scinote-eln/scinote-web
1
1
Fork 0
mirror of https://github.com/scinote-eln/scinote-web.git synced 2024-12-31 04:32:06 +08:00
Code Issues Projects Releases Packages Wiki Activity

Merge pull request #1209 from ZmagoD/zd_SCI_2165

Browse source 
Update team migration script to support "list of values" and "file" repository columns/cells [fixes SCI-2165]
This commit is contained in:
Zmago Devetak 2018-06-27 15:31:27 +02:00 committed by GitHub
commit 54a17e0574
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
2 changed files with 70 additions and 115 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

34
app/services/team_exporter.rb
View file

@ -48,7 +48,7 @@ class TeamExporter
end
yield if block_given?
dir = FileUtils.mkdir_p(File.join(dir_name, a.id.to_s)).first
if defined?(S3_BUCKET)
if ENV['S3_BUCKET']
s3_asset =
S3_BUCKET.object(a.public_send(attachment_name).path.remove(%r{^/}))
file_name = a.public_send(attachment_name).original_filename
@ -77,9 +77,6 @@ class TeamExporter
.includes(:user_notifications)
.where('user_notifications.user_id': team.users)
.map { |n| notification(n) },
samples: team.samples.map { |s| sample(s) },
sample_groups: team.sample_groups,
sample_types: team.sample_types,
custom_fields: team.custom_fields,
repositories: team.repositories.map { |r| repository(r) },
tiny_mce_assets: team.tiny_mce_assets,
@ -110,7 +107,6 @@ class TeamExporter
user: user_json,
user_notifications: user.user_notifications,
user_identities: user.user_identities,
samples_tables: user.samples_tables.where(team: @team),
repository_table_states:
user.repository_table_states.where(repository: @team.repositories)
}
@ -150,7 +146,6 @@ class TeamExporter
my_module_tags: my_module.my_module_tags,
task_comments: my_module.task_comments,
my_module_repository_rows: my_module.my_module_repository_rows,
sample_my_modules: my_module.sample_my_modules,
user_my_modules: my_module.user_my_modules,
protocols: my_module.protocols.map { |pr| protocol(pr) },
results: my_module.results.map { |res| result(res) }
@ -204,17 +199,12 @@ class TeamExporter
}
end
def sample(sample)
{
sample: sample,
sample_custom_fields: sample.sample_custom_fields
}
end
def repository(repository)
{
repository: repository,
repository_columns: repository.repository_columns,
repository_columns: repository.repository_columns.map do |c|
repository_column(c)
end,
repository_rows: repository.repository_rows.map do |r|
repository_row(r)
end
@ -234,7 +224,21 @@ class TeamExporter
def repository_cell(cell)
{
repository_cell: cell,
repository_value: cell.value
repository_value: cell.value,
repository_value_asset: get_cell_value_asset(cell)
}
end
def repository_column(column)
{
repository_column: column,
repository_list_items: column.repository_list_items
}
end
def get_cell_value_asset(cell)
return unless cell.value_type == 'RepositoryAssetValue'
@assets_to_copy.push(cell.value.asset)
cell.value.asset
end
end

151
app/services/team_importer.rb
View file

@ -3,10 +3,7 @@ class TeamImporter
@user_mappings = {}
@notification_mappings = {}
@repository_mappings = {}
@sample_group_mappings = {}
@sample_type_mappings = {}
@custom_field_mappings = {}
@sample_mappings = {}
@project_mappings = {}
@repository_column_mappings = {}
@experiment_mappings = {}
@ -19,6 +16,7 @@ class TeamImporter
@tag_mappings = {}
@result_text_mappings = {}
@repository_row_mappings = {}
@repository_list_item_mappings = {}
@result_mappings = {}
@checklist_mappings = {}
@table_mappings = {}
@ -28,7 +26,6 @@ class TeamImporter
@repository_row_counter = 0
@protocol_counter = 0
@step_counter = 0
@sample_counter = 0
@report_counter = 0
@my_module_counter = 0
@notification_counter = 0
@ -70,10 +67,7 @@ class TeamImporter
user_team.save!
end
create_sample_groups(team_json['sample_groups'], team)
create_sample_types(team_json['sample_types'], team)
create_custom_fields(team_json['custom_fields'], team)
create_samples(team_json['samples'], team)
create_protocol_keywords(team_json['protocol_keywords'], team)
create_protocols(team_json['protocols'], nil, team)
create_projects(team_json['projects'], team)
@ -114,7 +108,7 @@ class TeamImporter
team_json['repositories'].each do |repository_json|
repository_json['repository_rows'].each do |repository_row_json|
create_repository_cells(repository_row_json['repository_cells'])
create_repository_cells(repository_row_json['repository_cells'], team)
end
end
@ -132,7 +126,6 @@ class TeamImporter
puts "Imported reports: #{@report_counter}"
puts "Imported repositories: #{@repository_counter}"
puts "Imported repository rows: #{@repository_row_counter}"
puts "Imported samples: #{@sample_counter}"
puts "Imported tasks: #{@my_module_counter}"
puts "Imported protocols: #{@protocol_counter}"
puts "Imported steps: #{@step_counter}"
@ -184,11 +177,6 @@ class TeamImporter
step.save! if update_annotation(step.description)
end
end
team.samples.each do |sample|
sample.sample_custom_fields.find_each do |cf|
cf.save! if update_annotation(cf.value)
end
end
team.repositories.each do |rep|
rep.repository_rows.find_each do |row|
row.repository_cells.each do |cell|
@ -202,7 +190,7 @@ class TeamImporter
def update_annotation(text)
return false if text.nil?
updated = false
%w(prj exp tsk sam).each do |name|
%w(prj exp tsk rep_item).each do |name|
text.scan(/~#{name}~\w+\]/).each do |text_match|
orig_id_encoded = text_match.match(/~#{name}~(\w+)\]/)[1]
orig_id = orig_id_encoded.base62_decode
@ -214,8 +202,8 @@ class TeamImporter
@experiment_mappings[orig_id]
when 'tsk'
@my_module_mappings[orig_id]
when 'sam'
@sample_mappings[orig_id]
when 'rep_item'
@repository_row_mappings[orig_id]
end
next unless new_id
new_id_encoded = new_id.base62_encode
@ -317,13 +305,6 @@ class TeamImporter
user_identity.user_id = user.id
user_identity.save!
end
user_json['samples_tables'].each do |samples_table_json|
samples_table = SamplesTable.new(samples_table_json)
samples_table.id = nil
samples_table.user_id = user.id
samples_table.team_id = team.id
samples_table.save!
end
end
end
@ -353,7 +334,10 @@ class TeamImporter
@repository_mappings[orig_repository_id] = repository.id
@repository_counter += 1
repository_json['repository_columns'].each do |repository_column_json|
repository_column = RepositoryColumn.new(repository_column_json)
repository_column = RepositoryColumn.new(
repository_column_json['repository_column']
)
orig_rep_col_id = repository_column.id
repository_column.id = nil
repository_column.repository = repository
@ -361,6 +345,18 @@ class TeamImporter
find_user(repository_column.created_by_id)
repository_column.save!
@repository_column_mappings[orig_rep_col_id] = repository_column.id
next unless repository_column.data_type == 'RepositoryListValue'
repository_column_json['repository_list_items'].each do |list_item|
created_by_id = find_user(repository_column.created_by_id)
repository_list_item = RepositoryListItem.new(data: list_item['data'])
repository_list_item.repository_column = repository_column
repository_list_item.repository = repository
repository_list_item.created_by_id = created_by_id
repository_list_item.last_modified_by_id = created_by_id
repository_list_item.save!
@repository_list_item_mappings[list_item['id']] =
repository_list_item.id
end
end
create_repository_rows(repository_json['repository_rows'], repository)
end
@ -390,7 +386,7 @@ class TeamImporter
end
end
def create_repository_cells(repository_cells_json)
def create_repository_cells(repository_cells_json, team)
repository_cells_json.each do |repository_cell_json|
repository_cell =
RepositoryCell.new(repository_cell_json['repository_cell'])
@ -399,44 +395,9 @@ class TeamImporter
@repository_column_mappings[repository_cell.repository_column_id]
repository_cell.repository_row_id =
@repository_row_mappings[repository_cell.repository_row_id]
repository_value =
RepositoryTextValue.new(repository_cell_json['repository_value'])
repository_value.id = nil
repository_value.created_by_id = find_user(repository_value.created_by_id)
repository_value.last_modified_by_id =
find_user(repository_value.last_modified_by_id)
repository_value.repository_cell = repository_cell
repository_value.save!
end
end
def create_sample_groups(sample_groups_json, team)
puts 'Creating sample groups...'
sample_groups_json.each do |sample_group_json|
sample_group = SampleGroup.new(sample_group_json)
orig_group_id = sample_group.id
sample_group.id = nil
sample_group.team = team
sample_group.created_by_id = find_user(sample_group.created_by_id)
sample_group.last_modified_by_id =
find_user(sample_group.last_modified_by_id)
sample_group.save!
@sample_group_mappings[orig_group_id] = sample_group.id
end
end
def create_sample_types(sample_types_json, team)
puts 'Creating sample types...'
sample_types_json.each do |sample_type_json|
sample_type = SampleType.new(sample_type_json)
orig_type_id = sample_type.id
sample_type.id = nil
sample_type.team = team
sample_type.created_by_id = find_user(sample_type.created_by_id)
sample_type.last_modified_by_id =
find_user(sample_type.last_modified_by_id)
sample_type.save!
@sample_type_mappings[orig_type_id] = sample_type.id
create_cell_value(repository_cell,
repository_cell_json,
team)
end
end
@ -455,31 +416,6 @@ class TeamImporter
end
end
def create_samples(samples_json, team)
puts 'Creating samples...'
samples_json.each do |sample_json|
sample = Sample.new(sample_json['sample'])
orig_sample_id = sample.id
sample.id = nil
sample.team = team
sample.user_id = find_user(sample.user_id)
sample.sample_group_id = @sample_group_mappings[sample.sample_group_id]
sample.sample_type_id = @sample_type_mappings[sample.sample_type_id]
sample.last_modified_by_id = find_user(sample.last_modified_by_id)
sample.save!
@sample_mappings[orig_sample_id] = sample.id
@sample_counter += 1
sample_json['sample_custom_fields'].each do |s_custom_field_json|
s_custom_field = SampleCustomField.new(s_custom_field_json)
s_custom_field.id = nil
s_custom_field.sample = sample
s_custom_field.custom_field_id =
@custom_field_mappings[s_custom_field.custom_field_id]
s_custom_field.save!
end
end
end
def create_protocol_keywords(protocol_keywords_json, team)
puts 'Creating keywords...'
protocol_keywords_json.each do |protocol_keyword_json|
@ -607,17 +543,6 @@ class TeamImporter
task_comment.save!
end
my_module_json['sample_my_modules'].each do |sample_module_json|
sample_module = SampleMyModule.new(sample_module_json)
sample_module.id = nil
sample_module.sample_id =
@sample_mappings[sample_module.sample_id]
sample_module.my_module = my_module
sample_module.assigned_by_id =
find_user(sample_module.assigned_by_id)
sample_module.save!
end
my_module_json['user_my_modules'].each do |user_module_json|
user_module = UserMyModule.new(user_module_json)
user_module.id = nil
@ -875,4 +800,30 @@ class TeamImporter
return nil if user_id.nil?
@user_mappings[user_id] ? @user_mappings[user_id] : @admin_id
end
def find_list_item_id(list_item_id)
@repository_list_item_mappings[list_item_id]
end
def create_cell_value(repository_cell, value_json, team)
cell_json = value_json['repository_value']
case repository_cell.value_type
when 'RepositoryListValue'
list_item_id = find_list_item_id(cell_json['repository_list_item_id'])
repository_value = RepositoryListValue.new(
repository_list_item_id: list_item_id.to_i
)
when 'RepositoryTextValue'
repository_value = RepositoryTextValue.new(cell_json)
when 'RepositoryAssetValue'
asset = create_asset(value_json['repository_value_asset'], team)
repository_value = RepositoryAssetValue.new(asset: asset)
end
repository_value.id = nil
repository_value.created_by_id = find_user(cell_json['created_by_id'])
repository_value.last_modified_by_id =
find_user(cell_json['last_modified_by_id'])
repository_value.repository_cell = repository_cell
repository_value.save!
end
end