mirror of
https://github.com/scinote-eln/scinote-web.git
synced 2025-02-27 09:13:46 +08:00
renamed utilities
This commit is contained in:
zmagod
parent
9ae799d52c
commit
a6285f0431
5 changed files with 255 additions and 239 deletions
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@ -30,7 +30,7 @@ module DelayedUploaderTutorial
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temp_result.save
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temp_asset.save
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temp_asset.post_process_file(my_module.experiment.project.organization)
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temp_asset.post_process_file(my_module.experiment.project.team)
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# Create result activity
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Activity.new(
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@ -51,6 +51,6 @@ module DelayedUploaderTutorial
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def self.add_step_asset(step:, current_user:, file_name:)
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temp_asset = DelayedUploaderTutorial.get_asset(current_user, file_name)
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step.assets << temp_asset
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temp_asset.post_process_file(step.my_module.experiment.project.organization)
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temp_asset.post_process_file(step.my_module.experiment.project.team)
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end
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end
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@ -1,58 +1,61 @@
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module FirstTimeDataGenerator
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# Create data for tutorial for new users
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def seed_demo_data user
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def seed_demo_data(user)
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@user = user
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# First organization that this user created
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# First team that this user created
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# should contain the "intro" project
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if cookies[:repeat_tutorial_org_id]
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org = Organization.find(cookies[:repeat_tutorial_org_id])
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cookies.delete :repeat_tutorial_org_id
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if cookies[:repeat_tutorial_org_id] && cookies[:repeat_tutorial_team_id]
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team = Team.find_by_id(cookies[:repeat_tutorial_org_id])
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team ||= Team.find_by_id(cookies[:repeat_tutorial_team_id])
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cookies.delete :repeat_tutorial_org_id if cookies[:repeat_tutorial_org_id]
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if cookies[:repeat_tutorial_team_id]
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cookies.delete :repeat_tutorial_team_id
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end
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else
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org = user
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.organizations
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.where(created_by: user)
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.order(created_at: :asc)
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.first
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team = user
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.teams
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.where(created_by: user)
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.order(created_at: :asc)
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.first
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end
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# If private private organization does not exist,
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# If private private team does not exist,
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# there was something wrong with user creation.
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# Do nothing
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return unless org
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return unless team
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# Create sample types
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SampleType.create(
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name: "Potato leaves",
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organization: org
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name: 'Potato leaves',
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team: team
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)
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SampleType.create(
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name: "Tea leaves",
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organization: org
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name: 'Tea leaves',
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team: team
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)
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SampleType.create(
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name: "Potato bug",
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organization: org
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name: 'Potato bug',
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team: team
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)
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SampleGroup.create(
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name: "Fodder",
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organization: org,
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name: 'Fodder',
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team: team,
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color: Constants::TAG_COLORS[1]
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)
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SampleGroup.create(
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name: "Nutrient",
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organization: org,
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name: 'Nutrient',
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team: team,
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color: Constants::TAG_COLORS[0]
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)
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SampleGroup.create(
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name: "Seed",
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organization: org,
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name: 'Seed',
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team: team,
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color: Constants::TAG_COLORS[2]
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)
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@ -63,10 +66,10 @@ module FirstTimeDataGenerator
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for i in 1..5
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samples << Sample.create(
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name: sample_name + i.to_s,
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organization: org,
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team: team,
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user: user,
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sample_type: rand < 0.8 ? pluck_random(org.sample_types) : nil,
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sample_group: rand < 0.8 ? pluck_random(org.sample_groups) : nil
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sample_type: rand < 0.8 ? pluck_random(team.sample_types) : nil,
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sample_group: rand < 0.8 ? pluck_random(team.sample_groups) : nil
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)
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end
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@ -74,21 +77,22 @@ module FirstTimeDataGenerator
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for i in 1..5
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samples << Sample.create(
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name: sample_name + i.to_s,
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organization: org,
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team: team,
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user: user,
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sample_type: rand < 0.8 ? pluck_random(org.sample_types) : nil,
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sample_group: rand < 0.8 ? pluck_random(org.sample_groups) : nil
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sample_type: rand < 0.8 ? pluck_random(team.sample_types) : nil,
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sample_group: rand < 0.8 ? pluck_random(team.sample_groups) : nil
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)
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end
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name = "Demo project - qPCR"
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exp_name = "My first experiment"
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name = 'Demo project - qPCR'
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exp_name = 'My first experiment'
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# If there is an existing demo project, archive and rename it
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if org.projects.where(name: name).present?
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old = org.projects.where(name: "Demo project - qPCR")[0]
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if team.projects.where(name: name).present?
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# TODO: check if we still need this code
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# old = team.projects.where(name: 'Demo project - qPCR')[0]
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# old.archive! user
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i = 1
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while org.projects.where(name: name = "Demo project - qPCR (#{i})").present?
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while team.projects.where(name: name = "Demo project - qPCR (#{i})").present?
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i += 1
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end
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end
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@ -97,7 +101,7 @@ module FirstTimeDataGenerator
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visibility: 0,
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name: name,
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due_date: nil,
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organization: org,
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team: team,
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created_by: user,
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created_at: generate_random_time(1.week.ago),
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last_modified_by: user,
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@ -106,7 +110,7 @@ module FirstTimeDataGenerator
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experiment = Experiment.create(
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name: exp_name,
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description: "This is my very first experiment",
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description: 'This is my very first experiment',
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project: project,
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created_by: user,
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created_at: project.created_at + 5.minutes,
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@ -127,7 +131,7 @@ module FirstTimeDataGenerator
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user: user,
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project: project,
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message: I18n.t(
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"activities.create_project",
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'activities.create_project',
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user: user.full_name,
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project: project.name
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),
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@ -138,36 +142,36 @@ module FirstTimeDataGenerator
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generate_project_comment(
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project,
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user,
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"I've created a demo project"
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'I\'ve created a demo project'
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)
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# Create a module group
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my_module_group = MyModuleGroup.create(
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name: "Potato qPCR workflow",
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name: 'Potato qPCR workflow',
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experiment: experiment
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)
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# Create project modules
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my_modules = []
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my_module_names = [
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"Experiment design",
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"Sampling biological material",
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"RNA isolation",
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"RNA quality & quantity - BIOANALYSER",
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"Reverse transcription",
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"qPCR",
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"Data quality control",
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"Data analysis - ddCq"
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'Experiment design',
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'Sampling biological material',
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'RNA isolation',
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'RNA quality & quantity - BIOANALYSER',
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'Reverse transcription',
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'qPCR',
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'Data quality control',
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'Data analysis - ddCq'
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]
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qpcr_module_description = "PCR is a method where an enzyme
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qpcr_module_description = 'PCR is a method where an enzyme
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(thermostable DNA polymerase, originally isolated in 1960s
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from bacterium Thermus aquaticus, growing in hot lakes of
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Yellowstone park, USA) amplifies a short specific part of
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the template DNA (amplicon) in cycles. In every cycle the
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number of short specific sections of DNA is doubled, leading
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to an exponential amplification of targets. More on how
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conventional PCR works can be found here."
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conventional PCR works can be found here.'
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my_module_names.each_with_index do |name, i|
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my_module = MyModule.create(
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@ -189,7 +193,7 @@ module FirstTimeDataGenerator
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if i > 0
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Connection.create(
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input_id: my_module.id,
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output_id: my_modules[i-1].id
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output_id: my_modules[i - 1].id
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)
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end
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@ -200,7 +204,7 @@ module FirstTimeDataGenerator
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project: project,
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my_module: my_module,
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message: I18n.t(
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"activities.create_module",
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'activities.create_module',
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user: user.full_name,
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module: my_module.name
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),
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@ -219,7 +223,7 @@ module FirstTimeDataGenerator
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project: project,
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my_module: my_module,
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message: I18n.t(
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"activities.assign_user_to_module",
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'activities.assign_user_to_module',
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assigned_user: user.full_name,
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module: my_module.name,
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assigned_by_user: user.full_name
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@ -230,7 +234,7 @@ module FirstTimeDataGenerator
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# Create an archived module
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archived_module = MyModule.create(
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name: "Data analysis - Pfaffl method",
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name: 'Data analysis - Pfaffl method',
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created_by: user,
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created_at: generate_random_time(6.days.ago),
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due_date: Time.now + 1.week,
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@ -252,7 +256,7 @@ module FirstTimeDataGenerator
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project: project,
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my_module: archived_module,
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message: I18n.t(
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"activities.create_module",
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'activities.create_module',
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user: user.full_name,
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module: archived_module.name
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),
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@ -266,7 +270,7 @@ module FirstTimeDataGenerator
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project: project,
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my_module: archived_module,
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message: I18n.t(
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"activities.archive_module",
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'activities.archive_module',
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user: user.full_name,
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module: archived_module.name
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),
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@ -286,7 +290,7 @@ module FirstTimeDataGenerator
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project: project,
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my_module: archived_module,
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message: I18n.t(
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"activities.assign_user_to_module",
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'activities.assign_user_to_module',
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assigned_user: user.full_name,
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module: archived_module.name,
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assigned_by_user: user.full_name
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@ -305,7 +309,6 @@ module FirstTimeDataGenerator
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samples_to_assign << sample
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end
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my_modules[1].get_downstream_modules.each do |mm|
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samples_to_assign.each do |s|
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SampleMyModule.create(
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@ -359,21 +362,21 @@ module FirstTimeDataGenerator
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# Create tags and add them to module
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drylab_tag = Tag.create(
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name: "Drylab",
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name: 'Drylab',
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color: Constants::TAG_COLORS[8],
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project: project,
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created_by: user,
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last_modified_by: user
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)
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wetlab_tag = Tag.create(
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name: "Wetlab",
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name: 'Wetlab',
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color: Constants::TAG_COLORS[14],
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project: project,
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created_by: user,
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last_modified_by: user
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)
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decide_tag = Tag.create(
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name: "Decide",
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name: 'Decide',
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color: Constants::TAG_COLORS[5],
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project: project,
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created_by: user,
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@ -396,29 +399,34 @@ module FirstTimeDataGenerator
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my_modules[7].save
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# Load table contents yaml file
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tab_content = YAML.load_file("#{Rails.root}/app/assets/tutorial_files/tables_content.yaml")
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tab_content = YAML.load_file(
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"#{Rails.root}/app/assets/tutorial_files/tables_content.yaml"
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)
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# Create module content
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# ----------------- Module 1 ------------------
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module_step_names = [
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"Gene expression"
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'Gene expression'
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]
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module_step_descriptions = [
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"Compare response of PVYNTN, cab4 and PR1 genes in mock/virus inoculated potatoes & in time"
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'Compare response of PVYNTN, cab4 and PR1 genes in mock/virus ' \
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'inoculated potatoes & in time'
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]
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generate_module_steps(my_modules[0], module_step_names, module_step_descriptions)
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generate_module_steps(my_modules[0],
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module_step_names,
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module_step_descriptions)
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# Results
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DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
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my_module: my_modules[0],
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current_user: user,
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result_name: "sF",
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result_name: 'sF',
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created_at: generate_random_time(my_modules[0].created_at, 2.days),
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file_name: "samples.txt"
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file_name: 'samples.txt'
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)
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temp_result = Result.new(
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name: "Experimental design",
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name: 'Experimental design',
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my_module: my_modules[0],
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created_at: generate_random_time(my_modules[0].created_at, 1.days),
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user: user
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@ -430,63 +438,70 @@ module FirstTimeDataGenerator
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)
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temp_result.table = Table.new(
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created_by: user,
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contents: tab_content["module1"]["experimental_design"]
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contents: tab_content['module1']['experimental_design']
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)
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temp_result.save
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# ----------------- Module 2 ------------------
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module_step_names = [
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"Inoculation of potatoes",
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"Collection of potatoes",
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"Store samples"
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'Inoculation of potatoes',
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'Collection of potatoes',
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'Store samples'
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]
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module_step_descriptions = [
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"50% of samples should be mock inoculated while other 50% with PVY NTN virus.",
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"50% of PVYNTN inoculated potatos and 50% of Mock inoculated potatos collect 1 day post inocullation while other halph of samples collect 6 days post inoculation.",
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"Collect samples in 2ml tubes and put them in liquid nitrogen and store at 80°C."
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'50% of samples should be mock inoculated while other 50% with ' \
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'PVY NTN virus.',
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'50% of PVYNTN inoculated potatos and 50% of Mock inoculated potatos ' \
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'collect 1 day post inocullation while other halph of samples collect ' \
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'6 days post inoculation.',
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'Collect samples in 2ml tubes and put them in liquid nitrogen '\
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'and store at 80°C.'
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]
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generate_module_steps(my_modules[1], module_step_names, module_step_descriptions)
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generate_module_steps(my_modules[1],
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module_step_names,
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module_step_descriptions)
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# Add file to existig step
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DelayedUploaderTutorial.delay(queue: :tutorial).add_step_asset(
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step: my_modules[1].protocol.steps.where("position = 0").take,
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step: my_modules[1].protocol.steps.where('position = 0').take,
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current_user: user,
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file_name: "sample-potatoe.txt"
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file_name: 'sample-potatoe.txt'
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)
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# Results
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DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
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my_module: my_modules[1],
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current_user: user,
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result_name: "PVY-inoculated plant, symptoms",
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result_name: 'PVY-inoculated plant, symptoms',
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created_at: generate_random_time(my_modules[1].created_at, 1.days),
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file_name: "DSCN0660.JPG"
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file_name: 'DSCN0660.JPG'
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)
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DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
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my_module: my_modules[1],
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current_user: user,
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result_name: "mock-inoculated plant",
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result_name: 'mock-inoculated plant',
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created_at: generate_random_time(my_modules[1].created_at, 2.days),
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file_name: "DSCN0354.JPG"
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file_name: 'DSCN0354.JPG'
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)
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DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
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my_module: my_modules[1],
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current_user: user,
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result_name: "Height of plants at 6dpi",
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result_name: 'Height of plants at 6dpi',
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created_at: generate_random_time(my_modules[1].created_at, 3.days),
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file_name: "6dpi_height.JPG"
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file_name: '6dpi_height.JPG'
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)
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# Add a text result
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temp_result = Result.new(
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name: "Number of samples",
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name: 'Number of samples',
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my_module: my_modules[1],
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user: user,
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created_at: generate_random_time(my_modules[1].created_at, 4.days)
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)
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temp_text = "There are many biological replicates we harvested for each type of sample (code-names):\n\n"
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temp_text = "There are many biological replicates we harvested " \
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"for each type of sample (code-names):\n\n"
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samples_to_assign.each do |s|
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temp_text << "* #{s.name}\n\n"
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end
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|
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@ -504,32 +519,32 @@ module FirstTimeDataGenerator
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user: user,
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created_at: temp_result.created_at,
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message: I18n.t(
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"activities.add_text_result",
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'activities.add_text_result',
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user: user.full_name,
|
||||
result: temp_result.name
|
||||
)
|
||||
).sneaky_save
|
||||
# ----------------- Module 3 ------------------
|
||||
module_step_names = [
|
||||
"Homogenization of the material",
|
||||
"Isolation of RNA with RNeasy plant mini kit"
|
||||
'Homogenization of the material',
|
||||
'Isolation of RNA with RNeasy plant mini kit'
|
||||
]
|
||||
module_step_descriptions = [
|
||||
" Use tissue lyser: 1 min on step 3.",
|
||||
' Use tissue lyser: 1 min on step 3.',
|
||||
nil
|
||||
]
|
||||
generate_module_steps(my_modules[2], module_step_names, module_step_descriptions)
|
||||
|
||||
# Add file to existig step
|
||||
DelayedUploaderTutorial.delay(queue: :tutorial).add_step_asset(
|
||||
step: my_modules[2].protocol.steps.where("position = 1").take,
|
||||
step: my_modules[2].protocol.steps.where('position = 1').take,
|
||||
current_user: user,
|
||||
file_name: "RNeasy-Plant-Mini-Kit-EN.pdf"
|
||||
file_name: 'RNeasy-Plant-Mini-Kit-EN.pdf'
|
||||
)
|
||||
|
||||
# Results
|
||||
temp_result = Result.new(
|
||||
name: "Nanodrop results",
|
||||
name: 'Nanodrop results',
|
||||
my_module: my_modules[2],
|
||||
created_at: generate_random_time(my_modules[2].created_at, 1.days),
|
||||
user: user
|
||||
|
|
@ -542,7 +557,7 @@ module FirstTimeDataGenerator
|
|||
)
|
||||
temp_result.table = Table.new(
|
||||
created_by: user,
|
||||
contents: tab_content["module3"]["nanodrop"]
|
||||
contents: tab_content['module3']['nanodrop']
|
||||
)
|
||||
temp_result.save
|
||||
|
||||
|
|
@ -554,7 +569,7 @@ module FirstTimeDataGenerator
|
|||
user: user,
|
||||
created_at: temp_result.created_at,
|
||||
message: I18n.t(
|
||||
"activities.add_text_result",
|
||||
'activities.add_text_result',
|
||||
user: user.full_name,
|
||||
result: temp_result.name
|
||||
)
|
||||
|
|
@ -564,14 +579,14 @@ module FirstTimeDataGenerator
|
|||
DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
|
||||
my_module: my_modules[2],
|
||||
current_user: user,
|
||||
result_name: "Agarose gel electrophoresis of totRNA samples",
|
||||
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"
|
||||
file_name: 'totRNA_gel.jpg'
|
||||
)
|
||||
|
||||
# ----------------- Module 4 ------------------
|
||||
module_step_names = [
|
||||
"Use Nano chip for testing RNA integrity"
|
||||
'Use Nano chip for testing RNA integrity'
|
||||
]
|
||||
module_step_descriptions = [
|
||||
nil
|
||||
|
|
@ -580,47 +595,49 @@ module FirstTimeDataGenerator
|
|||
|
||||
# Add file to existig step
|
||||
DelayedUploaderTutorial.delay(queue: :tutorial).add_step_asset(
|
||||
step: my_modules[3].protocol.steps.where("position = 0").take,
|
||||
step: my_modules[3].protocol.steps.where('position = 0').take,
|
||||
current_user: user,
|
||||
file_name: "G2938-90034_KitRNA6000Nano_ebook.pdf"
|
||||
file_name: 'G2938-90034_KitRNA6000Nano_ebook.pdf'
|
||||
)
|
||||
|
||||
# Results
|
||||
DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
|
||||
my_module: my_modules[3],
|
||||
current_user: user,
|
||||
result_name: "Result of RNA integrity",
|
||||
result_name: 'Result of RNA integrity',
|
||||
created_at: generate_random_time(my_modules[3].created_at, 2.days),
|
||||
file_name: "Bioanalyser_result.JPG"
|
||||
file_name: 'Bioanalyser_result.JPG'
|
||||
)
|
||||
|
||||
# ----------------- Module 5 ------------------
|
||||
module_step_names = [
|
||||
"RNA denaturation",
|
||||
"Prepare mastermix for RT",
|
||||
"RT reaction"
|
||||
'RNA denaturation',
|
||||
'Prepare mastermix for RT',
|
||||
'RT reaction'
|
||||
]
|
||||
module_step_descriptions = [
|
||||
"1 ug of RNA denature at 80°C for 5 min --> ice",
|
||||
"High Capacity cDNA Reverse Transcription Kit (Applied Biosystems)",
|
||||
"25°C for 10 min 37°C for 2 h"
|
||||
'1 ug of RNA denature at 80°C for 5 min --> ice',
|
||||
'High Capacity cDNA Reverse Transcription Kit (Applied Biosystems)',
|
||||
'25°C for 10 min 37°C for 2 h'
|
||||
]
|
||||
generate_module_steps(my_modules[4], module_step_names, module_step_descriptions)
|
||||
generate_module_steps(my_modules[4],
|
||||
module_step_names,
|
||||
module_step_descriptions)
|
||||
|
||||
module_checklist_items = [
|
||||
"RT buffer",
|
||||
"dNTP mix",
|
||||
"Random Primers",
|
||||
"RNase inhibitor",
|
||||
"Reverse transcriptase",
|
||||
"Optional: Luciferase mRNA (denatured)",
|
||||
"H2O to 12.5 ul"
|
||||
'RT buffer',
|
||||
'dNTP mix',
|
||||
'Random Primers',
|
||||
'RNase inhibitor',
|
||||
'Reverse transcriptase',
|
||||
'Optional: Luciferase mRNA (denatured)',
|
||||
'H2O to 12.5 ul'
|
||||
]
|
||||
|
||||
# Add checklist to step
|
||||
step = my_modules[4].protocol.steps.where("position = 1").take
|
||||
step = my_modules[4].protocol.steps.where('position = 1').take
|
||||
checklist = Checklist.new(
|
||||
name: "Mastermix",
|
||||
name: 'Mastermix',
|
||||
step: step
|
||||
)
|
||||
|
||||
|
|
@ -633,58 +650,62 @@ module FirstTimeDataGenerator
|
|||
|
||||
# ----------------- Module 6 ------------------
|
||||
module_step_names = [
|
||||
"Sample preparation",
|
||||
"Reaction setup",
|
||||
"Use Applied Biosystem 7300 instrument for qPCR",
|
||||
"Setup of the 96 plate"
|
||||
'Sample preparation',
|
||||
'Reaction setup',
|
||||
'Use Applied Biosystem 7300 instrument for qPCR',
|
||||
'Setup of the 96 plate'
|
||||
]
|
||||
module_step_descriptions = [
|
||||
nil,
|
||||
nil,
|
||||
"Use following cycling condtions:",
|
||||
"Template of the 96-well plate"
|
||||
'Use following cycling condtions:',
|
||||
'Template of the 96-well plate'
|
||||
]
|
||||
generate_module_steps(my_modules[5], module_step_names, module_step_descriptions)
|
||||
generate_module_steps(my_modules[5],
|
||||
module_step_names,
|
||||
module_step_descriptions)
|
||||
|
||||
# Add file to existig steps
|
||||
DelayedUploaderTutorial.delay(queue: :tutorial).add_step_asset(
|
||||
step: my_modules[5].protocol.steps.where("position = 0").take,
|
||||
step: my_modules[5].protocol.steps.where('position = 0').take,
|
||||
current_user: user,
|
||||
file_name: "sample_preparation.JPG"
|
||||
file_name: 'sample_preparation.JPG'
|
||||
)
|
||||
|
||||
DelayedUploaderTutorial.delay(queue: :tutorial).add_step_asset(
|
||||
step: my_modules[5].protocol.steps.where("position = 1").take,
|
||||
step: my_modules[5].protocol.steps.where('position = 1').take,
|
||||
current_user: user,
|
||||
file_name: "reaction_setup.JPG"
|
||||
file_name: 'reaction_setup.JPG'
|
||||
)
|
||||
|
||||
DelayedUploaderTutorial.delay(queue: :tutorial).add_step_asset(
|
||||
step: my_modules[5].protocol.steps.where("position = 2").take,
|
||||
step: my_modules[5].protocol.steps.where('position = 2').take,
|
||||
current_user: user,
|
||||
file_name: "cycling_conditions.JPG"
|
||||
file_name: 'cycling_conditions.JPG'
|
||||
)
|
||||
|
||||
DelayedUploaderTutorial.delay(queue: :tutorial).add_step_asset(
|
||||
step: my_modules[5].protocol.steps.where("position = 3").take,
|
||||
step: my_modules[5].protocol.steps.where('position = 3').take,
|
||||
current_user: user,
|
||||
file_name: "96plate.doc"
|
||||
file_name: '96plate.doc'
|
||||
)
|
||||
|
||||
# Results
|
||||
# Add a hard-coded table result
|
||||
temp_result = Result.new(
|
||||
name: "Sample distribution on the plate",
|
||||
name: 'Sample distribution on the plate',
|
||||
my_module: my_modules[5],
|
||||
user: user,
|
||||
created_at: generate_random_time(my_modules[5].created_at, 1.days)
|
||||
)
|
||||
temp_result.table = Table.new(
|
||||
created_by: user,
|
||||
contents: tab_content["module6"]["distribution"] % {sample0: samples_to_assign[0].name,
|
||||
sample1: samples_to_assign[1].name,
|
||||
sample2: samples_to_assign[2].name,
|
||||
sample3: samples_to_assign[3].name}
|
||||
contents: tab_content['module6']['distribution'] % {
|
||||
sample0: samples_to_assign[0].name,
|
||||
sample1: samples_to_assign[1].name,
|
||||
sample2: samples_to_assign[2].name,
|
||||
sample3: samples_to_assign[3].name
|
||||
}
|
||||
)
|
||||
temp_result.save
|
||||
|
||||
|
|
@ -696,7 +717,7 @@ module FirstTimeDataGenerator
|
|||
user: user,
|
||||
created_at: temp_result.created_at,
|
||||
message: I18n.t(
|
||||
"activities.add_table_result",
|
||||
'activities.add_table_result',
|
||||
user: user.full_name,
|
||||
result: temp_result.name
|
||||
)
|
||||
|
|
@ -706,40 +727,45 @@ module FirstTimeDataGenerator
|
|||
DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
|
||||
my_module: my_modules[5],
|
||||
current_user: user,
|
||||
result_name: "Mixtures and plate setup",
|
||||
result_name: 'Mixtures and plate setup',
|
||||
created_at: generate_random_time(my_modules[5].created_at, 2.days),
|
||||
file_name: "Mixes_Templats.xls"
|
||||
file_name: 'Mixes_Templats.xls'
|
||||
)
|
||||
|
||||
DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
|
||||
my_module: my_modules[5],
|
||||
current_user: user,
|
||||
result_name: "Raw data from ABI 7300",
|
||||
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"
|
||||
file_name: 'BootCamp-Experiment-results-20122.sds'
|
||||
)
|
||||
|
||||
DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
|
||||
my_module: my_modules[5],
|
||||
current_user: user,
|
||||
result_name: "All results - curves",
|
||||
result_name: 'All results - curves',
|
||||
created_at: generate_random_time(my_modules[5].created_at, 4.days),
|
||||
file_name: "curves.JPG"
|
||||
file_name: 'curves.JPG'
|
||||
)
|
||||
|
||||
# ----------------- Module 7 ------------------
|
||||
module_step_names = [
|
||||
"Check negative controls NTC",
|
||||
"Eliminate results that have positive NTCs"
|
||||
'Check negative controls NTC',
|
||||
'Eliminate results that have positive NTCs'
|
||||
]
|
||||
module_step_descriptions = [
|
||||
"They have to be negative when using TaqMan assays. If they are positive when using SYBR assays check also melitng curve where signal comes from. - if it is primer dimer result is negative - If it is specific signal it is positive",
|
||||
"And repeat procedure"
|
||||
'They have to be negative when using TaqMan assays. If they are ' \
|
||||
'positive when using SYBR assays check also melitng curve where signal ' \
|
||||
'comes from. - if it is primer dimer result is negative - If it is ' \
|
||||
'specific signal it is positive',
|
||||
'And repeat procedure'
|
||||
]
|
||||
generate_module_steps(my_modules[6], module_step_names, module_step_descriptions)
|
||||
generate_module_steps(my_modules[6],
|
||||
module_step_names,
|
||||
module_step_descriptions)
|
||||
|
||||
# Add comment to step
|
||||
step = my_modules[6].protocol.steps.where("position = 1").take
|
||||
step = my_modules[6].protocol.steps.where('position = 1').take
|
||||
step.save
|
||||
generate_step_comment(
|
||||
step,
|
||||
|
|
@ -749,53 +775,57 @@ module FirstTimeDataGenerator
|
|||
|
||||
# ----------------- Module 8 ------------------
|
||||
module_step_names = [
|
||||
"Template for ddCq analysis"
|
||||
'Template for ddCq analysis'
|
||||
]
|
||||
module_step_descriptions = [
|
||||
nil
|
||||
]
|
||||
generate_module_steps(my_modules[7], module_step_names, module_step_descriptions)
|
||||
|
||||
generate_module_steps(my_modules[7],
|
||||
module_step_names,
|
||||
module_step_descriptions)
|
||||
|
||||
# Add file to existig step
|
||||
DelayedUploaderTutorial.delay(queue: :tutorial).add_step_asset(
|
||||
step: my_modules[7].protocol.steps.where("position = 0").take,
|
||||
step: my_modules[7].protocol.steps.where('position = 0').take,
|
||||
current_user: user,
|
||||
file_name: "ddCq-quantification_diagnostics-template.xls"
|
||||
file_name: 'ddCq-quantification_diagnostics-template.xls'
|
||||
)
|
||||
|
||||
# Add result
|
||||
DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
|
||||
my_module: my_modules[7],
|
||||
current_user: user,
|
||||
result_name: "Results of ddCq method",
|
||||
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"
|
||||
file_name: 'ddCq-quantification_diagnostics-results.xls'
|
||||
)
|
||||
|
||||
DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
|
||||
my_module: my_modules[7],
|
||||
current_user: user,
|
||||
result_name: "Dilution curve and efficiency",
|
||||
result_name: 'Dilution curve and efficiency',
|
||||
created_at: generate_random_time(my_modules[7].created_at, 2.days),
|
||||
file_name: "dilution_curve-efficiency.JPG"
|
||||
file_name: 'dilution_curve-efficiency.JPG'
|
||||
)
|
||||
|
||||
DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
|
||||
my_module: my_modules[7],
|
||||
current_user: user,
|
||||
result_name: "Relative quantification results",
|
||||
result_name: 'Relative quantification results',
|
||||
created_at: generate_random_time(my_modules[7].created_at, 3.days),
|
||||
file_name: "result-ddCq.JPG"
|
||||
file_name: 'result-ddCq.JPG'
|
||||
)
|
||||
|
||||
# Add a text result
|
||||
temp_result = Result.new(
|
||||
name: "Markdown remarks",
|
||||
name: 'Markdown remarks',
|
||||
my_module: my_modules[7],
|
||||
user: user,
|
||||
created_at: generate_random_time(my_modules[7].created_at, 4.days)
|
||||
)
|
||||
temp_text = "__Bolded text__\n\ndouble Enter to go to new line\n\n- bulletpoint"
|
||||
temp_text = "__Bolded text__\n\ndouble Enter " \
|
||||
"to go to new line\n\n- bulletpoint"
|
||||
temp_result.result_text = ResultText.new(
|
||||
text: temp_text
|
||||
)
|
||||
|
|
@ -809,7 +839,7 @@ module FirstTimeDataGenerator
|
|||
user: user,
|
||||
created_at: temp_result.created_at,
|
||||
message: I18n.t(
|
||||
"activities.add_text_result",
|
||||
'activities.add_text_result',
|
||||
user: user.full_name,
|
||||
result: temp_result.name
|
||||
)
|
||||
|
|
@ -820,17 +850,14 @@ module FirstTimeDataGenerator
|
|||
|
||||
# Lastly, create cookie with according ids
|
||||
# so tutorial steps can be properly positioned
|
||||
JSON.generate([
|
||||
organization: org.id,
|
||||
project: project.id,
|
||||
qpcr_module: my_modules[5].id
|
||||
])
|
||||
JSON.generate([team: team.id,
|
||||
project: project.id,
|
||||
qpcr_module: my_modules[5].id])
|
||||
end
|
||||
|
||||
|
||||
# WARNING: This only works on PostgreSQL
|
||||
def pluck_random(scope)
|
||||
scope.order("RANDOM()").first
|
||||
scope.order('RANDOM()').first
|
||||
end
|
||||
|
||||
def generate_random_time(*args)
|
||||
|
|
@ -844,14 +871,13 @@ module FirstTimeDataGenerator
|
|||
end
|
||||
end
|
||||
|
||||
|
||||
# Create steps for given module
|
||||
def generate_module_steps(my_module, step_names, step_descriptions)
|
||||
step_names.each_with_index do |name, i|
|
||||
created_at = generate_random_time(my_module.created_at, 5.hours)
|
||||
completed = rand <= 0.3
|
||||
completed_on = completed ?
|
||||
generate_random_time(created_at, 10.hours) : nil
|
||||
completed_on = nil
|
||||
completed_on = generate_random_time(created_at, 10.hours) if completed
|
||||
|
||||
step = Step.create(
|
||||
created_at: created_at,
|
||||
|
|
@ -872,13 +898,13 @@ module FirstTimeDataGenerator
|
|||
user: step.user,
|
||||
created_at: created_at,
|
||||
message: I18n.t(
|
||||
"activities.create_step",
|
||||
'activities.create_step',
|
||||
user: step.user.full_name,
|
||||
step: i,
|
||||
step_name: step.name
|
||||
)
|
||||
).sneaky_save
|
||||
if completed then
|
||||
if completed
|
||||
Activity.new(
|
||||
type_of: :complete_step,
|
||||
project: my_module.experiment.project,
|
||||
|
|
@ -886,22 +912,22 @@ module FirstTimeDataGenerator
|
|||
user: step.user,
|
||||
created_at: completed_on,
|
||||
message: I18n.t(
|
||||
"activities.complete_step",
|
||||
'activities.complete_step',
|
||||
user: step.user.full_name,
|
||||
step: i+1,
|
||||
step: i + 1,
|
||||
step_name: step.name,
|
||||
completed: my_module.protocol.completed_steps.count,
|
||||
all: i+1
|
||||
all: i + 1
|
||||
)
|
||||
).sneaky_save
|
||||
|
||||
# Also add random comments to completed steps
|
||||
if rand < 0.3
|
||||
polite_comment = "This looks well."
|
||||
polite_comment = 'This looks well.'
|
||||
elsif rand < 0.4
|
||||
polite_comment = "Seems satisfactory."
|
||||
polite_comment = 'Seems satisfactory.'
|
||||
elsif rand < 0.4
|
||||
polite_comment = "Try a bit harder next time."
|
||||
polite_comment = 'Try a bit harder next time.'
|
||||
end
|
||||
if polite_comment
|
||||
commented_on = generate_random_time(completed_on)
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
module ProtocolsImporter
|
||||
include RenamingUtil
|
||||
|
||||
def import_new_protocol(protocol_json, organization, type, user)
|
||||
def import_new_protocol(protocol_json, team, type, user)
|
||||
remove_empty_inputs(protocol_json)
|
||||
protocol = Protocol.new(
|
||||
name: protocol_json["name"],
|
||||
|
|
@ -10,7 +10,7 @@ module ProtocolsImporter
|
|||
protocol_type: (type == :public ? :in_repository_public : :in_repository_private),
|
||||
published_on: (type == :public ? Time.now : nil),
|
||||
added_by: user,
|
||||
organization: @organization
|
||||
team: @team
|
||||
)
|
||||
|
||||
# Try to rename record
|
||||
|
|
@ -127,7 +127,7 @@ module ProtocolsImporter
|
|||
|
||||
# Post process assets
|
||||
asset_ids.each do |asset_id|
|
||||
Asset.find(asset_id).post_process_file(protocol.organization)
|
||||
Asset.find(asset_id).post_process_file(protocol.team)
|
||||
end
|
||||
end
|
||||
|
||||
|
|
|
|||
|
|
@ -2,18 +2,18 @@ class SmartAnnotation
|
|||
include ActionView::Helpers::SanitizeHelper
|
||||
include ActionView::Helpers::TextHelper
|
||||
|
||||
attr_writer :current_user, :current_organization, :query
|
||||
attr_writer :current_user, :current_team, :query
|
||||
|
||||
def initialize(current_user, current_organization, query)
|
||||
def initialize(current_user, current_team, query)
|
||||
@current_user = current_user
|
||||
@current_organization = current_organization
|
||||
@current_team = current_team
|
||||
@query = query
|
||||
end
|
||||
|
||||
def my_modules
|
||||
# Search tasks
|
||||
res = MyModule
|
||||
.search(@current_user, false, @query, 1, @current_organization)
|
||||
.search(@current_user, false, @query, 1, @current_team)
|
||||
.limit(Constants::ATWHO_SEARCH_LIMIT)
|
||||
|
||||
modules_list = []
|
||||
|
|
@ -40,7 +40,7 @@ class SmartAnnotation
|
|||
def projects
|
||||
# Search projects
|
||||
res = Project
|
||||
.search(@current_user, false, @query, 1, @current_organization)
|
||||
.search(@current_user, false, @query, 1, @current_team)
|
||||
.limit(Constants::ATWHO_SEARCH_LIMIT)
|
||||
|
||||
projects_list = []
|
||||
|
|
@ -57,7 +57,7 @@ class SmartAnnotation
|
|||
def experiments
|
||||
# Search experiments
|
||||
res = Experiment
|
||||
.search(@current_user, false, @query, 1, @current_organization)
|
||||
.search(@current_user, false, @query, 1, @current_team)
|
||||
.limit(Constants::ATWHO_SEARCH_LIMIT)
|
||||
|
||||
experiments_list = []
|
||||
|
|
@ -78,7 +78,7 @@ class SmartAnnotation
|
|||
def samples
|
||||
# Search samples
|
||||
res = Sample
|
||||
.search(@current_user, false, @query, 1, @current_organization)
|
||||
.search(@current_user, false, @query, 1, @current_team)
|
||||
.limit(Constants::ATWHO_SEARCH_LIMIT)
|
||||
|
||||
samples_list = []
|
||||
|
|
|
|||
|
|
@ -1,5 +1,4 @@
|
|||
module UsersGenerator
|
||||
|
||||
# Simply validate the user with the given data,
|
||||
# and return an array of errors (which is 0-length
|
||||
# if user is valid)
|
||||
|
|
@ -8,65 +7,57 @@ module UsersGenerator
|
|||
email,
|
||||
password
|
||||
)
|
||||
nu = User.new({
|
||||
full_name: full_name,
|
||||
initials: get_user_initials(full_name),
|
||||
email: email,
|
||||
password: password
|
||||
})
|
||||
nu = User.new(full_name: full_name,
|
||||
initials: get_user_initials(full_name),
|
||||
email: email,
|
||||
password: password)
|
||||
nu.validate
|
||||
nu.errors
|
||||
end
|
||||
|
||||
# If confirmed == true, the user is automatically confirmed;
|
||||
# otherwise, sciNote sends the "confirmation" email to the user
|
||||
# If private_org_name == nil, private organization is not created.
|
||||
def create_user(
|
||||
full_name,
|
||||
email,
|
||||
password,
|
||||
confirmed,
|
||||
private_org_name,
|
||||
org_ids)
|
||||
nu = User.new({
|
||||
full_name: full_name,
|
||||
initials: get_user_initials(full_name),
|
||||
email: email,
|
||||
password: password,
|
||||
password_confirmation: password
|
||||
})
|
||||
if confirmed then
|
||||
nu.confirmed_at = Time.now
|
||||
end
|
||||
# If private_team_name == nil, private taem is not created.
|
||||
def create_user(full_name,
|
||||
email,
|
||||
password,
|
||||
confirmed,
|
||||
private_team_name,
|
||||
team_ids)
|
||||
nu = User.new(full_name: full_name,
|
||||
initials: get_user_initials(full_name),
|
||||
email: email,
|
||||
password: password,
|
||||
password_confirmation: password)
|
||||
|
||||
nu.confirmed_at = Time.now if confirmed
|
||||
nu.save!
|
||||
|
||||
# TODO: If user is not confirmed, maybe additional email
|
||||
# needs to be sent with his/her password & email?
|
||||
|
||||
# Create user's own organization of needed
|
||||
if private_org_name.present? then
|
||||
create_private_user_organization(nu, private_org_name)
|
||||
# Create user's own team of needed
|
||||
if private_team_name.present?
|
||||
create_private_user_team(nu, private_team_name)
|
||||
end
|
||||
|
||||
# Assign user to additional organizations
|
||||
org_ids.each do |org_id|
|
||||
org = Organization.find_by_id(org_id)
|
||||
if org.present?
|
||||
UserOrganization.create({ user: nu, organization: org, role: :admin })
|
||||
end
|
||||
# Assign user to additional teams
|
||||
team_ids.each do |team_id|
|
||||
team = Team.find_by_id(team_id)
|
||||
UserTeam.create(user: nu, team: team, role: :admin) if team.present?
|
||||
end
|
||||
|
||||
# Assign user organization as user current organization
|
||||
nu.current_organization_id = nu.organizations.first.id
|
||||
# Assign user team as user current team
|
||||
nu.current_team_id = nu.teams.first.id
|
||||
nu.save!
|
||||
|
||||
nu.reload
|
||||
return nu
|
||||
nu
|
||||
end
|
||||
|
||||
def create_private_user_organization(user, private_org_name)
|
||||
no = Organization.create({ name: private_org_name, created_by: user })
|
||||
UserOrganization.create({ user: user, organization: no, role: :admin })
|
||||
def create_private_user_team(user, private_team_name)
|
||||
no = Team.create(name: private_team_name, created_by: user)
|
||||
UserTeam.create(user: user, team: no, role: :admin)
|
||||
end
|
||||
|
||||
def print_user(user, password)
|
||||
|
|
@ -76,8 +67,8 @@ module UsersGenerator
|
|||
puts " Email: #{user.email}"
|
||||
puts " Password: #{password}"
|
||||
puts " Confirmed at: #{user.confirmed_at}"
|
||||
orgs = user.organizations.collect{ |org| org.name }.join(", ")
|
||||
puts " Member of organizations: #{orgs}"
|
||||
teams = user.teams.collect(&:name).join(', ')
|
||||
puts " Member of teams: #{teams}"
|
||||
end
|
||||
|
||||
def generate_user_password
|
||||
|
|
@ -86,7 +77,6 @@ module UsersGenerator
|
|||
end
|
||||
|
||||
def get_user_initials(full_name)
|
||||
full_name.split(" ").collect{ |n| n.capitalize[0] }.join[0..3]
|
||||
full_name.split(' ').collect { |n| n.capitalize[0] }.join[0..3]
|
||||
end
|
||||
|
||||
end
|
||||
|
|
|
|||
Loading…
Reference in a new issue