
table.created_by = current_user if table.new_record?
table.last_modified_by = current_user unless table.new_record?
table.team = current_team
end
if @step.save
@step.reload

1
app/models/asset.rb
View file

@ -48,6 +48,7 @@ class Asset < ActiveRecord::Base
belongs_to :last_modified_by,
foreign_key: 'last_modified_by_id',
class_name: 'User'
belongs_to :team
has_one :step_asset,
inverse_of: :asset,
dependent: :destroy

4
app/models/protocol.rb
View file

@ -291,8 +291,6 @@ class Protocol < ActiveRecord::Base
)
item2.created_by = current_user
item2.last_modified_by = current_user
p item
p item2
item2.save
end
@ -306,6 +304,7 @@ class Protocol < ActiveRecord::Base
asset.file_file_size
)
asset2.created_by = current_user
asset2.team = dest.team
asset2.last_modified_by = current_user
asset2.file_processing = true if asset.is_image?
asset2.save
@ -323,6 +322,7 @@ class Protocol < ActiveRecord::Base
table2 = Table.new(name: table.name, contents: table.contents)
table2.created_by = current_user
table2.last_modified_by = current_user
table2.team = dest.team
step2.tables << table2
end
end

1
app/models/table.rb
View file

@ -10,6 +10,7 @@ class Table < ActiveRecord::Base
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'
belongs_to :team
has_one :step_table, inverse_of: :table
has_one :step, through: :step_table

11
app/utilities/delayed_uploader_tutorial.rb
View file

@ -1,11 +1,12 @@
module DelayedUploaderTutorial
# Get asset from tutorial_files folder
def self.get_asset(user, file_name)
def self.get_asset(user, team, file_name)
Asset.new(
file: File.open(
"#{Rails.root}/app/assets/tutorial_files/#{file_name}", 'r'
),
created_by: user,
team: team,
last_modified_by: user
)
end
@ -15,11 +16,12 @@ module DelayedUploaderTutorial
def self.generate_result_asset(
my_module:,
current_user:,
current_team:,
result_name:,
created_at: Time.now,
file_name:
)
temp_asset = get_asset(current_user, file_name)
temp_asset = get_asset(current_user, current_team, file_name)
temp_result = Result.new(
created_at: created_at,
user: current_user,
@ -48,8 +50,9 @@ module DelayedUploaderTutorial
end
# Adds asset to existing step
def self.add_step_asset(step:, current_user:, file_name:)
temp_asset = DelayedUploaderTutorial.get_asset(current_user, file_name)
def self.add_step_asset(step:, current_user:, current_team:, file_name:)
temp_asset =
DelayedUploaderTutorial.get_asset(current_user, current_team, file_name)
step.assets << temp_asset
temp_asset.post_process_file(step.my_module.experiment.project.team)
end

23
app/utilities/first_time_data_generator.rb
View file

@ -422,6 +422,7 @@ module FirstTimeDataGenerator
DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
my_module: my_modules[0],
current_user: user,
current_team: team,
result_name: 'sF',
created_at: generate_random_time(my_modules[0].created_at, 2.days),
file_name: 'samples.txt'
@ -440,6 +441,7 @@ module FirstTimeDataGenerator
)
temp_result.table = Table.new(
created_by: user,
team: team,
contents: tab_content['module1']['experimental_design']
)
temp_result.save
@ -467,6 +469,7 @@ module FirstTimeDataGenerator
DelayedUploaderTutorial.delay(queue: :tutorial).add_step_asset(
step: my_modules[1].protocol.steps.where('position = 0').take,
current_user: user,
current_team: team,
file_name: 'sample-potatoe.txt'
)
@ -474,6 +477,7 @@ module FirstTimeDataGenerator
DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
my_module: my_modules[1],
current_user: user,
current_team: team,
result_name: 'PVY-inoculated plant, symptoms',
created_at: generate_random_time(my_modules[1].created_at, 1.days),
file_name: 'DSCN0660.JPG'
@ -482,6 +486,7 @@ module FirstTimeDataGenerator
DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
my_module: my_modules[1],
current_user: user,
current_team: team,
result_name: 'mock-inoculated plant',
created_at: generate_random_time(my_modules[1].created_at, 2.days),
file_name: 'DSCN0354.JPG'
@ -490,6 +495,7 @@ module FirstTimeDataGenerator
DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
my_module: my_modules[1],
current_user: user,
current_team: team,
result_name: 'Height of plants at 6dpi',
created_at: generate_random_time(my_modules[1].created_at, 3.days),
file_name: '6dpi_height.JPG'
@ -541,6 +547,7 @@ module FirstTimeDataGenerator
DelayedUploaderTutorial.delay(queue: :tutorial).add_step_asset(
step: my_modules[2].protocol.steps.where('position = 1').take,
current_user: user,
current_team: team,
file_name: 'RNeasy-Plant-Mini-Kit-EN.pdf'
)
@ -559,6 +566,7 @@ module FirstTimeDataGenerator
)
temp_result.table = Table.new(
created_by: user,
team: team,
contents: tab_content['module3']['nanodrop']
)
temp_result.save
@ -581,6 +589,7 @@ module FirstTimeDataGenerator
DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
my_module: my_modules[2],
current_user: user,
current_team: team,
result_name: 'Agarose gel electrophoresis of totRNA samples',
created_at: generate_random_time(my_modules[2].created_at, 3.days),
file_name: 'totRNA_gel.jpg'
@ -599,6 +608,7 @@ module FirstTimeDataGenerator
DelayedUploaderTutorial.delay(queue: :tutorial).add_step_asset(
step: my_modules[3].protocol.steps.where('position = 0').take,
current_user: user,
current_team: team,
file_name: 'G2938-90034_KitRNA6000Nano_ebook.pdf'
)
@ -606,6 +616,7 @@ module FirstTimeDataGenerator
DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
my_module: my_modules[3],
current_user: user,
current_team: team,
result_name: 'Result of RNA integrity',
created_at: generate_random_time(my_modules[3].created_at, 2.days),
file_name: 'Bioanalyser_result.JPG'
@ -671,24 +682,28 @@ module FirstTimeDataGenerator
DelayedUploaderTutorial.delay(queue: :tutorial).add_step_asset(
step: my_modules[5].protocol.steps.where('position = 0').take,
current_user: user,
current_team: team,
file_name: 'sample_preparation.JPG'
)
DelayedUploaderTutorial.delay(queue: :tutorial).add_step_asset(
step: my_modules[5].protocol.steps.where('position = 1').take,
current_user: user,
current_team: team,
file_name: 'reaction_setup.JPG'
)
DelayedUploaderTutorial.delay(queue: :tutorial).add_step_asset(
step: my_modules[5].protocol.steps.where('position = 2').take,
current_user: user,
current_team: team,
file_name: 'cycling_conditions.JPG'
)
DelayedUploaderTutorial.delay(queue: :tutorial).add_step_asset(
step: my_modules[5].protocol.steps.where('position = 3').take,
current_user: user,
current_team: team,
file_name: '96plate.doc'
)
@ -702,6 +717,7 @@ module FirstTimeDataGenerator
)
temp_result.table = Table.new(
created_by: user,
team: team,
contents: tab_content['module6']['distribution'] % {
sample0: samples_to_assign[0].name,
sample1: samples_to_assign[1].name,
@ -729,6 +745,7 @@ module FirstTimeDataGenerator
DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
my_module: my_modules[5],
current_user: user,
current_team: team,
result_name: 'Mixtures and plate setup',
created_at: generate_random_time(my_modules[5].created_at, 2.days),
file_name: 'Mixes_Templats.xls'
@ -737,6 +754,7 @@ module FirstTimeDataGenerator
DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
my_module: my_modules[5],
current_user: user,
current_team: team,
result_name: 'Raw data from ABI 7300',
created_at: generate_random_time(my_modules[5].created_at, 3.days),
file_name: 'BootCamp-Experiment-results-20122.sds'
@ -745,6 +763,7 @@ module FirstTimeDataGenerator
DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
my_module: my_modules[5],
current_user: user,
current_team: team,
result_name: 'All results - curves',
created_at: generate_random_time(my_modules[5].created_at, 4.days),
file_name: 'curves.JPG'
@ -791,6 +810,7 @@ module FirstTimeDataGenerator
DelayedUploaderTutorial.delay(queue: :tutorial).add_step_asset(
step: my_modules[7].protocol.steps.where('position = 0').take,
current_user: user,
current_team: team,
file_name: 'ddCq-quantification_diagnostics-template.xls'
)
@ -798,6 +818,7 @@ module FirstTimeDataGenerator
DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
my_module: my_modules[7],
current_user: user,
current_team: team,
result_name: 'Results of ddCq method',
created_at: generate_random_time(my_modules[7].created_at, 1.days),
file_name: 'ddCq-quantification_diagnostics-results.xls'
@ -806,6 +827,7 @@ module FirstTimeDataGenerator
DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
my_module: my_modules[7],
current_user: user,
current_team: team,
result_name: 'Dilution curve and efficiency',
created_at: generate_random_time(my_modules[7].created_at, 2.days),
file_name: 'dilution_curve-efficiency.JPG'
@ -814,6 +836,7 @@ module FirstTimeDataGenerator
DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
my_module: my_modules[7],
current_user: user,
current_team: team,
result_name: 'Relative quantification results',
created_at: generate_random_time(my_modules[7].created_at, 3.days),
file_name: 'result-ddCq.JPG'

14
app/utilities/protocols_importer.rb
View file

@ -22,18 +22,18 @@ module ProtocolsImporter
protocol.save!
# Protocol is saved, populate it
populate_protocol(protocol, protocol_json, user)
populate_protocol(protocol, protocol_json, user, team)
return protocol
end
def import_into_existing(protocol, protocol_json, user)
def import_into_existing(protocol, protocol_json, user, team)
# Firstly, destroy existing protocol's contents
protocol.destroy_contents(user)
protocol.reload
# Alright, now populate the protocol
populate_protocol(protocol, protocol_json, user)
populate_protocol(protocol, protocol_json, user, team)
protocol.reload
# Unlink the protocol
@ -43,7 +43,7 @@ module ProtocolsImporter
private
def populate_protocol(protocol, protocol_json, user)
def populate_protocol(protocol, protocol_json, user, team)
protocol.reload
asset_ids = []
@ -93,7 +93,8 @@ module ProtocolsImporter
name: table_json['name'],
contents: Base64.decode64(table_json['contents']),
created_by: user,
last_modified_by: user
last_modified_by: user,
team: team
)
StepTable.create!(
step: step,
@ -106,7 +107,8 @@ module ProtocolsImporter
step_json["assets"].values.each do |asset_json|
asset = Asset.new(
created_by: user,
last_modified_by: user
last_modified_by: user,
team: team
)
# Decode the file bytes

29
db/migrate/20170322095856_add_team_id_to_asset_and_tables.rb Normal file
View file

@ -0,0 +1,29 @@
class AddTeamIdToAssetAndTables < ActiveRecord::Migration
def change
add_column :assets, :team_id, :integer
add_index :assets, :team_id
add_column :tables, :team_id, :integer
add_index :tables, :team_id
Asset.find_each do |asset|
if asset.result
asset.update_columns(
team_id: asset.result.my_module.experiment.project.team_id
)
elsif asset.step
asset.update_columns(team_id: asset.step.protocol.team_id)
end
end
Table.find_each do |table|
if table.result
table.update_columns(
team_id: table.result.my_module.experiment.project.team_id
)
elsif table.step
table.update_columns(team_id: table.step.protocol.team_id)
end
end
end
end