Cdx parser

.gitignore

@@ -58,14 +58,14 @@
 /public/images/*
 !/public/images/wild_card/
 
-/uploads/attachments/*
-/uploads/thumbnails
+/uploads/*
 !/public/attachments/.keep
 
+
 /public/docx/*
 !/public/docx/.keep
 
-/public/assets/*.js
+/public/assets/*
 
 /coverage/
 

.rubocop.yml

@@ -1,3 +1,7 @@
+AllCops:
+  DisplayCopNames: true
+  TargetRubyVersion: 2.3
+
 Style/BlockDelimiters:
   EnforcedStyle: semantic
   FunctionalMethods:
@@ -15,6 +19,8 @@ Metrics/ModuleLength:
 Metrics/BlockLength:
   Exclude:
     - "**/*_spec.rb"
-
 Metrics/LineLength:
   Max: 100
+
+Metrics/MethodLength:
+  Max: 20

Gemfile

@@ -106,6 +106,7 @@ gem 'rubocop', require: false
 gem 'yaml_db'
 
 gem 'ruby-ole'
+gem 'ruby-geometry', require: 'geometry'
 
 # CI
 gem 'coveralls', require: false
@@ -114,8 +115,8 @@ gem 'coveralls', require: false
 # to compile from github/openbabel/openbabel master
 # gem 'openbabel', '2.4.1.2', git: 'https://github.com/ComPlat/openbabel-gem'
 # to compile from github/openbabel/openbabel branch openbabel-2-4-x
-gem 'openbabel', '2.4.0.1', git: 'https://github.com/ComPlat/openbabel-gem',
-                            branch: 'openbabel-2-4-x'
+gem 'openbabel', '2.4.1.2', git: 'https://github.com/ComPlat/openbabel-gem',
+                            branch: 'cdx-extraction'
 
 gem 'barby'
 gem 'prawn'

Gemfile.lock

@@ -15,10 +15,10 @@ GIT
 
 GIT
   remote: https://github.com/ComPlat/openbabel-gem
-  revision: 837eec9e660b6dbc9d2517889de39a6e93bb4b98
-  branch: openbabel-2-4-x
+  revision: b651909dc84ea33ab79a8e95dc50486ba272a3d4
+  branch: cdx-extraction
   specs:
-    openbabel (2.4.0.1)
+    openbabel (2.4.1.2)
 
 GIT
   remote: https://github.com/ComPlat/sablon
@@ -333,6 +333,7 @@ GEM
       skinny (~> 0.2.3)
       sqlite3 (~> 1.3)
       thin (~> 1.5.0)
+    memoist (0.16.0)
     memory_profiler (0.9.7)
     meta_request (0.4.3)
       callsite (~> 0.0, >= 0.0.11)
@@ -469,6 +470,9 @@ GEM
       rainbow (>= 1.99.1, < 3.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (~> 1.0, >= 1.0.1)
+    ruby-geometry (0.0.6)
+      activesupport
+      memoist
     ruby-mailchecker (3.0.27)
     ruby-ole (1.2.12)
     ruby-progressbar (1.8.1)
@@ -632,7 +636,7 @@ DEPENDENCIES
   net-sftp
   net-ssh
   nokogiri
-  openbabel (= 2.4.0.1)!
+  openbabel (= 2.4.1.2)!
   paranoia (~> 2.0)
   pg (~> 0.20.0)
   pg_search
@@ -648,6 +652,7 @@ DEPENDENCIES
   rspec-rails
   rtf
   rubocop
+  ruby-geometry
   ruby-mailchecker
   ruby-ole
   rubyXL (= 3.3.26)

app/api/api.rb

@@ -190,7 +190,7 @@ def to_molecule_array(hash_groups)
   mount Chemotion::DevicesAnalysisAPI
   mount Chemotion::GeneralAPI
   mount Chemotion::V1PublicAPI
-  mount Chemotion::DocxAPI
   mount Chemotion::GateAPI
   mount Chemotion::ElementAPI
+  mount Chemotion::ChemReadAPI
 end

app/api/chemotion/chem_read_api.rb

@@ -0,0 +1,69 @@
+# frozen_string_literal: true
+
+# Belong to Chemotion module
+module Chemotion
+  require 'open3'
+  require 'ole/storage'
+
+  # API for ChemRead manipulation
+  class ChemReadAPI < Grape::API
+    helpers ChemReadHelpers
+
+    resource :chemread do
+      resource :embedded do
+        desc 'Upload import files'
+        params do
+          requires :get_mol, type: Boolean, default: false, desc: ''
+        end
+
+        post 'upload' do
+          smi_arr = []
+
+          get_mol = params[:get_mol]
+          params.delete('get_mol')
+
+          params.each do |uid, file|
+            temp_file = file.tempfile
+            temp_path = temp_file.to_path
+            extn = File.extname temp_path
+            tmp_dir = Dir.mktmpdir([uid, File.basename(temp_path, extn)])
+
+            info = read_uploaded_file(temp_file, tmp_dir, get_mol)
+            smi_obj = { uid: uid, name: file.filename, info: info }
+
+            temp_file.close
+            temp_file.unlink
+            FileUtils.remove_dir tmp_dir, true
+            smi_arr.push(smi_obj)
+          end
+
+          smi_arr
+        end
+      end
+
+      resource :svg do
+        desc 'Convert svg from smi'
+        params do
+          requires :smiArr, type: Array, desc: 'Files and uids'
+        end
+
+        post 'smi' do
+          smi_arr = params[:smiArr]
+          res = []
+          smi_arr.each do |smi|
+            res.push(
+              uid: smi[:uid],
+              smiIdx: smi[:smiIdx],
+              svg: SVG::ReactionComposer.cr_reaction_svg_from_rsmi(
+                smi[:newSmi],
+                ChemReadHelpers::SOLVENTS_SMI,
+                ChemReadHelpers::REAGENTS_SMI
+              )
+            )
+          end
+          res
+        end
+      end
+    end
+  end
+end