')
+ end
+ mdl_lines.push('$$$$') if mdl_lines.last.strip != '$$$$'
+
+ update(extended_metadata: ext_data, mdl: mdl_lines.join("\n"))
+ end
+ end
+end
diff --git a/app/models/chemscanner/reaction.rb b/app/models/chemscanner/reaction.rb
new file mode 100644
index 000000000..98d35b00f
--- /dev/null
+++ b/app/models/chemscanner/reaction.rb
@@ -0,0 +1,113 @@
+# frozen_string_literal: true
+
+# == Schema Information
+#
+# Table name: chemscanner_reactions
+#
+# id :integer not null, primary key
+# scheme_id :integer not null
+# external_id :integer not null
+# clone_from :integer
+# description :string
+# temperature :string
+# time :string
+# status :string
+# yield :float
+# details :jsonb
+# extended_metadata :jsonb
+# is_approved :boolean default(FALSE)
+# imported_id :integer
+# created_at :datetime not null
+# updated_at :datetime not null
+# deleted_at :datetime
+#
+
+
+module Chemscanner
+ # ChemScanner scanned reaction(s)
+ class Reaction < ApplicationRecord
+ acts_as_paranoid
+
+ belongs_to :scheme, class_name: 'Scheme', foreign_key: :scheme_id
+
+ has_many :steps, class_name: 'ReactionStep', foreign_key: :reaction_id
+
+ has_many :reactions_molecules, dependent: :destroy
+ has_many :molecules, through: :reactions_molecules, source: :molecule
+
+ has_many :reactions_reactant_molecules,
+ class_name: 'ReactionsReactantMolecule',
+ dependent: :destroy
+ has_many :reactants,
+ through: :reactions_reactant_molecules, source: :molecule
+
+ has_many :reactions_reagent_molecules,
+ class_name: 'ReactionsReagentMolecule',
+ dependent: :destroy
+ has_many :reagents,
+ through: :reactions_reagent_molecules, source: :molecule
+
+ has_many :reactions_solvent_molecules,
+ class_name: 'ReactionsSolventMolecule',
+ dependent: :destroy
+ has_many :solvents,
+ through: :reactions_solvent_molecules, source: :molecule
+
+ has_many :reactions_product_molecules,
+ class_name: 'ReactionsProductMolecule',
+ dependent: :destroy
+ has_many :products,
+ through: :reactions_product_molecules,
+ source: :molecule
+
+ def assign_from_chemscanner(reaction)
+ assign_attributes(
+ external_id: reaction.arrow_id,
+ clone_from: reaction.clone_from,
+ description: reaction.description,
+ temperature: reaction.temperature,
+ time: reaction.time,
+ status: reaction.status,
+ yield: reaction.yield,
+ details: reaction.details.to_h.to_json
+ )
+ end
+
+ def remove_reagent_smiles(smiles)
+ to_remove = reagents.select { |m| smiles.include?(m.cano_smiles) }
+ ids = to_remove.map(&:id)
+ to_remove.each(&:destroy)
+
+ save!
+ ids
+ end
+
+ def add_reagent_smiles(smiles)
+ max_id = (reactants + reagents + products).map(&:external_id).max
+
+ added = []
+ smiles.each do |s|
+ rw_mol = RDKitChem::RWMol.mol_from_smiles(s)
+
+ m = Molecule.create(
+ cano_smiles: s,
+ scheme_id: scheme_id,
+ mdl: rw_mol.mol_to_mol_block(true, -1, false),
+ external_id: max_id += 1
+ )
+
+ rm = ReactionsMolecule.create(
+ type: 'Chemscanner::ReactionsReagentMolecule',
+ reaction_id: id,
+ molecule_id: m.id
+ )
+ reactions_reagent_molecules << rm
+ added.push(m)
+ end
+
+ save!
+
+ added
+ end
+ end
+end
diff --git a/app/models/chemscanner/reaction_step.rb b/app/models/chemscanner/reaction_step.rb
new file mode 100644
index 000000000..91c0e7f75
--- /dev/null
+++ b/app/models/chemscanner/reaction_step.rb
@@ -0,0 +1,38 @@
+# frozen_string_literal: true
+
+# == Schema Information
+#
+# Table name: chemscanner_reaction_steps
+#
+# id :integer not null, primary key
+# reaction_id :integer not null
+# reaction_external_id :integer not null
+# reagent_ids :integer default([]), is an Array
+# reagent_smiles :string default([]), is an Array
+# step_number :integer not null
+# description :string
+# temperature :string
+# time :string
+# created_at :datetime not null
+# updated_at :datetime not null
+# deleted_at :datetime
+#
+
+
+# ChemScanner scanned reaction(s)
+module Chemscanner
+ # ChemScanner reaction steps
+ class ReactionStep < ApplicationRecord
+ acts_as_paranoid
+
+ belongs_to :reaction, class_name: 'Reaction', foreign_key: :output_id
+
+ def assign_from_chemscanner(step)
+ assign_attributes(
+ description: step.description,
+ temperature: step.temperature,
+ time: step.time
+ )
+ end
+ end
+end
diff --git a/app/models/chemscanner/reactions_molecule.rb b/app/models/chemscanner/reactions_molecule.rb
new file mode 100644
index 000000000..37e804a8b
--- /dev/null
+++ b/app/models/chemscanner/reactions_molecule.rb
@@ -0,0 +1,37 @@
+# frozen_string_literal: true
+
+# == Schema Information
+#
+# Table name: chemscanner_reactions_molecules
+#
+# id :integer not null, primary key
+# reaction_id :integer not null
+# molecule_id :integer not null
+# type :string not null
+# created_at :datetime not null
+# updated_at :datetime not null
+# deleted_at :datetime
+#
+
+
+module Chemscanner
+ # Chemscanner reaction molecule join table
+ class ReactionsMolecule < ApplicationRecord
+ acts_as_paranoid
+
+ belongs_to :reaction
+ belongs_to :molecule
+ end
+
+ class ReactionsReactantMolecule < ReactionsMolecule
+ end
+
+ class ReactionsReagentMolecule < ReactionsMolecule
+ end
+
+ class ReactionsSolventMolecule < ReactionsMolecule
+ end
+
+ class ReactionsProductMolecule < ReactionsMolecule
+ end
+end
diff --git a/app/models/chemscanner/reactions_product_molecule.rb b/app/models/chemscanner/reactions_product_molecule.rb
new file mode 100644
index 000000000..4f8277bbf
--- /dev/null
+++ b/app/models/chemscanner/reactions_product_molecule.rb
@@ -0,0 +1,22 @@
+# frozen_string_literal: true
+
+# == Schema Information
+#
+# Table name: chemscanner_reactions_molecules
+#
+# id :integer not null, primary key
+# reaction_id :integer not null
+# molecule_id :integer not null
+# type :string not null
+# created_at :datetime not null
+# updated_at :datetime not null
+# deleted_at :datetime
+#
+
+
+module Chemscanner
+ class ReactionsProductMolecule < ReactionsMolecule
+ # STI: this file is only here because of rails model autoloading.
+ # place all code in app/models/chemscanner/reactions_molecule.rb.
+ end
+end
diff --git a/app/models/chemscanner/reactions_reactant_molecule.rb b/app/models/chemscanner/reactions_reactant_molecule.rb
new file mode 100644
index 000000000..1b14aaf1c
--- /dev/null
+++ b/app/models/chemscanner/reactions_reactant_molecule.rb
@@ -0,0 +1,22 @@
+# frozen_string_literal: true
+
+# == Schema Information
+#
+# Table name: chemscanner_reactions_molecules
+#
+# id :integer not null, primary key
+# reaction_id :integer not null
+# molecule_id :integer not null
+# type :string not null
+# created_at :datetime not null
+# updated_at :datetime not null
+# deleted_at :datetime
+#
+
+
+module Chemscanner
+ class ReactionsReactantMolecule < ReactionsMolecule
+ # STI: this file is only here because of rails model autoloading.
+ # place all code in app/models/chemscanner/reactions_molecule.rb.
+ end
+end
diff --git a/app/models/chemscanner/reactions_reagent_molecule.rb b/app/models/chemscanner/reactions_reagent_molecule.rb
new file mode 100644
index 000000000..a27ade2fa
--- /dev/null
+++ b/app/models/chemscanner/reactions_reagent_molecule.rb
@@ -0,0 +1,22 @@
+# frozen_string_literal: true
+
+# == Schema Information
+#
+# Table name: chemscanner_reactions_molecules
+#
+# id :integer not null, primary key
+# reaction_id :integer not null
+# molecule_id :integer not null
+# type :string not null
+# created_at :datetime not null
+# updated_at :datetime not null
+# deleted_at :datetime
+#
+
+
+module Chemscanner
+ class ReactionsReagentMolecule < ReactionsMolecule
+ # STI: this file is only here because of rails model autoloading.
+ # place all code in app/models/chemscanner/reactions_molecule.rb.
+ end
+end
diff --git a/app/models/chemscanner/reactions_solvent_molecule.rb b/app/models/chemscanner/reactions_solvent_molecule.rb
new file mode 100644
index 000000000..8823e496b
--- /dev/null
+++ b/app/models/chemscanner/reactions_solvent_molecule.rb
@@ -0,0 +1,22 @@
+# frozen_string_literal: true
+
+# == Schema Information
+#
+# Table name: chemscanner_reactions_molecules
+#
+# id :integer not null, primary key
+# reaction_id :integer not null
+# molecule_id :integer not null
+# type :string not null
+# created_at :datetime not null
+# updated_at :datetime not null
+# deleted_at :datetime
+#
+
+
+module Chemscanner
+ class ReactionsSolventMolecule < ReactionsMolecule
+ # STI: this file is only here because of rails model autoloading.
+ # place all code in app/models/chemscanner/reactions_molecule.rb.
+ end
+end
diff --git a/app/models/chemscanner/scheme.rb b/app/models/chemscanner/scheme.rb
new file mode 100644
index 000000000..684cb6706
--- /dev/null
+++ b/app/models/chemscanner/scheme.rb
@@ -0,0 +1,87 @@
+# frozen_string_literal: true
+
+# == Schema Information
+#
+# Table name: chemscanner_schemes
+#
+# id :integer not null, primary key
+# source_id :integer not null
+# is_approved :boolean default(FALSE)
+# extended_metadata :jsonb
+# index :integer default(0)
+# image_data :string default("")
+# version :string default("")
+# created_by :integer not null
+# created_at :datetime not null
+# updated_at :datetime not null
+# deleted_at :datetime
+#
+
+
+module Chemscanner
+ # Hold ChemScanner output information
+ class Scheme < ApplicationRecord
+ acts_as_paranoid
+
+ belongs_to :creator, foreign_key: :created_by, class_name: 'User'
+ belongs_to :source, foreign_key: :source_id, class_name: 'Chemscanner::Source'
+
+ has_many :reactions,
+ class_name: 'Reaction', foreign_key: :scheme_id,
+ dependent: :destroy
+
+ has_many :molecules,
+ class_name: 'Molecule', foreign_key: :scheme_id,
+ dependent: :destroy
+
+ accepts_nested_attributes_for :reactions, :molecules
+
+ scope :for_user, ->(user_id) { where('created_by = ?', user_id) }
+
+ def file_uuid
+ source.file_uuid
+ end
+
+ def empty?
+ reactions.empty? && molecules.empty?
+ end
+
+ def add_doi(doi)
+ return if doi.empty?
+
+ ext_data = extended_metadata
+ return if ext_data.key?(:doi)
+
+ update!(extended_metadata: ext_data.merge(doi: doi.strip))
+ end
+
+ def destroy_version(version)
+ destroy if self.version == version
+ end
+
+ def approve(val)
+ reactions.update_all(is_approved: val)
+ molecules.update_all(is_approved: val)
+
+ {
+ scheme_ids: [id],
+ reaction_ids: reactions.map(&:id),
+ molecule_ids: molecules.map(&:id)
+ }
+ end
+
+ class << self
+ def save_png(png_list)
+ png_list.each do |file_info|
+ id = file_info['id']
+ scheme = find(id)
+ next if scheme.nil?
+
+ scheme.image_data = file_info['imageData']
+ scheme.save!
+ end
+ end
+ # handle_asynchronously :save_png
+ end
+ end
+end
diff --git a/app/models/chemscanner/source.rb b/app/models/chemscanner/source.rb
new file mode 100644
index 000000000..87fdff9dc
--- /dev/null
+++ b/app/models/chemscanner/source.rb
@@ -0,0 +1,138 @@
+# frozen_string_literal: true
+
+# == Schema Information
+#
+# Table name: chemscanner_sources
+#
+# id :integer not null, primary key
+# parent_id :integer
+# file_id :integer not null
+# extended_metadata :jsonb
+# created_by :integer not null
+# created_at :datetime not null
+# updated_at :datetime not null
+#
+
+
+# Storing uploaded file for ChemScanner processing
+module Chemscanner
+ # Uploaded files for scanning
+ class Source < ActiveRecord::Base
+ belongs_to :creator, foreign_key: :created_by, class_name: 'User'
+
+ belongs_to :file, -> { where attachable_type: 'ChemscannerSource' },
+ class_name: 'Attachment', foreign_key: :file_id,
+ foreign_type: :attachable_type
+
+ # has_one :file, as: :attachable
+
+ has_many :schemes,
+ foreign_key: :source_id, class_name: 'Scheme',
+ dependent: :destroy
+
+ accepts_nested_attributes_for :schemes
+
+ has_many :reactions, through: :schemes
+ has_many :molecules, through: :schemes
+
+ has_closure_tree dependent: :destroy
+
+ # _ct from closure_tree gem
+ scope :full_tree, -> { _ct.default_tree_scope(all) }
+
+ scope :for_user, ->(user_id) { where('created_by = ?', user_id) }
+
+ MIME_TYPE = {
+ cdx: 'chemical/cdx',
+ cdxml: 'text/xml',
+ xml: 'text/xml',
+ doc: 'application/msword',
+ docx: 'application/vnd.openxmlformats-officedocument.wordprocessingml.document',
+ json: 'application/json'
+ }.freeze
+
+ def file_uuid
+ file.identifier
+ end
+
+ def scan
+ filename = file.filename
+ extn = File.extname(filename).downcase
+
+ func_name = "#{extn[1..-1]}_process".to_sym
+ return unless Chemscanner::Process.respond_to?(func_name)
+
+ Chemscanner::Process.send(func_name, self)
+ end
+
+ def create_child(child_path)
+ user_id = created_by
+ source = self.class.new(created_by: user_id)
+ ext = File.extname(child_path)
+ basename = File.basename(child_path)
+
+ source.build_file(
+ filename: basename,
+ file_path: child_path,
+ identifier: SecureRandom.uuid,
+ created_by: user_id,
+ created_for: user_id,
+ attachable_type: 'ChemscannerSource',
+ content_type: MIME_TYPE[ext.to_sym]
+ )
+ source.parent = self
+ children << source
+
+ source
+ end
+
+ def approve(val)
+ reactions.update_all(is_approved: val)
+ molecules.update_all(is_approved: val)
+
+ file_ids = [id]
+ scheme_ids = schemes.map(&:id)
+ reaction_ids = reactions.map(&:id)
+ molecule_ids = molecules.map(&:id)
+
+ children.each do |child|
+ info = child.approve(val)
+
+ file_ids.concat(info[:file_ids] || [])
+ scheme_ids.concat(info[:scheme_ids] || [])
+ reaction_ids.concat(info[:reaction_ids] || [])
+ molecule_ids.concat(info[:molecule_ids] || [])
+ end
+
+ {
+ file_ids: file_ids,
+ scheme_ids: scheme_ids,
+ reaction_ids: reaction_ids,
+ molecule_ids: molecule_ids
+ }
+ end
+
+ class << self
+ def create_from_uploaded_file(file, uid, user)
+ user_id = user.nil? ? nil : user.id
+ temp_file = file['tempfile']
+ file_path = temp_file.to_path
+ extn = File.extname(file_path)[1..-1]
+
+ source = Source.new(created_by: user_id)
+
+ source.build_file(
+ filename: file['filename'],
+ file_path: file_path,
+ identifier: uid,
+ created_by: user_id,
+ created_for: user_id,
+ attachable_type: 'ChemscannerSource',
+ content_type: MIME_TYPE[extn.to_sym] || ''
+ )
+
+ source
+ end
+ end
+ end
+end
diff --git a/app/models/collaborator.rb b/app/models/collaborator.rb
new file mode 100644
index 000000000..7b6626dfa
--- /dev/null
+++ b/app/models/collaborator.rb
@@ -0,0 +1,55 @@
+# == Schema Information
+#
+# Table name: users
+#
+# id :integer not null, primary key
+# email :string default(""), not null
+# encrypted_password :string default(""), not null
+# reset_password_token :string
+# reset_password_sent_at :datetime
+# remember_created_at :datetime
+# sign_in_count :integer default(0), not null
+# current_sign_in_at :datetime
+# last_sign_in_at :datetime
+# current_sign_in_ip :inet
+# last_sign_in_ip :inet
+# created_at :datetime not null
+# updated_at :datetime not null
+# name :string
+# first_name :string not null
+# last_name :string not null
+# deleted_at :datetime
+# counters :hstore not null
+# name_abbreviation :string(12)
+# type :string default("Person")
+# reaction_name_prefix :string(3) default("R")
+# layout :hstore not null
+# confirmation_token :string
+# confirmed_at :datetime
+# confirmation_sent_at :datetime
+# unconfirmed_email :string
+# selected_device_id :integer
+# failed_attempts :integer default(0), not null
+# unlock_token :string
+# locked_at :datetime
+# account_active :boolean
+# matrix :integer default(0)
+# providers :jsonb
+#
+# Indexes
+#
+# index_users_on_confirmation_token (confirmation_token) UNIQUE
+# index_users_on_deleted_at (deleted_at)
+# index_users_on_email (email) UNIQUE
+# index_users_on_name_abbreviation (name_abbreviation) UNIQUE WHERE (name_abbreviation IS NOT NULL)
+# index_users_on_reset_password_token (reset_password_token) UNIQUE
+# index_users_on_unlock_token (unlock_token) UNIQUE
+#
+
+class Collaborator < User
+ def send_on_create_confirmation_instructions
+
+ end
+ end
+
+
diff --git a/app/models/collection.rb b/app/models/collection.rb
index f04251b92..cb48c1007 100644
--- a/app/models/collection.rb
+++ b/app/models/collection.rb
@@ -33,6 +33,7 @@ class Collection < ApplicationRecord
acts_as_paranoid
belongs_to :user, optional: true
has_ancestry
+ include Publishing
has_many :collections_samples, dependent: :destroy
has_many :collections_reactions, dependent: :destroy
@@ -51,6 +52,8 @@ class Collection < ApplicationRecord
has_many :sync_collections_users, foreign_key: :collection_id, dependent: :destroy
has_many :shared_users, through: :sync_collections_users, source: :user
+ has_one :doi, as: :doiable
+
# A collection is locked if it is not allowed to rename or rearrange it
scope :unlocked, -> { where(is_locked: false) }
scope :locked, -> { where(is_locked: true) }
@@ -72,6 +75,55 @@ class Collection < ApplicationRecord
default_scope { ordered }
+ def self.public_collection_id
+ ENV['PUBLIC_COLL_ID']&.to_i
+ end
+
+ def self.public_collection
+ find_by(id: ENV['PUBLIC_COLL_ID']) || find_by(
+ user_id: User.chemotion_user.id,
+ label: ENV['PUBLIC_COLL']
+ )
+ end
+
+ def self.scheme_only_reactions_collection
+ find_by(id: ENV['SCHEME_ONLY_REACTIONS_COLL_ID']) || find_by(
+ user_id: User.chemotion_user.id,
+ label: ENV['SCHEME_ONLY_REACTIONS_COLL']
+ ) || find_by(
+ user_id: User.chemotion_user.id,
+ label: 'Scheme-only reactions'
+ )
+ end
+
+ def self.scheme_only_reactions_collection_id
+ ENV['SCHEME_ONLY_REACTIONS_COLL_ID']&.to_i
+ end
+
+ def self.embargo_accepted_collection
+ find_by(
+ user_id: User.chemotion_user.id,
+ label: 'Embargo Accepted',
+ is_synchronized: true
+ )
+ end
+
+ def self.element_to_review_collection
+ where(
+ user_id: User.chemotion_user.id,
+ label: 'Element To Review',
+ is_synchronized: true
+ )
+ end
+
+ def self.reviewed_collection
+ where(
+ user_id: User.chemotion_user.id,
+ label: 'Reviewed',
+ is_synchronized: true
+ )
+ end
+
def self.get_all_collection_for_user(user_id)
find_by(user_id: user_id, label: 'All', is_locked: true)
end
@@ -141,4 +193,23 @@ def self.reject_shared(user_id, collection_id)
Collection.where(id: collection_id, user_id: user_id, is_shared: true)
.each(&:destroy)
end
+
+ def self.all_embargos(user_id)
+ if user_id.nil?
+ Collection.where(
+ <<~SQL
+ id in (select c2.id from collections c2 where c2.ancestry in (select c.id::text from collections c where c.label = 'Published Elements'))
+ SQL
+ )
+ else
+ Collection.where(
+ <<~SQL
+ id in (
+ select c2.id from collections c2 where c2.ancestry in (select c.id::text from collections c where c.label = 'Published Elements') union
+ select co.id from collections co where co.ancestry in (select c.id::text from collections c, sync_collections_users scu
+ where c.label = 'Embargoed Publications' and scu.collection_id = c.id and scu.user_id = #{user_id}))
+ SQL
+ )
+ end
+ end
end
diff --git a/app/models/collections_reaction.rb b/app/models/collections_reaction.rb
index e78683c4e..08e4c3720 100644
--- a/app/models/collections_reaction.rb
+++ b/app/models/collections_reaction.rb
@@ -37,6 +37,8 @@ def self.remove_in_collection(reaction_ids, collection_ids)
def self.move_to_collection(reaction_ids, from_col_ids, to_col_ids)
# Get associated samples
sample_ids = Reaction.get_associated_samples(reaction_ids)
+ # exclude samples which are already public, they are not supposed to be moved
+ sample_ids = sample_ids.difference(Collection.public_collection.samples.where(id: sample_ids).pluck(:id))
# Delete reactions from collection
delete_in_collection(reaction_ids, from_col_ids)
# Move associated samples in current collection
diff --git a/app/models/compound_open_data.rb b/app/models/compound_open_data.rb
new file mode 100644
index 000000000..1a5074375
--- /dev/null
+++ b/app/models/compound_open_data.rb
@@ -0,0 +1,21 @@
+# == Schema Information
+#
+# Table name: compound_open_data_locals
+#
+# x_id :integer
+# x_sample_id :integer
+# x_data :jsonb
+# x_created_at :datetime
+# x_updated_at :datetime
+# x_inchikey :string
+# x_sum_formular :string
+# x_cano_smiles :string
+# x_external_label :string
+# x_short_label :string
+# x_name :string
+# x_stereo :jsonb
+#
+
+class CompoundOpenData < ApplicationRecord
+ default_scope { order(x_created_at: :desc) }
+end
diff --git a/app/models/concerns/attachment_converter.rb b/app/models/concerns/attachment_converter.rb
index 2842081ab..758d7b727 100644
--- a/app/models/concerns/attachment_converter.rb
+++ b/app/models/concerns/attachment_converter.rb
@@ -14,8 +14,8 @@ def init_converter
def exec_converter
return if !Rails.configuration.try(:converter).try(:url) || !ACCEPTED_FORMATS.include?(File.extname(filename&.downcase)) || aasm_state != 'queueing'
- resp = Analyses::Converter.jcamp_converter(id)
- self.aasm_state = resp.success? ? 'done' : 'failure'
+ state = Analyses::Converter.jcamp_converter(id)
+ self.aasm_state = state if %w[done failure].include?(state)
end
end
end
diff --git a/app/models/concerns/attachment_jcamp_aasm.rb b/app/models/concerns/attachment_jcamp_aasm.rb
index 642ffda3e..c7dfc8114 100644
--- a/app/models/concerns/attachment_jcamp_aasm.rb
+++ b/app/models/concerns/attachment_jcamp_aasm.rb
@@ -3,7 +3,7 @@
# - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# State machine for attachment Jcamp handle
module AttachmentJcampAasm
- FILE_EXT_SPECTRA = %w[dx jdx jcamp mzml mzxml raw cdf zip].freeze
+ FILE_EXT_SPECTRA = %w[dx jdx jcamp mzml mzxml raw cdf zip nmrium].freeze
extend ActiveSupport::Concern
@@ -15,7 +15,7 @@ module AttachmentJcampAasm
aasm do
state :idle, initial: true
state :queueing, :regenerating, :done
- state :peaked, :edited, :backup, :image, :json
+ state :peaked, :edited, :backup, :image, :json, :csv, :nmrium
state :failure
state :non_jcamp
state :oo_editing
@@ -29,25 +29,25 @@ module AttachmentJcampAasm
end
event :set_queueing do
- transitions from: %i[idle done backup failure non_jcamp queueing regenerating],
+ transitions from: %i[idle done backup failure non_jcamp queueing regenerating nmrium],
to: :queueing
end
event :set_regenerating do
- transitions from: %i[idle done backup failure non_jcamp queueing regenerating],
+ transitions from: %i[idle done backup failure non_jcamp queueing regenerating nmrium],
to: :regenerating
end
event :set_force_peaked do
- transitions from: %i[queueing regenerating], to: :peaked
+ transitions from: %i[queueing regenerating nmrium], to: :peaked
end
event :set_edited do
- transitions from: %i[peaked queueing regenerating], to: :edited
+ transitions from: %i[peaked queueing regenerating nmrium], to: :edited
end
event :set_backup do
- transitions from: %i[peaked edited failure], to: :backup
+ transitions from: %i[peaked edited failure nmrium], to: :backup
end
event :set_non_jcamp do
@@ -55,7 +55,7 @@ module AttachmentJcampAasm
end
event :set_done do
- transitions from: %i[queueing regenerating], to: :done
+ transitions from: %i[queueing regenerating nmrium], to: :done
end
event :set_image do
@@ -63,11 +63,19 @@ module AttachmentJcampAasm
end
event :set_json do
- transitions from: %i[idle peaked non_jcamp], to: :json
+ transitions from: %i[idle peaked non_jcamp json], to: :json
+ end
+
+ event :set_csv do
+ transitions from: %i[idle peaked non_jcamp], to: :csv
+ end
+
+ event :set_nmrium do
+ transitions from: %i[idle peaked edited non_jcamp queueing regenerating], to: :nmrium
end
event :set_failure do
- transitions from: %i[idle queueing regenerating failure], to: :failure
+ transitions from: %i[idle queueing regenerating failure nmrium], to: :failure
end
end
end
@@ -103,8 +111,8 @@ def require_peaks_generation? # rubocop:disable all
is_peak_edit = %w[peak edit].include?(typname)
return generate_img_only(typname) if is_peak_edit
- generate_spectrum(true, false) if queueing? && !new_upload
- generate_spectrum(true, true) if regenerating? && !new_upload
+ generate_spectrum(true, false) if queueing?
+ generate_spectrum(true, true) if regenerating?
end
def belong_to_analysis?
@@ -122,6 +130,7 @@ def generate_att(meta_tmp, addon, to_edit = false, ext = nil)
meta_filename = Chemotion::Jcamp::Gen.filename(filename_parts, addon, ext)
content_type = ext == 'png' ? 'image/png' : 'application/octet-stream'
+
att = Attachment.new(
filename: meta_filename,
file_path: meta_tmp.path,
@@ -135,7 +144,12 @@ def generate_att(meta_tmp, addon, to_edit = false, ext = nil)
att.set_edited if ext != 'png' && to_edit
att.set_image if ext == 'png'
att.set_json if ext == 'json'
+ att.set_csv if ext == 'csv'
+ att.set_nmrium if ext == 'nmrium'
att.update!(storage: Rails.configuration.storage.primary_store)
+ # att.update!(
+ # attachable_id: attachable_id, attachable_type: 'Container'
+ # )
att
end
@@ -152,6 +166,14 @@ def generate_json_att(json_tmp, addon, to_edit = false)
generate_att(json_tmp, addon, to_edit, 'json')
end
+ def generate_csv_att(csv_tmp, addon, to_edit = false)
+ generate_att(csv_tmp, addon, to_edit, 'csv')
+ end
+
+ def generate_nmrium_att(nmrium_tmp, addon, to_edit = false)
+ generate_att(nmrium_tmp, addon, to_edit, 'nmrium')
+ end
+
def build_params(params = {})
_, extname = extension_parts
params[:mass] = 0.0
@@ -163,15 +185,17 @@ def build_params(params = {})
params
end
+ # TODO: Fix bugs and improve code
def get_infer_json_content
- atts = Attachment.where(attachable_id: attachable_id)
+ atts = Attachment.where(attachable_id: attachable_id) # might break on multiple Attachments with the same ID but different types
+ # shorten this whole block to a single find with '{}' fallback if none is found
infers = atts.map do |att|
keyword, _extname = att.extension_parts
keep = att.json? && keyword == 'infer'
keep ? att : nil
end.select(&:present?)
- !infers.empty? ? infers[0].read_file : '{}'
+ infers.empty? ? '{}' : infers[0].read_file
end
def update_prediction(params, spc_type, is_regen)
@@ -184,38 +208,87 @@ def update_prediction(params, spc_type, is_regen)
def create_process(is_regen)
params = build_params
- tmp_jcamp, tmp_img, spc_type = Tempfile.create('molfile') do |t_molfile|
- if attachable&.root_element.is_a?(Sample)
- t_molfile.write(attachable.root_element.molecule.molfile)
- t_molfile.rewind
- end
- Chemotion::Jcamp::Create.spectrum(
- abs_path, t_molfile.path, is_regen, params
- )
+
+ if params[:ext] == 'nmrium'
+ return generate_spectrum_from_nmrium
+ end
+
+ tmp_jcamp, tmp_img, arr_jcamp, arr_img, arr_csv, arr_nmrium, spc_type, invalid_molfile = generate_spectrum_data(params, is_regen)
+
+ check_invalid_molfile(invalid_molfile)
+
+ if spc_type == 'bagit'
+ read_bagit_data(arr_jcamp, arr_img, arr_csv, spc_type, is_regen)
+ elsif arr_jcamp.length > 1
+ read_processed_data(arr_jcamp, arr_img, spc_type, is_regen)
+ else
+ jcamp_att = generate_jcamp_att(tmp_jcamp, 'peak')
+ jcamp_att.auto_infer_n_clear_json(spc_type, is_regen)
+ img_att = generate_img_att(tmp_img, 'peak')
+
+ tmp_files_to_be_deleted = [tmp_jcamp, tmp_img]
+ tmp_files_to_be_deleted.push(*arr_img)
+
+ set_done
+ delete_tmps(tmp_files_to_be_deleted)
+ delete_related_imgs(img_att)
+ delete_edit_peak_after_done
+
+ jcamp_att
+ end
+ end
+
+ def edit_process(is_regen, orig_params)
+ params = build_params(orig_params)
+ tmp_jcamp, tmp_img, _, _, arr_csv, arr_nmrium, spc_type, invalid_molfile = generate_spectrum_data(params, is_regen)
+
+ check_invalid_molfile(invalid_molfile)
+
+ jcamp_att = generate_jcamp_att(tmp_jcamp, 'edit', true)
+ jcamp_att.update_prediction(params, spc_type, is_regen)
+ img_att = generate_img_att(tmp_img, 'edit', true)
+
+ tmp_files_to_be_deleted = [tmp_jcamp, tmp_img]
+
+ unless arr_csv.nil? || arr_csv.length == 0
+ curr_tmp_csv = arr_csv[0]
+ csv_att = generate_csv_att(curr_tmp_csv, 'edit', false)
+ tmp_files_to_be_deleted.push(*arr_csv)
+ delete_related_csv(csv_att)
end
- if tmp_img.nil? && spc_type.nil? && tmp_jcamp['invalid_molfile'] == true
+ # set_backup
+ unless arr_nmrium.nil? || arr_nmrium.length == 0
+ curr_tmp_nmrium = arr_nmrium[0]
+ nmrium_att = generate_nmrium_att(curr_tmp_nmrium, '', false)
+ tmp_files_to_be_deleted.push(*arr_nmrium)
+ delete_related_nmrium(nmrium_att)
+ end
+
+ set_backup
+ delete_tmps(tmp_files_to_be_deleted)
+ delete_related_imgs(img_att)
+ delete_related_edit_peak(jcamp_att)
+ jcamp_att
+ end
+
+ def check_invalid_molfile(invalid_molfile = false)
+ if invalid_molfile == true
# add message when invalid molfile
Message.create_msg_notification(
channel_subject: Channel::CHEM_SPECTRA_NOTIFICATION,
message_from: attachable.root_element.created_by,
- data_args: { 'msg': 'Invalid molfile' }
+ data_args: { msg: 'Invalid molfile' },
)
end
-
- jcamp_att = generate_jcamp_att(tmp_jcamp, 'peak')
- jcamp_att.auto_infer_n_clear_json(spc_type, is_regen)
- img_att = generate_img_att(tmp_img, 'peak')
- set_done
- delete_tmps([tmp_jcamp, tmp_img])
- delete_related_imgs(img_att)
- delete_edit_peak_after_done
- jcamp_att
end
- def edit_process(is_regen, orig_params)
- params = build_params(orig_params)
- tmp_jcamp, tmp_img, spc_type = Tempfile.create('molfile') do |t_molfile|
+ def generate_spectrum_data(params, is_regen)
+ if params[:ext] == 'nmrium'
+ return
+ end
+
+ tmp_jcamp, tmp_img, arr_jcamp, arr_img, arr_csv, arr_nmrium, spc_type, invalid_molfile = Tempfile.create('molfile') do |t_molfile|
if attachable&.root_element.is_a?(Sample)
t_molfile.write(attachable.root_element.molecule.molfile)
t_molfile.rewind
@@ -224,33 +297,105 @@ def edit_process(is_regen, orig_params)
abs_path, t_molfile.path, is_regen, params
)
end
+ end
- if tmp_img.nil? && spc_type.nil? && tmp_jcamp['invalid_molfile'] == true
- # add message when invalid molfile
- Message.create_msg_notification(
- channel_subject: Channel::CHEM_SPECTRA_NOTIFICATION,
- message_from: attachable.root_element.created_by,
- data_args: { 'msg': 'Invalid molfile' }
- )
+ def generate_spectrum(is_create = false, is_regen = false, params = {})
+ is_create ? create_process(is_regen) : edit_process(is_regen, params)
+ rescue StandardError => e
+ set_failure
+ Rails.logger.info('**** Jcamp Peaks Generation fails ***')
+ Rails.logger.error(e)
+ end
+
+ def read_processed_data(arr_jcamp, arr_img, spc_type, is_regen)
+ jcamp_att = nil
+ tmp_to_be_deleted = []
+ tmp_img_to_deleted = []
+ arr_jcamp.each_with_index do |jcamp, idx|
+ file_name_to_generate = idx == 0 ? 'peak' : "processed_#{idx}"
+
+ curr_jcamp_att = generate_jcamp_att(jcamp, file_name_to_generate)
+ curr_jcamp_att.auto_infer_n_clear_json(spc_type, is_regen)
+ jcamp_att = curr_jcamp_att if idx == 0
+
+ curr_tmp_img = arr_img[idx]
+ img_att = generate_img_att(curr_tmp_img, file_name_to_generate)
+
+ tmp_to_be_deleted.push(jcamp, curr_tmp_img)
+ tmp_img_to_deleted.push(img_att)
end
- jcamp_att = generate_jcamp_att(tmp_jcamp, 'edit', true)
- jcamp_att.update_prediction(params, spc_type, is_regen)
- img_att = generate_img_att(tmp_img, 'edit', true)
- set_backup
- delete_tmps([tmp_jcamp, tmp_img])
- delete_related_imgs(img_att)
+
+ set_done
+ delete_tmps(tmp_to_be_deleted)
+ delete_related_arr_img(tmp_img_to_deleted)
delete_edit_peak_after_done
jcamp_att
end
- def generate_spectrum(is_create = false, is_regen = false, params = {})
- is_create ? create_process(is_regen) : edit_process(is_regen, params)
+ def read_bagit_data(arr_jcamp, arr_img, arr_csv, spc_type, is_regen)
+ jcamp_att = nil
+ tmp_to_be_deleted = []
+ tmp_img_to_deleted = []
+ arr_jcamp.each_with_index do |jcamp, idx|
+ curr_jcamp_att = generate_jcamp_att(jcamp, "#{idx + 1}_bagit")
+ curr_jcamp_att.auto_infer_n_clear_json(spc_type, is_regen)
+ curr_tmp_img = arr_img[idx]
+ img_att = generate_img_att(curr_tmp_img, "#{idx + 1}_bagit")
+ tmp_to_be_deleted.push(jcamp, curr_tmp_img)
+ tmp_img_to_deleted.push(img_att)
+
+ curr_tmp_csv = arr_csv[idx]
+ _ = generate_csv_att(curr_tmp_csv, "#{idx + 1}_bagit")
+ tmp_to_be_deleted.push(curr_tmp_csv)
+
+ jcamp_att = curr_jcamp_att if idx == 0
+ end
+ set_done
+ delete_tmps(tmp_to_be_deleted)
+ delete_related_arr_img(tmp_img_to_deleted)
+ delete_edit_peak_after_done
+ jcamp_att
+ end
+
+ def generate_spectrum_from_nmrium
+ tmp_jcamp = Chemotion::Jcamp::CreateFromNMRium.jcamp_from_nmrium(abs_path)
+ jcamp_att = generate_jcamp_att(tmp_jcamp, 'edit', true)
+
+ set_nmrium
+
+ tmp_files_to_be_deleted = [tmp_jcamp]
+ delete_tmps(tmp_files_to_be_deleted)
+ delete_related_edited_jcamp(jcamp_att)
+ delete_related_edit_peak_with_att(jcamp_att)
+ delete_related_nmrium(self)
+ jcamp_att
rescue StandardError => e
set_failure
- Rails.logger.info('**** Jcamp Peaks Generation fails ***')
+ Rails.logger.info('**** Jcamp Edit from NMRium Generation fails ***')
Rails.logger.error(e)
end
+ def delete_related_edit_peak_with_att(attachment)
+ return unless attachment
+
+ atts = Attachment.where(attachable_id: attachable_id)
+ valid_name = fname_wo_ext(self)
+ atts.each do |att|
+ edit_jdx_name = File.basename(att.filename, '.edit.jdx')
+ peak_jdx_name = File.basename(att.filename, '.peak.jdx')
+ edit_image_name = File.basename(att.filename, '.edit.png')
+ peak_image_name = File.basename(att.filename, '.peak.png')
+ array_valid_names = [edit_jdx_name, peak_jdx_name, edit_image_name, peak_image_name]
+
+ is_delete = (
+ (att.edited? || att.peaked? || att.image?) &&
+ att.id != attachment.id &&
+ (array_valid_names.include? valid_name)
+ )
+ att.delete if is_delete
+ end
+ end
+
def delete_tmps(tmp_arr)
tmp_arr.each do |tmp|
next unless tmp
@@ -265,9 +410,24 @@ def delete_edit_peak_after_done
destroy if %w[edit peak].include?(typname)
end
+ def delete_related_edit_peak(jcamp_att)
+ return unless jcamp_att
+
+ atts = Attachment.where(attachable_id: attachable_id)
+ valid_name = fname_wo_ext(self)
+ atts.each do |att|
+ is_delete = (
+ (att.edited? || att.peaked?) &&
+ att.id != jcamp_att.id &&
+ valid_name == fname_wo_ext(att)
+ )
+ att.delete if is_delete
+ end
+ end
+
def fname_wo_ext(target)
parts = target.filename_parts
- ending = parts.length == 2 ? -2 : -3
+ ending = parts.length == 2 || parts.length == 3 ? -2 : -3
parts[0..ending].join('_')
end
@@ -286,6 +446,70 @@ def delete_related_imgs(img_att)
end
end
+ def delete_related_arr_img(arr_img)
+ return unless arr_img
+
+ arr_img.each do |img_att|
+ next unless img_att
+
+ atts = Attachment.where(attachable_id: attachable_id)
+ valid_name = fname_wo_ext(img_att)
+ atts.each do |att|
+ is_delete = (
+ att.image? &&
+ att.id != img_att.id &&
+ valid_name == fname_wo_ext(att)
+ )
+ att.delete if is_delete
+ end
+ end
+ end
+
+ def delete_related_csv(csv_att)
+ return unless csv_att
+
+ atts = Attachment.where(attachable_id: attachable_id)
+ valid_name = fname_wo_ext(self)
+ atts.each do |att|
+ is_delete = (
+ att.csv? &&
+ att.id != csv_att.id &&
+ valid_name == fname_wo_ext(att)
+ )
+ att.delete if is_delete
+ end
+ end
+
+ def delete_related_nmrium(nmrium_att)
+ return unless nmrium_att
+
+ atts = Attachment.where(attachable_id: attachable_id)
+ valid_name = filename_parts[0]
+ atts.each do |att|
+ is_delete = (
+ att.nmrium? &&
+ att.id != nmrium_att.id &&
+ valid_name == fname_wo_ext(att)
+ )
+ att.delete if is_delete
+ end
+ end
+
+ def delete_related_edited_jcamp(jcamp_att)
+ return unless jcamp_att
+
+ atts = Attachment.where(attachable_id: jcamp_att.attachable_id)
+ valid_name = fname_wo_ext(self)
+ atts.each do |att|
+ is_delete = (
+ att.edited? &&
+ att.id != jcamp_att.id &&
+ valid_name == att.filename_parts[0]
+ )
+ att.delete if is_delete
+ end
+ end
+
def generate_img_only(typname)
_, tmp_img = Chemotion::Jcamp::CreateImg.spectrum_img_gene(abs_path)
img_att = generate_img_att(tmp_img, typname)
@@ -326,7 +550,7 @@ def infer_base_on_type(t_molfile, params)
params[:layout],
params[:peaks] || '[]',
params[:shift] || '{}',
- t_spectrum
+ t_spectrum,
)
end
end
diff --git a/app/models/concerns/metadata_jsonld.rb b/app/models/concerns/metadata_jsonld.rb
new file mode 100644
index 000000000..1cc8dba33
--- /dev/null
+++ b/app/models/concerns/metadata_jsonld.rb
@@ -0,0 +1,275 @@
+# frozen_string_literal: true
+require 'json'
+require 'open-uri'
+require 'nokogiri'
+
+module MetadataJsonld
+ extend ActiveSupport::Concern
+
+ def json_ld
+ if element_type == 'Sample'
+ json_ld_sample_root
+ elsif element_type == 'Reaction'
+ json_ld_reaction
+ elsif element_type == 'Container'
+ json_ld_container
+ end
+ end
+
+ def json_ld_sample_root(pub = self)
+ json = json_ld_study
+ json['about'] = [json_ld_sample]
+ json
+ end
+
+ def json_ld_study(pub = self)
+ json = {}
+ json['@context'] = 'https://schema.org'
+ json['@type'] = 'Study'
+ json['@id'] = "https://doi.org/#{doi.full_doi}"
+ json['dct:conformsTo'] = {
+ "@id": 'https://bioschemas.org/profiles/Study/0.3-DRAFT',
+ "@type": 'CreativeWork'
+ }
+ json['publisher'] = json_ld_publisher
+ json['dateCreated'] = pub.published_at&.strftime('%Y-%m-%d')
+ json['datePublished'] = pub.published_at&.strftime('%Y-%m-%d')
+ json['author'] = json_ld_authors(pub.taggable_data)
+ json['contributor'] = json_ld_contributor(pub.taggable_data["contributors"])
+ json['citation'] = json_ld_citations(pub.element.literatures, pub.element.id)
+ json['includedInDataCatalog'] = json_ld_data_catalog(pub)
+ json
+ end
+
+ def json_ld_data_catalog(pub = self)
+ json = {}
+ json['@context'] = 'https://schema.org'
+ json['@type'] = 'DataCatalog'
+ json['@id'] = 'https://www.chemotion-repository.net'
+ json['dct:conformsTo'] = {
+ "@id": 'https://bioschemas.org/profiles/DataCatalog/0.3-RELEASE-2019_07_01',
+ "@type": 'CreativeWork'
+ }
+ json['description'] = 'Chemotion Repository'
+ json['name'] = 'Chemotion Repository'
+ json['url'] = 'https://www.chemotion-repository.net'
+ json
+
+ end
+
+ def conforms_to
+ {
+ "@id": "https://bioschemas.org/profiles/Study/0.3-DRAFT",
+ "@type": "CreativeWork"
+ }
+ end
+
+ def json_ld_sample(pub = self)
+ # metadata_xml
+ json = {}
+ json['@context'] = 'https://schema.org'
+ json['@type'] = 'ChemicalSubstance'
+ json['@id'] = "https://doi.org/#{pub.doi.full_doi}"
+ json['identifier'] = "CRS-#{pub.id}"
+ json['url'] = "https://www.chemotion-repository.net/inchikey/#{pub.doi.suffix}"
+ json['name'] = pub.element.molecule_name&.name
+ json['alternateName'] = pub.element.molecule.inchistring
+ # json['image'] = element.sample_svg_file
+ json['image'] = 'https://www.chemotion-repository.net/images/samples/' + pub.element.sample_svg_file if pub&.element&.sample_svg_file.present?
+ json['description'] = json_ld_description(pub.element.description)
+ #json['author'] = json_ld_authors(pub.taggable_data)
+ json['hasBioChemEntityPart'] = json_ld_moelcule_entity(pub)
+ json['subjectOf'] = json_ld_subjectOf(pub)
+ #json_object = JSON.parse(json)
+ #JSON.pretty_generate(json_object)
+ json
+ # formatted_json = JSON.pretty_generate(json)
+ # formatted_json
+ end
+
+
+ def json_ld_reaction
+ json = {}
+ json['@context'] = 'https://schema.org'
+ json['@type'] = 'Study'
+ json['@id'] = "https://doi.org/#{doi.full_doi}"
+ json['identifier'] = "CRR-#{id}"
+ json['url'] = "https://www.chemotion-repository.net/inchikey/#{doi.suffix}"
+ json['additionalType'] = 'Reaction'
+ json['name'] = element.rinchi_short_key
+ json['author'] = json_ld_authors(taggable_data)
+ json['description'] = json_ld_description(element.description)
+ json['license'] = rights_data[:rightsURI]
+ json['datePublished'] = published_at&.strftime('%Y-%m-%d')
+ json['dateCreated'] = created_at&.strftime('%Y-%m-%d')
+ json['publisher'] = json_ld_publisher
+ json['provider'] = json_ld_publisher
+ json['keywords'] = 'chemical reaction: structures conditions'
+ json['citation'] = json_ld_citations(element.literatures, element.id)
+ json['subjectOf'] = json_ld_reaction_has_part
+ json
+ end
+
+ def json_ld_embargo
+ json = {}
+ json['@context'] = 'https://schema.org'
+ json['@type'] = 'Study'
+ # json['startDate'] = embargo_start_date&.strftime('%Y-%m-%d')
+ json
+ end
+
+ def json_ld_lab_protocol
+ json = {}
+ json['@context'] = 'https://schema.org'
+ json['@type'] = 'LabProtocol'
+ json['@id'] = "https://doi.org/#{doi.full_doi}"
+ json
+ end
+
+ def json_ld_reaction_has_part
+ json = []
+ children&.each do |pub|
+ json.push(json_ld_sample(pub)) if pub.element_type == 'Sample'
+ json.push(json_ld_analysis(pub)) if pub.element_type == 'Container'
+ end
+ json
+ end
+
+ def json_ld_reaction_has_part_product
+ end
+
+ def json_ld_description(desc)
+ REXML::Text.new(Nokogiri::HTML( Chemotion::QuillToHtml.new.convert(desc.to_json)).text, false, nil, false).to_s
+ #persit_datacite_metadata_xml! unless metadata_xml.present?
+ #xml_data = Nokogiri::XML(metadata_xml)
+ #desc = xml_data.search('description')&.text&.strip
+ #desc
+ end
+
+ def json_ld_container
+ json_ld_analysis
+ end
+
+
+ def json_ld_subjectOf(pub = self)
+ arr = []
+ # arr.push(json_ld_creative_work(pub))
+ pub.children&.each do |ana|
+ arr.push(json_ld_analysis(ana))
+ end
+ arr
+ end
+
+ def json_ld_analysis(pub = self)
+ json = {}
+ json['@context'] = 'https://schema.org'
+ json['@type'] = 'Dataset'
+ json['@id'] = "https://doi.org/#{pub.doi.full_doi}"
+ json['identifier'] = "CRD-#{pub.id}"
+ json['url'] = "https://www.chemotion-repository.net/inchikey/#{pub.doi.suffix}"
+ json['name'] = pub.element.extended_metadata['kind'] || '' if pub&.element&.extended_metadata.present?
+ json['author'] = json_ld_authors(pub.taggable_data)
+ json['description'] = json_ld_analysis_description(pub)
+ json
+ end
+
+ def json_ld_analysis_description(pub)
+ #xml_data = Nokogiri::XML(metadata_xml)
+ #desc = xml_data.search('description')&.text&.strip
+ #desc
+ element = pub.element
+ kind = 'dataset for ' + (element.extended_metadata['kind'] || '')&.split('|').pop + '\n'
+ desc = element.extended_metadata['description'] || '' + '\n'
+ content = REXML::Text.new(Nokogiri::HTML( Chemotion::QuillToHtml.new.convert(element.extended_metadata['content'] || '')).text, false, nil, false).to_s
+
+ kind + desc + content
+ end
+
+
+ def json_ld_citations(literatures, id)
+ json = []
+ literatures.each do |lit|
+ json.push(json_ld_citation(lit, id))
+ end
+ json
+ end
+
+ def json_ld_citation(lit, id)
+ json = {}
+ json['@type'] = 'CreativeWork'
+ bib = lit[:refs] && lit[:refs]['bibtex']
+ bb = DataCite::LiteraturePaser.parse_bibtex!(bib, id)
+ bb = DataCite::LiteraturePaser.get_metadata(bb, lit[:doi], id) unless bb.class == BibTeX::Entry
+ dc_lit = DataCite::LiteraturePaser.report_hash(lit, bb) if bb.class == BibTeX::Entry
+ json['name'] = dc_lit[:title] unless dc_lit.blank?
+ json['author'] = dc_lit[:author] unless dc_lit.blank?
+ json['url'] = dc_lit[:url] unless dc_lit.blank?
+ json
+ end
+
+ def json_ld_publisher
+ json = {}
+ json['@type'] = 'Organization'
+ json['name'] = 'chemotion-repository'
+ json
+ end
+
+
+ def json_ld_authors(taggable_data)
+ creators = taggable_data["creators"] || []
+ arr = []
+ creators.each do |author|
+ json = {}
+ json['@type'] = 'Person'
+ json['name'] = author['name']
+ json['identifier'] = author['ORCID'] if author['ORCID'].present?
+ json['familyName'] = author["familyName"]
+ json['givenName'] = author["givenName"]
+ json['affiliation'] = json_ld_affiliation(author['affiliationIds']&.first, taggable_data)
+ arr.push(json)
+ end
+ arr
+ end
+
+ def json_ld_contributor(contributor)
+ return {} unless contributor.present?
+
+ json = {}
+ json['@type'] = 'Person'
+ json['name'] = contributor['name']
+ json['identifier'] = contributor['ORCID'] if contributor['ORCID'].present?
+ json['familyName'] = contributor["familyName"]
+ json['givenName'] = contributor["givenName"]
+ # json['affiliation'] = json_ld_affiliation(author['affiliationIds']&.first)
+ json
+ end
+
+ def json_ld_affiliation(aff_id, taggable_data)
+ json = {}
+ json['@type'] = 'Organization'
+ json['name'] = taggable_data['affiliations'][aff_id.to_s]
+ json
+ end
+
+ def json_ld_molecular_weight(mol)
+ json ={}
+ json['@type'] = 'QuantitativeValue'
+ json['value'] = mol.molecular_weight
+ json['unitCode'] = 'g/mol'
+ json
+ end
+
+ def json_ld_moelcule_entity(pub = self)
+ mol = pub.element.molecule
+ json = {}
+ json['@type'] = 'MolecularEntity'
+ json['smiles'] = mol.cano_smiles
+ json['inChIKey'] = mol.inchikey
+ json['inChI'] = mol.inchistring
+ json['name'] = pub.element.molecule_name&.name
+ json['molecularFormula'] = mol.sum_formular
+ json['molecularWeight'] = json_ld_molecular_weight(mol)
+ json['iupacName'] = mol.iupac_name
+ json
+ end
+end
diff --git a/app/models/concerns/publishing.rb b/app/models/concerns/publishing.rb
new file mode 100644
index 000000000..91f021e0c
--- /dev/null
+++ b/app/models/concerns/publishing.rb
@@ -0,0 +1,334 @@
+module Publishing
+ class Net::FTP
+ def puttextcontent(content, remotefile, &block)
+ f = StringIO.new(content)
+ begin
+ storlines('STOR ' + remotefile, f, &block)
+ ensure
+ f.close
+ end
+ end
+ end
+
+ extend ActiveSupport::Concern
+
+ included do
+
+ has_one :publication, as: :element
+ has_one :publication_as_source, as: :original_element
+
+ def publication_tag
+ self.tag.taggable_data['publication']
+ end
+
+ def reserve_suffix
+ return Doi.create_for_element!(self) unless (d = self.doi)
+
+ if self.is_a?(Sample) && d.inchikey != self.molecule.inchikey
+ d.update!(doiable: nil)
+ return Doi.create_for_element!(self)
+ elsif self.is_a?(Reaction) && (d.inchikey.tr('reaction/','') != self.products_short_rinchikey_trimmed)
+ d.update!(doiable: nil)
+ return Doi.create_for_element!(self)
+ end
+ d
+ end
+
+ def reserve_suffix_analyses(as = Container.none)
+ ids = as.map(&:id)
+ if self.is_a?(Sample)
+ ik = self.molecule.inchikey
+ analysis_set = self.analyses.where(id: ids)
+ elsif self.is_a?(Reaction)
+ ik = self.products_short_rinchikey_trimmed
+ analysis_set = self.analyses.where(id: ids) |
+ Container.where(id: (self.samples.map(&:analyses).flatten.map(&:id) & ids))
+ end
+
+ analysis_set.each do |analysis|
+ if (doi = analysis.doi)
+ type = analysis.extended_metadata['kind'].delete(' ')
+ if (doi&.inchikey != ik) || (type != doi&.analysis_type)
+ doi.update!(doiable: nil)
+ doi = Doi.create_for_analysis!(analysis)
+ end
+ else
+ doi = Doi.create_for_analysis!(analysis)
+ end
+ end
+ end
+
+ def full_doi
+ return nil unless (d = Doi.find_by(doiable: self))
+ d.full_doi
+ end
+
+ def generate_doi(version)
+ version_str = version.to_i.zero? ? '' : '.' + version.to_s
+ inchikey_version = self.molecule.inchikey + version_str
+ "#{Datacite::Mds.new.doi_prefix}/#{inchikey_version}"
+ end
+
+ def create_publication_tag(contributor, author_ids, license)
+ authors = User.where(id: author_ids, type: %w(Person Collaborator))
+ .includes(:affiliations)
+ .order("position(users.id::text in '#{author_ids}')")
+ affiliations = authors.map(&:current_affiliations)
+ affiliations_output = {}
+ affiliations.flatten.each do |aff|
+ affiliations_output[aff.id] = aff.output_full
+ end
+ publication = {
+ published_by: author_ids[0],
+ author_ids: author_ids,
+ creators: authors.map { |author|
+ {
+ 'givenName' => author.first_name,
+ 'familyName' => author.last_name,
+ 'name' => author.name,
+ 'ORCID' => author.orcid,
+ 'affiliationIds' => author.current_affiliations.map(&:id),
+ 'id' => author.id
+ }
+ },
+ contributors: {
+ 'givenName' => contributor.first_name,
+ 'familyName' => contributor.last_name,
+ 'name' => contributor.name,
+ 'ORCID' => contributor.orcid,
+ 'affiliations' => contributor.current_affiliations.map{ |aff| aff.output_full },
+ 'id' => contributor.id
+ },
+ affiliations: affiliations_output,
+ affiliation_ids: affiliations.map { |as| as.map(&:id) },
+ queued_at: DateTime.now,
+ license: license
+ }
+ et = self.tag
+ et.update!(
+ taggable_data: (et.taggable_data || {}).merge(publication: publication)
+ )
+ end
+
+ ##
+ # Update the tag['publication'] for a (being) published public sample
+
+ def update_publication_tag(**args)
+ data = args.slice(
+ :doi_reg_at, :pubchem_reg_at, :published_at, :sample_version, :doi, :chem_first
+ )
+ et = self.tag
+ td = et.taggable_data
+ td['publication'].merge!(data)
+
+ ## update molecule tag
+ if self.is_a?(Sample)
+ mt = self.molecule.tag
+ mt_data = mt.taggable_data || {}
+ # chemotion_first unless already chemotion_first
+ mt_data['chemotion'] ||= {}
+
+ if args[:chem_first] && mt_data['chemotion']['chemotion_first'].blank?
+ mt_data['chemotion']['chemotion_first'] = args[:chem_first]
+ end
+
+ mt_data['chemotion']['doi'] = args[:doi] unless mt_data['chemotion']['doi'].present?
+ mt_data['chemotion']['last_published_at'] = args[:published_at]
+
+ mt.update!(taggable_data: mt_data)
+ end
+ et.save!
+ end
+
+ ##
+ # Update the tag of the original sample (and of its analysis) used for publication
+
+ def tag_as_published(pub_sample, ori_analyses)
+ et = self.tag
+ if (pub_sample.is_a? Reaction)
+ et.update!(
+ taggable_data: (et.taggable_data || {}).merge(public_reaction: pub_sample.id, publish_pending: true)
+ )
+ else
+ et.update!(
+ taggable_data: (et.taggable_data || {}).merge(public_sample: pub_sample.id, publish_pending: true)
+ )
+ end
+
+ ori_analyses.each do |analysis|
+ analysis.reload
+ aid = pub_sample.analyses.select { |a| a.extended_metadata == analysis.extended_metadata }&.first&.id || true
+ at = analysis.tag
+ at.update!(
+ taggable_data: (at.taggable_data || {}).merge(public_analysis: aid)
+ )
+ xm = analysis.extended_metadata
+ xm.delete('publish')
+ xm['public_analysis'] = aid
+ analysis.update!(extended_metadata: xm)
+ end
+ end
+
+ def tag_as_new_version(previous_element, scheme_only: false)
+ previous_license = previous_element&.tag&.taggable_data['publication']['license']
+ previous_users = previous_element&.tag&.taggable_data['publication']['creators']
+
+ element_tag = self.tag
+ element_tag.update!(
+ taggable_data: (element_tag.taggable_data || {}).merge(
+ previous_version: {
+ id: previous_element.id,
+ doi: {
+ id: previous_element&.doi&.id
+ },
+ license: previous_license,
+ scheme_only: scheme_only,
+ users: previous_users
+ }
+ )
+ )
+ end
+
+ def tag_replace_in_publication
+ element_tag = self.tag
+ element_tag.update!(
+ taggable_data: (element_tag.taggable_data || {}).merge(
+ replace_in_publication: true
+ )
+ )
+ end
+
+ def untag_replace_in_publication
+ element_tag = self.tag
+
+ taggable_data = element_tag.taggable_data || {}
+ taggable_data.delete('replace_in_publication')
+
+ element_tag.update!(
+ taggable_data: taggable_data
+ )
+ end
+
+ def update_versions_tag
+ element_tag = self.tag
+
+ if element_tag.taggable_data['new_version'].nil?
+ # recursively find all versions of the latest element
+ versions = self.find_versions
+ else
+ # copy the list of versions from the latest element
+ new_version = self.class.find_by(id: element_tag.taggable_data['new_version']['id'])
+ versions = new_version&.tag&.taggable_data['versions']
+ end
+
+ element_tag.update!(
+ taggable_data: (element_tag.taggable_data || {}).merge(
+ versions: versions
+ )
+ )
+
+ # call this method recursively for all versions
+ unless element_tag.taggable_data['previous_version'].nil?
+ previous_version = self.class.find_by(id: element_tag.taggable_data['previous_version']['id'])
+ previous_version.update_versions_tag
+ end
+ end
+
+ def find_versions
+ element_tag = self.tag
+ versions = [self.id]
+
+ unless element_tag.taggable_data['previous_version'].nil?
+ previous_version = self.class.find_by(id: element_tag.taggable_data['previous_version']['id'])
+ versions += previous_version.find_versions
+ end
+
+ return versions
+ end
+
+ def tag_as_previous_version(new_element)
+ element_tag = self.tag
+ element_tag.update!(
+ taggable_data: (element_tag.taggable_data || {}).merge(
+ new_version: {
+ id: new_element.id
+ })
+ )
+ end
+
+ def untag_as_previous_version
+ element_tag = self.tag
+ taggable_data = element_tag.taggable_data || {}
+ taggable_data.delete('new_version')
+ element_tag.update!(taggable_data: taggable_data)
+ end
+
+ def tag_reserved_suffix(ori_analyses)
+ et = self.tag
+ et.update!(
+ taggable_data: (et.taggable_data || {}).merge(reserved_doi: self.doi.full_doi)
+ )
+ ori_analyses.each do |analysis|
+ at = analysis.tag
+ d = analysis.doi.full_doi
+ at.update!(
+ taggable_data: (at.taggable_data || {}).merge(reserved_doi: d)
+ )
+ xm = analysis.extended_metadata
+ xm['reserved_doi'] = d
+ xm['publish'] = true
+ analysis.update!(extended_metadata: xm)
+ end
+ end
+
+ def untag_reserved_suffix()
+ et = self.tag
+ taggable_data = et.taggable_data || {}
+ taggable_data.delete('reserved_doi')
+ et.update!(taggable_data: taggable_data)
+
+ self.analyses.each do |analysis|
+ at = analysis.tag
+ td = at.taggable_data
+ td.delete('reserved_doi')
+ at.update!(taggable_data: td)
+
+ xm = analysis.extended_metadata
+ xm.delete('reserved_doi')
+ analysis.update!(extended_metadata: xm)
+ end
+ end
+
+ # remove doi link if molecule changes
+ def check_doi
+ d = self.doi
+ return true unless d
+ if self.is_a?(Sample) && molecule_id_changed?
+ d.update!(doiable: nil)
+ self.untag_reserved_suffix
+
+ elsif self.is_a?(Reaction) && (d.inchikey.tr('reaction/', '') != self.products_short_rinchikey_trimmed)
+ d.update!(doiable: nil)
+ self.untag_reserved_suffix
+ self.products.each do |s|
+ sd = s.doi
+ sd.update!(doiable: nil) unless sd.nil?
+ s.untag_reserved_suffix
+ end
+ end
+ true
+ end
+
+ def get_new_version_short_label
+ m = self.previous_version.short_label.match /^(.*)-V(\d+)$/
+ if m
+ # increment the version part of the short_label of the previous version
+ version = Integer(m[2]) + 1
+ self.short_label = "#{m[1]}-V#{version}"
+ else
+ # append "-V1" to the short_label of the previous version
+ self.short_label = "#{self.previous_version.short_label}-V1"
+ end
+ end
+ end
+end
diff --git a/app/models/concerns/reaction_rinchi.rb b/app/models/concerns/reaction_rinchi.rb
index 75f47bd20..5cc3a8406 100644
--- a/app/models/concerns/reaction_rinchi.rb
+++ b/app/models/concerns/reaction_rinchi.rb
@@ -45,11 +45,46 @@ def retrieve_molfiles
def no_structure
<<~MOLFILE
-
+
ACCLDraw04191619342D
-
+
0 0 0 0 0 0 0 0 0 0999 V2000
M END
MOLFILE
end
+
+ def products_rinchis
+ mols_rcts, mols_prds, mols_agts = self.retrieve_molfiles
+ rcts = Rinchi::MolVect.new
+ # mols_rcts.each do |rct| rcts.push(rct) end
+ [].each do |rct| rcts.push(rct) end
+ prds = Rinchi::MolVect.new
+ mols_prds.each do |prd| prds.push(prd) end
+ agts = Rinchi::MolVect.new
+ # mols_agts.each do |agt| agts.push(agt) end
+ [].each do |agt| agts.push(agt) end
+ Rinchi.convert(rcts, prds, agts)
+ end
+
+ def no_structure_rinchis
+ prds = Rinchi::MolVect.new
+ mols_prds = []
+ mols_prds.push(no_structure)
+ mols_prds.each { |prd| prds.push(prd) }
+ Rinchi.convert(Rinchi::MolVect.new, prds, Rinchi::MolVect.new)
+ end
+
+ def products_short_rinchikey
+ _, _, result, _ = products_rinchis
+ result
+ end
+
+ def products_short_rinchikey_trimmed
+ if products_short_rinchikey.blank?
+ _, _, result, _ = no_structure_rinchis
+ result&.sub(/Short-RInChIKey=/, '')
+ else
+ products_short_rinchikey.sub(/Short-RInChIKey=/, '')
+ end
+ end
end
diff --git a/app/models/concerns/reaction_sample_collections.rb b/app/models/concerns/reaction_sample_collections.rb
index e2b49410b..63601e3a0 100644
--- a/app/models/concerns/reaction_sample_collections.rb
+++ b/app/models/concerns/reaction_sample_collections.rb
@@ -9,7 +9,14 @@ module ReactionSampleCollections
def assign_sample_to_collections
self.reaction.collections.each do |c|
- CollectionsSample.where(sample: self.sample, collection: c).first_or_create
+ # same as CollectionsSample.where(sample: self.sample, collection: c).first_or_create
+ # but should work with act_as_paranoid
+ collection_sample = CollectionsSample.where(sample: self.sample, collection: c).with_deleted.first
+ if collection_sample.nil?
+ CollectionsSample.new(sample: self.sample, collection: c).save!
+ elsif collection_sample.deleted?
+ collection_sample.restore
+ end
end
end
end
diff --git a/app/models/concerns/segmentable.rb b/app/models/concerns/segmentable.rb
index a77c95ec9..383df68c1 100644
--- a/app/models/concerns/segmentable.rb
+++ b/app/models/concerns/segmentable.rb
@@ -7,9 +7,38 @@ module Segmentable
has_many :segments, as: :element, dependent: :destroy
end
- def save_segments(**args)
+ def copy_segments(**args)
return if args[:segments].nil?
+ segments = save_segments(segments: args[:segments], current_user_id: args[:current_user_id])
+ segments.each do |segment|
+ properties = segment.properties
+ properties['layers'].keys.each do |key|
+ layer = properties['layers'][key]
+ field_uploads = layer['fields'].select { |ss| ss['type'] == 'upload' }
+ field_uploads&.each do |upload|
+ idx = properties['layers'][key]['fields'].index(upload)
+ files = upload["value"] && upload["value"]["files"]
+ files&.each_with_index do |fi, fdx|
+ aid = properties['layers'][key]['fields'][idx]['value']['files'][fdx]['aid']
+ unless aid.nil?
+ copied_att = Attachment.find(aid)&.copy(attachable_type: 'SegmentProps', attachable_id: segment.id, transferred: true)
+ unless copied_att.nil?
+ copied_att.save!
+ properties['layers'][key]['fields'][idx]['value']['files'][fdx]['aid'] = copied_att.id
+ properties['layers'][key]['fields'][idx]['value']['files'][fdx]['uid'] = copied_att.identifier
+ end
+ end
+ end
+ end
+ end
+ segment.update!(properties: properties)
+ end
+ end
+
+ def save_segments(**args)
+ return if args[:segments].nil?
+ segments = []
args[:segments].each do |seg|
klass = SegmentKlass.find_by(id: seg['segment_klass_id'])
uuid = SecureRandom.uuid
@@ -29,7 +58,9 @@ def save_segments(**args)
props['klass_uuid'] = klass.uuid
props['eln'] = Chemotion::Application.config.version
props['klass'] = 'Segment'
- Segment.create!(segment_klass_id: seg['segment_klass_id'], element_type: self.class.name, element_id: self.id, properties: props, created_by: args[:current_user_id], uuid: uuid, klass_uuid: klass.uuid)
+ segment = Segment.create!(segment_klass_id: seg['segment_klass_id'], element_type: self.class.name, element_id: self.id, properties: props, created_by: args[:current_user_id], uuid: uuid, klass_uuid: klass.uuid)
+ segments.push(segment)
end
+ segments
end
end
diff --git a/app/models/concerns/taggable.rb b/app/models/concerns/taggable.rb
index 94fc5abf5..5e01c2647 100644
--- a/app/models/concerns/taggable.rb
+++ b/app/models/concerns/taggable.rb
@@ -61,12 +61,13 @@ def collection_tag
cols = []
send(klass).each do |cc|
next unless c = cc.collection
- next if c.label == 'All' && c.is_locked
+ next if (c.label == 'All' && c.is_locked)
cols.push({
name: c.label, is_shared: c.is_shared, user_id: c.user_id,
id: c.id, shared_by_id: c.shared_by_id,
is_synchronized: false
})
+ next if (c.id == Collection.public_collection_id) || (c.id == Collection.scheme_only_reactions_collection_id)
if c.is_synchronized
c.sync_collections_users&.each do |syn|
cols.push({
@@ -81,8 +82,14 @@ def collection_tag
end
def grouped_analyses
- analyses.map(&:extended_metadata).map { |x| x.extract!('kind', 'status') }
- .group_by { |x| x['status'] }
+ analyses_extended_metadata = analyses.map(&:extended_metadata)
+ links_extended_metadata = links.map do |container|
+ target_container = Container.find(container.extended_metadata['target_id'])
+ target_container[:extended_metadata]
+ end
+ extended_metadata = analyses_extended_metadata.concat(links_extended_metadata)
+ extended_metadata.map { |x| x.extract!('kind', 'status') }
+ .group_by { |x| x['status'] }
end
def count_by_kind(analyses)
@@ -90,7 +97,7 @@ def count_by_kind(analyses)
end
def analyses_tag
- return nil unless is_a?(Sample) && analyses.count.positive?
+ return nil unless is_a?(Sample) && (analyses.count.positive? || links.count.positive?)
grouped_analyses.map { |key, val|
vv = count_by_kind(val)
kk = key.to_s.downcase
diff --git a/app/models/container.rb b/app/models/container.rb
index e300d393a..97003554f 100644
--- a/app/models/container.rb
+++ b/app/models/container.rb
@@ -25,10 +25,14 @@ class Container < ApplicationRecord
belongs_to :containable, polymorphic: true, optional: true
has_many :attachments, as: :attachable
+ has_one :publication, as: :element
+ include Taggable
+
+ has_one :doi, as: :doiable
# TODO: dependent destroy for attachments should be implemented when attachment get paranoidized instead of this DJ
before_destroy :delete_attachment
before_destroy :destroy_datasetable
- has_closure_tree
+ has_closure_tree order: Arel.sql("extended_metadata->'index' asc")
scope :analyses_for_root, ->(root_id) {
where(container_type: 'analysis').joins(
@@ -36,10 +40,32 @@ class Container < ApplicationRecord
)
}
+ scope :links_for_root, ->(root_id) {
+ where(container_type: 'link').joins(
+ "inner join container_hierarchies ch on ch.generations = 2 and ch.ancestor_id = #{root_id} and ch.descendant_id = containers.id "
+ )
+ }
+
+ scope :analyses_container, ->(id) {
+ where(container_type: 'analyses').joins(
+ <<~SQL
+ inner join container_hierarchies ch
+ on (ch.ancestor_id = #{id} and ch.descendant_id = containers.id)
+ or (ch.descendant_id = #{id} and ch.ancestor_id = containers.id)
+ SQL
+ )
+ }
+
+ before_save :check_doi
+
def analyses
Container.analyses_for_root(self.id)
end
+ def links
+ Container.links_for_root(self.id)
+ end
+
def root_element
self.root.containable
end
@@ -50,8 +76,6 @@ def self.create_root_container(**args)
root_con
end
- private
-
def delete_attachment
if Rails.env.production?
attachments.each { |attachment|
@@ -61,4 +85,41 @@ def delete_attachment
attachments.each(&:destroy!)
end
end
+
+ def generate_doi version
+ type = self.extended_metadata['kind'].delete(' ') if self.extended_metadata['kind']
+ version_str = version.to_i == 0 ? "" : "." + version.to_s
+ term_id = (type || '').split('|').first.sub!(':','')
+ if self.root.containable.respond_to? :molecule
+ ds_version = self.root.containable.molecule.inchikey + "/" + term_id + version_str
+ elsif self.root.containable.respond_to? :products_short_rinchikey_trimmed
+ ds_version = "reaction/" + self.root.containable.products_short_rinchikey_trimmed+ "/" + term_id + version_str
+ else
+ ds_version = term_id + version_str
+ end
+ "#{Datacite::Mds.new.doi_prefix}/#{ds_version}"
+ end
+
+ def full_doi
+ return nil unless (d = Doi.find_by(doiable: self))
+ d.full_doi
+ end
+
+ def unassociate_doi(d = self.doi)
+ d.update(doiable: nil) unless d.nil?
+ self.extended_metadata.delete('reserved_doi')
+ at = self.tag
+ at.taggable_data.delete('reserved_doi')
+ at.save
+ end
+
+ def check_doi
+ # unassoicate doi if type has changed
+ if (d = self.doi) && self.container_type == 'analysis' && self.publication&.state != 'completed'
+ if self.extended_metadata['kind']&.delete(' ') != d.analysis_type
+ unassociate_doi(d)
+ end
+ end
+ true
+ end
end
diff --git a/app/models/device.rb b/app/models/device.rb
index fe09f938f..301bd21da 100644
--- a/app/models/device.rb
+++ b/app/models/device.rb
@@ -23,19 +23,18 @@
# name_abbreviation :string(12)
# type :string default("Person")
# reaction_name_prefix :string(3) default("R")
+# layout :hstore not null
# confirmation_token :string
# confirmed_at :datetime
# confirmation_sent_at :datetime
# unconfirmed_email :string
-# layout :hstore not null
# selected_device_id :integer
# failed_attempts :integer default(0), not null
# unlock_token :string
# locked_at :datetime
# account_active :boolean
# matrix :integer default(0)
-# omniauth_provider :string
-# omniauth_uid :string
+# providers :jsonb
#
# Indexes
#
diff --git a/app/models/doi.rb b/app/models/doi.rb
new file mode 100644
index 000000000..633df5ae9
--- /dev/null
+++ b/app/models/doi.rb
@@ -0,0 +1,201 @@
+# == Schema Information
+#
+# Table name: dois
+#
+# id :integer not null, primary key
+# molecule_id :integer
+# inchikey :string
+# molecule_count :integer
+# analysis_id :integer
+# analysis_type :string
+# analysis_count :integer
+# metadata :jsonb
+# minted :boolean default(FALSE)
+# minted_at :datetime
+# created_at :datetime not null
+# updated_at :datetime not null
+# doiable_id :integer
+# doiable_type :string
+# suffix :string
+# version_count :integer default(0)
+#
+# Indexes
+#
+# index_dois_on_suffix (suffix) UNIQUE
+# index_on_dois (inchikey,molecule_count,analysis_type,analysis_count,version_count) UNIQUE
+#
+# Foreign Keys
+#
+# fk_rails_... (molecule_id => molecules.id)
+#
+
+class Doi < ApplicationRecord
+
+ belongs_to :doiable, polymorphic: true, optional: true
+ belongs_to :molecule, class_name: 'Molecule', optional: true
+ belongs_to :analysis, class_name: 'Container', optional: true
+
+ before_save :align_suffix
+
+ def build_suffix
+ s = "#{inchikey}"
+ s += ".#{molecule_count}" if molecule_count.to_i > 0
+ if analysis_type.present?
+ term_id = analysis_type.split('|').first.sub!(':','')
+ s += "/#{term_id}"
+ s += ".#{analysis_count}" if analysis_count.to_i > 0
+ end
+ s += "/#{version_count}" if version_count.to_i > 0
+ s
+ end
+
+ def generate_doi
+ "#{Datacite::Mds.new.doi_prefix}/#{suffix}"
+ end
+
+ def full_doi
+ "#{Datacite::Mds.new.doi_prefix}/#{suffix}"
+ end
+
+ def self.find_by_doi(doi)
+ d = split_doi(doi)
+ find_by(suffix: d[:suffix])
+ end
+
+ def self.find_by_split_suffix(suffix)
+ split_suffix = split_suffix(suffix)
+ find_by(split_suffix)
+ end
+
+ def self.create_for_analysis!(analysis, ik = nil)
+ if !ik
+ rt = analysis.root_element
+ ik = (rt.is_a?(Sample) && rt.molecule.inchikey) ||
+ (rt.is_a?(Reaction) && rt.products_short_rinchikey_trimmed)
+ raise "only works with sample/reaction analysis" unless ik
+ end
+
+ type = analysis.extended_metadata['kind'].delete(' ')
+ type = type.presence || 'nd'
+ term_id = type.split('|').first.sub!(':','')
+
+ if (previous_version_doi_id = analysis.extended_metadata['previous_version_doi_id'])
+ previous_doi = Doi.find_by(id: previous_version_doi_id)
+ ac = previous_doi.analysis_count
+ ac_string = ".#{ac}"
+ vc = previous_doi.version_count.to_i + 1
+ vc_string = "/#{vc}"
+ suffix = "#{ik}/#{term_id}#{ac_string}#{vc_string}"
+ else
+ ds = Doi.select("*, coalesce(analysis_count, 0) as real_count")
+ .where(inchikey: ik, analysis_type: type)
+ .order('real_count desc')
+ if ds.blank?
+ ac = 0
+ ac_string = ''
+ else
+ ac = ds.first.analysis_count.to_i.next
+ ac_string = ".#{ac}"
+ end
+ vc = 0
+ suffix = "#{ik}/#{term_id}#{ac_string}"
+ end
+
+ Doi.create!(
+ inchikey: ik,
+ doiable_id: analysis.id,
+ doiable_type: analysis.class.name,
+ analysis_count: ac,
+ version_count: vc,
+ suffix: suffix,
+ analysis_type: type
+ )
+ end
+
+ def self.create_for_element!(element, ik = nil)
+ klass = element.class.name
+ ik ||= case klass
+ when 'Sample'
+ element.molecule.inchikey
+ when 'Collection'
+ "collection/" + element.label
+ when 'Reaction'
+ "reaction/" + element.products_short_rinchikey_trimmed
+ end
+
+ if (previous_version = element.tag.taggable_data['previous_version'])
+ previous_doi = Doi.find_by(id: previous_version['doi']['id'])
+ mc = previous_doi.molecule_count
+ mc_string = ".#{mc}"
+ vc = previous_doi.version_count.to_i + 1
+ vc_string = "/#{vc}"
+ suffix = "#{ik}#{mc_string}#{vc_string}"
+ else
+ ds = Doi.select("*, coalesce(molecule_count, 0) as real_count")
+ .where(inchikey: ik)
+ .order('real_count desc')
+ if ds.blank?
+ mc = 0
+ mc_string = ''
+ else
+ mc = ds.first.molecule_count.to_i.next
+ mc_string = ".#{mc}"
+ end
+ vc = 0
+ suffix = "#{ik}#{mc_string}"
+ end
+
+ d = Doi.create!(
+ inchikey: ik,
+ doiable_id: element.id,
+ doiable_type: klass,
+ molecule_count: mc,
+ version_count: vc,
+ suffix: suffix
+ )
+ end
+
+ private
+
+ def self.extract_suffix(doi)
+ if doi.match(/(10\..+?)\//)
+ $'
+ end
+ end
+
+ def self.split_doi(doi)
+ if doi.match(/(10\..+?)\//)
+ { prefix: $1, suffix: $', split_suffix: split_suffix($') }
+ else
+ {}
+ end
+ end
+
+ def self.split_suffix(suffix)
+ if suffix.match(/([\w-]+)(?:\.(\d+))?(?:\/((?:.+62\.5)|(?:[^.]+))?(?:\.(\d+))?)?\z/)
+ {
+ inchikey: $1,
+ molecule_count: $2,
+ analysis_type: $3,
+ analysis_count: $4,
+ }
+ else
+ {}
+ end
+ end
+
+ def align_suffix
+ if suffix_changed? && !inchikey_changed? && !analysis_type_changed?
+ s = self.class.split_suffix(suffix)
+ self.inchikey = s[:inchikey]
+ self.molecule_count = s[:molecule_count]
+ self.analysis_type = s[:analysis_type]
+ self.analysis_count = s[:analysis_count]
+ else !suffix_changed? && inchikey_changed?
+ self.suffix = build_suffix
+ end
+ # throw(:abort) unless suffix == build_suffix
+ suffix == build_suffix
+ end
+
+end
diff --git a/app/models/group.rb b/app/models/group.rb
index 07ed20677..2d307e4b8 100644
--- a/app/models/group.rb
+++ b/app/models/group.rb
@@ -23,19 +23,18 @@
# name_abbreviation :string(12)
# type :string default("Person")
# reaction_name_prefix :string(3) default("R")
+# layout :hstore not null
# confirmation_token :string
# confirmed_at :datetime
# confirmation_sent_at :datetime
# unconfirmed_email :string
-# layout :hstore not null
# selected_device_id :integer
# failed_attempts :integer default(0), not null
# unlock_token :string
# locked_at :datetime
# account_active :boolean
# matrix :integer default(0)
-# omniauth_provider :string
-# omniauth_uid :string
+# providers :jsonb
#
# Indexes
#
diff --git a/app/models/literature.rb b/app/models/literature.rb
index 1e3af44d1..c2398ca27 100644
--- a/app/models/literature.rb
+++ b/app/models/literature.rb
@@ -34,7 +34,7 @@ class Literature < ApplicationRecord
scope :add_user_info, -> {
joins("inner join users on users.id = literals.user_id")
- .select("literatures.*, literals.id as literal_id, literals.user_id, literals.litype, (users.first_name || chr(32) || users.last_name) as user_name")
+ .select("literatures.*, literals.id as literal_id, literals.element_type, literals.user_id, literals.litype, (users.first_name || chr(32) || users.last_name) as user_name")
}
scope :add_element_and_user_info, -> {
diff --git a/app/models/molecule.rb b/app/models/molecule.rb
index 42e2a96bc..c910635c4 100644
--- a/app/models/molecule.rb
+++ b/app/models/molecule.rb
@@ -135,6 +135,8 @@ def assign_molecule_data(babel_info, pubchem_info = {})
self.names = pubchem_info[:names]
self.pcid = pubchem_info[:cid]
self.check_sum_formular # correct exact and average MW for resins
+ svg = Molecule.svg_reprocess(babel_info[:svg], molfile)
+ attach_svg svg
#self.attach_svg babel_info[:svg]
svg = Chemotion::OpenBabelService.svg_from_molfile(self.molfile)
@@ -151,12 +153,12 @@ def pubchem_lcss
mol_tag = self.tag
mol_tag_data = mol_tag.taggable_data || {}
if mol_tag_data['pubchem_lcss'] && mol_tag_data['pubchem_lcss'].length > 0
- mol_tag_data['pubchem_lcss'];
+ mol_tag_data['pubchem_lcss']
else
mol_tag_data['pubchem_lcss'] = Chemotion::PubchemService.lcss_from_cid(cid)
# updated_at of element_tags(not molecule) is updated
mol_tag.update_attributes taggable_data: mol_tag_data
- mol_tag_data['pubchem_lcss'];
+ mol_tag_data['pubchem_lcss']
end
end
@@ -234,6 +236,20 @@ def unique_molecule_name(new_name)
!mns.include?(new_name)
end
+ def self.svg_reprocess(svg, molfile)
+ return svg unless Rails.configuration.try(:ketcher_service).try(:url).present?
+ return svg if svg.present? && !svg&.include?('Open Babel')
+
+ svg = KetcherService::RenderSvg.svg(molfile)
+
+ if svg&.present?
+ svg = Ketcherails::SVGProcessor.new(svg)
+ svg.centered_and_scaled_svg
+ else
+ Chemotion::OpenBabelService.svg_from_molfile(molfile)
+ end
+ end
+
private
# TODO: check that molecules are OK and remove this method. fix is in editor
diff --git a/app/models/person.rb b/app/models/person.rb
index 84427b6be..ccc2bfc7d 100644
--- a/app/models/person.rb
+++ b/app/models/person.rb
@@ -23,19 +23,18 @@
# name_abbreviation :string(12)
# type :string default("Person")
# reaction_name_prefix :string(3) default("R")
+# layout :hstore not null
# confirmation_token :string
# confirmed_at :datetime
# confirmation_sent_at :datetime
# unconfirmed_email :string
-# layout :hstore not null
# selected_device_id :integer
# failed_attempts :integer default(0), not null
# unlock_token :string
# locked_at :datetime
# account_active :boolean
# matrix :integer default(0)
-# omniauth_provider :string
-# omniauth_uid :string
+# providers :jsonb
#
# Indexes
#
diff --git a/app/models/publication.rb b/app/models/publication.rb
new file mode 100644
index 000000000..0c44cf85a
--- /dev/null
+++ b/app/models/publication.rb
@@ -0,0 +1,740 @@
+# == Schema Information
+#
+# Table name: publications
+#
+# id :integer not null, primary key
+# state :string
+# metadata :jsonb
+# taggable_data :jsonb
+# dois :jsonb
+# element_type :string
+# element_id :integer
+# doi_id :integer
+# created_at :datetime
+# updated_at :datetime
+# deleted_at :datetime
+# original_element_type :string
+# original_element_id :integer
+# ancestry :string
+# metadata_xml :text
+# published_by :integer
+# published_at :datetime
+# review :jsonb
+# accepted_at :datetime
+# oai_metadata_xml :text
+#
+# Indexes
+#
+# index_publications_on_ancestry (ancestry)
+# publications_element_idx (element_type,element_id,deleted_at)
+#
+class Publication < ActiveRecord::Base
+ class Net::FTP
+ def puttextcontent(content, remotefile, &block)
+ f = StringIO.new(content)
+ begin
+ storlines('STOR ' + remotefile, f, &block)
+ ensure
+ f.close
+ end
+ end
+ end
+
+ acts_as_paranoid
+ include MetadataJsonld
+ has_ancestry
+ belongs_to :element, polymorphic: true
+ belongs_to :original_element, polymorphic: true, optional: true
+ belongs_to :doi
+
+ STATE_START = 'start'
+
+ STATE_DC_METADATA_UPLOADING = 'dc_metadata_uploading'
+ STATE_DC_METADATA_UPLOADED = 'dc_metadata_uploaded'
+
+ # STATE_DC_METADATA_ANALYSES_UPLOADING = 'dc_metadata_analyses_uploading'
+ # STATE_DC_METADATA_ANALYSES_UPLOADED = 'dc_metadata_analyses_uploaded'
+
+ STATE_DC_DOI_REGISTERING = 'dc_doi_registering'
+ STATE_DC_DOI_REGISTERED = 'dc_doi_registered'
+
+ STATE_PUBCHEM_REGISTERING = 'pubchem_registering'
+ STATE_PUBCHEM_REGISTERED = 'pubchem_registered'
+
+ # STATE_DC_DOI_MINT_ANALYSES_START = 'dc_doi_mint_analyses_start'
+ # STATE_DC_DOI_MINT_ANALYSES_DONE = 'dc_doi_mint_analyses_done'
+
+ STATE_COMPLETING = 'completing'
+ STATE_COMPLETED = 'completed'
+ STATE_PUBLISHED = 'published'
+
+ STATE_ACCEPTED = 'accepted'
+ STATE_PENDING = 'pending'
+ STATE_DECLINED = 'declined'
+ STATE_REVIEWED = 'reviewed'
+ STATE_RETRACTED = 'retracted'
+
+ def embargoed?(root_publication = root)
+ cid = User.find(root_publication.published_by).publication_embargo_collection.id
+ embargo_col = root_publication.element.collections.select { |c| c['ancestry'].to_i == cid }
+ embargo_col.present? ? true : false
+ end
+
+ # Moving publication element to collections according to publication state
+
+ def update_state(new_state)
+ update_columns(state: new_state)
+ descendants.each { |d| d.update_columns(state: new_state) }
+ update_columns(accepted_at: Time.now.utc) if new_state == Publication::STATE_ACCEPTED
+ descendants.each { |d| d.update_columns(accepted_at: Time.now.utc) } if new_state == Publication::STATE_ACCEPTED
+
+ process_element(new_state)
+ end
+
+ def process_element(new_state = state)
+ case new_state
+ when Publication::STATE_PENDING
+ move_to_pending_collection
+ group_review_collection
+ when Publication::STATE_REVIEWED
+ move_to_review_collection
+ group_review_collection
+ when Publication::STATE_ACCEPTED
+ move_to_accepted_collection
+ group_review_collection
+ when Publication::STATE_DECLINED
+ if element&.tag&.taggable_data['previous_version'].nil?
+ declined_reverse_original_element
+ declined_move_collections
+ group_review_collection
+ end
+ end
+ end
+
+ # WARNING: for STATE_ACCEPTED the method does more than just notify users (see ChemotionRepoPublishingJob)
+ # TODO: separate publishing responsability
+ def inform_users(new_state = state, current_user_id = 0)
+ method = if ENV['PUBLISH_MODE'] == 'production' && Rails.env.production?
+ :perform_later
+ elsif ENV['PUBLISH_MODE'] == 'staging'
+ :perform_now
+ end
+ return unless method
+
+ queue_name = new_state.to_s
+ klass = if new_state == Publication::STATE_ACCEPTED && !embargoed?
+ queue_name = 'publishing'
+ ChemotionRepoPublishingJob
+ else
+ ChemotionRepoReviewingJob
+ end
+ klass.set(queue: "#{queue_name} #{id}").send(method, id, new_state, current_user_id)
+ end
+
+ # remove publication element from editable collections
+ def move_to_accepted_collection
+ pub_user = User.find(published_by)
+ return false unless pub_user && element
+ return true unless embargoed?
+
+ ## do not move if in reviewing, but why ???
+ # reviewing_col = element.collections.where(id: pub_user.reviewing_collection.id).pluck(:id)
+ # return false if reviewing_col.present?
+
+ case element_type
+ when 'Sample'
+ CollectionsSample
+ when 'Reaction'
+ CollectionsReaction
+ end.move_to_collection(
+ element.id,
+ element.collections.where(
+ id: [pub_user.pending_collection.id, pub_user.reviewing_collection.id]
+ ).pluck(:id) + Collection.element_to_review_collection.pluck(:id),
+ [Collection.embargo_accepted_collection&.id]
+ )
+ end
+
+ # move publication element from reviewer editable collection to submitter editable collection
+ # move publication element from submitter readable collection to reviewer readable collection
+ def move_to_review_collection
+ pub_user = User.find(published_by)
+ return false unless pub_user && element
+
+ case element_type
+ when 'Sample'
+ CollectionsSample
+ when 'Reaction'
+ CollectionsReaction
+ end.move_to_collection(
+ element.id,
+ [pub_user.pending_collection.id] + Collection.element_to_review_collection.pluck(:id),
+ [pub_user.reviewing_collection.id] + Collection.reviewed_collection.pluck(:id)
+ )
+ end
+
+ def move_to_pending_collection
+ pub_user = User.find(published_by)
+ return false unless pub_user && element
+
+ case element_type
+ when 'Sample'
+ CollectionsSample
+ when 'Reaction'
+ CollectionsReaction
+ end.move_to_collection(
+ element.id,
+ [pub_user.reviewing_collection.id] + Collection.reviewed_collection.pluck(:id),
+ [pub_user.pending_collection.id] + Collection.element_to_review_collection.pluck(:id)
+ )
+ end
+
+ def declined_reverse_original_element
+ oet = original_element&.tag
+ oet&.taggable_data&.delete('publish_pending')
+ oet&.taggable_data&.delete('public_reaction') if element_type == 'Reaction'
+ oet&.taggable_data&.delete('public_sample') if element_type == 'Sample'
+ oet&.save!
+ original_element&.analyses&.each do |a|
+ a.reload
+ a.tag&.taggable_data&.delete('public_analysis') && a.tag.save!
+ a.extended_metadata&.delete('public_analysis') && a.save!
+ end
+ declined_reverse_original_reaction_elements
+ end
+
+ def group_review_collection
+ pub_user = User.find(published_by)
+ return false unless pub_user && element
+
+ group_reviewers = review['reviewers']
+ reviewers = User.where(id: group_reviewers) if group_reviewers.present?
+ return false if reviewers&.empty?
+
+ reviewers&.each do |user|
+ ## user = User.find(gl_id)
+ col = user.find_or_create_grouplead_collection
+ case element_type
+ when 'Sample'
+ CollectionsSample
+ when 'Reaction'
+ CollectionsReaction
+ end.create_in_collection([element.id], [col.id])
+ end
+
+ end
+
+ def declined_reverse_original_reaction_elements
+ element_type == 'Reaction' && original_element&.samples&.each do |s|
+ spp = s.tag&.taggable_data&.delete('publish_pending')
+ sps = s.tag&.taggable_data&.delete('public_sample')
+ s.tag&.save! unless spp.nil? && sps.nil?
+ original_element&.analyses&.each do |a|
+ a.reload
+ a.tag&.taggable_data&.delete('public_analysis') && a.tag.save!
+ a.extended_metadata&.delete('public_analysis') && a.save!
+ end
+ end
+ end
+
+ def declined_move_collections
+ all_col_id = User.find(published_by).all_collection&.id
+ return unless element && all_col_id
+
+ col_ids = element&.collections&.pluck(:id)
+ et = element.tag
+ et.taggable_data = et.taggable_data.merge(decline: true)
+ tag_pub = et.taggable_data&.delete('publication')
+ et.save!
+ case element_type
+ when 'Reaction'
+ CollectionsReaction
+ when 'Sample'
+ CollectionsSample
+ end.move_to_collection(element_id, col_ids, all_col_id)
+ end
+
+ # NB: ?NOT USED? Was it meant for declining/rejecting publication
+ # NB: was Moved to model from ChemotionRepoReviewingJob
+ # TODO: move this to publising concern ?
+ # def release_original_element
+ # ot = original_element&.tag&.taggable_data&.delete("publish_#{element_type.downcase}")
+ # original_element.tag.save! unless ot.nil?
+ #
+ # case element_type
+ # when 'Sample'
+ # clear_orig_analyses(original_element)
+ # when 'Reaction'
+ # clear_orig_analyses(original_element)
+ # original_element&.samples&.each do |s|
+ # t = s.tag&.taggable_data&.delete('publish_sample')
+ # s.tag.save! unless t.nil?
+ # clear_orig_analyses(s)
+ # end
+ # end
+ # end
+
+ # TODO: mv this to publishing concern ??
+ # def clear_orig_analyses(el = element)
+ # el&.analyses&.each do |a|
+ # t = a.tag&.taggable_data&.delete('publish_analysis')
+ # a.tag.save! unless t.nil?
+ # end
+ # end
+
+ def publication_logger
+ @@publication_logger ||= Logger.new(File.join(Rails.root, 'log', 'publication.log'))
+ end
+
+ def doi_bag
+ d = doi
+ case element_type
+ when 'Collection'
+ dois = {
+ collection: {
+ DOI: d.full_doi,
+ suffix: d.suffix,
+ inchikey: d.inchikey,
+ count: d.molecule_count
+ },
+ element_dois: {}
+ }
+ eids = taggable_data["eids"]
+ eids.each do |eid|
+ sp = Publication.find(eid)
+ sd = sp.doi
+ dois[:element_dois][sp.element_id.to_s] = {
+ DOI: sd.full_doi,
+ suffix: sd.suffix,
+ type: sd.analysis_type,
+ count: sd.analysis_count
+ }
+ end
+ when 'Sample'
+ dois = {
+ sample: {
+ DOI: d.full_doi,
+ suffix: d.suffix,
+ inchikey: d.inchikey,
+ count: d.molecule_count
+ },
+ analyses_dois: {}
+ }
+ children.each do |a|
+ d = a.doi
+ dois[:analyses_dois][a.element_id.to_s] = {
+ DOI: d.full_doi,
+ suffix: d.suffix,
+ type: d.analysis_type,
+ count: d.analysis_count
+ }
+ end
+ when 'Reaction'
+ dois = {
+ reaction: {
+ DOI: d.full_doi,
+ suffix: d.suffix,
+ inchikey: d.inchikey,
+ count: d.molecule_count
+ },
+ analyses_dois: {}
+ }
+ children.where(element_type: 'Container').each do |a|
+ d = a.doi
+ dois[:analyses_dois][a.element_id.to_s] = {
+ DOI: d.full_doi,
+ suffix: d.suffix,
+ type: d.analysis_type,
+ count: d.analysis_count
+ }
+ end
+ dois['samples'] = {}
+ children.where(element_type: 'Sample').each do |new_sample|
+ d = new_sample.doi
+ if d
+ dois['samples'][new_sample.element_id.to_s] = {
+ sample: {
+ DOI: d.full_doi,
+ suffix: d.suffix,
+ inchikey: d.inchikey,
+ count: d.molecule_count
+ },
+ analyses_dois: {}
+ }
+ end
+ end
+ when 'Container'
+ parent_doi = parent.doi
+ dois = {
+ analysis: {
+ DOI: d.full_doi,
+ suffix: d.suffix,
+ inchikey: d.inchikey,
+ count: d.molecule_count
+ },
+ parent_element: {
+ DOI: parent_doi.full_doi,
+ suffix: parent_doi.suffix,
+ inchikey: parent_doi.inchikey,
+ count: parent_doi.molecule_count
+ }
+ }
+ end
+ return dois
+ end
+
+ def scheme_only
+ taggable_data && taggable_data['scheme_only'] == true ? true : false
+ end
+
+ def rights_data
+ rights = {
+ schemeURI: 'https://spdx.org/licenses/',
+ rightsIdentifierScheme: 'SPDX',
+ rightsIdentifier: 'CC-BY-SA-4.0',
+ rightsURI: 'http://creativecommons.org/licenses/by-sa/4.0/',
+ rightsName: 'Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)'
+ }
+ if taggable_data && taggable_data['license'].present?
+ case taggable_data['license']
+ when 'CC BY'
+ rights[:rightsIdentifier] = 'CC-BY-4.0'
+ rights[:rightsURI] = 'http://creativecommons.org/licenses/by/4.0/'
+ rights[:rightsName] = 'Attribution 4.0 International (CC BY 4.0)'
+ when 'CC0'
+ rights[:rightsIdentifier] = 'CC0-1.0'
+ rights[:rightsURI] = 'http://creativecommons.org/publicdomain/zero/1.0/'
+ rights[:rightsName] = 'CC0 1.0 Universal'
+ when 'No License'
+ rights[:rightsIdentifier] = ''
+ rights[:rightsURI] = ''
+ rights[:rightsName] = ''
+ rights[:schemeURI] = ''
+ rights[:rightsIdentifierScheme] = ''
+ end
+ end
+ rights
+ end
+
+ def datacite_metadata_xml
+ previous_version = element.tag.taggable_data['previous_version']
+ unless previous_version.nil?
+ previous_version_tag = ElementTag.find_by(taggable_type: element_type,
+ taggable_id: previous_version['id'])
+ previous_version_doi = previous_version_tag.taggable_data.fetch('publication', {}).fetch('doi')
+ end
+
+ if parent.nil? && %w[Sample Reaction].include?(element_type)
+ coly = element.collections.where(
+ <<~SQL
+ collections.id in (select element_id from publications pub where element_type = 'Collection' and element_id = collections.id)
+ SQL
+ ).last
+ cdoi = coly.publication&.doi&.full_doi if coly.present?
+ end
+ parent_element = parent&.element
+ literals = ActiveRecord::Base.connection.exec_query(literals_sql(element_id, element_type))
+ metadata_obj = OpenStruct.new(pub: self, element: element, pub_tag: taggable_data, dois: doi_bag,
+ parent_element: parent_element.presence, previous_version_doi: previous_version_doi,
+ rights: rights_data, lits: literals, col_doi: cdoi, cust_sample: cust_sample)
+ erb_file = if element_type == 'Container'
+ "app/publish/datacite_metadata_#{parent_element.class.name.downcase}_#{element_type.downcase}.html.erb"
+ else
+ "app/publish/datacite_metadata_#{element_type.downcase}.html.erb"
+ end
+ metadata_file = ERB.new(File.read(File.join(
+ Rails.root,
+ erb_file
+ )))
+ metadata_file.result(metadata_obj.instance_eval { binding })
+ end
+
+ def persit_datacite_metadata_xml!
+ mt = datacite_metadata_xml
+ self.update!(metadata_xml: mt, oai_metadata_xml: mt)
+ mt
+ end
+
+ def persit_oai_metadata_xml!
+ mt = datacite_metadata_xml
+ self.update_columns(oai_metadata_xml: mt)
+ mt
+ end
+
+ def transition_from_start_to_metadata_uploading!
+ return unless valid_transition(STATE_DC_METADATA_UPLOADING)
+ mt = datacite_metadata_xml
+ self.update!(metadata_xml: mt, oai_metadata_xml: mt, state: STATE_DC_METADATA_UPLOADING)
+ end
+
+ def transition_from_metadata_uploading_to_uploaded!
+ return unless valid_transition(STATE_DC_METADATA_UPLOADED)
+ if (ENV['DATACITE_MODE'] == 'test' || ENV['PUBLISH_MODE'] == 'production') && scheme_only == false
+ resp = Datacite::Mds.new.upload_metadata(metadata_xml)
+ success = resp.is_a?(Net::HTTPSuccess)
+ message = "#{resp.inspect}: metadata upload#{"ing fail" if !success}ed"
+ else
+ success = true
+ message = "metadata not uploaded in mode #{ENV['PUBLISH_MODE']}"
+ end
+ logger([message, metadata])
+ raise "#{message}" unless success
+ self.update!(state: STATE_DC_METADATA_UPLOADED)
+ end
+
+ def transition_from_metadata_uploaded_to_doi_registering!
+ return unless valid_transition(STATE_DC_DOI_REGISTERING)
+ self.update!(state: STATE_DC_DOI_REGISTERING)
+ end
+
+ def transition_from_doi_registering_to_registered!
+ return unless valid_transition(STATE_DC_DOI_REGISTERED)
+ mds = Datacite::Mds.new
+ suffix = doi.suffix
+ short_doi = "#{mds.doi_prefix}/#{suffix}"
+ url = "https://#{mds.doi_domain}/inchikey/#{suffix}"
+ if (ENV['DATACITE_MODE'] == 'test' || ENV['PUBLISH_MODE'] == 'production') && scheme_only == false
+ resp = mds.mint(short_doi, url)
+ success = resp.is_a?(Net::HTTPSuccess)
+ message = "#{resp.inspect}: DOI mint#{'ing fail' unless success}ed"
+ else
+ success = true
+ message = "DOI not minted in mode #{ENV['PUBLISH_MODE']}"
+ end
+ logger([message, "doi: #{short_doi}", "url: #{url}"])
+ raise "#{message}:\n #{short_doi} <-> #{url}" unless success
+ doi_date = DateTime.now
+ case element_type
+ when 'Sample'
+ chem_first = element.pubchem_cid.blank?
+ tag_data = {
+ doi_reg_at: doi_date,
+ sample_version: doi.molecule_count,
+ doi: short_doi
+ }
+ tag_data[:chem_first] = doi_date if chem_first
+ element.update_publication_tag(tag_data)
+ when 'Container'
+ et = ElementTag.find_or_create_by(
+ taggable_type: 'Container', taggable_id: element_id
+ )
+ tag_data = parent.element.publication_tag.merge({
+ published_at: doi_date,
+ dataset_version: doi.analysis_count,
+ analysis_doi: short_doi
+ })
+ et.update!(
+ taggable_data: (et.taggable_data || {}).merge(publication: tag_data)
+ )
+ when 'Reaction'
+ tag_data = {
+ doi_reg_at: doi_date,
+ reaction_version: doi.molecule_count,
+ doi: short_doi
+ }
+ element.update_publication_tag(tag_data)
+ when 'Collection'
+ tag_data = {
+ doi_reg_at: doi_date,
+ doi: short_doi
+ }
+ end
+
+ pd = taggable_data.merge(tag_data)
+ self.update!(state: STATE_DC_DOI_REGISTERED,taggable_data: taggable_data.merge(pd))
+ end
+
+ def transition_from_doi_registered_to_pubchem_registering!
+ return unless valid_transition(STATE_PUBCHEM_REGISTERING)
+ self.update!(state: STATE_PUBCHEM_REGISTERING)
+ end
+
+ def transition_from_doi_pubchem_registering_to_registered!
+ return unless valid_transition(STATE_PUBCHEM_REGISTERED)
+ if element_type == 'Sample'
+ metadata_obj = OpenStruct.new(sample: element)
+ metadata_file = ERB.new(File.read(
+ File.join(Rails.root,'app', 'publish', 'pubchem_metadata.sdf.erb')
+ ))
+ mt = metadata_file.result(metadata_obj.instance_eval { binding })
+ if (production = Rails.env.production? && ENV['PUBLISH_MODE'] == 'production') && scheme_only == false
+ ftp = Net::FTP.new('ftp-private.ncbi.nlm.nih.gov')
+ ftp.passive = true
+ ftp.login(ENV['PUBCHEM_LOGIN'], ENV['PUBCHEM_PASSWORD'])
+ ftp.puttextcontent(mt, doi.suffix + '.sdf.in')
+ ftp.close
+ end
+ message = "\n---MOLFILE START---"
+ element.update_publication_tag(pubchem_reg_at: DateTime.now)
+ pd = taggable_data.merge(pubchem_reg_at: DateTime.now)
+ logger([message, mt, "Pubchem FTP upload #{production ? '' : 'NOT'} sent (mode: #{ENV['PUBLISH_MODE']})"])
+ end
+ self.update!(state: STATE_PUBCHEM_REGISTERED, taggable_data: taggable_data.merge(pd))
+ end
+
+ def transition_from_pubchem_registered_to_completing!
+ return unless valid_transition(STATE_COMPLETING)
+ self.update!(state: STATE_COMPLETING)
+ end
+
+ def transition_from_doi_registered_to_completing!
+ return unless valid_transition(STATE_COMPLETING)
+ self.update!(state: STATE_COMPLETING)
+ end
+
+ def transition_from_completing_to_completed!
+ return unless valid_transition(STATE_COMPLETED)
+ pd = {}
+ time = DateTime.now
+ if element_type != 'Container' && element_type != 'Collection'
+ creator_ids = taggable_data['author_ids']
+ su_id = User.chemotion_user.id
+
+ pending_collection_ids = Collection.joins(
+ "INNER JOIN sync_collections_users ON sync_collections_users.collection_id = collections.id"
+ ).where("sync_collections_users.shared_by_id = ?", su_id)
+ .where("sync_collections_users.user_id in (?)", published_by)
+ .where("collections.label = 'Pending Publications'").pluck(:id)
+
+ my_published_collection_ids = Collection.joins(
+ "INNER JOIN sync_collections_users ON sync_collections_users.collection_id = collections.id"
+ ).where("sync_collections_users.shared_by_id = ?", User.chemotion_user.id)
+ .where("sync_collections_users.user_id in (?)", [published_by] + creator_ids)
+ .where("collections.label = 'Published Elements'")
+ .pluck(:id)
+
+ if element_type == 'Reaction' && scheme_only
+ published_collection_ids = my_published_collection_ids + [Collection.scheme_only_reactions_collection.id]
+ else
+ published_collection_ids = my_published_collection_ids + [Collection.public_collection_id]
+ end
+ collections_klass = "Collections#{element_type}".constantize
+ if element_type == 'Sample'
+ gl_col_ids = collections_klass.joins(:collection).where(sample_id: element_id).where("collections.label = 'Group Lead Review'").pluck :collection_id
+ end
+ if element_type == 'Reaction'
+ gl_col_ids = collections_klass.joins(:collection).where(reaction_id: element_id).where("collections.label = 'Group Lead Review'").pluck :collection_id
+ end
+ collections_klass.remove_in_collection([element_id], gl_col_ids ) if gl_col_ids.present?
+ collections_klass.remove_in_collection([element_id], pending_collection_ids)
+ collections_klass.remove_in_collection([element_id], Collection.element_to_review_collection.pluck(:id))
+ collections_klass.remove_in_collection([element_id], [Collection.embargo_accepted_collection&.id])
+ collections_klass.create_in_collection([element_id], published_collection_ids)
+
+ element.update_publication_tag(published_at: time)
+ pd = taggable_data.merge(published_at: time)
+ logger(['moved to collections'])
+ end
+ self.update!(state: STATE_COMPLETED, taggable_data: taggable_data.merge(pd), published_at: time)
+ end
+
+ def default_line
+ @default_line ||= "#{element_type} #{element_id}: "
+ end
+
+ def valid_transition(to_state)
+ case to_state
+ when STATE_START
+ valid = [STATE_START].include?(state)
+
+ when STATE_ACCEPTED
+ valid = [STATE_ACCEPTED].include?(state)
+
+ when STATE_DC_METADATA_UPLOADING
+ valid = [STATE_ACCEPTED].include?(state)
+
+ when STATE_DC_METADATA_UPLOADED
+ valid = [STATE_DC_METADATA_UPLOADING].include?(state)
+
+ when STATE_DC_DOI_REGISTERING
+ valid = [STATE_DC_METADATA_UPLOADED].include?(state)
+
+ when STATE_DC_DOI_REGISTERED
+ valid = [STATE_DC_DOI_REGISTERING].include?(state)
+
+ when STATE_PUBCHEM_REGISTERING
+ valid = (element_type == 'Sample') && [STATE_DC_DOI_REGISTERED].include?(state)
+
+ when STATE_PUBCHEM_REGISTERED
+ valid = [STATE_PUBCHEM_REGISTERING].include?(state)
+
+ when STATE_COMPLETING
+ valid = if element_type == 'Sample'
+ [STATE_PUBCHEM_REGISTERED].include?(state)
+ else
+ [STATE_DC_DOI_REGISTERED, STATE_COMPLETING].include?(state)
+ end
+
+ when STATE_COMPLETED
+ valid = [STATE_COMPLETING].include?(state)
+ end
+
+ log_invalid_transition(to_state) unless valid
+ valid
+ end
+
+ def literals_sql(e_id, e_type)
+ <<~SQL
+ select l.*,
+ case l.litype
+ when 'citedOwn' then 'IsCitedBy'
+ when 'citedRef' then 'Continues'
+ when 'referTo' then 'References'
+ end relationtype,
+ case
+ when nullif(l2.doi,'') is not null then 'DOI' || ' {|} ' || 'https://dx.doi.org/' || doi
+ when nullif(l2.isbn,'') is not null then 'ISBN' || ' {|} ' || isbn
+ when nullif(l2.url,'') is not null then 'URL' || ' {|} ' || url
+ end relatedIdentifiertype,
+ l2.title, l2.url, l2.refs, l2.doi, l2.isbn
+ from literals l
+ join literatures l2 on l.literature_id = l2.id
+ where l.element_id = #{e_id} and l.element_type = '#{e_type}' and l.litype in ('citedOwn', 'citedRef', 'referTo')
+ SQL
+ end
+
+ def get_xvial(xvial)
+ com_config = Rails.configuration.compound_opendata
+ return nil unless com_config.present? && xvial.present?
+
+ CompoundOpenData.where("x_data ->> 'xid' = ?", xvial)
+ end
+
+ def cust_sample
+ if element_type == 'Sample'
+ desc_type = "#{element.decoupled ? 'de' : ''}coupled_sample#{element.molecule_inchikey == 'DUMMY' ? '' : '_structure'}"
+ melting_point = range_to_s(element.melting_point)
+ boiling_point = range_to_s(element.boiling_point)
+
+ { type: desc_type, melting_point: melting_point, boiling_point: boiling_point, x_id: get_xvial(element.tag&.taggable_data&.dig('xvial','num'))&.first&.x_short_label }
+ else
+ {}
+ end
+ end
+
+ def range_to_s(val)
+ if val.begin == -Float::INFINITY && val.end == Float::INFINITY
+ ''
+ else
+ start = val.begin == -Float::INFINITY ? '' : val.begin.to_f
+ finish = val.end == Float::INFINITY ? '' : val.end.to_f
+ "#{start}#{start == '' || finish == '' ? '' : ' - '}#{finish} (°C)"
+ end
+ end
+
+ def log_invalid_transition(to_state)
+ logger("CANNOT TRANSITION from #{state} to #{to_state}")
+ end
+
+ def logger(message_arr)
+ message = [message_arr].flatten.join("\n")
+ publication_logger.info(
+ <<~INFO
+ ******** MODE #{ENV['PUBLISH_MODE']}********
+ Publication #{id}. STATE: #{state}: #{default_line}
+ #{message}
+ ********************************************************************************
+ INFO
+ )
+ end
+end
diff --git a/app/models/publication_authors.rb b/app/models/publication_authors.rb
new file mode 100644
index 000000000..e7cdd72b8
--- /dev/null
+++ b/app/models/publication_authors.rb
@@ -0,0 +1,14 @@
+# == Schema Information
+#
+# Table name: publication_authors
+#
+# author_id :text
+# element_id :integer
+# element_type :string
+# state :string
+# doi_id :integer
+# ancestry :string
+#
+
+class PublicationAuthors < ApplicationRecord
+end
diff --git a/app/models/publication_collections.rb b/app/models/publication_collections.rb
new file mode 100644
index 000000000..11a87c7a6
--- /dev/null
+++ b/app/models/publication_collections.rb
@@ -0,0 +1,16 @@
+# == Schema Information
+#
+# Table name: publication_collections
+#
+# id :integer
+# state :string
+# element_id :integer
+# label :text
+# doi :text
+# elobj :jsonb
+# doi_id :integer
+# published_by :integer
+#
+
+class PublicationCollections < ApplicationRecord
+end
diff --git a/app/models/publication_ontologies.rb b/app/models/publication_ontologies.rb
new file mode 100644
index 000000000..d37396c64
--- /dev/null
+++ b/app/models/publication_ontologies.rb
@@ -0,0 +1,15 @@
+# == Schema Information
+#
+# Table name: publication_ontologies
+#
+# element_type :string
+# element_id :integer
+# container_id :integer
+# published_at :datetime
+# ontologies :text
+# term_id :text
+# label :text
+#
+
+class PublicationOntologies < ApplicationRecord
+end
diff --git a/app/models/reaction.rb b/app/models/reaction.rb
index 2cefabe77..37cd5bcac 100644
--- a/app/models/reaction.rb
+++ b/app/models/reaction.rb
@@ -50,6 +50,7 @@ class Reaction < ApplicationRecord
include Taggable
include ReactionRinchi
include Segmentable
+ include Publishing
serialize :description, Hash
serialize :observation, Hash
@@ -57,6 +58,7 @@ class Reaction < ApplicationRecord
multisearchable against: %i[name short_label rinchi_string]
attr_accessor :can_copy
+ attr_accessor :previous_version
# search scopes for exact matching
pg_search_scope :search_by_reaction_name, against: :name
@@ -136,6 +138,7 @@ class Reaction < ApplicationRecord
has_many :sync_collections_users, through: :collections
has_many :private_notes, as: :noteable, dependent: :destroy
+ has_one :doi, as: :doiable
belongs_to :creator, foreign_key: :created_by, class_name: 'User'
validates :creator, presence: true
@@ -143,10 +146,13 @@ class Reaction < ApplicationRecord
before_save :update_svg_file!
before_save :cleanup_array_fields
before_save :auto_format_temperature!
+ before_save :check_doi
before_create :auto_set_short_label
after_create :update_counter
+ before_destroy :remove_from_previous_version
+
has_one :container, :as => :containable
def self.get_associated_samples(reaction_ids)
@@ -157,6 +163,10 @@ def analyses
self.container ? self.container.analyses : []
end
+ def links
+ self.container ? self.container.links : []
+ end
+
def auto_format_temperature!
valueUnitCheck = (temperature['valueUnit'] =~ /^(°C|°F|K)$/).present?
temperature['valueUnit'] = '°C' if (!valueUnitCheck)
@@ -215,7 +225,7 @@ def update_svg_file!
paths[prop] = collection.map do |reactions_sample|
sample = reactions_sample.sample
params = [
- svg_path(sample.sample_svg_file, sample.molecule.molecule_svg_file)
+ svg_path(sample&.sample_svg_file, sample&.molecule&.molecule_svg_file)
]
params[0] = sample.svg_text_path if reactions_sample.show_label
params.append(yield_amount(sample.id)) if prop == :products
@@ -245,7 +255,8 @@ def svg_path(sample_svg, molecule_svg)
end
def yield_amount(sample_id)
- ReactionsProductSample.find_by(reaction_id: self.id, sample_id: sample_id).try(:equivalent)
+ rps = ReactionsProductSample.find_by(reaction_id: self.id, sample_id: sample_id)
+ rps.scheme_yield || rps.equivalent
end
def solvents_in_svg
@@ -259,12 +270,24 @@ def cleanup_array_fields
end
def auto_set_short_label
- prefix = creator.reaction_name_prefix
- counter = creator.counters['reactions'].succ
- self.short_label = "#{creator.initials}-#{prefix}#{counter}"
+ unless self.previous_version.present?
+ prefix = creator.reaction_name_prefix
+ counter = creator.counters['reactions'].succ
+ self.short_label = "#{creator.initials}-#{prefix}#{counter}"
+ else
+ self.short_label = get_new_version_short_label
+ end
end
def update_counter
self.creator.increment_counter 'reactions'
end
+
+ def remove_from_previous_version
+ previous_version = self.tag&.taggable_data['previous_version']
+ if previous_version
+ previous_element = Reaction.find_by(id: previous_version['id'])
+ previous_element.untag_as_previous_version
+ end
+ end
end
diff --git a/app/models/reactions_product_sample.rb b/app/models/reactions_product_sample.rb
index 50d1beebf..f74dbcce2 100644
--- a/app/models/reactions_product_sample.rb
+++ b/app/models/reactions_product_sample.rb
@@ -2,17 +2,18 @@
#
# Table name: reactions_samples
#
-# id :integer not null, primary key
-# reaction_id :integer
-# sample_id :integer
-# reference :boolean
-# equivalent :float
-# position :integer
-# type :string
-# deleted_at :datetime
-# waste :boolean default(FALSE)
-# coefficient :float default(1.0)
-# show_label :boolean default(FALSE), not null
+# id :integer not null, primary key
+# reaction_id :integer
+# sample_id :integer
+# reference :boolean
+# equivalent :float
+# position :integer
+# type :string
+# deleted_at :datetime
+# waste :boolean default(FALSE)
+# coefficient :float default(1.0)
+# scheme_yield :float
+# show_label :boolean default(FALSE), not null
#
# Indexes
#
diff --git a/app/models/reactions_purification_solvent_sample.rb b/app/models/reactions_purification_solvent_sample.rb
index aa2c1c9fa..dcca1d83a 100644
--- a/app/models/reactions_purification_solvent_sample.rb
+++ b/app/models/reactions_purification_solvent_sample.rb
@@ -2,17 +2,18 @@
#
# Table name: reactions_samples
#
-# id :integer not null, primary key
-# reaction_id :integer
-# sample_id :integer
-# reference :boolean
-# equivalent :float
-# position :integer
-# type :string
-# deleted_at :datetime
-# waste :boolean default(FALSE)
-# coefficient :float default(1.0)
-# show_label :boolean default(FALSE), not null
+# id :integer not null, primary key
+# reaction_id :integer
+# sample_id :integer
+# reference :boolean
+# equivalent :float
+# position :integer
+# type :string
+# deleted_at :datetime
+# waste :boolean default(FALSE)
+# coefficient :float default(1.0)
+# scheme_yield :float
+# show_label :boolean default(FALSE), not null
#
# Indexes
#
diff --git a/app/models/reactions_reactant_sample.rb b/app/models/reactions_reactant_sample.rb
index 958da1b44..a0f0b2d89 100644
--- a/app/models/reactions_reactant_sample.rb
+++ b/app/models/reactions_reactant_sample.rb
@@ -2,17 +2,18 @@
#
# Table name: reactions_samples
#
-# id :integer not null, primary key
-# reaction_id :integer
-# sample_id :integer
-# reference :boolean
-# equivalent :float
-# position :integer
-# type :string
-# deleted_at :datetime
-# waste :boolean default(FALSE)
-# coefficient :float default(1.0)
-# show_label :boolean default(FALSE), not null
+# id :integer not null, primary key
+# reaction_id :integer
+# sample_id :integer
+# reference :boolean
+# equivalent :float
+# position :integer
+# type :string
+# deleted_at :datetime
+# waste :boolean default(FALSE)
+# coefficient :float default(1.0)
+# scheme_yield :float
+# show_label :boolean default(FALSE), not null
#
# Indexes
#
diff --git a/app/models/reactions_sample.rb b/app/models/reactions_sample.rb
index c3c3e64b0..c41e40a76 100644
--- a/app/models/reactions_sample.rb
+++ b/app/models/reactions_sample.rb
@@ -2,17 +2,18 @@
#
# Table name: reactions_samples
#
-# id :integer not null, primary key
-# reaction_id :integer
-# sample_id :integer
-# reference :boolean
-# equivalent :float
-# position :integer
-# type :string
-# deleted_at :datetime
-# waste :boolean default(FALSE)
-# coefficient :float default(1.0)
-# show_label :boolean default(FALSE), not null
+# id :integer not null, primary key
+# reaction_id :integer
+# sample_id :integer
+# reference :boolean
+# equivalent :float
+# position :integer
+# type :string
+# deleted_at :datetime
+# waste :boolean default(FALSE)
+# coefficient :float default(1.0)
+# scheme_yield :float
+# show_label :boolean default(FALSE), not null
#
# Indexes
#
diff --git a/app/models/reactions_solvent_sample.rb b/app/models/reactions_solvent_sample.rb
index 947359f81..c180548f1 100644
--- a/app/models/reactions_solvent_sample.rb
+++ b/app/models/reactions_solvent_sample.rb
@@ -2,17 +2,18 @@
#
# Table name: reactions_samples
#
-# id :integer not null, primary key
-# reaction_id :integer
-# sample_id :integer
-# reference :boolean
-# equivalent :float
-# position :integer
-# type :string
-# deleted_at :datetime
-# waste :boolean default(FALSE)
-# coefficient :float default(1.0)
-# show_label :boolean default(FALSE), not null
+# id :integer not null, primary key
+# reaction_id :integer
+# sample_id :integer
+# reference :boolean
+# equivalent :float
+# position :integer
+# type :string
+# deleted_at :datetime
+# waste :boolean default(FALSE)
+# coefficient :float default(1.0)
+# scheme_yield :float
+# show_label :boolean default(FALSE), not null
#
# Indexes
#
diff --git a/app/models/reactions_starting_material_sample.rb b/app/models/reactions_starting_material_sample.rb
index cc73df342..7e12a1956 100644
--- a/app/models/reactions_starting_material_sample.rb
+++ b/app/models/reactions_starting_material_sample.rb
@@ -2,17 +2,18 @@
#
# Table name: reactions_samples
#
-# id :integer not null, primary key
-# reaction_id :integer
-# sample_id :integer
-# reference :boolean
-# equivalent :float
-# position :integer
-# type :string
-# deleted_at :datetime
-# waste :boolean default(FALSE)
-# coefficient :float default(1.0)
-# show_label :boolean default(FALSE), not null
+# id :integer not null, primary key
+# reaction_id :integer
+# sample_id :integer
+# reference :boolean
+# equivalent :float
+# position :integer
+# type :string
+# deleted_at :datetime
+# waste :boolean default(FALSE)
+# coefficient :float default(1.0)
+# scheme_yield :float
+# show_label :boolean default(FALSE), not null
#
# Indexes
#
diff --git a/app/models/report.rb b/app/models/report.rb
index 610ebe7b7..32753ec65 100644
--- a/app/models/report.rb
+++ b/app/models/report.rb
@@ -20,7 +20,7 @@
# updated_at :datetime not null
# template :string default("standard")
# mol_serials :text default([])
-# si_reaction_settings :text default({"Name"=>true, "CAS"=>true, "Formula"=>true, "Smiles"=>true, "InCHI"=>true, "Molecular Mass"=>true, "Exact Mass"=>true, "EA"=>true})
+# si_reaction_settings :text default({:Name=>true, :CAS=>true, :Formula=>true, :Smiles=>true, :InCHI=>true, :"Molecular Mass"=>true, :"Exact Mass"=>true, :EA=>true})
# prd_atts :text default([])
# report_templates_id :integer
#
@@ -92,6 +92,10 @@ def create_docx
Reporter::WorkerRxnList.new(
report: self, template_path: tpl_path, ext: 'html'
).process
+ when 'doi_list_xlsx'
+ Reporter::WorkerDoiList.new(
+ report: self, ext: 'xlsx'
+ ).process
else
Reporter::Worker.new(
report: self, template_path: tpl_path
diff --git a/app/models/sample.rb b/app/models/sample.rb
index ca0810d1a..bee4ee311 100644
--- a/app/models/sample.rb
+++ b/app/models/sample.rb
@@ -12,7 +12,6 @@
# molecule_id :integer
# molfile :binary
# purity :float default(1.0)
-# deprecated_solvent :string default("")
# impurities :string default("")
# location :string default("")
# is_top_secret :boolean default(FALSE)
@@ -53,6 +52,11 @@
#
class Sample < ApplicationRecord
+
+ require 'net/ftp'
+ require 'erb'
+ require 'ostruct'
+
acts_as_paranoid
include ElementUIStateScopes
include PgSearch
@@ -62,6 +66,7 @@ class Sample < ApplicationRecord
include UnitConvertable
include Taggable
include Segmentable
+ include Publishing
STEREO_ABS = ['any', 'rac', 'meso', 'delta', 'lambda', '(S)', '(R)', '(Sp)', '(Rp)', '(Sa)', '(Ra)'].freeze
STEREO_REL = ['any', 'syn', 'anti', 'p-geminal', 'p-ortho', 'p-meta', 'p-para', 'cis', 'trans', 'fac', 'mer'].freeze
@@ -72,6 +77,8 @@ class Sample < ApplicationRecord
:molecule_iupac_name, :molecule_inchistring, :molecule_inchikey, :molecule_cano_smiles
]
+ attr_accessor :previous_version
+
# search scopes for exact matching
pg_search_scope :search_by_sum_formula, against: :sum_formula, associated_against: {
molecule: :sum_formular
@@ -160,12 +167,15 @@ class Sample < ApplicationRecord
before_save :attach_svg, :init_elemental_compositions,
:set_loading_from_ea
before_save :auto_set_short_label
+ before_save :check_doi
before_create :check_molecule_name
before_create :set_boiling_melting_points
after_save :update_counter
after_create :create_root_container
after_save :update_data_for_reactions
+ before_destroy :remove_from_previous_version
+
has_many :collections_samples, inverse_of: :sample, dependent: :destroy
has_many :collections, through: :collections_samples
@@ -181,7 +191,7 @@ class Sample < ApplicationRecord
has_many :reactions_as_reactant, through: :reactions_reactant_samples, source: :reaction
has_many :reactions_as_solvent, through: :reactions_solvent_samples, source: :reaction
has_many :reactions_as_product, through: :reactions_product_samples, source: :reaction
-
+
has_many :literals, as: :element, dependent: :destroy
has_many :literatures, through: :literals
@@ -208,6 +218,8 @@ class Sample < ApplicationRecord
belongs_to :creator, foreign_key: :created_by, class_name: 'User'
belongs_to :molecule, optional: true
+ has_one :doi, as: :doiable
+
accepts_nested_attributes_for :molecule_name
accepts_nested_attributes_for :collections_samples
accepts_nested_attributes_for :molecule, update_only: true
@@ -221,6 +233,14 @@ class Sample < ApplicationRecord
delegate :computed_props, to: :molecule, prefix: true
delegate :inchikey, to: :molecule, prefix: true, allow_nil: true
+ def molfile_pubchem
+ version = Chemotion::OpenBabelService.molfile_version(self.molfile)
+ mf = Chemotion::OpenBabelService.mofile_clear_coord_bonds(self.molfile, version)
+ mf = molfile unless mf
+ mf&.split(/^\$\$\$\$/).first
+ end
+
+
def molecule_sum_formular
(decoupled? ? sum_formula : molecule&.sum_formular) || ''
end
@@ -245,6 +265,22 @@ def analyses
self.container ? self.container.analyses : Container.none
end
+ def links
+ self.container ? self.container.links : Container.none
+ end
+
+ #TODO move to molecule (chemotion_ELN)
+ def pubchem_cid
+ mol = self.molecule
+ cid = mol.tag && mol.tag.taggable_data && mol.tag.taggable_data['pubchem_cid']
+ if cid
+ cid
+ else
+ mol.update_tag!(pubchem_tag: true)
+ mol.tag.taggable_data['pubchem_cid']
+ end
+ end
+
def self.associated_by_user_id_and_reaction_ids(user_id, reaction_ids)
(for_user(user_id).by_reaction_ids(reaction_ids)).distinct
end
@@ -341,24 +377,45 @@ def loading
self.residues[0] && self.residues[0].custom_info['loading'].to_f
end
+ def full_svg_path(svg_file_name = sample_svg_file)
+ Rails.public_path.join('images', 'samples', svg_file_name)
+ end
+
def attach_svg
svg = self.sample_svg_file
return unless svg.present?
svg_file_name = "#{SecureRandom.hex(64)}.svg"
- if svg =~ /TMPFILE[0-9a-f]{64}.svg/
- svg_path = Rails.public_path.join('images', 'samples', svg.to_s).to_s
- FileUtils.mv(svg_path, svg_path.gsub(/(TMPFILE\S+)/, svg_file_name))
- self.sample_svg_file = svg_file_name
- elsif svg.start_with?(' 1,
'reaction' => 2,
@@ -271,6 +299,130 @@ def all_sync_in_collections_users
SyncCollectionsUser.where('user_id IN (?) ', [id] + group_ids)
end
+ def self.is_public
+ self.find_by(email: ENV['SYS_EMAIL'])
+ end
+
+ # TODO: mv to initializers
+ def self.reviewer_ids
+ (ENV['REVIEWERS'] || '').split(',').map(&:to_i)
+ end
+
+ def is_reviewer
+ (ENV['REVIEWERS'] || "").split(",").include?(self.id.to_s)
+ end
+
+ def is_article_editor
+ (ENV['NEWSROOM_EDITOR'] || "").split(",").include?(self.id.to_s)
+ end
+
+ def is_howto_editor
+ (ENV['HOWTO_EDITOR'] || "").split(",").include?(self.id.to_s)
+ end
+
+ def pending_collection
+ su_id = User.chemotion_user.id
+ Collection.joins(
+ "INNER JOIN sync_collections_users ON " +
+ "sync_collections_users.collection_id = collections.id")
+ .where("sync_collections_users.shared_by_id = #{su_id}")
+ .where("sync_collections_users.user_id = #{self.id}")
+ .where("collections.label = 'Pending Publications'").first
+ end
+
+ def versions_collection
+ su_id = User.chemotion_user.id
+ Collection.joins(
+ "INNER JOIN sync_collections_users ON " +
+ "sync_collections_users.collection_id = collections.id")
+ .where("sync_collections_users.shared_by_id = #{su_id}")
+ .where("sync_collections_users.user_id = #{self.id}")
+ .where("collections.label = 'New Versions'").first
+ end
+
+ def reviewing_collection
+ su_id = User.chemotion_user.id
+ Collection.joins(
+ "INNER JOIN sync_collections_users ON " +
+ "sync_collections_users.collection_id = collections.id")
+ .where("sync_collections_users.shared_by_id = #{su_id}")
+ .where("sync_collections_users.user_id = #{self.id}")
+ .where("collections.label = 'Reviewing'").first
+ end
+
+ def sync_reviewing_collection
+ su_id = User.chemotion_user.id
+ SyncCollectionsUser.joins(
+ "INNER JOIN collections ON " +
+ "sync_collections_users.collection_id = collections.id")
+ .where("sync_collections_users.shared_by_id = #{su_id}")
+ .where("sync_collections_users.user_id = #{self.id}")
+ .where("collections.label = 'Reviewing'").first
+ end
+
+
+ def sync_element_to_review_collection
+ su_id = User.chemotion_user.id
+ SyncCollectionsUser.joins(
+ "INNER JOIN collections ON " +
+ "sync_collections_users.collection_id = collections.id")
+ .where("sync_collections_users.shared_by_id = #{su_id}")
+ .where("sync_collections_users.user_id = #{self.id}")
+ .where("collections.label = 'Element To Review'").first
+ end
+
+ def find_or_create_grouplead_collection
+ chemotion_user = User.chemotion_user
+ sys_review_from = Collection.find_or_create_by(user_id: chemotion_user.id, label: 'Group Lead Review from', is_locked: true, is_shared: false)
+ sys_review_collection = Collection.find_or_create_by(user: chemotion_user, label: 'Group Lead Review', ancestry: "#{sys_review_from.id}", shared_by_id: id)
+
+ col_attributes = {
+ user: self,
+ shared_by_id: chemotion_user.id,
+ is_locked: true,
+ is_shared: true
+ }
+
+ rc = Collection.find_by(col_attributes)
+ unless rc.nil?
+ SyncCollectionsUser.find_or_create_by(user: self, shared_by_id: chemotion_user.id, collection_id: sys_review_collection.id,
+ permission_level: 3, sample_detail_level: 10, reaction_detail_level: 10, fake_ancestry: rc.id.to_s)
+ end
+ sys_review_collection
+ end
+
+ def published_collection
+ su_id = User.chemotion_user.id
+ Collection.joins("INNER JOIN sync_collections_users ON sync_collections_users.collection_id = collections.id")
+ .where("sync_collections_users.shared_by_id = #{su_id}")
+ .where("sync_collections_users.user_id = #{self.id}")
+ .where("collections.label = 'Published Elements'").first
+ end
+
+ def sync_published_collection
+ SyncCollectionsUser.joins("INNER JOIN collections on collections.id = sync_collections_users.collection_id")
+ .where("sync_collections_users.user_id = #{self.id}")
+ .where("collections.id = #{Collection.public_collection_id}").first
+
+ end
+
+ def publication_embargo_collection
+ su_id = User.chemotion_user.id
+ Collection.joins("INNER JOIN sync_collections_users ON sync_collections_users.collection_id = collections.id")
+ .where("sync_collections_users.shared_by_id = #{su_id}")
+ .where("sync_collections_users.user_id = #{self.id}")
+ .where("collections.label = 'Embargoed Publications'").first
+ end
+
+ def all_collection
+ Collection.where(user: self, label: 'All', is_locked: true, position: 0)&.first
+
+ end
+
+ def self.chemotion_user
+ find_by(email: ENV['SYS_EMAIL'])
+ end
+
def current_affiliations
Affiliation.joins(
'INNER JOIN user_affiliations ua ON ua.affiliation_id = affiliations.id'
@@ -288,6 +440,10 @@ def molecule_editor
profile&.data&.fetch('molecule_editor', false)
end
+ def converter_admin
+ profile&.data&.fetch('converter_admin', false)
+ end
+
def matrix_check_by_name(name)
mx = Matrice.find_by(name: name)
return false if mx.nil?
@@ -345,27 +501,31 @@ def create_text_template
end
def self.from_omniauth(provider, uid, email, first_name, last_name)
- where(omniauth_provider: provider, omniauth_uid: uid).first_or_create do |user|
- # update the email, the first_name, and the last_name on every login
- user.email = email
- user.first_name = first_name
- user.last_name = last_name
- user.password = Devise.friendly_token[0,20]
+ user = find_by(email: email)
+ if user.present?
+ providers = user.providers || {}
+ providers[provider] = uid
+ user.providers = providers
+ user.save!
+ else
+ user = User.new(
+ email: email,
+ first_name: first_name,
+ last_name: last_name,
+ password: Devise.friendly_token[0, 20],
+ )
end
+ user
end
def link_omniauth(provider, uid)
- if User.where(omniauth_provider: provider, omniauth_uid: uid).exists?
- return nil
- else
- self.omniauth_provider = provider
- self.omniauth_uid = uid
- self.save
- end
+ providers = {} if providers.nil?
+ providers[provider] = uid
+ save!
end
def password_required?
- super && omniauth_provider.blank?
+ super && provider.blank?
end
private
@@ -377,6 +537,7 @@ def password_required?
# - delete it
def create_all_collection
+ return if self.type == 'Anonymous'
Collection.create(user: self, label: 'All', is_locked: true, position: 0)
end
@@ -386,8 +547,40 @@ def new_user_text_template
def create_chemotion_public_collection
return unless self.type == 'Person'
+ chemotion_user = User.chemotion_user
+ # Collection.create(user: self, label: 'chemotion.net', is_locked: true, position: 1)
+ Collection.find_or_create_by(user: self, label: 'ELN Gate', is_locked: true, position: 1)
+ Collection.find_or_create_by(user: self, label: 'My Data', is_locked: true, position: 2)
+
+ sys_published_by = Collection.find_or_create_by(user_id: chemotion_user.id, label: 'Published by')
+ sys_pending_from = Collection.find_or_create_by(user_id: chemotion_user.id, label: 'Pending Publication from')
+ sys_versions_from = Collection.find_or_create_by(user_id: chemotion_user.id, label: 'New Versions from')
+ sys_reviewing_from = Collection.find_or_create_by(user_id: chemotion_user.id, label: 'Reviewing Publication from')
+ sys_ready_publish_from = Collection.find_or_create_by(user_id: chemotion_user.id, label: 'Embargoed Publications from')
+
+ sys_reviewing_collection = self.reviewing_collection || Collection.create(user: chemotion_user, label: 'Reviewing', ancestry: "#{sys_reviewing_from.id}")
+ sys_pending_collection = self.pending_collection || Collection.create(user: chemotion_user, label: 'Pending Publications', ancestry: "#{sys_pending_from.id}")
+ sys_versions_collection = self.versions_collection || Collection.create(user: chemotion_user, label: 'New Versions', ancestry: "#{sys_versions_from.id}")
+ sys_published_collection = self.published_collection || Collection.create(user: chemotion_user, label: 'Published Elements', ancestry: "#{sys_published_by.id}")
+ sys_publication_embargo_collection = self.publication_embargo_collection || Collection.create(user: chemotion_user, label: 'Embargoed Publications', ancestry: "#{sys_ready_publish_from.id}")
+
+ root_label = "with %s" %chemotion_user.name_abbreviation
+ root_collection_attributes = {
+ label: root_label,
+ user: self,
+ shared_by_id: chemotion_user.id,
+ is_locked: true,
+ is_shared: true
+ }
+ rc = Collection.find_or_create_by(root_collection_attributes)
- Collection.create(user: self, label: 'chemotion-repository.net', is_locked: true, position: 1)
+ SyncCollectionsUser.find_or_create_by(user: self, shared_by_id: chemotion_user.id, collection_id: Collection.public_collection_id, permission_level: 0, sample_detail_level: 10, reaction_detail_level: 10, fake_ancestry: rc.id.to_s)
+ SyncCollectionsUser.find_or_create_by(user: self, shared_by_id: chemotion_user.id, collection_id: Collection.scheme_only_reactions_collection.id, permission_level: 0, sample_detail_level: 10, reaction_detail_level: 10, fake_ancestry: rc.id.to_s)
+ SyncCollectionsUser.find_or_create_by(user: self, shared_by_id: chemotion_user.id, collection_id: sys_published_collection.id, permission_level: 0, sample_detail_level: 10, reaction_detail_level: 10, fake_ancestry: rc.id.to_s)
+ SyncCollectionsUser.find_or_create_by(user: self, shared_by_id: chemotion_user.id, collection_id: sys_pending_collection.id, permission_level: 0, sample_detail_level: 10, reaction_detail_level: 10, fake_ancestry: rc.id.to_s)
+ SyncCollectionsUser.find_or_create_by(user: self, shared_by_id: chemotion_user.id, collection_id: sys_versions_collection.id, permission_level: 3, sample_detail_level: 10, reaction_detail_level: 10, fake_ancestry: rc.id.to_s)
+ SyncCollectionsUser.find_or_create_by(user: self, shared_by_id: chemotion_user.id, collection_id: sys_reviewing_collection.id, permission_level: 3, sample_detail_level: 10, reaction_detail_level: 10, fake_ancestry: rc.id.to_s)
+ SyncCollectionsUser.find_or_create_by(user: self, shared_by_id: chemotion_user.id, collection_id: sys_publication_embargo_collection.id, permission_level: 0, sample_detail_level: 10, reaction_detail_level: 10, fake_ancestry: rc.id.to_s)
end
def set_account_active
@@ -406,12 +599,13 @@ def send_welcome_email
def delete_data
# TODO: logic to check if user can be really destroy or which data can be deleted
count = samples.count
- # + self.reactions.count
- # + self.wellplates.count
- # + self.screens.count
- # + self.research_plans.count
+ # + self.reactions.count
+ # + self.wellplates.count
+ # + self.screens.count
+ # + self.research_plans.count
update_columns(email: "#{id}_#{name_abbreviation}@deleted")
update_columns(name_abbreviation: nil) if count.zero?
+ update_columns(providers: nil)
end
end
diff --git a/app/models/users_collaborator.rb b/app/models/users_collaborator.rb
new file mode 100644
index 000000000..7db9e81e2
--- /dev/null
+++ b/app/models/users_collaborator.rb
@@ -0,0 +1,11 @@
+# == Schema Information
+#
+# Table name: users_collaborators
+#
+# id :integer not null, primary key
+# user_id :integer
+# collaborator_id :integer
+#
+
+class UsersCollaborator < ApplicationRecord
+end
diff --git a/app/packs/entrypoints/application.js b/app/packs/entrypoints/application.js
index f8b16999e..29655a565 100644
--- a/app/packs/entrypoints/application.js
+++ b/app/packs/entrypoints/application.js
@@ -12,4 +12,10 @@ var OmniauthCredential = require('../src/components/sso/OmniauthCredential');
var UserCounter = require('../src/components/elements/UserCounter');
var ScifinderCredential = require('../src/components/scifinder/ScifinderCredential');
var mydb = require('../src/components/App');
-
+var UserCounter = require('../src/components/elements/UserCounter');
+var RepoNewsEditor = require('../src/libHome/RepoNewsEditor');
+var RepoNewsReader = require('../src/libHome/RepoNewsReader');
+var RepoHowToEditor = require('../src/libHome/RepoHowToEditor');
+var RepoHowToReader = require('../src/libHome/RepoHowToReader');
+var LoginOptions = require('../src/components/sso/LoginOptions');
+var ConverterAdmin = require('../src/admin/converter/ConverterAdmin');
diff --git a/app/packs/src/admin/AdminHome.js b/app/packs/src/admin/AdminHome.js
index 8dc0f649c..74929a677 100644
--- a/app/packs/src/admin/AdminHome.js
+++ b/app/packs/src/admin/AdminHome.js
@@ -19,7 +19,6 @@ import SegmentElementAdmin from './SegmentElementAdmin';
import DatasetElementAdmin from './DatasetElementAdmin';
import DelayedJobs from './DelayedJobs';
import TemplateManagement from './TemplateManagement';
-import ConverterAdmin from './converter/AdminApp';
class AdminHome extends React.Component {
constructor(props) {
@@ -78,8 +77,6 @@ class AdminHome extends React.Component {
return this.renderTemplateManagement();
} else if (pageIndex === 13) {
return this.renderDelayedJobs();
- } else if (pageIndex === 14) {
- return this.renderConverterAdmin();
}
return ();
@@ -100,7 +97,6 @@ class AdminHome extends React.Component {
Groups & Devices
Data Collector
NoVNC Settings
- Converter Profiles
UI features
Text Templates
Generic Elements (BETA)
@@ -206,15 +202,6 @@ class AdminHome extends React.Component {
);
}
- renderConverterAdmin() {
- const { contentClassName } = this.state;
- return (
-
-
-
- );
- }
-
renderTemplateManagement() {
const { contentClassName } = this.state;
return (
diff --git a/app/packs/src/admin/TemplateManagement.js b/app/packs/src/admin/TemplateManagement.js
index 0fc151d53..7cf5886ee 100644
--- a/app/packs/src/admin/TemplateManagement.js
+++ b/app/packs/src/admin/TemplateManagement.js
@@ -366,7 +366,7 @@ export default class TemplateManagement extends React.Component {
{idx + 1}
| {g.name} |
- {this.state.reportTemplateTypes.find(({ value }) => value === g.report_type).label} |
+ {(this.state.reportTemplateTypes.find(({ value }) => value === g.report_type) || {}).label} |
{g.id} |
diff --git a/app/packs/src/admin/UserManagement.js b/app/packs/src/admin/UserManagement.js
index c65eb8ed9..4fd8421f8 100644
--- a/app/packs/src/admin/UserManagement.js
+++ b/app/packs/src/admin/UserManagement.js
@@ -52,6 +52,8 @@ const confirmUserTooltip = confirm this account (confirm email:
{email});
const disableTooltip = lock this account;
const enableTooltip = unlock this account;
+const converterEnableTooltip = Enable Converter profiles editing for this user (currently disabled);
+const converterDisableTooltip = Disable Converter profiles editing for this user (currently enabled);
const templateModeratorEnableTooltip = Enable Ketcher template editing for this user (currently disabled);
const templateModeratorDisableTooltip = Disable Ketcher template editing for this user (currently enabled);
const moleculeModeratorEnableTooltip = Enable editing the representation of the global molecules for this user (currently disabled);
@@ -152,6 +154,15 @@ export default class UserManagement extends React.Component {
});
}
+ handleConverterAdmin(id, isConverterAdmin) {
+ AdminFetcher.updateAccount({ user_id: id, converter_admin: !isConverterAdmin })
+ .then((result) => {
+ this.handleFetchUsers();
+ const message = isConverterAdmin === true ? 'Disable Converter profiles editing for this user' : 'Enable Converter profiles editing for this user';
+ alert(message);
+ });
+ }
+
handleTemplatesModerator(id, isTemplatesModerator) {
AdminFetcher.updateAccount({ user_id: id, is_templates_moderator: !isTemplatesModerator })
.then((result) => {
@@ -851,6 +862,16 @@ export default class UserManagement extends React.Component {
+
+
+
+
|